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PubMed Central Canada to be taken offline in February 2018

On February 23, 2018, PubMed Central Canada (PMC Canada) will be taken offline permanently. No author manuscripts will be deleted, and the approximately 2,900 manuscripts authored by Canadian Institutes of Health Research (CIHR)-funded researchers currently in the archive will be copied to the National Research Council’s (NRC) Digital Repository over the coming months. These manuscripts along with all other content will also remain publicly searchable on PubMed Central (US) and Europe PubMed Central, meaning such manuscripts will continue to be compliant with the Tri-Agency Open Access Policy on Publications.

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1.  Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution 
Leung, Wilson | Shaffer, Christopher D. | Reed, Laura K. | Smith, Sheryl T. | Barshop, William | Dirkes, William | Dothager, Matthew | Lee, Paul | Wong, Jeannette | Xiong, David | Yuan, Han | Bedard, James E. J. | Machone, Joshua F. | Patterson, Seantay D. | Price, Amber L. | Turner, Bryce A. | Robic, Srebrenka | Luippold, Erin K. | McCartha, Shannon R. | Walji, Tezin A. | Walker, Chelsea A. | Saville, Kenneth | Abrams, Marita K. | Armstrong, Andrew R. | Armstrong, William | Bailey, Robert J. | Barberi, Chelsea R. | Beck, Lauren R. | Blaker, Amanda L. | Blunden, Christopher E. | Brand, Jordan P. | Brock, Ethan J. | Brooks, Dana W. | Brown, Marie | Butzler, Sarah C. | Clark, Eric M. | Clark, Nicole B. | Collins, Ashley A. | Cotteleer, Rebecca J. | Cullimore, Peterson R. | Dawson, Seth G. | Docking, Carter T. | Dorsett, Sasha L. | Dougherty, Grace A. | Downey, Kaitlyn A. | Drake, Andrew P. | Earl, Erica K. | Floyd, Trevor G. | Forsyth, Joshua D. | Foust, Jonathan D. | Franchi, Spencer L. | Geary, James F. | Hanson, Cynthia K. | Harding, Taylor S. | Harris, Cameron B. | Heckman, Jonathan M. | Holderness, Heather L. | Howey, Nicole A. | Jacobs, Dontae A. | Jewell, Elizabeth S. | Kaisler, Maria | Karaska, Elizabeth A. | Kehoe, James L. | Koaches, Hannah C. | Koehler, Jessica | Koenig, Dana | Kujawski, Alexander J. | Kus, Jordan E. | Lammers, Jennifer A. | Leads, Rachel R. | Leatherman, Emily C. | Lippert, Rachel N. | Messenger, Gregory S. | Morrow, Adam T. | Newcomb, Victoria | Plasman, Haley J. | Potocny, Stephanie J. | Powers, Michelle K. | Reem, Rachel M. | Rennhack, Jonathan P. | Reynolds, Katherine R. | Reynolds, Lyndsey A. | Rhee, Dong K. | Rivard, Allyson B. | Ronk, Adam J. | Rooney, Meghan B. | Rubin, Lainey S. | Salbert, Luke R. | Saluja, Rasleen K. | Schauder, Taylor | Schneiter, Allison R. | Schulz, Robert W. | Smith, Karl E. | Spencer, Sarah | Swanson, Bryant R. | Tache, Melissa A. | Tewilliager, Ashley A. | Tilot, Amanda K. | VanEck, Eve | Villerot, Matthew M. | Vylonis, Megan B. | Watson, David T. | Wurzler, Juliana A. | Wysocki, Lauren M. | Yalamanchili, Monica | Zaborowicz, Matthew A. | Emerson, Julia A. | Ortiz, Carlos | Deuschle, Frederic J. | DiLorenzo, Lauren A. | Goeller, Katie L. | Macchi, Christopher R. | Muller, Sarah E. | Pasierb, Brittany D. | Sable, Joseph E. | Tucci, Jessica M. | Tynon, Marykathryn | Dunbar, David A. | Beken, Levent H. | Conturso, Alaina C. | Danner, Benjamin L. | DeMichele, Gabriella A. | Gonzales, Justin A. | Hammond, Maureen S. | Kelley, Colleen V. | Kelly, Elisabeth A. | Kulich, Danielle | Mageeney, Catherine M. | McCabe, Nikie L. | Newman, Alyssa M. | Spaeder, Lindsay A. | Tumminello, Richard A. | Revie, Dennis | Benson, Jonathon M. | Cristostomo, Michael C. | DaSilva, Paolo A. | Harker, Katherine S. | Jarrell, Jenifer N. | Jimenez, Luis A. | Katz, Brandon M. | Kennedy, William R. | Kolibas, Kimberly S. | LeBlanc, Mark T. | Nguyen, Trung T. | Nicolas, Daniel S. | Patao, Melissa D. | Patao, Shane M. | Rupley, Bryan J. | Sessions, Bridget J. | Weaver, Jennifer A. | Goodman, Anya L. | Alvendia, Erica L. | Baldassari, Shana M. | Brown, Ashley S. | Chase, Ian O. | Chen, Maida | Chiang, Scott | Cromwell, Avery B. | Custer, Ashley F. | DiTommaso, Tia M. | El-Adaimi, Jad | Goscinski, Nora C. | Grove, Ryan A. | Gutierrez, Nestor | Harnoto, Raechel S. | Hedeen, Heather | Hong, Emily L. | Hopkins, Barbara L. | Huerta, Vilma F. | Khoshabian, Colin | LaForge, Kristin M. | Lee, Cassidy T. | Lewis, Benjamin M. | Lydon, Anniken M. | Maniaci, Brian J. | Mitchell, Ryan D. | Morlock, Elaine V. | Morris, William M. | Naik, Priyanka | Olson, Nicole C. | Osterloh, Jeannette M. | Perez, Marcos A. | Presley, Jonathan D. | Randazzo, Matt J. | Regan, Melanie K. | Rossi, Franca G. | Smith, Melanie A. | Soliterman, Eugenia A. | Sparks, Ciani J. | Tran, Danny L. | Wan, Tiffany | Welker, Anne A. | Wong, Jeremy N. | Sreenivasan, Aparna | Youngblom, Jim | Adams, Andrew | Alldredge, Justin | Bryant, Ashley | Carranza, David | Cifelli, Alyssa | Coulson, Kevin | Debow, Calise | Delacruz, Noelle | Emerson, Charlene | Farrar, Cassandra | Foret, Don | Garibay, Edgar | Gooch, John | Heslop, Michelle | Kaur, Sukhjit | Khan, Ambreen | Kim, Van | Lamb, Travis | Lindbeck, Peter | Lucas, Gabi | Macias, Elizabeth | Martiniuc, Daniela | Mayorga, Lissett | Medina, Joseph | Membreno, Nelson | Messiah, Shady | Neufeld, Lacey | Nguyen, San Francisco | Nichols, Zachary | Odisho, George | Peterson, Daymon | Rodela, Laura | Rodriguez, Priscilla | Rodriguez, Vanessa | Ruiz, Jorge | Sherrill, Will | Silva, Valeria | Sparks, Jeri | Statton, Geeta | Townsend, Ashley | Valdez, Isabel | Waters, Mary | Westphal, Kyle | Winkler, Stacey | Zumkehr, Joannee | DeJong, Randall J. | Hoogewerf, Arlene J. | Ackerman, Cheri M. | Armistead, Isaac O. | Baatenburg, Lara | Borr, Matthew J. | Brouwer, Lindsay K. | Burkhart, Brandon J. | Bushhouse, Kelsey T. | Cesko, Lejla | Choi, Tiffany Y. Y. | Cohen, Heather | Damsteegt, Amanda M. | Darusz, Jess M. | Dauphin, Cory M. | Davis, Yelena P. | Diekema, Emily J. | Drewry, Melissa | Eisen, Michelle E. M. | Faber, Hayley M. | Faber, Katherine J. | Feenstra, Elizabeth | Felzer-Kim, Isabella T. | Hammond, Brandy L. | Hendriksma, Jesse | Herrold, Milton R. | Hilbrands, Julia A. | Howell, Emily J. | Jelgerhuis, Sarah A. | Jelsema, Timothy R. | Johnson, Benjamin K. | Jones, Kelly K. | Kim, Anna | Kooienga, Ross D. | Menyes, Erika E. | Nollet, Eric A. | Plescher, Brittany E. | Rios, Lindsay | Rose, Jenny L. | Schepers, Allison J. | Scott, Geoff | Smith, Joshua R. | Sterling, Allison M. | Tenney, Jenna C. | Uitvlugt, Chris | VanDyken, Rachel E. | VanderVennen, Marielle | Vue, Samantha | Kokan, Nighat P. | Agbley, Kwabea | Boham, Sampson K. | Broomfield, Daniel | Chapman, Kayla | Dobbe, Ali | Dobbe, Ian | Harrington, William | Ibrahem, Marwan | Kennedy, Andre | Koplinsky, Chad A. | Kubricky, Cassandra | Ladzekpo, Danielle | Pattison, Claire | Ramirez, Roman E. | Wande, Lucia | Woehlke, Sarah | Wawersik, Matthew | Kiernan, Elizabeth | Thompson, Jeffrey S. | Banker, Roxanne | Bartling, Justina R. | Bhatiya, Chinmoy I. | Boudoures, Anna L. | Christiansen, Lena | Fosselman, Daniel S. | French, Kristin M. | Gill, Ishwar S. | Havill, Jessen T. | Johnson, Jaelyn L. | Keny, Lauren J. | Kerber, John M. | Klett, Bethany M. | Kufel, Christina N. | May, Francis J. | Mecoli, Jonathan P. | Merry, Callie R. | Meyer, Lauren R. | Miller, Emily G. | Mullen, Gregory J. | Palozola, Katherine C. | Pfeil, Jacob J. | Thomas, Jessica G. | Verbofsky, Evan M. | Spana, Eric P. | Agarwalla, Anant | Chapman, Julia | Chlebina, Ben | Chong, Insun | Falk, I.N. | Fitzgibbons, John D. | Friedman, Harrison | Ighile, Osagie | Kim, Andrew J. | Knouse, Kristin A. | Kung, Faith | Mammo, Danny | Ng, Chun Leung | Nikam, Vinayak S. | Norton, Diana | Pham, Philip | Polk, Jessica W. | Prasad, Shreya | Rankin, Helen | Ratliff, Camille D. | Scala, Victoria | Schwartz, Nicholas U. | Shuen, Jessica A. | Xu, Amy | Xu, Thomas Q. | Zhang, Yi | Rosenwald, Anne G. | Burg, Martin G. | Adams, Stephanie J. | Baker, Morgan | Botsford, Bobbi | Brinkley, Briana | Brown, Carter | Emiah, Shadie | Enoch, Erica | Gier, Chad | Greenwell, Alyson | Hoogenboom, Lindsay | Matthews, Jordan E. | McDonald, Mitchell | Mercer, Amanda | Monsma, Nicholaus | Ostby, Kristine | Ramic, Alen | Shallman, Devon | Simon, Matthew | Spencer, Eric | Tomkins, Trisha | Wendland, Pete | Wylie, Anna | Wolyniak, Michael J. | Robertson, Gregory M. | Smith, Samuel I. | DiAngelo, Justin R. | Sassu, Eric D. | Bhalla, Satish C. | Sharif, Karim A. | Choeying, Tenzin | Macias, Jason S. | Sanusi, Fareed | Torchon, Karvyn | Bednarski, April E. | Alvarez, Consuelo J. | Davis, Kristen C. | Dunham, Carrie A. | Grantham, Alaina J. | Hare, Amber N. | Schottler, Jennifer | Scott, Zackary W. | Kuleck, Gary A. | Yu, Nicole S. | Kaehler, Marian M. | Jipp, Jacob | Overvoorde, Paul J. | Shoop, Elizabeth | Cyrankowski, Olivia | Hoover, Betsy | Kusner, Matt | Lin, Devry | Martinov, Tijana | Misch, Jonathan | Salzman, Garrett | Schiedermayer, Holly | Snavely, Michael | Zarrasola, Stephanie | Parrish, Susan | Baker, Atlee | Beckett, Alissa | Belella, Carissa | Bryant, Julie | Conrad, Turner | Fearnow, Adam | Gomez, Carolina | Herbstsomer, Robert A. | Hirsch, Sarah | Johnson, Christen | Jones, Melissa | Kabaso, Rita | Lemmon, Eric | Vieira, Carolina Marques dos Santos | McFarland, Darryl | McLaughlin, Christopher | Morgan, Abbie | Musokotwane, Sepo | Neutzling, William | Nietmann, Jana | Paluskievicz, Christina | Penn, Jessica | Peoples, Emily | Pozmanter, Caitlin | Reed, Emily | Rigby, Nichole | Schmidt, Lasse | Shelton, Micah | Shuford, Rebecca | Tirasawasdichai, Tiara | Undem, Blair | Urick, Damian | Vondy, Kayla | Yarrington, Bryan | Eckdahl, Todd T. | Poet, Jeffrey L. | Allen, Alica B. | Anderson, John E. | Barnett, Jason M. | Baumgardner, Jordan S. | Brown, Adam D. | Carney, Jordan E. | Chavez, Ramiro A. | Christgen, Shelbi L. | Christie, Jordan S. | Clary, Andrea N. | Conn, Michel A. | Cooper, Kristen M. | Crowley, Matt J. | Crowley, Samuel T. | Doty, Jennifer S. | Dow, Brian A. | Edwards, Curtis R. | Elder, Darcie D. | Fanning, John P. | Janssen, Bridget M. | Lambright, Anthony K. | Lane, Curtiss E. | Limle, Austin B. | Mazur, Tammy | McCracken, Marly R. | McDonough, Alexa M. | Melton, Amy D. | Minnick, Phillip J. | Musick, Adam E. | Newhart, William H. | Noynaert, Joseph W. | Ogden, Bradley J. | Sandusky, Michael W. | Schmuecker, Samantha M. | Shipman, Anna L. | Smith, Anna L. | Thomsen, Kristen M. | Unzicker, Matthew R. | Vernon, William B. | Winn, Wesley W. | Woyski, Dustin S. | Zhu, Xiao | Du, Chunguang | Ament, Caitlin | Aso, Soham | Bisogno, Laura Simone | Caronna, Jason | Fefelova, Nadezhda | Lopez, Lenin | Malkowitz, Lorraine | Marra, Jonathan | Menillo, Daniella | Obiorah, Ifeanyi | Onsarigo, Eric Nyabeta | Primus, Shekerah | Soos, Mahdi | Tare, Archana | Zidan, Ameer | Jones, Christopher J. | Aronhalt, Todd | Bellush, James M. | Burke, Christa | DeFazio, Steve | Does, Benjamin R. | Johnson, Todd D. | Keysock, Nicholas | Knudsen, Nelson H. | Messler, James | Myirski, Kevin | Rekai, Jade Lea | Rempe, Ryan Michael | Salgado, Michael S. | Stagaard, Erica | Starcher, Justin R. | Waggoner, Andrew W. | Yemelyanova, Anastasia K. | Hark, Amy T. | Bertolet, Anne | Kuschner, Cyrus E. | Parry, Kesley | Quach, Michael | Shantzer, Lindsey | Shaw, Mary E. | Smith, Mary A. | Glenn, Omolara | Mason, Portia | Williams, Charlotte | Key, S. Catherine Silver | Henry, Tyneshia C. P. | Johnson, Ashlee G. | White, Jackie X. | Haberman, Adam | Asinof, Sam | Drumm, Kelly | Freeburg, Trip | Safa, Nadia | Schultz, Darrin | Shevin, Yakov | Svoronos, Petros | Vuong, Tam | Wellinghoff, Jules | Hoopes, Laura L. M. | Chau, Kim M. | Ward, Alyssa | Regisford, E. Gloria C. | Augustine, LaJerald | Davis-Reyes, Brionna | Echendu, Vivienne | Hales, Jasmine | Ibarra, Sharon | Johnson, Lauriaun | Ovu, Steven | Braverman, John M. | Bahr, Thomas J. | Caesar, Nicole M. | Campana, Christopher | Cassidy, Daniel W. | Cognetti, Peter A. | English, Johnathan D. | Fadus, Matthew C. | Fick, Cameron N. | Freda, Philip J. | Hennessy, Bryan M. | Hockenberger, Kelsey | Jones, Jennifer K. | King, Jessica E. | Knob, Christopher R. | Kraftmann, Karen J. | Li, Linghui | Lupey, Lena N. | Minniti, Carl J. | Minton, Thomas F. | Moran, Joseph V. | Mudumbi, Krishna | Nordman, Elizabeth C. | Puetz, William J. | Robinson, Lauren M. | Rose, Thomas J. | Sweeney, Edward P. | Timko, Ashley S. | Paetkau, Don W. | Eisler, Heather L. | Aldrup, Megan E. | Bodenberg, Jessica M. | Cole, Mara G. | Deranek, Kelly M. | DeShetler, Megan | Dowd, Rose M. | Eckardt, Alexandra K. | Ehret, Sharon C. | Fese, Jessica | Garrett, Amanda D. | Kammrath, Anna | Kappes, Michelle L. | Light, Morgan R. | Meier, Anne C. | O’Rouke, Allison | Perella, Mallory | Ramsey, Kimberley | Ramthun, Jennifer R. | Reilly, Mary T. | Robinett, Deirdre | Rossi, Nadine L. | Schueler, Mary Grace | Shoemaker, Emma | Starkey, Kristin M. | Vetor, Ashley | Vrable, Abby | Chandrasekaran, Vidya | Beck, Christopher | Hatfield, Kristen R. | Herrick, Douglas A. | Khoury, Christopher B. | Lea, Charlotte | Louie, Christopher A. | Lowell, Shannon M. | Reynolds, Thomas J. | Schibler, Jeanine | Scoma, Alexandra H. | Smith-Gee, Maxwell T. | Tuberty, Sarah | Smith, Christopher D. | Lopilato, Jane E. | Hauke, Jeanette | Roecklein-Canfield, Jennifer A. | Corrielus, Maureen | Gilman, Hannah | Intriago, Stephanie | Maffa, Amanda | Rauf, Sabya A. | Thistle, Katrina | Trieu, Melissa | Winters, Jenifer | Yang, Bib | Hauser, Charles R. | Abusheikh, Tariq | Ashrawi, Yara | Benitez, Pedro | Boudreaux, Lauren R. | Bourland, Megan | Chavez, Miranda | Cruz, Samantha | Elliott, GiNell | Farek, Jesse R. | Flohr, Sarah | Flores, Amanda H. | Friedrichs, Chelsey | Fusco, Zach | Goodwin, Zane | Helmreich, Eric | Kiley, John | Knepper, John Mark | Langner, Christine | Martinez, Megan | Mendoza, Carlos | Naik, Monal | Ochoa, Andrea | Ragland, Nicolas | Raimey, England | Rathore, Sunil | Reza, Evangelina | Sadovsky, Griffin | Seydoux, Marie-Isabelle B. | Smith, Jonathan E. | Unruh, Anna K. | Velasquez, Vicente | Wolski, Matthew W. | Gosser, Yuying | Govind, Shubha | Clarke-Medley, Nicole | Guadron, Leslie | Lau, Dawn | Lu, Alvin | Mazzeo, Cheryl | Meghdari, Mariam | Ng, Simon | Pamnani, Brad | Plante, Olivia | Shum, Yuki Kwan Wa | Song, Roy | Johnson, Diana E. | Abdelnabi, Mai | Archambault, Alexi | Chamma, Norma | Gaur, Shailly | Hammett, Deborah | Kandahari, Adrese | Khayrullina, Guzal | Kumar, Sonali | Lawrence, Samantha | Madden, Nigel | Mandelbaum, Max | Milnthorp, Heather | Mohini, Shiv | Patel, Roshni | Peacock, Sarah J. | Perling, Emily | Quintana, Amber | Rahimi, Michael | Ramirez, Kristen | Singhal, Rishi | Weeks, Corinne | Wong, Tiffany | Gillis, Aubree T. | Moore, Zachary D. | Savell, Christopher D. | Watson, Reece | Mel, Stephanie F. | Anilkumar, Arjun A. | Bilinski, Paul | Castillo, Rostislav | Closser, Michael | Cruz, Nathalia M. | Dai, Tiffany | Garbagnati, Giancarlo F. | Horton, Lanor S. | Kim, Dongyeon | Lau, Joyce H. | Liu, James Z. | Mach, Sandy D. | Phan, Thu A. | Ren, Yi | Stapleton, Kenneth E. | Strelitz, Jean M. | Sunjed, Ray | Stamm, Joyce | Anderson, Morgan C. | Bonifield, Bethany Grace | Coomes, Daniel | Dillman, Adam | Durchholz, Elaine J. | Fafara-Thompson, Antoinette E. | Gross, Meleah J. | Gygi, Amber M. | Jackson, Lesley E. | Johnson, Amy | Kocsisova, Zuzana | Manghelli, Joshua L. | McNeil, Kylie | Murillo, Michael | Naylor, Kierstin L. | Neely, Jessica | Ogawa, Emmy E. | Rich, Ashley | Rogers, Anna | Spencer, J. Devin | Stemler, Kristina M. | Throm, Allison A. | Van Camp, Matt | Weihbrecht, Katie | Wiles, T. Aaron | Williams, Mallory A. | Williams, Matthew | Zoll, Kyle | Bailey, Cheryl | Zhou, Leming | Balthaser, Darla M. | Bashiri, Azita | Bower, Mindy E. | Florian, Kayla A. | Ghavam, Nazanin | Greiner-Sosanko, Elizabeth S. | Karim, Helmet | Mullen, Victor W. | Pelchen, Carly E. | Yenerall, Paul M. | Zhang, Jiayu | Rubin, Michael R. | Arias-Mejias, Suzette M. | Bermudez-Capo, Armando G. | Bernal-Vega, Gabriela V. | Colon-Vazquez, Mariela | Flores-Vazquez, Arelys | Gines-Rosario, Mariela | Llavona-Cartagena, Ivan G. | Martinez-Rodriguez, Javier O. | Ortiz-Fuentes, Lionel | Perez-Colomba, Eliezer O. | Perez-Otero, Joseph | Rivera, Elisandra | Rodriguez-Giron, Luke J. | Santiago-Sanabria, Arnaldo J. | Senquiz-Gonzalez, Andrea M. | delValle, Frank R. Soto | Vargas-Franco, Dorianmarie | Velázquez-Soto, Karla I. | Zambrana-Burgos, Joan D. | Martinez-Cruzado, Juan Carlos | Asencio-Zayas, Lillyann | Babilonia-Figueroa, Kevin | Beauchamp-Pérez, Francis D. | Belén-Rodríguez, Juliana | Bracero-Quiñones, Luciann | Burgos-Bula, Andrea P. | Collado-Méndez, Xavier A. | Colón-Cruz, Luis R. | Correa-Muller, Ana I. | Crooke-Rosado, Jonathan L. | Cruz-García, José M. | Defendini-Ávila, Marianna | Delgado-Peraza, Francheska M. | Feliciano-Cancela, Alex J. | Gónzalez-Pérez, Valerie M. | Guiblet, Wilfried | Heredia-Negrón, Aldo | Hernández-Muñiz, Jennifer | Irizarry-González, Lourdes N. | Laboy-Corales, Ángel L. | Llaurador-Caraballo, Gabriela A. | Marín-Maldonado, Frances | Marrero-Llerena, Ulises | Martell-Martínez, Héctor A. | Martínez-Traverso, Idaliz M. | Medina-Ortega, Kiara N. | Méndez-Castellanos, Sonya G. | Menéndez-Serrano, Krizia C. | Morales-Caraballo, Carol I. | Ortiz-DeChoudens, Saryleine | Ortiz-Ortiz, Patricia | Pagán-Torres, Hendrick | Pérez-Afanador, Diana | Quintana-Torres, Enid M. | Ramírez-Aponte, Edwin G. | Riascos-Cuero, Carolina | Rivera-Llovet, Michelle S. | Rivera-Pagán, Ingrid T. | Rivera-Vicéns, Ramón E. | Robles-Juarbe, Fabiola | Rodríguez-Bonilla, Lorraine | Rodríguez-Echevarría, Brian O. | Rodríguez-García, Priscila M. | Rodríguez-Laboy, Abneris E. | Rodríguez-Santiago, Susana | Rojas-Vargas, Michael L. | Rubio-Marrero, Eva N. | Santiago-Colón, Albeliz | Santiago-Ortiz, Jorge L. | Santos-Ramos, Carlos E. | Serrano-González, Joseline | Tamayo-Figueroa, Alina M. | Tascón-Peñaranda, Edna P. | Torres-Castillo, José L. | Valentín-Feliciano, Nelson A. | Valentín-Feliciano, Yashira M. | Vargas-Barreto, Nadyan M. | Vélez-Vázquez, Miguel | Vilanova-Vélez, Luis R. | Zambrana-Echevarría, Cristina | MacKinnon, Christy | Chung, Hui-Min | Kay, Chris | Pinto, Anthony | Kopp, Olga R. | Burkhardt, Joshua | Harward, Chris | Allen, Robert | Bhat, Pavan | Chang, Jimmy Hsiang-Chun | Chen, York | Chesley, Christopher | Cohn, Dara | DuPuis, David | Fasano, Michael | Fazzio, Nicholas | Gavinski, Katherine | Gebreyesus, Heran | Giarla, Thomas | Gostelow, Marcus | Greenstein, Rachel | Gunasinghe, Hashini | Hanson, Casey | Hay, Amanda | He, Tao Jian | Homa, Katie | Howe, Ruth | Howenstein, Jeff | Huang, Henry | Khatri, Aaditya | Kim, Young Lu | Knowles, Olivia | Kong, Sarah | Krock, Rebecca | Kroll, Matt | Kuhn, Julia | Kwong, Matthew | Lee, Brandon | Lee, Ryan | Levine, Kevin | Li, Yedda | Liu, Bo | Liu, Lucy | Liu, Max | Lousararian, Adam | Ma, Jimmy | Mallya, Allyson | Manchee, Charlie | Marcus, Joseph | McDaniel, Stephen | Miller, Michelle L. | Molleston, Jerome M. | Diez, Cristina Montero | Ng, Patrick | Ngai, Natalie | Nguyen, Hien | Nylander, Andrew | Pollack, Jason | Rastogi, Suchita | Reddy, Himabindu | Regenold, Nathaniel | Sarezky, Jon | Schultz, Michael | Shim, Jien | Skorupa, Tara | Smith, Kenneth | Spencer, Sarah J. | Srikanth, Priya | Stancu, Gabriel | Stein, Andrew P. | Strother, Marshall | Sudmeier, Lisa | Sun, Mengyang | Sundaram, Varun | Tazudeen, Noor | Tseng, Alan | Tzeng, Albert | Venkat, Rohit | Venkataram, Sandeep | Waldman, Leah | Wang, Tracy | Yang, Hao | Yu, Jack Y. | Zheng, Yin | Preuss, Mary L. | Garcia, Angelica | Juergens, Matt | Morris, Robert W. | Nagengast, Alexis A. | Azarewicz, Julie | Carr, Thomas J. | Chichearo, Nicole | Colgan, Mike | Donegan, Megan | Gardner, Bob | Kolba, Nik | Krumm, Janice L. | Lytle, Stacey | MacMillian, Laurell | Miller, Mary | Montgomery, Andrew | Moretti, Alysha | Offenbacker, Brittney | Polen, Mike | Toth, John | Woytanowski, John | Kadlec, Lisa | Crawford, Justin | Spratt, Mary L. | Adams, Ashley L. | Barnard, Brianna K. | Cheramie, Martin N. | Eime, Anne M. | Golden, Kathryn L. | Hawkins, Allyson P. | Hill, Jessica E. | Kampmeier, Jessica A. | Kern, Cody D. | Magnuson, Emily E. | Miller, Ashley R. | Morrow, Cody M. | Peairs, Julia C. | Pickett, Gentry L. | Popelka, Sarah A. | Scott, Alexis J. | Teepe, Emily J. | TerMeer, Katie A. | Watchinski, Carmen A. | Watson, Lucas A. | Weber, Rachel E. | Woodard, Kate A. | Barnard, Daron C. | Appiah, Isaac | Giddens, Michelle M. | McNeil, Gerard P. | Adebayo, Adeola | Bagaeva, Kate
G3: Genes|Genomes|Genetics  2015;5(5):719-740.
The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.
doi:10.1534/g3.114.015966
PMCID: PMC4426361  PMID: 25740935
codon bias; evolution of heterochromatin; gene size; melting characteristics; transposons
2.  Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions 
The American naturalist  2016;188(4):379-397.
Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outlier methods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scan methods, including correcting for the confounding influence of a species’ demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, we make suggestions for best practices for maximizing the accuracy and efficiency of genome scans to detect the underlying genetic basis of local adaptation. With attention to their current limitations, genome scan methods can be an important tool in finding the genetic basis of adaptive evolutionary change.
doi:10.1086/688018
PMCID: PMC5457800  PMID: 27622873
local adaptation; genome scans; FST outliers; differentiation outlier; genetic-environment association; genetics of adaptation
3.  Discrepant Alcohol Use, Intimate Partner Violence, and Relationship Adjustment among Lesbian Women and their Relationship Partners 
Journal of family violence  2015;30(8):977-986.
This study examined the association between relationship adjustment and discrepant alcohol use among lesbian women and their same-sex intimate partners after controlling for verbal and physical aggression. Lesbian women (N = 819) who were members of online marketing research panels completed an online survey in which they reported both their own and same-sex intimate partner’s alcohol use, their relationship adjustment, and their own and their partner’s physical aggression and psychological aggression (i.e., verbal aggression and dominance/isolation). Partners’ alcohol use was moderately correlated. Discrepancy in alcohol use was associated with poorer relationship adjustment after controlling for psychological aggression and physical aggression. Results are discussed in terms of the similarity and differences with previous literature primarily focused on heterosexual couples.
doi:10.1007/s10896-015-9743-5
PMCID: PMC4607288  PMID: 26478657
lesbian women; same-sex intimate partner violence; relationship adjustment
4.  Common genetic variants in the CLDN2 and PRSS1-PRSS2 loci alter risk for alcohol-related and sporadic pancreatitis 
Whitcomb, David C. | LaRusch, Jessica | Krasinskas, Alyssa M. | Klei, Lambertus | Smith, Jill P. | Brand, Randall E. | Neoptolemos, John P. | Lerch, Markus M. | Tector, Matt | Sandhu, Bimaljit S. | Guda, Nalini M. | Orlichenko, Lidiya | Alkaade, Samer | Amann, Stephen T. | Anderson, Michelle A. | Baillie, John | Banks, Peter A. | Conwell, Darwin | Coté, Gregory A. | Cotton, Peter B. | DiSario, James | Farrer, Lindsay A. | Forsmark, Chris E. | Johnstone, Marianne | Gardner, Timothy B. | Gelrud, Andres | Greenhalf, William | Haines, Jonathan L. | Hartman, Douglas J. | Hawes, Robert A. | Lawrence, Christopher | Lewis, Michele | Mayerle, Julia | Mayeux, Richard | Melhem, Nadine M. | Money, Mary E. | Muniraj, Thiruvengadam | Papachristou, Georgios I. | Pericak-Vance, Margaret A. | Romagnuolo, Joseph | Schellenberg, Gerard D. | Sherman, Stuart | Simon, Peter | Singh, Vijay K. | Slivka, Adam | Stolz, Donna | Sutton, Robert | Weiss, Frank Ulrich | Wilcox, C. Mel | Zarnescu, Narcis Octavian | Wisniewski, Stephen R. | O'Connell, Michael R. | Kienholz, Michelle L. | Roeder, Kathryn | Barmada, M. Michael | Yadav, Dhiraj | Devlin, Bernie | Albert, Marilyn S. | Albin, Roger L. | Apostolova, Liana G. | Arnold, Steven E. | Baldwin, Clinton T. | Barber, Robert | Barnes, Lisa L. | Beach, Thomas G. | Beecham, Gary W. | Beekly, Duane | Bennett, David A. | Bigio, Eileen H. | Bird, Thomas D. | Blacker, Deborah | Boxer, Adam | Burke, James R. | Buxbaum, Joseph D. | Cairns, Nigel J. | Cantwell, Laura B. | Cao, Chuanhai | Carney, Regina M. | Carroll, Steven L. | Chui, Helena C. | Clark, David G. | Cribbs, David H. | Crocco, Elizabeth A. | Cruchaga, Carlos | DeCarli, Charles | Demirci, F. Yesim | Dick, Malcolm | Dickson, Dennis W. | Duara, Ranjan | Ertekin-Taner, Nilufer | Faber, Kelley M. | Fallon, Kenneth B. | Farlow, Martin R. | Ferris, Steven | Foroud, Tatiana M. | Frosch, Matthew P. | Galasko, Douglas R. | Ganguli, Mary | Gearing, Marla | Geschwind, Daniel H. | Ghetti, Bernardino | Gilbert, John R. | Gilman, Sid | Glass, Jonathan D. | Goate, Alison M. | Graff-Radford, Neill R. | Green, Robert C. | Growdon, John H. | Hakonarson, Hakon | Hamilton-Nelson, Kara L. | Hamilton, Ronald L. | Harrell, Lindy E. | Head, Elizabeth | Honig, Lawrence S. | Hulette, Christine M. | Hyman, Bradley T. | Jicha, Gregory A. | Jin, Lee-Way | Jun, Gyungah | Kamboh, M. Ilyas | Karydas, Anna | Kaye, Jeffrey A. | Kim, Ronald | Koo, Edward H. | Kowall, Neil W. | Kramer, Joel H. | Kramer, Patricia | Kukull, Walter A. | LaFerla, Frank M. | Lah, James J. | Leverenz, James B. | Levey, Allan I. | Li, Ge | Lin, Chiao-Feng | Lieberman, Andrew P. | Lopez, Oscar L. | Lunetta, Kathryn L. | Lyketsos, Constantine G. | Mack, Wendy J. | Marson, Daniel C. | Martin, Eden R. | Martiniuk, Frank | Mash, Deborah C. | Masliah, Eliezer | McKee, Ann C. | Mesulam, Marsel | Miller, Bruce L. | Miller, Carol A. | Miller, Joshua W. | Montine, Thomas J. | Morris, John C. | Murrell, Jill R. | Naj, Adam C. | Olichney, John M. | Parisi, Joseph E. | Peskind, Elaine | Petersen, Ronald C. | Pierce, Aimee | Poon, Wayne W. | Potter, Huntington | Quinn, Joseph F. | Raj, Ashok | Raskind, Murray | Reiman, Eric M. | Reisberg, Barry | Reitz, Christiane | Ringman, John M. | Roberson, Erik D. | Rosen, Howard J. | Rosenberg, Roger N. | Sano, Mary | Saykin, Andrew J. | Schneider, Julie A. | Schneider, Lon S. | Seeley, William W. | Smith, Amanda G. | Sonnen, Joshua A. | Spina, Salvatore | Stern, Robert A. | Tanzi, Rudolph E. | Trojanowski, John Q. | Troncoso, Juan C. | Tsuang, Debby W. | Valladares, Otto | Van Deerlin, Vivianna M. | Van Eldik, Linda J. | Vardarajan, Badri N. | Vinters, Harry V. | Vonsattel, Jean Paul | Wang, Li-San | Weintraub, Sandra | Welsh-Bohmer, Kathleen A. | Williamson, Jennifer | Woltjer, Randall L. | Wright, Clinton B. | Younkin, Steven G. | Yu, Chang-En | Yu, Lei
Nature genetics  2012;44(12):1349-1354.
Pancreatitis is a complex, progressively destructive inflammatory disorder. Alcohol was long thought to be the primary causative agent, but genetic contributions have been of interest since the discovery that rare PRSS1, CFTR, and SPINK1 variants were associated with pancreatitis risk. We now report two significant genome-wide associations identified and replicated at PRSS1-PRSS2 (1×10-12) and x-linked CLDN2 (p < 1×10-21) through a two-stage genome-wide study (Stage 1, 676 cases and 4507 controls; Stage 2, 910 cases and 4170 controls). The PRSS1 variant affects susceptibility by altering expression of the primary trypsinogen gene. The CLDN2 risk allele is associated with atypical localization of claudin-2 in pancreatic acinar cells. The homozygous (or hemizygous male) CLDN2 genotype confers the greatest risk, and its alleles interact with alcohol consumption to amplify risk. These results could partially explain the high frequency of alcohol-related pancreatitis in men – male hemizygous frequency is 0.26, female homozygote is 0.07.
doi:10.1038/ng.2466
PMCID: PMC3510344  PMID: 23143602
5.  Effects of low-fat dairy intake on blood pressure, endothelial function, and lipoprotein lipids in subjects with prehypertension or stage 1 hypertension 
Objective
This randomized crossover trial assessed the effects of 5 weeks of consuming low-fat dairy (one serving/day each of 1% fluid milk, low-fat cheese, and low-fat yogurt) versus nondairy products (one serving/day each of apple juice, pretzels, and cereal bar) on systolic and diastolic blood pressures (SBP and DBP), vascular function (reactive hyperemia index [RHI] and augmentation index), and plasma lipids.
Methods
Patients were 62 men and women (mean age 54.5 years, body mass index 29.2 kg/m2) with prehypertension or stage 1 hypertension (mean resting SBP/DBP 129.8 mmHg/80.8 mmHg) while not receiving antihypertensive medications. A standard breakfast meal challenge including two servings of study products was administered at the end of each treatment period.
Results
Dairy and nondairy treatments did not produce significantly different mean SBP or DBP in the resting postprandial state or from premeal to 3.5 hours postmeal (SBP, 126.3 mmHg versus 124.9 mmHg; DBP, 76.5 mmHg versus 75.7 mmHg), premeal (2.35 versus 2.20) or 2 hours postmeal (2.33 versus 2.30) RHI, and premeal (22.5 versus 23.8) or 2 hours postmeal (12.4 versus 13.2) augmentation index. Among subjects with endothelial dysfunction (RHI ≤ 1.67; n = 14) during the control treatment, premeal RHI was significantly higher in the dairy versus nondairy condition (2.32 versus 1.50, P = 0.002). Fasting lipoprotein lipid values were not significantly different between treatments overall, or in subgroup analyses.
Conclusion
No significant effects of consuming low-fat dairy products, compared with low-fat nondairy products, were observed for blood pressures, measures of vascular function, or lipid variables in the overall sample, but results from subgroup analyses were consistent with the hypothesis that dairy foods might improve RHI in those with endothelial dysfunction.
doi:10.2147/VHRM.S45684
PMCID: PMC3726585  PMID: 23901280
blood pressure; dairy; endothelial function; hypertension; lipids
6.  Toward a Neuroimaging Treatment Selection Biomarker for Major Depressive Disorder 
JAMA psychiatry  2013;70(8):821-829.
IMPORTANCE
Currently, fewer than 40% of patients treated for major depressive disorder achieve remission with initial treatment. Identification of a biological marker that might improve these odds could have significant health and economic impact.
OBJECTIVE
To identify a candidate neuroimaging “treatment-specific biomarker” that predicts differential outcome to either medication or psychotherapy.
DESIGN
Brain glucose metabolism was measured with positron emission tomography prior to treatment randomization to either escitalopram oxalate or cognitive behavior therapy for 12 weeks. Patients who did not remit on completion of their phase 1 treatment were offered enrollment in phase 2 comprising an additional 12 weeks of treatment with combination escitalopram and cognitive behavior therapy.
SETTING
Mood and anxiety disorders research program at an academic medical center.
PARTICIPANTS
Men and women aged 18 to 60 years with currently untreated major depressive disorder.
INTERVENTION
Randomized assignment to 12 weeks of treatment with either escitalopram oxalate (10–20 mg/d) or 16 sessions of manual-based cognitive behavior therapy.
MAIN OUTCOME AND MEASURE
Remission, defined as a 17-item Hamilton Depression Rating Scale score of 7 or less at both weeks 10 and 12, as assessed by raters blinded to treatment.
RESULTS
Positive and negative predictors of remission were identified with a 2-way analysis of variance treatment (escitalopram or cognitive behavior therapy) × outcome (remission or nonresponse) interaction. Of 65 protocol completers, 38 patients with clear outcomes and usable positron emission tomography scans were included in the primary analysis: 12 remitters to cognitive behavior therapy, 11 remitters to escitalopram, 9 nonresponders to cognitive behavior therapy, and 6 nonresponders to escitalopram. Six limbic and cortical regions were identified, with the right anterior insula showing the most robust discriminant properties across groups (effect size = 1.43). Insula hypometabolism (relative to whole-brain mean) was associated with remission to cognitive behavior therapy and poor response to escitalopram, while insula hypermetabolism was associated with remission to escitalopram and poor response to cognitive behavior therapy.
CONCLUSIONS AND RELEVANCE
If verified with prospective testing, the insula metabolism-based treatment-specific biomarker defined in this study provides the first objective marker, to our knowledge, to guide initial treatment selection for depression.
TRIAL REGISTRATION
Registered at clinicaltrials.gov (NCT00367341)
doi:10.1001/jamapsychiatry.2013.143
PMCID: PMC4413467  PMID: 23760393
7.  Identification of six new susceptibility loci for invasive epithelial ovarian cancer 
Kuchenbaecker, Karoline B. | Ramus, Susan J. | Tyrer, Jonathan | Lee, Andrew | Shen, Howard C. | Beesley, Jonathan | Lawrenson, Kate | McGuffog, Lesley | Healey, Sue | Lee, Janet M. | Spindler, Tassja J. | Lin, Yvonne G. | Pejovic, Tanja | Bean, Yukie | Li, Qiyuan | Coetzee, Simon | Hazelett, Dennis | Miron, Alexander | Southey, Melissa | Terry, Mary Beth | Goldgar, David E. | Buys, Saundra S. | Janavicius, Ramunas | Dorfling, Cecilia M. | van Rensburg, Elizabeth J. | Neuhausen, Susan L. | Ding, Yuan Chun | Hansen, Thomas V. O. | Jønson, Lars | Gerdes, Anne-Marie | Ejlertsen, Bent | Barrowdale, Daniel | Dennis, Joe | Benitez, Javier | Osorio, Ana | Garcia, Maria Jose | Komenaka, Ian | Weitzel, Jeffrey N. | Ganschow, Pamela | Peterlongo, Paolo | Bernard, Loris | Viel, Alessandra | Bonanni, Bernardo | Peissel, Bernard | Manoukian, Siranoush | Radice, Paolo | Papi, Laura | Ottini, Laura | Fostira, Florentia | Konstantopoulou, Irene | Garber, Judy | Frost, Debra | Perkins, Jo | Platte, Radka | Ellis, Steve | Godwin, Andrew K. | Schmutzler, Rita Katharina | Meindl, Alfons | Engel, Christoph | Sutter, Christian | Sinilnikova, Olga M. | Damiola, Francesca | Mazoyer, Sylvie | Stoppa-Lyonnet, Dominique | Claes, Kathleen | De Leeneer, Kim | Kirk, Judy | Rodriguez, Gustavo C. | Piedmonte, Marion | O'Malley, David M. | de la Hoya, Miguel | Caldes, Trinidad | Aittomäki, Kristiina | Nevanlinna, Heli | Collée, J. Margriet | Rookus, Matti A. | Oosterwijk, Jan C. | Tihomirova, Laima | Tung, Nadine | Hamann, Ute | Isaacs, Claudine | Tischkowitz, Marc | Imyanitov, Evgeny N. | Caligo, Maria A. | Campbell, Ian | Hogervorst, Frans B.L. | Olah, Edith | Diez, Orland | Blanco, Ignacio | Brunet, Joan | Lazaro, Conxi | Pujana, Miquel Angel | Jakubowska, Anna | Gronwald, Jacek | Lubinski, Jan | Sukiennicki, Grzegorz | Barkardottir, Rosa B. | Plante, Marie | Simard, Jacques | Soucy, Penny | Montagna, Marco | Tognazzo, Silvia | Teixeira, Manuel R. | Pankratz, Vernon S. | Wang, Xianshu | Lindor, Noralane | Szabo, Csilla I. | Kauff, Noah | Vijai, Joseph | Aghajanian, Carol A. | Pfeiler, Georg | Berger, Andreas | Singer, Christian F. | Tea, Muy-Kheng | Phelan, Catherine M. | Greene, Mark H. | Mai, Phuong L. | Rennert, Gad | Mulligan, Anna Marie | Tchatchou, Sandrine | Andrulis, Irene L. | Glendon, Gord | Toland, Amanda Ewart | Jensen, Uffe Birk | Kruse, Torben A. | Thomassen, Mads | Bojesen, Anders | Zidan, Jamal | Friedman, Eitan | Laitman, Yael | Soller, Maria | Liljegren, Annelie | Arver, Brita | Einbeigi, Zakaria | Stenmark-Askmalm, Marie | Olopade, Olufunmilayo I. | Nussbaum, Robert L. | Rebbeck, Timothy R. | Nathanson, Katherine L. | Domchek, Susan M. | Lu, Karen H. | Karlan, Beth Y. | Walsh, Christine | Lester, Jenny | Hein, Alexander | Ekici, Arif B. | Beckmann, Matthias W. | Fasching, Peter A. | Lambrechts, Diether | Nieuwenhuysen, Els Van | Vergote, Ignace | Lambrechts, Sandrina | Dicks, Ed | Doherty, Jennifer A. | Wicklund, Kristine G. | Rossing, Mary Anne | Rudolph, Anja | Chang-Claude, Jenny | Wang-Gohrke, Shan | Eilber, Ursula | Moysich, Kirsten B. | Odunsi, Kunle | Sucheston-Campbell, Lara | Lele, Shashi | Wilkens, Lynne R. | Goodman, Marc T. | Thompson, Pamela J. | Shvetsov, Yurii B. | Runnebaum, Ingo B. | Dürst, Matthias | Hillemanns, Peter | Dörk, Thilo | Antonenkova, Natalia | Bogdanova, Natalia | Leminen, Arto | Pelttari, Liisa M. | Butzow, Ralf | Modugno, Francesmary | Kelley, Joseph L. | Edwards, Robert P. | Ness, Roberta B. | du Bois, Andreas | Heitz, Florian | Schwaab, Ira | Harter, Philipp | Matsuo, Keitaro | Hosono, Satoyo | Orsulic, Sandra | Jensen, Allan | Kjaer, Susanne Kruger | Hogdall, Estrid | Hasmad, Hanis Nazihah | Noor Azmi, Mat Adenan | Teo, Soo-Hwang | Woo, Yin-Ling | Fridley, Brooke L. | Goode, Ellen L. | Cunningham, Julie M. | Vierkant, Robert A. | Bruinsma, Fiona | Giles, Graham G. | Liang, Dong | Hildebrandt, Michelle A.T. | Wu, Xifeng | Levine, Douglas A. | Bisogna, Maria | Berchuck, Andrew | Iversen, Edwin S. | Schildkraut, Joellen M. | Concannon, Patrick | Weber, Rachel Palmieri | Cramer, Daniel W. | Terry, Kathryn L. | Poole, Elizabeth M. | Tworoger, Shelley S. | Bandera, Elisa V. | Orlow, Irene | Olson, Sara H. | Krakstad, Camilla | Salvesen, Helga B. | Tangen, Ingvild L. | Bjorge, Line | van Altena, Anne M. | Aben, Katja K.H. | Kiemeney, Lambertus A. | Massuger, Leon F.A.G. | Kellar, Melissa | Brooks-Wilson, Angela | Kelemen, Linda E. | Cook, Linda S. | Le, Nhu D. | Cybulski, Cezary | Yang, Hannah | Lissowska, Jolanta | Brinton, Louise A. | Wentzensen, Nicolas | Hogdall, Claus | Lundvall, Lene | Nedergaard, Lotte | Baker, Helen | Song, Honglin | Eccles, Diana | McNeish, Ian | Paul, James | Carty, Karen | Siddiqui, Nadeem | Glasspool, Rosalind | Whittemore, Alice S. | Rothstein, Joseph H. | McGuire, Valerie | Sieh, Weiva | Ji, Bu-Tian | Zheng, Wei | Shu, Xiao-Ou | Gao, Yu-Tang | Rosen, Barry | Risch, Harvey A. | McLaughlin, John R. | Narod, Steven A. | Monteiro, Alvaro N. | Chen, Ann | Lin, Hui-Yi | Permuth-Wey, Jenny | Sellers, Thomas A. | Tsai, Ya-Yu | Chen, Zhihua | Ziogas, Argyrios | Anton-Culver, Hoda | Gentry-Maharaj, Aleksandra | Menon, Usha | Harrington, Patricia | Lee, Alice W. | Wu, Anna H. | Pearce, Celeste L. | Coetzee, Gerhard A. | Pike, Malcolm C. | Dansonka-Mieszkowska, Agnieszka | Timorek, Agnieszka | Rzepecka, Iwona K. | Kupryjanczyk, Jolanta | Freedman, Matt | Noushmehr, Houtan | Easton, Douglas F. | Offit, Kenneth | Couch, Fergus J. | Gayther, Simon | Pharoah, Paul P. | Antoniou, Antonis C. | Chenevix-Trench, Georgia
Nature genetics  2015;47(2):164-171.
doi:10.1038/ng.3185
PMCID: PMC4445140  PMID: 25581431
8.  Common variants in MS4A4/MS4A6E, CD2uAP, CD33, and EPHA1 are associated with late-onset Alzheimer’s disease 
Naj, Adam C | Jun, Gyungah | Beecham, Gary W | Wang, Li-San | Vardarajan, Badri Narayan | Buros, Jacqueline | Gallins, Paul J | Buxbaum, Joseph D | Jarvik, Gail P | Crane, Paul K | Larson, Eric B | Bird, Thomas D | Boeve, Bradley F | Graff-Radford, Neill R | De Jager, Philip L | Evans, Denis | Schneider, Julie A | Carrasquillo, Minerva M | Ertekin-Taner, Nilufer | Younkin, Steven G | Cruchaga, Carlos | Kauwe, John SK | Nowotny, Petra | Kramer, Patricia | Hardy, John | Huentelman, Matthew J | Myers, Amanda J | Barmada, Michael M | Demirci, F. Yesim | Baldwin, Clinton T | Green, Robert C | Rogaeva, Ekaterina | St George-Hyslop, Peter | Arnold, Steven E | Barber, Robert | Beach, Thomas | Bigio, Eileen H | Bowen, James D | Boxer, Adam | Burke, James R | Cairns, Nigel J | Carlson, Chris S | Carney, Regina M | Carroll, Steven L | Chui, Helena C | Clark, David G | Corneveaux, Jason | Cotman, Carl W | Cummings, Jeffrey L | DeCarli, Charles | DeKosky, Steven T | Diaz-Arrastia, Ramon | Dick, Malcolm | Dickson, Dennis W | Ellis, William G | Faber, Kelley M | Fallon, Kenneth B | Farlow, Martin R | Ferris, Steven | Frosch, Matthew P | Galasko, Douglas R | Ganguli, Mary | Gearing, Marla | Geschwind, Daniel H | Ghetti, Bernardino | Gilbert, John R | Gilman, Sid | Giordani, Bruno | Glass, Jonathan D | Growdon, John H | Hamilton, Ronald L | Harrell, Lindy E | Head, Elizabeth | Honig, Lawrence S | Hulette, Christine M | Hyman, Bradley T | Jicha, Gregory A | Jin, Lee-Way | Johnson, Nancy | Karlawish, Jason | Karydas, Anna | Kaye, Jeffrey A | Kim, Ronald | Koo, Edward H | Kowall, Neil W | Lah, James J | Levey, Allan I | Lieberman, Andrew P | Lopez, Oscar L | Mack, Wendy J | Marson, Daniel C | Martiniuk, Frank | Mash, Deborah C | Masliah, Eliezer | McCormick, Wayne C | McCurry, Susan M | McDavid, Andrew N | McKee, Ann C | Mesulam, Marsel | Miller, Bruce L | Miller, Carol A | Miller, Joshua W | Parisi, Joseph E | Perl, Daniel P | Peskind, Elaine | Petersen, Ronald C | Poon, Wayne W | Quinn, Joseph F | Rajbhandary, Ruchita A | Raskind, Murray | Reisberg, Barry | Ringman, John M | Roberson, Erik D | Rosenberg, Roger N | Sano, Mary | Schneider, Lon S | Seeley, William | Shelanski, Michael L | Slifer, Michael A | Smith, Charles D | Sonnen, Joshua A | Spina, Salvatore | Stern, Robert A | Tanzi, Rudolph E | Trojanowski, John Q | Troncoso, Juan C | Deerlin, Vivianna M Van | Vinters, Harry V | Vonsattel, Jean Paul | Weintraub, Sandra | Welsh-Bohmer, Kathleen A | Williamson, Jennifer | Woltjer, Randall L | Cantwell, Laura B | Dombroski, Beth A | Beekly, Duane | Lunetta, Kathryn L | Martin, Eden R | Kamboh, M. Ilyas | Saykin, Andrew J | Reiman, Eric M | Bennett, David A | Morris, John C | Montine, Thomas J | Goate, Alison M | Blacker, Deborah | Tsuang, Debby W | Hakonarson, Hakon | Kukull, Walter A | Foroud, Tatiana M | Haines, Jonathan L | Mayeux, Richard | Pericak-Vance, Margaret A | Farrer, Lindsay A | Schellenberg, Gerard D
Nature genetics  2011;43(5):436-441.
The Alzheimer Disease Genetics Consortium (ADGC) performed a genome-wide association study (GWAS) of late-onset Alzheimer disease (LOAD) using a 3 stage design consisting of a discovery stage (Stage 1) and two replication stages (Stages 2 and 3). Both joint and meta-analysis analysis approaches were used. We obtained genome-wide significant results at MS4A4A [rs4938933; Stages 1+2, meta-analysis (PM) = 1.7 × 10−9, joint analysis (PJ) = 1.7 × 10−9; Stages 1–3, PM = 8.2 × 10−12], CD2AP (rs9349407; Stages 1–3, PM = 8.6 × 10−9), EPHA1 (rs11767557; Stages 1–3 PM = 6.0 × 10−10), and CD33 (rs3865444; Stages 1–3, PM = 1.6 × 10−9). We confirmed that CR1 (rs6701713; PM = 4.6×10−10, PJ = 5.2×10−11), CLU (rs1532278; PM = 8.3 × 10−8, PJ = 1.9×10−8), BIN1 (rs7561528; PM = 4.0×10−14; PJ = 5.2×10−14), and PICALM (rs561655; PM = 7.0 × 10−11, PJ = 1.0×10−10) but not EXOC3L2 are LOAD risk loci1–3.
doi:10.1038/ng.801
PMCID: PMC3090745  PMID: 21460841
9.  Assessment of variation in immunosuppressive pathway genes reveals TGFBR2 to be associated with risk of clear cell ovarian cancer 
Hampras, Shalaka S. | Sucheston-Campbell, Lara E. | Cannioto, Rikki | Chang-Claude, Jenny | Modugno, Francesmary | Dörk, Thilo | Hillemanns, Peter | Preus, Leah | Knutson, Keith L. | Wallace, Paul K. | Hong, Chi-Chen | Friel, Grace | Davis, Warren | Nesline, Mary | Pearce, Celeste L. | Kelemen, Linda E. | Goodman, Marc T. | Bandera, Elisa V. | Terry, Kathryn L. | Schoof, Nils | Eng, Kevin H. | Clay, Alyssa | Singh, Prashant K. | Joseph, Janine M. | Aben, Katja K.H. | Anton-Culver, Hoda | Antonenkova, Natalia | Baker, Helen | Bean, Yukie | Beckmann, Matthias W. | Bisogna, Maria | Bjorge, Line | Bogdanova, Natalia | Brinton, Louise A. | Brooks-Wilson, Angela | Bruinsma, Fiona | Butzow, Ralf | Campbell, Ian G. | Carty, Karen | Cook, Linda S. | Cramer, Daniel W. | Cybulski, Cezary | Dansonka-Mieszkowska, Agnieszka | Dennis, Joe | Despierre, Evelyn | Dicks, Ed | Doherty, Jennifer A. | du Bois, Andreas | Dürst, Matthias | Easton, Doug | Eccles, Diana | Edwards, Robert P. | Ekici, Arif B. | Fasching, Peter A. | Fridley, Brooke L. | Gao, Yu-Tang | Gentry-Maharaj, Aleksandra | Giles, Graham G. | Glasspool, Rosalind | Gronwald, Jacek | Harrington, Patricia | Harter, Philipp | Hasmad, Hanis Nazihah | Hein, Alexander | Heitz, Florian | Hildebrandt, Michelle A.T. | Hogdall, Claus | Hogdall, Estrid | Hosono, Satoyo | Iversen, Edwin S. | Jakubowska, Anna | Jensen, Allan | Ji, Bu-Tian | Karlan, Beth Y. | Kellar, Melissa | Kelley, Joseph L. | Kiemeney, Lambertus A. | Klapdor, Rüdiger | Kolomeyevskaya, Nonna | Krakstad, Camilla | Kjaer, Susanne K. | Kruszka, Bridget | Kupryjanczyk, Jolanta | Lambrechts, Diether | Lambrechts, Sandrina | Le, Nhu D. | Lee, Alice W. | Lele, Shashikant | Leminen, Arto | Lester, Jenny | Levine, Douglas A. | Liang, Dong | Lissowska, Jolanta | Liu, Song | Lu, Karen | Lubinski, Jan | Lundvall, Lene | Massuger, Leon F.A.G. | Matsuo, Keitaro | McGuire, Valeria | McLaughlin, John R. | McNeish, Ian | Menon, Usha | Moes-Sosnowska, Joanna | Narod, Steven A. | Nedergaard, Lotte | Nevanlinna, Heli | Nickels, Stefan | Olson, Sara H. | Orlow, Irene | Weber, Rachel Palmieri | Paul, James | Pejovic, Tanja | Pelttari, Liisa M. | Perkins, Barbara | Permuth-Wey, Jenny | Pike, Malcolm C. | Plisiecka-Halasa, Joanna | Poole, Elizabeth M. | Risch, Harvey A. | Rossing, Mary Anne | Rothstein, Joseph H. | Rudolph, Anja | Runnebaum, Ingo B. | Rzepecka, Iwona K. | Salvesen, Helga B. | Schernhammer, Eva | Schmitt, Kristina | Schwaab, Ira | Shu, Xiao-Ou | Shvetsov, Yurii B | Siddiqui, Nadeem | Sieh, Weiva | Song, Honglin | Southey, Melissa C. | Tangen, Ingvild L. | Teo, Soo-Hwang | Thompson, Pamela J. | Timorek, Agnieszka | Tsai, Ya-Yu | Tworoger, Shelley S. | Tyrer, Jonathan | van Altena, Anna M. | Vergote, Ignace | Vierkant, Robert A. | Walsh, Christine | Wang-Gohrke, Shan | Wentzensen, Nicolas | Whittemore, Alice S. | Wicklund, Kristine G. | Wilkens, Lynne R. | Wu, Anna H. | Wu, Xifeng | Woo, Yin-Ling | Yang, Hannah | Zheng, Wei | Ziogas, Argyrios | Gayther, Simon A. | Ramus, Susan J. | Sellers, Thomas A. | Schildkraut, Joellen M. | Phelan, Catherine M. | Berchuck, Andrew | Chenevix-Trench, Georgia | Cunningham, Julie M. | Pharoah, Paul P. | Ness, Roberta B. | Odunsi, Kunle | Goode, Ellen L. | Moysich, Kirsten B.
Oncotarget  2016;7(43):69097-69110.
Background
Regulatory T (Treg) cells, a subset of CD4+ T lymphocytes, are mediators of immunosuppression in cancer, and, thus, variants in genes encoding Treg cell immune molecules could be associated with ovarian cancer.
Methods
In a population of 15,596 epithelial ovarian cancer (EOC) cases and 23,236 controls, we measured genetic associations of 1,351 SNPs in Treg cell pathway genes with odds of ovarian cancer and tested pathway and gene-level associations, overall and by histotype, for the 25 genes, using the admixture likelihood (AML) method. The most significant single SNP associations were tested for correlation with expression levels in 44 ovarian cancer patients.
Results
The most significant global associations for all genes in the pathway were seen in endometrioid (p = 0.082) and clear cell (p = 0.083), with the most significant gene level association seen with (p = 0.001) and clear cell EOC. Gene associations with histotypes at< 0.05 included:(p = 0.005 and = 0.008, serous and high-grade serous, respectively), (p = 0.035, endometrioid and mucinous), (p = 0.03, mucinous), (p = 0.022, clear cell), (p = 0.021 endometrioid) and (p = 0.017 and = 0.025, endometrioid and mucinous, respectively).
Conclusions
Common inherited gene variation in Treg cell pathways shows some evidence of germline genetic contribution to odds of EOC that varies by histologic subtype and may be associated with mRNA expression of immune-complex receptor in EOC patients.
doi:10.18632/oncotarget.10215
PMCID: PMC5340115  PMID: 27533245
ovarian cancer; immunosuppression; biomarkers; genetic variation; TGFBR2
10.  Development of Functional Sex Differences in the Larynx of Xenopus laevis 
Developmental biology  1991;147(1):251-259.
Three laryngeal properties associated with the production of masculine song—laryngeal muscle tension, fiber twitch type, and fiber recruitment—are markedly sexually dimorphic in adult Xenopus laevis frogs. To elucidate the pattern of sexual differentiation, tension and fiber recruitment in male and female larynges and fiber twitch type in male larynges were examined throughout postmetamorphic development. Masculinization of male laryngeal properties begins early in postmetamorphic development and continues until adulthood. In contrast, tension and fiber recruitment in females do not change after the end of metamorphosis. Laryngeal muscle tension and fiber type are gradually and progressively masculinized; the temporal pattern of masculinization is very similar for these properties. Fiber recruitment, on the other hand, appears to masculinize in a stepwise manner. Masculinization of all three properties is highly correlated with larynx weight in males. We have used this relation to divide postmetamorphic development into seven stages associated with key events in sexual differentiation. This staging scheme provides an important experimental tool for studying the hormonal regulation of sexual differentiation, the subject of the accompanying paper.
PMCID: PMC3493208  PMID: 1879611
12.  Alternating Hemiplegia of Childhood: Retrospective Genetic Study and Genotype-Phenotype Correlations in 187 Subjects from the US AHCF Registry 
PLoS ONE  2015;10(5):e0127045.
Mutations in ATP1A3 cause Alternating Hemiplegia of Childhood (AHC) by disrupting function of the neuronal Na+/K+ ATPase. Published studies to date indicate 2 recurrent mutations, D801N and E815K, and a more severe phenotype in the E815K cohort. We performed mutation analysis and retrospective genotype-phenotype correlations in all eligible patients with AHC enrolled in the US AHC Foundation registry from 1997-2012. Clinical data were abstracted from standardized caregivers’ questionnaires and medical records and confirmed by expert clinicians. We identified ATP1A3 mutations by Sanger and whole genome sequencing, and compared phenotypes within and between 4 groups of subjects, those with D801N, E815K, other ATP1A3 or no ATP1A3 mutations. We identified heterozygous ATP1A3 mutations in 154 of 187 (82%) AHC patients. Of 34 unique mutations, 31 (91%) are missense, and 16 (47%) had not been previously reported. Concordant with prior studies, more than 2/3 of all mutations are clustered in exons 17 and 18. Of 143 simplex occurrences, 58 had D801N (40%), 38 had E815K (26%) and 11 had G937R (8%) mutations. Patients with an E815K mutation demonstrate an earlier age of onset, more severe motor impairment and a higher prevalence of status epilepticus. This study further expands the number and spectrum of ATP1A3 mutations associated with AHC and confirms a more deleterious effect of the E815K mutation on selected neurologic outcomes. However, the complexity of the disorder and the extensive phenotypic variability among subgroups merits caution and emphasizes the need for further studies.
doi:10.1371/journal.pone.0127045
PMCID: PMC4440742  PMID: 25996915
13.  PALB2, CHEK2 and ATM rare variants and cancer risk: data from COGS 
Southey, Melissa C | Goldgar, David E | Winqvist, Robert | Pylkäs, Katri | Couch, Fergus | Tischkowitz, Marc | Foulkes, William D | Dennis, Joe | Michailidou, Kyriaki | van Rensburg, Elizabeth J | Heikkinen, Tuomas | Nevanlinna, Heli | Hopper, John L | Dörk, Thilo | Claes, Kathleen BM | Reis-Filho, Jorge | Teo, Zhi Ling | Radice, Paolo | Catucci, Irene | Peterlongo, Paolo | Tsimiklis, Helen | Odefrey, Fabrice A | Dowty, James G | Schmidt, Marjanka K | Broeks, Annegien | Hogervorst, Frans B | Verhoef, Senno | Carpenter, Jane | Clarke, Christine | Scott, Rodney J | Fasching, Peter A | Haeberle, Lothar | Ekici, Arif B | Beckmann, Matthias W | Peto, Julian | dos-Santos-Silva, Isabel | Fletcher, Olivia | Johnson, Nichola | Bolla, Manjeet K | Sawyer, Elinor J | Tomlinson, Ian | Kerin, Michael J | Miller, Nicola | Marme, Federik | Burwinkel, Barbara | Yang, Rongxi | Guénel, Pascal | Truong, Thérèse | Menegaux, Florence | Sanchez, Marie | Bojesen, Stig | Nielsen, Sune F | Flyger, Henrik | Benitez, Javier | Zamora, M Pilar | Perez, Jose Ignacio Arias | Menéndez, Primitiva | Anton-Culver, Hoda | Neuhausen, Susan | Ziogas, Argyrios | Clarke, Christina A | Brenner, Hermann | Arndt, Volker | Stegmaier, Christa | Brauch, Hiltrud | Brüning, Thomas | Ko, Yon-Dschun | Muranen, Taru A | Aittomäki, Kristiina | Blomqvist, Carl | Bogdanova, Natalia V | Antonenkova, Natalia N | Lindblom, Annika | Margolin, Sara | Mannermaa, Arto | Kataja, Vesa | Kosma, Veli-Matti | Hartikainen, Jaana M | Spurdle, Amanda B | Investigators, kConFab | Wauters, Els | Smeets, Dominiek | Beuselinck, Benoit | Floris, Giuseppe | Chang-Claude, Jenny | Rudolph, Anja | Seibold, Petra | Flesch-Janys, Dieter | Olson, Janet E | Vachon, Celine | Pankratz, Vernon S | McLean, Catriona | Haiman, Christopher A | Henderson, Brian E | Schumacher, Fredrick | Le Marchand, Loic | Kristensen, Vessela | Alnæs, Grethe Grenaker | Zheng, Wei | Hunter, David J | Lindstrom, Sara | Hankinson, Susan E | Kraft, Peter | Andrulis, Irene | Knight, Julia A | Glendon, Gord | Mulligan, Anna Marie | Jukkola-Vuorinen, Arja | Grip, Mervi | Kauppila, Saila | Devilee, Peter | Tollenaar, Robert A E M | Seynaeve, Caroline | Hollestelle, Antoinette | Garcia-Closas, Montserrat | Figueroa, Jonine | Chanock, Stephen J | Lissowska, Jolanta | Czene, Kamila | Darabi, Hatef | Eriksson, Mikael | Eccles, Diana M | Rafiq, Sajjad | Tapper, William J | Gerty, Sue M | Hooning, Maartje J | Martens, John W M | Collée, J Margriet | Tilanus-Linthorst, Madeleine | Hall, Per | Li, Jingmei | Brand, Judith S | Humphreys, Keith | Cox, Angela | Reed, Malcolm W R | Luccarini, Craig | Baynes, Caroline | Dunning, Alison M | Hamann, Ute | Torres, Diana | Ulmer, Hans Ulrich | Rüdiger, Thomas | Jakubowska, Anna | Lubinski, Jan | Jaworska, Katarzyna | Durda, Katarzyna | Slager, Susan | Toland, Amanda E | Ambrosone, Christine B | Yannoukakos, Drakoulis | Swerdlow, Anthony | Ashworth, Alan | Orr, Nick | Jones, Michael | González-Neira, Anna | Pita, Guillermo | Alonso, M Rosario | Álvarez, Nuria | Herrero, Daniel | Tessier, Daniel C | Vincent, Daniel | Bacot, Francois | Simard, Jacques | Dumont, Martine | Soucy, Penny | Eeles, Rosalind | Muir, Kenneth | Wiklund, Fredrik | Gronberg, Henrik | Schleutker, Johanna | Nordestgaard, Børge G | Weischer, Maren | Travis, Ruth C | Neal, David | Donovan, Jenny L | Hamdy, Freddie C | Khaw, Kay-Tee | Stanford, Janet L | Blot, William J | Thibodeau, Stephen | Schaid, Daniel J | Kelley, Joseph L | Maier, Christiane | Kibel, Adam S | Cybulski, Cezary | Cannon-Albright, Lisa | Butterbach, Katja | Park, Jong | Kaneva, Radka | Batra, Jyotsna | Teixeira, Manuel R | Kote-Jarai, Zsofia | Olama, Ali Amin Al | Benlloch, Sara | Renner, Stefan P | Hartmann, Arndt | Hein, Alexander | Ruebner, Matthias | Lambrechts, Diether | Van Nieuwenhuysen, Els | Vergote, Ignace | Lambretchs, Sandrina | Doherty, Jennifer A | Rossing, Mary Anne | Nickels, Stefan | Eilber, Ursula | Wang-Gohrke, Shan | Odunsi, Kunle | Sucheston-Campbell, Lara E | Friel, Grace | Lurie, Galina | Killeen, Jeffrey L | Wilkens, Lynne R | Goodman, Marc T | Runnebaum, Ingo | Hillemanns, Peter A | Pelttari, Liisa M | Butzow, Ralf | Modugno, Francesmary | Edwards, Robert P | Ness, Roberta B | Moysich, Kirsten B | du Bois, Andreas | Heitz, Florian | Harter, Philipp | Kommoss, Stefan | Karlan, Beth Y | Walsh, Christine | Lester, Jenny | Jensen, Allan | Kjaer, Susanne Krüger | Høgdall, Estrid | Peissel, Bernard | Bonanni, Bernardo | Bernard, Loris | Goode, Ellen L | Fridley, Brooke L | Vierkant, Robert A | Cunningham, Julie M | Larson, Melissa C | Fogarty, Zachary C | Kalli, Kimberly R | Liang, Dong | Lu, Karen H | Hildebrandt, Michelle A T | Wu, Xifeng | Levine, Douglas A | Dao, Fanny | Bisogna, Maria | Berchuck, Andrew | Iversen, Edwin S | Marks, Jeffrey R | Akushevich, Lucy | Cramer, Daniel W | Schildkraut, Joellen | Terry, Kathryn L | Poole, Elizabeth M | Stampfer, Meir | Tworoger, Shelley S | Bandera, Elisa V | Orlow, Irene | Olson, Sara H | Bjorge, Line | Salvesen, Helga B | van Altena, Anne M | Aben, Katja K H | Kiemeney, Lambertus A | Massuger, Leon F A G | Pejovic, Tanja | Bean, Yukie | Brooks-Wilson, Angela | Kelemen, Linda E | Cook, Linda S | Le, Nhu D | Górski, Bohdan | Gronwald, Jacek | Menkiszak, Janusz | Høgdall, Claus K | Lundvall, Lene | Nedergaard, Lotte | Engelholm, Svend Aage | Dicks, Ed | Tyrer, Jonathan | Campbell, Ian | McNeish, Iain | Paul, James | Siddiqui, Nadeem | Glasspool, Rosalind | Whittemore, Alice S | Rothstein, Joseph H | McGuire, Valerie | Sieh, Weiva | Cai, Hui | Shu, Xiao-Ou | Teten, Rachel T | Sutphen, Rebecca | McLaughlin, John R | Narod, Steven A | Phelan, Catherine M | Monteiro, Alvaro N | Fenstermacher, David | Lin, Hui-Yi | Permuth, Jennifer B | Sellers, Thomas A | Chen, Y Ann | Tsai, Ya-Yu | Chen, Zhihua | Gentry-Maharaj, Aleksandra | Gayther, Simon A | Ramus, Susan J | Menon, Usha | Wu, Anna H | Pearce, Celeste L | Van Den Berg, David | Pike, Malcolm C | Dansonka-Mieszkowska, Agnieszka | Plisiecka-Halasa, Joanna | Moes-Sosnowska, Joanna | Kupryjanczyk, Jolanta | Pharoah, Paul DP | Song, Honglin | Winship, Ingrid | Chenevix-Trench, Georgia | Giles, Graham G | Tavtigian, Sean V | Easton, Doug F | Milne, Roger L
Journal of Medical Genetics  2016;53(12):800-811.
Background
The rarity of mutations in PALB2, CHEK2 and ATM make it difficult to estimate precisely associated cancer risks. Population-based family studies have provided evidence that at least some of these mutations are associated with breast cancer risk as high as those associated with rare BRCA2 mutations. We aimed to estimate the relative risks associated with specific rare variants in PALB2, CHEK2 and ATM via a multicentre case-control study.
Methods
We genotyped 10 rare mutations using the custom iCOGS array: PALB2 c.1592delT, c.2816T>G and c.3113G>A, CHEK2 c.349A>G, c.538C>T, c.715G>A, c.1036C>T, c.1312G>T, and c.1343T>G and ATM c.7271T>G. We assessed associations with breast cancer risk (42 671 cases and 42 164 controls), as well as prostate (22 301 cases and 22 320 controls) and ovarian (14 542 cases and 23 491 controls) cancer risk, for each variant.
Results
For European women, strong evidence of association with breast cancer risk was observed for PALB2 c.1592delT OR 3.44 (95% CI 1.39 to 8.52, p=7.1×10−5), PALB2 c.3113G>A OR 4.21 (95% CI 1.84 to 9.60, p=6.9×10−8) and ATM c.7271T>G OR 11.0 (95% CI 1.42 to 85.7, p=0.0012). We also found evidence of association with breast cancer risk for three variants in CHEK2, c.349A>G OR 2.26 (95% CI 1.29 to 3.95), c.1036C>T OR 5.06 (95% CI 1.09 to 23.5) and c.538C>T OR 1.33 (95% CI 1.05 to 1.67) (p≤0.017). Evidence for prostate cancer risk was observed for CHEK2 c.1343T>G OR 3.03 (95% CI 1.53 to 6.03, p=0.0006) for African men and CHEK2 c.1312G>T OR 2.21 (95% CI 1.06 to 4.63, p=0.030) for European men. No evidence of association with ovarian cancer was found for any of these variants.
Conclusions
This report adds to accumulating evidence that at least some variants in these genes are associated with an increased risk of breast cancer that is clinically important.
doi:10.1136/jmedgenet-2016-103839
PMCID: PMC5200636  PMID: 27595995
Cancer: breast; Cancer: prostate; Genetics; Cancer: ovary; cancer predisposition
14.  PALB2, CHEK2 and ATM rare variants and cancer risk: data from COGS 
Southey, Melissa C | Goldgar, David E | Winqvist, Robert | Pylkäs, Katri | Couch, Fergus | Tischkowitz, Marc | Foulkes, William D | Dennis, Joe | Michailidou, Kyriaki | van Rensburg, Elizabeth J | Heikkinen, Tuomas | Nevanlinna, Heli | Hopper, John L | Dörk, Thilo | Claes, Kathleen BM | Reis-Filho, Jorge | Teo, Zhi Ling | Radice, Paolo | Catucci, Irene | Peterlongo, Paolo | Tsimiklis, Helen | Odefrey, Fabrice A | Dowty, James G | Schmidt, Marjanka K | Broeks, Annegien | Hogervorst, Frans B | Verhoef, Senno | Carpenter, Jane | Clarke, Christine | Scott, Rodney J | Fasching, Peter A | Haeberle, Lothar | Ekici, Arif B | Beckmann, Matthias W | Peto, Julian | dos-Santos-Silva, Isabel | Fletcher, Olivia | Johnson, Nichola | Bolla, Manjeet K | Sawyer, Elinor J | Tomlinson, Ian | Kerin, Michael J | Miller, Nicola | Marme, Federik | Burwinkel, Barbara | Yang, Rongxi | Guénel, Pascal | Truong, Thérèse | Menegaux, Florence | Sanchez, Marie | Bojesen, Stig | Nielsen, Sune F | Flyger, Henrik | Benitez, Javier | Zamora, M Pilar | Arias Perez, Jose Ignacio | Menéndez, Primitiva | Anton-Culver, Hoda | Neuhausen, Susan | Ziogas, Argyrios | Clarke, Christina A | Brenner, Hermann | Arndt, Volker | Stegmaier, Christa | Brauch, Hiltrud | Brüning, Thomas | Ko, Yon-Dschun | Muranen, Taru A | Aittomäki, Kristiina | Blomqvist, Carl | Bogdanova, Natalia V | Antonenkova, Natalia N | Lindblom, Annika | Margolin, Sara | Mannermaa, Arto | Kataja, Vesa | Kosma, Veli-Matti | Hartikainen, Jaana M | Spurdle, Amanda B | Wauters, Els | Smeets, Dominiek | Beuselinck, Benoit | Floris, Giuseppe | Chang-Claude, Jenny | Rudolph, Anja | Seibold, Petra | Flesch-Janys, Dieter | Olson, Janet E | Vachon, Celine | Pankratz, Vernon S | McLean, Catriona | Haiman, Christopher A | Henderson, Brian E | Schumacher, Fredrick | Le Marchand, Loic | Kristensen, Vessela | Alnæs, Grethe Grenaker | Zheng, Wei | Hunter, David J | Lindstrom, Sara | Hankinson, Susan E | Kraft, Peter | Andrulis, Irene | Knight, Julia A | Glendon, Gord | Mulligan, Anna Marie | Jukkola-Vuorinen, Arja | Grip, Mervi | Kauppila, Saila | Devilee, Peter | Tollenaar, Robert A E M | Seynaeve, Caroline | Hollestelle, Antoinette | Garcia-Closas, Montserrat | Figueroa, Jonine | Chanock, Stephen J | Lissowska, Jolanta | Czene, Kamila | Darabi, Hatef | Eriksson, Mikael | Eccles, Diana M | Rafiq, Sajjad | Tapper, William J | Gerty, Sue M | Hooning, Maartje J | Martens, John W M | Collée, J Margriet | Tilanus-Linthorst, Madeleine | Hall, Per | Li, Jingmei | Brand, Judith S | Humphreys, Keith | Cox, Angela | Reed, Malcolm W R | Luccarini, Craig | Baynes, Caroline | Dunning, Alison M | Hamann, Ute | Torres, Diana | Ulmer, Hans Ulrich | Rüdiger, Thomas | Jakubowska, Anna | Lubinski, Jan | Jaworska, Katarzyna | Durda, Katarzyna | Slager, Susan | Toland, Amanda E | Ambrosone, Christine B | Yannoukakos, Drakoulis | Swerdlow, Anthony | Ashworth, Alan | Orr, Nick | Jones, Michael | González-Neira, Anna | Pita, Guillermo | Alonso, M Rosario | Álvarez, Nuria | Herrero, Daniel | Tessier, Daniel C | Vincent, Daniel | Bacot, Francois | Simard, Jacques | Dumont, Martine | Soucy, Penny | Eeles, Rosalind | Muir, Kenneth | Wiklund, Fredrik | Gronberg, Henrik | Schleutker, Johanna | Nordestgaard, Børge G | Weischer, Maren | Travis, Ruth C | Neal, David | Donovan, Jenny L | Hamdy, Freddie C | Khaw, Kay-Tee | Stanford, Janet L | Blot, William J | Thibodeau, Stephen | Schaid, Daniel J | Kelley, Joseph L | Maier, Christiane | Kibel, Adam S | Cybulski, Cezary | Cannon-Albright, Lisa | Butterbach, Katja | Park, Jong | Kaneva, Radka | Batra, Jyotsna | Teixeira, Manuel R | Kote-Jarai, Zsofia | Al Olama, Ali Amin | Benlloch, Sara | Renner, Stefan P | Hartmann, Arndt | Hein, Alexander | Ruebner, Matthias | Lambrechts, Diether | Van Nieuwenhuysen, Els | Vergote, Ignace | Lambretchs, Sandrina | Doherty, Jennifer A | Rossing, Mary Anne | Nickels, Stefan | Eilber, Ursula | Wang-Gohrke, Shan | Odunsi, Kunle | Sucheston-Campbell, Lara E | Friel, Grace | Lurie, Galina | Killeen, Jeffrey L | Wilkens, Lynne R | Goodman, Marc T | Runnebaum, Ingo | Hillemanns, Peter A | Pelttari, Liisa M | Butzow, Ralf | Modugno, Francesmary | Edwards, Robert P | Ness, Roberta B | Moysich, Kirsten B | du Bois, Andreas | Heitz, Florian | Harter, Philipp | Kommoss, Stefan | Karlan, Beth Y | Walsh, Christine | Lester, Jenny | Jensen, Allan | Kjaer, Susanne Krüger | Høgdall, Estrid | Peissel, Bernard | Bonanni, Bernardo | Bernard, Loris | Goode, Ellen L | Fridley, Brooke L | Vierkant, Robert A | Cunningham, Julie M | Larson, Melissa C | Fogarty, Zachary C | Kalli, Kimberly R | Liang, Dong | Lu, Karen H | Hildebrandt, Michelle A T | Wu, Xifeng | Levine, Douglas A | Dao, Fanny | Bisogna, Maria | Berchuck, Andrew | Iversen, Edwin S | Marks, Jeffrey R | Akushevich, Lucy | Cramer, Daniel W | Schildkraut, Joellen | Terry, Kathryn L | Poole, Elizabeth M | Stampfer, Meir | Tworoger, Shelley S | Bandera, Elisa V | Orlow, Irene | Olson, Sara H | Bjorge, Line | Salvesen, Helga B | van Altena, Anne M | Aben, Katja K H | Kiemeney, Lambertus A | Massuger, Leon F A G | Pejovic, Tanja | Bean, Yukie | Brooks-Wilson, Angela | Kelemen, Linda E | Cook, Linda S | Le, Nhu D | Górski, Bohdan | Gronwald, Jacek | Menkiszak, Janusz | Høgdall, Claus K | Lundvall, Lene | Nedergaard, Lotte | Engelholm, Svend Aage | Dicks, Ed | Tyrer, Jonathan | Campbell, Ian | McNeish, Iain | Paul, James | Siddiqui, Nadeem | Glasspool, Rosalind | Whittemore, Alice S | Rothstein, Joseph H | McGuire, Valerie | Sieh, Weiva | Cai, Hui | Shu, Xiao-Ou | Teten, Rachel T | Sutphen, Rebecca | McLaughlin, John R | Narod, Steven A | Phelan, Catherine M | Monteiro, Alvaro N | Fenstermacher, David | Lin, Hui-Yi | Permuth, Jennifer B | Sellers, Thomas A | Chen, Y Ann | Tsai, Ya-Yu | Chen, Zhihua | Gentry-Maharaj, Aleksandra | Gayther, Simon A | Ramus, Susan J | Menon, Usha | Wu, Anna H | Pearce, Celeste L | Van Den Berg, David | Pike, Malcolm C | Dansonka-Mieszkowska, Agnieszka | Plisiecka-Halasa, Joanna | Moes-Sosnowska, Joanna | Kupryjanczyk, Jolanta | Pharoah, Paul DP | Song, Honglin | Winship, Ingrid | Chenevix-Trench, Georgia | Giles, Graham G | Tavtigian, Sean V | Easton, Doug F | Milne, Roger L
Journal of medical genetics  2016;53(12):800-811.
Background
The rarity of mutations in PALB2, CHEK2 and ATM make it difficult to estimate precisely associated cancer risks. Population-based family studies have provided evidence that at least some of these mutations are associated with breast cancer risk as high as those associated with rare BRCA2 mutations. We aimed to estimate the relative risks associated with specific rare variants in PALB2, CHEK2 and ATM via a multicentre case-control study.
Methods
We genotyped 10 rare mutations using the custom iCOGS array: PALB2 c.1592delT, c.2816T>G and c.3113G>A, CHEK2 c.349A>G, c.538C>T, c.715G>A, c.1036C>T, c.1312G>T, and c.1343T>G and ATM c.7271T>G. We assessed associations with breast cancer risk (42 671 cases and 42 164 controls), as well as prostate (22 301 cases and 22 320 controls) and ovarian (14 542 cases and 23 491 controls) cancer risk, for each variant.
Results
For European women, strong evidence of association with breast cancer risk was observed for PALB2 c.1592delT OR 3.44 (95% CI 1.39 to 8.52, p=7.1×10−5), PALB2 c.3113G>A OR 4.21 (95% CI 1.84 to 9.60, p=6.9×10−8) and ATM c.7271T>G OR 11.0 (95% CI 1.42 to 85.7, p=0.0012). We also found evidence of association with breast cancer risk for three variants in CHEK2, c.349A>G OR 2.26 (95% CI 1.29 to 3.95), c.1036C>T OR 5.06 (95% CI 1.09 to 23.5) and c.538C>T OR 1.33 (95% CI 1.05 to 1.67) (p≤0.017). Evidence for prostate cancer risk was observed for CHEK2 c.1343T>G OR 3.03 (95% CI 1.53 to 6.03, p=0.0006) for African men and CHEK2 c.1312G>T OR 2.21 (95% CI 1.06 to 4.63, p=0.030) for European men. No evidence of association with ovarian cancer was found for any of these variants.
Conclusions
This report adds to accumulating evidence that at least some variants in these genes are associated with an increased risk of breast cancer that is clinically important.
doi:10.1136/jmedgenet-2016-103839
PMCID: PMC5200636  PMID: 27595995
15.  Vocalizations by a Sexually Dimorphic Isolated Larynx: Peripheral Constraints on Behavioral Expression 
The clawed frog Xenopus laevis uses sexually dimorphic vocalizations, mate calling and ticking, to advertise reproductive state. The basic unit of vocalization is a brief click, produced by the movement of cartilagenous disks located within the larynx. The rate of click production in the male-specific mate call (71 Hz) is an order of magnitude faster than the rate of click production in female typical ticking (6 Hz). To determine if vocalization rate is constrained by the periphery, male and female larynges were isolated and response of the muscles to nerve stimulation was studied. Laryngeal muscle response is markedly dimorphic in the 2 sexes, both in the amplitude potentiation of electromyograms and in the rate at which discrete tension transients can be produced. At 6 Hz (ticking), both sexes generate discrete tension transients in response to each stimulus pulse. In response to nerve stimulation at 71 Hz (mate calling), male laryngeal muscle generates discrete tension transients while female laryngeal muscle does not.
Since expression of sex-specific vocalizations is regulated by androgenic hormones, responses of laryngeal muscle to nerve stimulation in androgen-treated adult females and castrated adult males were also examined. The responses of laryngeal muscle from castrated and intact males are similar. Androgen-treated female larynx is partially masculinized but does not produce tension transients at the mate call rate. These physiological results are in close agreement with behavioral observations.
Sounds produced by the isolated larynx were nearly identical in spectral properties to those produced by an intact male. We determined that the production of a discrete tension transient is prerequisite to click production. Thus, one reason females do not mate call, even when treated with androgens, is that female laryngeal muscle cannot produce discrete tension transients at a rapid rate.
PMCID: PMC3493245  PMID: 3668623
16.  Systematic underestimation of the age of selected alleles 
Frontiers in Genetics  2012;3:165.
A common interpretation of genome-wide selection scans is that the dispersal of anatomically modern humans out of Africa and into diverse environments led to a number of genetic adaptations. If so, patterns of polymorphism from non-African individuals should show the signature of adaptations dating to 40,000–100,000 Kya, coinciding with the main exodus from Africa. However, scans of polymorphism data from a few populations have yielded conflicting results about the chronology of local, population-specific adaptations. In particular, a number of papers report very recent ages for selected alleles in humans, which postdate the development of agriculture 10 Kya, and suggest that adaptive differences among human populations are much more recent. I present an analysis of simulations suggesting a downward bias in methods commonly used to estimate the age of selected alleles. These findings indicate that an estimate of a time to the most recent common ancestor (tMRCA) obtained using standard methods (used as a proxy for the age of an allele) of less than 10 Kya is consistent with an allele that actually became selected before the onset of agriculture and potentially as early as 50 Kya. These findings suggest that the genomic scans for selection may be consistent with selective pressures tied to the Out of Africa expansion of modern human populations.
doi:10.3389/fgene.2012.00165
PMCID: PMC3431732  PMID: 22969791
haplotype length; selected allele; selective sweep; allele age; time to most recent common ancestor; tMRCA
17.  Repression is relieved before attenuation in the trp operon of Escherichia coli as tryptophan starvation becomes increasingly severe. 
Journal of Bacteriology  1984;158(3):1018-1024.
Expression of the tryptophan operon of Escherichia coli is regulated over about a 500- to 600-fold range by the combined action of repression and attenuation. Repression regulates transcription initiation in response to variation in the intracellular concentration of tryptophan. Attenuation regulates transcription termination at a site in the leader region of the operon in response to changes in the extent of charging of tRNATrp. We measured repression independently of attenuation to ascertain whether these regulatory mechanisms were used differentially by the bacterium as the severity of tryptophan starvation was increased. We found that repression regulated transcription of the operon over the range from growth with excess tryptophan to growth under moderate tryptophan starvation. By contrast, attenuation (termination control) was not relaxed until tryptophan starvation was in the moderate-to-severe range. Thus, attenuation and repression were used to regulate transcription in response to different degrees of tryptophan deprivation. Consistent with this conclusion is the observation that when tryptophan starvation was sufficient to relieve repression 50 to 60%, 65% of the tRNATrp of the bacterium was charged. These findings provide a possible explanation for the existence of only two tryptophan codons in the coding region for the trp leader peptide of Enterobacteriaceae.
PMCID: PMC215544  PMID: 6233264
18.  A framework for human microbiome research 
Methé, Barbara A. | Nelson, Karen E. | Pop, Mihai | Creasy, Heather H. | Giglio, Michelle G. | Huttenhower, Curtis | Gevers, Dirk | Petrosino, Joseph F. | Abubucker, Sahar | Badger, Jonathan H. | Chinwalla, Asif T. | Earl, Ashlee M. | FitzGerald, Michael G. | Fulton, Robert S. | Hallsworth-Pepin, Kymberlie | Lobos, Elizabeth A. | Madupu, Ramana | Magrini, Vincent | Martin, John C. | Mitreva, Makedonka | Muzny, Donna M. | Sodergren, Erica J. | Versalovic, James | Wollam, Aye M. | Worley, Kim C. | Wortman, Jennifer R. | Young, Sarah K. | Zeng, Qiandong | Aagaard, Kjersti M. | Abolude, Olukemi O. | Allen-Vercoe, Emma | Alm, Eric J. | Alvarado, Lucia | Andersen, Gary L. | Anderson, Scott | Appelbaum, Elizabeth | Arachchi, Harindra M. | Armitage, Gary | Arze, Cesar A. | Ayvaz, Tulin | Baker, Carl C. | Begg, Lisa | Belachew, Tsegahiwot | Bhonagiri, Veena | Bihan, Monika | Blaser, Martin J. | Bloom, Toby | Vivien Bonazzi, J. | Brooks, Paul | Buck, Gregory A. | Buhay, Christian J. | Busam, Dana A. | Campbell, Joseph L. | Canon, Shane R. | Cantarel, Brandi L. | Chain, Patrick S. | Chen, I-Min A. | Chen, Lei | Chhibba, Shaila | Chu, Ken | Ciulla, Dawn M. | Clemente, Jose C. | Clifton, Sandra W. | Conlan, Sean | Crabtree, Jonathan | Cutting, Mary A. | Davidovics, Noam J. | Davis, Catherine C. | DeSantis, Todd Z. | Deal, Carolyn | Delehaunty, Kimberley D. | Dewhirst, Floyd E. | Deych, Elena | Ding, Yan | Dooling, David J. | Dugan, Shannon P. | Dunne, Wm. Michael | Durkin, A. Scott | Edgar, Robert C. | Erlich, Rachel L. | Farmer, Candace N. | Farrell, Ruth M. | Faust, Karoline | Feldgarden, Michael | Felix, Victor M. | Fisher, Sheila | Fodor, Anthony A. | Forney, Larry | Foster, Leslie | Di Francesco, Valentina | Friedman, Jonathan | Friedrich, Dennis C. | Fronick, Catrina C. | Fulton, Lucinda L. | Gao, Hongyu | Garcia, Nathalia | Giannoukos, Georgia | Giblin, Christina | Giovanni, Maria Y. | Goldberg, Jonathan M. | Goll, Johannes | Gonzalez, Antonio | Griggs, Allison | Gujja, Sharvari | Haas, Brian J. | Hamilton, Holli A. | Harris, Emily L. | Hepburn, Theresa A. | Herter, Brandi | Hoffmann, Diane E. | Holder, Michael E. | Howarth, Clinton | Huang, Katherine H. | Huse, Susan M. | Izard, Jacques | Jansson, Janet K. | Jiang, Huaiyang | Jordan, Catherine | Joshi, Vandita | Katancik, James A. | Keitel, Wendy A. | Kelley, Scott T. | Kells, Cristyn | Kinder-Haake, Susan | King, Nicholas B. | Knight, Rob | Knights, Dan | Kong, Heidi H. | Koren, Omry | Koren, Sergey | Kota, Karthik C. | Kovar, Christie L. | Kyrpides, Nikos C. | La Rosa, Patricio S. | Lee, Sandra L. | Lemon, Katherine P. | Lennon, Niall | Lewis, Cecil M. | Lewis, Lora | Ley, Ruth E. | Li, Kelvin | Liolios, Konstantinos | Liu, Bo | Liu, Yue | Lo, Chien-Chi | Lozupone, Catherine A. | Lunsford, R. Dwayne | Madden, Tessa | Mahurkar, Anup A. | Mannon, Peter J. | Mardis, Elaine R. | Markowitz, Victor M. | Mavrommatis, Konstantinos | McCorrison, Jamison M. | McDonald, Daniel | McEwen, Jean | McGuire, Amy L. | McInnes, Pamela | Mehta, Teena | Mihindukulasuriya, Kathie A. | Miller, Jason R. | Minx, Patrick J. | Newsham, Irene | Nusbaum, Chad | O’Laughlin, Michelle | Orvis, Joshua | Pagani, Ioanna | Palaniappan, Krishna | Patel, Shital M. | Pearson, Matthew | Peterson, Jane | Podar, Mircea | Pohl, Craig | Pollard, Katherine S. | Priest, Margaret E. | Proctor, Lita M. | Qin, Xiang | Raes, Jeroen | Ravel, Jacques | Reid, Jeffrey G. | Rho, Mina | Rhodes, Rosamond | Riehle, Kevin P. | Rivera, Maria C. | Rodriguez-Mueller, Beltran | Rogers, Yu-Hui | Ross, Matthew C. | Russ, Carsten | Sanka, Ravi K. | Pamela Sankar, J. | Sathirapongsasuti, Fah | Schloss, Jeffery A. | Schloss, Patrick D. | Schmidt, Thomas M. | Scholz, Matthew | Schriml, Lynn | Schubert, Alyxandria M. | Segata, Nicola | Segre, Julia A. | Shannon, William D. | Sharp, Richard R. | Sharpton, Thomas J. | Shenoy, Narmada | Sheth, Nihar U. | Simone, Gina A. | Singh, Indresh | Smillie, Chris S. | Sobel, Jack D. | Sommer, Daniel D. | Spicer, Paul | Sutton, Granger G. | Sykes, Sean M. | Tabbaa, Diana G. | Thiagarajan, Mathangi | Tomlinson, Chad M. | Torralba, Manolito | Treangen, Todd J. | Truty, Rebecca M. | Vishnivetskaya, Tatiana A. | Walker, Jason | Wang, Lu | Wang, Zhengyuan | Ward, Doyle V. | Warren, Wesley | Watson, Mark A. | Wellington, Christopher | Wetterstrand, Kris A. | White, James R. | Wilczek-Boney, Katarzyna | Wu, Yuan Qing | Wylie, Kristine M. | Wylie, Todd | Yandava, Chandri | Ye, Liang | Ye, Yuzhen | Yooseph, Shibu | Youmans, Bonnie P. | Zhang, Lan | Zhou, Yanjiao | Zhu, Yiming | Zoloth, Laurie | Zucker, Jeremy D. | Birren, Bruce W. | Gibbs, Richard A. | Highlander, Sarah K. | Weinstock, George M. | Wilson, Richard K. | White, Owen
Nature  2012;486(7402):215-221.
A variety of microbial communities and their genes (microbiome) exist throughout the human body, playing fundamental roles in human health and disease. The NIH funded Human Microbiome Project (HMP) Consortium has established a population-scale framework which catalyzed significant development of metagenomic protocols resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 to 18 body sites up to three times, which to date, have generated 5,177 microbial taxonomic profiles from 16S rRNA genes and over 3.5 Tb of metagenomic sequence. In parallel, approximately 800 human-associated reference genomes have been sequenced. Collectively, these data represent the largest resource to date describing the abundance and variety of the human microbiome, while providing a platform for current and future studies.
doi:10.1038/nature11209
PMCID: PMC3377744  PMID: 22699610
19.  Vital Signs: Update on Zika Virus–Associated Birth Defects and Evaluation of All U.S. Infants with Congenital Zika Virus Exposure — U.S. Zika Pregnancy Registry, 2016 
Reynolds, Megan R. | Jones, Abbey M. | Petersen, Emily E. | Lee, Ellen H. | Rice, Marion E. | Bingham, Andrea | Ellington, Sascha R. | Evert, Nicole | Reagan-Steiner, Sarah | Oduyebo, Titilope | Brown, Catherine M. | Martin, Stacey | Ahmad, Nina | Bhatnagar, Julu | Macdonald, Jennifer | Gould, Carolyn | Fine, Anne D. | Polen, Kara D. | Lake-Burger, Heather | Hillard, Christina L. | Hall, Noemi | Yazdy, Mahsa M. | Slaughter, Karnesha | Sommer, Jamie N. | Adamski, Alys | Raycraft, Meghan | Fleck-Derderian, Shannon | Gupta, Jyoti | Newsome, Kimberly | Baez-Santiago, Madelyn | Slavinski, Sally | White, Jennifer L. | Moore, Cynthia A. | Shapiro-Mendoza, Carrie K. | Petersen, Lyle | Boyle, Coleen | Jamieson, Denise J. | Meaney-Delman, Dana | Honein, Margaret A. | Adair, Jennifer | Ruberto, Irene | Haselow, Dirk T. | Im, Lucille | Jilek, Wendy | Lehmann, Monica S. | Olney, Richard | Porse, Charsey Cole | Ramstrom, Karen C. | Sowunmi, Similoluwa | Marzec, Natalie S. | Davis, Karin | Esponda-Morrison, Brenda | Fraser, M. Zachariah | O'Connor, Colleen Ann | Chung, Wendy | Richardson, Folasuyi | Sexton, Taylor | Stocks, Meredith E. | Woldai, Senait | Bundek, Amanda M. | Zambri, Jennifer | Goldberg, Cynthia | Eisenstein, Leah | Jackson, Jennifer | Kopit, Russell | Logue, Teresa | Mendoza, Raphael | Feldpausch, Amanda | Graham, Teri | Mann, Sylvia | Park, Sarah Y. | Carter, Kris Kelly | Potts, Emily J. | Stevens, Taryn | Simonson, Sean | Tonzel, Julius L. | Davis, Shari | Robinson, Sara | Hyun, Judie K. | Jenkins, Erin M. | Piccardi, Monika | Reid, Lawrence D. | Dunn, Julie E. | Higgins, Cathleen A. | Lin, Angela E. | Munshi, Gerlinde S. | Sandhu, Kayleigh | Scotland, Sarah J. | Soliva, Susan | Copeland, Glenn | Signs, Kimberly A. | Schiffman, Elizabeth | Byers, Paul | Hand, Sheryl | Mulgrew, Christine L. | Hamik, Jeff | Koirala, Samir | Ludwig, Lisa A. | Fredette, Carolyn Rose | Garafalo, Kristin | Worthington, Karen | Ropri, Abubakar | Ade, Julius Nchangtachi | Alaali, Zahra S. | Blog, Debra | Brunt, Scott J. | Bryant, Patrick | Burns, Amy E. | Bush, Steven | Carson, Kyle | Dean, Amy B. | Demarest, Valerie | Dufort, Elizabeth M. | Dupuis II, Alan P. | Sullivan-Frohm, Ann | Furuya, Andrea Marias | Fuschino, Meghan | Glaze, Viola H. | Griffin, Jacquelin | Hidalgo, Christina | Kulas, Karen E. | Lamson, Daryl M. | Lance, Lou Ann | Lee, William T. | Limberger, Ronald | Many, Patricia S. | Marchewka, Mary J. | Naizby, Brenda Elizabeth | Polfleit, MaryJo | Popowich, Michael | Rahman, Tabassum | Rem, Timothy | Robbins, Amy E. | Rowlands, Jemma V. | Seaver, Chantelle | Seward, Kimberley A. | Smith, Lou | Sohi, Inderbir | St. George, Kirsten | Souto, Maria I. | Wester, Rachel Elizabeth | Wong, Susan J. | Zeng, Li | Ackelsberg, Joel | Alex, Byron | Ballen, Vennus | Baumgartner, Jennifer | Bloch, Danielle | Clark, Sandhya | Conners, Erin | Cooper, Hannah | Davidson, Alexander | Dentinger, Catherine | Deocharan, Bisram | DeVito, Andrea | Fu, Jie | Hrusa, Gili | Iqbal, Maryam | Iwamoto, Martha | Jones, Lucretia | Kubinson, Hannah | Lash, Maura | Layton, Marcelle | Lee, Christopher T. | Liu, Dakai | McGibbon, Emily | Moy, Morgan | Ngai, Stephanie | Parton, Hilary B. | Peterson, Eric | Poy, Jose | Rakeman, Jennifer | Stoute, Alaina | Thompson, Corinne | Weiss, Don | Westheimer, Emily | Winters, Ann | Younis, Mohammad | Chan, Ronna L. | Cronquist, Laura Jean | Caton, Lisa | Lind, Leah | Nalluswami, Kumar | Perella, Dana | Brady, Diane S. | Gosciminski, Michael | McAuley, Patricia | Drociuk, Daniel | Leedom, Vinita | Witrick, Brian | Bollock, Jan | Hartel, Marie Bottomley | Lucinski, Loraine Swanson | McDonald, Morgan | Miller, Angela M. | Ponson, Tori Armand | Price, Laura | Nance, Amy E. | Peterson, Dallin | Cook, Sally | Martin, Brennan | Oltean, Hanna | Neary, Jillian | Baker, Melissa A. | Cummons, Kathy | Bryan, Katie | Arnold, Kathryn E. | Arth, Annelise C. | Bollweg, Brigid C. | Cragan, Janet D. | Dawson, April L. | Denison, Amy M. | Dziuban, Eric J. | Estetter, Lindsey | Silva-Flannery, Luciana | Free, Rebecca J. | Galang, Romeo R. | Gary, Joy | Goldsmith, Cynthia S. | Green, Caitlin | Hale, Gillian L. | Hayes, Heather M. | Igbinosa, Irogue | Keating, M. Kelly | Khan, Sumaiya | Kim, Shin Y. | Lampe, Margaret | Lewis, Amanda | Mai, Cara | Martines, Roosecelis Brasil | Miers, Brooke | Moore, Jazmyn | Muehlenbachs, Atis | Nahabedian, John | Panella, Amanda | Parihar, Vaunita | Patel, Mitesh M. | Rabeneck, D. Brett | Rasmussen, Sonja A. | Ritter, Jana M. | Rollin, Dominique C. | Sanders, Jeanine H. | Shieh, Wun-Ju | Simeone, Regina M. | Simon, Elizabeth L. | Sims, John R. | Spivey, Pamela J. | Talley-McRae, Helen | Tshiwala, Alphonse K. | VanMaldeghem, Kelley | Viens, Laura | Wainscott-Sargent, Anne | Williams, Tonya | Zaki, Sherif
Background
In collaboration with state, tribal, local, and territorial health departments, CDC established the U.S. Zika Pregnancy Registry (USZPR) in early 2016 to monitor pregnant women with laboratory evidence of possible recent Zika virus infection and their infants.
Methods
This report includes an analysis of completed pregnancies (which include live births and pregnancy losses, regardless of gestational age) in the 50 U.S. states and the District of Columbia (DC) with laboratory evidence of possible recent Zika virus infection reported to the USZPR from January 15 to December 27, 2016. Birth defects potentially associated with Zika virus infection during pregnancy include brain abnormalities and/or microcephaly, eye abnormalities, other consequences of central nervous system dysfunction, and neural tube defects and other early brain malformations.
Results
During the analysis period, 1,297 pregnant women in 44 states were reported to the USZPR. Zika virus–associated birth defects were reported for 51 (5%) of the 972 fetuses/infants from completed pregnancies with laboratory evidence of possible recent Zika virus infection (95% confidence interval [CI] = 4%–7%); the proportion was higher when restricted to pregnancies with laboratory-confirmed Zika virus infection (24/250 completed pregnancies [10%, 95% CI = 7%–14%]). Birth defects were reported in 15% (95% CI = 8%–26%) of fetuses/infants of completed pregnancies with confirmed Zika virus infection in the first trimester. Among 895 liveborn infants from pregnancies with possible recent Zika virus infection, postnatal neuroimaging was reported for 221 (25%), and Zika virus testing of at least one infant specimen was reported for 585 (65%).
Conclusions and Implications for Public Health Practice
These findings highlight why pregnant women should avoid Zika virus exposure. Because the full clinical spectrum of congenital Zika virus infection is not yet known, all infants born to women with laboratory evidence of possible recent Zika virus infection during pregnancy should receive postnatal neuroimaging and Zika virus testing in addition to a comprehensive newborn physical exam and hearing screen. Identification and follow-up care of infants born to women with laboratory evidence of possible recent Zika virus infection during pregnancy and infants with possible congenital Zika virus infection can ensure that appropriate clinical services are available.
doi:10.15585/mmwr.mm6613e1
PMCID: PMC5657905  PMID: 28384133
20.  The association of place characteristics with HIV and HCV risk behaviors among racial/ethnic groups of people who inject drugs in the United States 
Annals of epidemiology  2016;26(9):619-630.e2.
Purpose
Investigate whether characteristics of geographic areas are associated with condomless sex and injection-related risk behavior among racial/ethnic groups of people who inject drugs (PWID) in the United States.
Methods
PWID were recruited from 19 metropolitan statistical areas (MSAs) for 2009 National HIV Behavioral Surveillance. Administrative data described ZIP codes, counties, and MSAs where PWID lived. Multilevel models, stratified by racial/ethnic group, were used to assess relationships of place-based characteristics to condomless sex and injection-related risk behavior (sharing injection equipment).
Results
Among black PWID, living in the South (vs. Northeast) was associated with injection-related risk behavior [Adjusted Odds Ratio (AOR)=2.24, 95% Confidence Interval (CI)=1.37,4.34;p-value=0.011] and living in counties with higher percentages of unaffordable rental housing was associated with condomless sex [AOR=1.02, 95% CI=1.00,1.04; p-value=0.046]. Among white PWID, living in ZIP codes with greater access to drug treatment was negatively associated with condomless sex [AOR=0.93, 95% CI=0.88,1.00;p-value=0.038).
Discussion
Policies that increase access to affordable housing and drug treatment may make environments more conducive to safe sexual behaviors among black and white PWID. Future research designed to longitudinally explore the association between residence in the south and injection-related risk behavior might identify specific place-based features that sustain patterns of injection-related risk behavior.
doi:10.1016/j.annepidem.2016.07.012
PMCID: PMC5110217  PMID: 27576908
HIV; HCV; injection; condom use; PWID; housing; drug treatment
21.  Common variants at the CHEK2 gene locus and risk of epithelial ovarian cancer 
Lawrenson, Kate | Iversen, Edwin S. | Tyrer, Jonathan | Weber, Rachel Palmieri | Concannon, Patrick | Hazelett, Dennis J. | Li, Qiyuan | Marks, Jeffrey R. | Berchuck, Andrew | Lee, Janet M. | Aben, Katja K.H. | Anton-Culver, Hoda | Antonenkova, Natalia | Bandera, Elisa V. | Bean, Yukie | Beckmann, Matthias W. | Bisogna, Maria | Bjorge, Line | Bogdanova, Natalia | Brinton, Louise A. | Brooks-Wilson, Angela | Bruinsma, Fiona | Butzow, Ralf | Campbell, Ian G. | Carty, Karen | Chang-Claude, Jenny | Chenevix-Trench, Georgia | Chen, Ann | Chen, Zhihua | Cook, Linda S. | Cramer, Daniel W. | Cunningham, Julie M. | Cybulski, Cezary | Plisiecka-Halasa, Joanna | Dennis, Joe | Dicks, Ed | Doherty, Jennifer A. | Dörk, Thilo | du Bois, Andreas | Eccles, Diana | Easton, Douglas T. | Edwards, Robert P. | Eilber, Ursula | Ekici, Arif B. | Fasching, Peter A. | Fridley, Brooke L. | Gao, Yu-Tang | Gentry-Maharaj, Aleksandra | Giles, Graham G. | Glasspool, Rosalind | Goode, Ellen L. | Goodman, Marc T. | Gronwald, Jacek | Harter, Philipp | Hasmad, Hanis Nazihah | Hein, Alexander | Heitz, Florian | Hildebrandt, Michelle A.T. | Hillemanns, Peter | Hogdall, Estrid | Hogdall, Claus | Hosono, Satoyo | Jakubowska, Anna | Paul, James | Jensen, Allan | Karlan, Beth Y. | Kjaer, Susanne Kruger | Kelemen, Linda E. | Kellar, Melissa | Kelley, Joseph L. | Kiemeney, Lambertus A. | Krakstad, Camilla | Lambrechts, Diether | Lambrechts, Sandrina | Le, Nhu D. | Lee, Alice W. | Cannioto, Rikki | Leminen, Arto | Lester, Jenny | Levine, Douglas A. | Liang, Dong | Lissowska, Jolanta | Lu, Karen | Lubinski, Jan | Lundvall, Lene | Massuger, Leon F.A.G. | Matsuo, Keitaro | McGuire, Valerie | McLaughlin, John R. | Nevanlinna, Heli | McNeish, Iain | Menon, Usha | Modugno, Francesmary | Moysich, Kirsten B. | Narod, Steven A. | Nedergaard, Lotte | Ness, Roberta B. | Noor Azmi, Mat Adenan | Odunsi, Kunle | Olson, Sara H. | Orlow, Irene | Orsulic, Sandra | Pearce, Celeste L. | Pejovic, Tanja | Pelttari, Liisa M. | Permuth-Wey, Jennifer | Phelan, Catherine M. | Pike, Malcolm C. | Poole, Elizabeth M. | Ramus, Susan J. | Risch, Harvey A. | Rosen, Barry | Rossing, Mary Anne | Rothstein, Joseph H. | Rudolph, Anja | Runnebaum, Ingo B. | Rzepecka, Iwona K. | Salvesen, Helga B. | Budzilowska, Agnieszka | Sellers, Thomas A. | Shu, Xiao-Ou | Shvetsov, Yurii B. | Siddiqui, Nadeem | Sieh, Weiva | Song, Honglin | Southey, Melissa C. | Sucheston, Lara | Tangen, Ingvild L. | Teo, Soo-Hwang | Terry, Kathryn L. | Thompson, Pamela J. | Timorek, Agnieszka | Tworoger, Shelley S. | Nieuwenhuysen, Els Van | Vergote, Ignace | Vierkant, Robert A. | Wang-Gohrke, Shan | Walsh, Christine | Wentzensen, Nicolas | Whittemore, Alice S. | Wicklund, Kristine G. | Wilkens, Lynne R. | Woo, Yin-Ling | Wu, Xifeng | Wu, Anna H. | Yang, Hannah | Zheng, Wei | Ziogas, Argyrios | Coetzee, Gerhard A. | Freedman, Matthew L. | Monteiro, Alvaro N.A. | Moes-Sosnowska, Joanna | Kupryjanczyk, Jolanta | Pharoah, Paul D. | Gayther, Simon A. | Schildkraut, Joellen M.
Carcinogenesis  2015;36(11):1341-1353.
Summary
Associations with EOC for variants at CHEK2 were found with the strongest association for the CHEK2 SNP rs6005807 with serous EOC. Common variants at 22q12.1 are associated with risk of serous EOC and CHEK2 as a plausible target susceptibility gene.
Genome-wide association studies have identified 20 genomic regions associated with risk of epithelial ovarian cancer (EOC), but many additional risk variants may exist. Here, we evaluated associations between common genetic variants [single nucleotide polymorphisms (SNPs) and indels] in DNA repair genes and EOC risk. We genotyped 2896 common variants at 143 gene loci in DNA samples from 15 397 patients with invasive EOC and controls. We found evidence of associations with EOC risk for variants at FANCA, EXO1, E2F4, E2F2, CREB5 and CHEK2 genes (P ≤ 0.001). The strongest risk association was for CHEK2 SNP rs17507066 with serous EOC (P = 4.74 x 10–7). Additional genotyping and imputation of genotypes from the 1000 genomes project identified a slightly more significant association for CHEK2 SNP rs6005807 (r 2 with rs17507066 = 0.84, odds ratio (OR) 1.17, 95% CI 1.11–1.24, P = 1.1×10−7). We identified 293 variants in the region with likelihood ratios of less than 1:100 for representing the causal variant. Functional annotation identified 25 candidate SNPs that alter transcription factor binding sites within regulatory elements active in EOC precursor tissues. In The Cancer Genome Atlas dataset, CHEK2 gene expression was significantly higher in primary EOCs compared to normal fallopian tube tissues (P = 3.72×10−8). We also identified an association between genotypes of the candidate causal SNP rs12166475 (r 2 = 0.99 with rs6005807) and CHEK2 expression (P = 2.70×10-8). These data suggest that common variants at 22q12.1 are associated with risk of serous EOC and CHEK2 as a plausible target susceptibility gene.
doi:10.1093/carcin/bgv138
PMCID: PMC4635670  PMID: 26424751
22.  Cis-eQTL Analysis And Functional Validation Of Candidate Susceptibility Genes For High-Grade Serous Ovarian Cancer 
Lawrenson, Kate | Li, Qiyuan | Kar, Siddhartha | Seo, Ji-Heui | Tyrer, Jonathan | Spindler, Tassja J. | Lee, Janet | Chen, Yibu | Karst, Alison | Drapkin, Ronny | Aben, Katja K.H. | Anton-Culver, Hoda | Antonenkova, Natalia | Baker, Helen | Bandera, Elisa V. | Bean, Yukie | Beckmann, Matthias W. | Berchuck, Andrew | Bisogna, Maria | Bjorge, Line | Bogdanova, Natalia | Brinton, Louise A. | Brooks-Wilson, Angela | Bruinsma, Fiona | Butzow, Ralf | Campbell, Ian G. | Carty, Karen | Chang-Claude, Jenny | Chenevix-Trench, Georgia | Chen, Anne | Chen, Zhihua | Cook, Linda S. | Cramer, Daniel W. | Cunningham, Julie M. | Cybulski, Cezary | Dansonka-Mieszkowska, Agnieszka | Dennis, Joe | Dicks, Ed | Doherty, Jennifer A. | Dörk, Thilo | du Bois, Andreas | Dürst, Matthias | Eccles, Diana | Easton, Douglas T. | Edwards, Robert P. | Eilber, Ursula | Ekici, Arif B. | Fasching, Peter A. | Fridley, Brooke L. | Gao, Yu-Tang | Gentry-Maharaj, Aleksandra | Giles, Graham G. | Glasspool, Rosalind | Goode, Ellen L. | Goodman, Marc T. | Grownwald, Jacek | Harrington, Patricia | Harter, Philipp | Hasmad, Hanis Nazihah | Hein, Alexander | Heitz, Florian | Hildebrandt, Michelle A.T. | Hillemanns, Peter | Hogdall, Estrid | Hogdall, Claus | Hosono, Satoyo | Iversen, Edwin S. | Jakubowska, Anna | James, Paul | Jensen, Allan | Ji, Bu-Tian | Karlan, Beth Y | Kjaer, Susanne Kruger | Kelemen, Linda E. | Kellar, Melissa | Kelley, Joseph L. | Kiemeney, Lambertus A. | Krakstad, Camilla | Kupryjanczyk, Jolanta | Lambrechts, Diether | Lambrechts, Sandrina | Le, Nhu D. | Lee, Alice W. | Lele, Shashi | Leminen, Arto | Lester, Jenny | Levine, Douglas A. | Liang, Dong | Lissowska, Jolanta | Lu, Karen | Lubinski, Jan | Lundvall, Lene | Massuger, Leon F.A.G. | Matsuo, Keitaro | McGuire, Valerie | McLaughlin, John R. | Nevanlinna, Heli | McNeish, Ian | Menon, Usha | Modugno, Francesmary | Moysich, Kirsten B. | Narod, Steven A. | Nedergaard, Lotte | Ness, Roberta B. | Azmi, Mat Adenan Noor | Odunsi, Kunle | Olson, Sara H. | Orlow, Irene | Orsulic, Sandra | Weber, Rachel Palmieri | Pearce, Celeste L. | Pejovic, Tanja | Pelttari, Liisa M. | Permuth-Wey, Jennifer | Phelan, Catherine M. | Pike, Malcolm C. | Poole, Elizabeth M. | Ramus, Susan J. | Risch, Harvey A. | Rosen, Barry | Rossing, Mary Anne | Rothstein, Joseph H. | Rudolph, Anja | Runnebaum, Ingo B. | Rzepecka, Iwona K. | Salvesen, Helga B. | Schildkraut, Joellen M. | Schwaab, Ira | Sellers, Thomas A. | Shu, Xiao-Ou | Shvetsov, Yurii B | Siddiqui, Nadeem | Sieh, Weiva | Song, Honglin | Southey, Melissa C. | Sucheston, Lara | Tangen, Ingvild L. | Teo, Soo-Hwang | Terry, Kathryn L. | Thompson, Pamela J | Timorek, Agnieszka | Tsai, Ya-Yu | Tworoger, Shelley S. | van Altena, Anne M. | Van Nieuwenhuysen, Els | Vergote, Ignace | Vierkant, Robert A. | Wang-Gohrke, Shan | Walsh, Christine | Wentzensen, Nicolas | Whittemore, Alice S. | Wicklund, Kristine G. | Wilkens, Lynne R. | Woo, Yin-Ling | Wu, Xifeng | Wu, Anna H. | Yang, Hannah | Zheng, Wei | Ziogas, Argyrios | Monteiro, Alvaro | Pharoah, Paul D. | Gayther, Simon A. | Freedman, Matthew L. | Bowtell, David | Webb, Penelope M. | deFazio, Anna
Nature communications  2015;6:8234.
Genome-wide association studies have reported eleven regions conferring risk of high-grade serous epithelial ovarian cancer (HGSOC). Expression quantitative trait locus (eQTL) analyses can identify candidate susceptibility genes at risk loci. Here we evaluate cis-eQTL associations at 47 regions associated with HGSOC risk (P≤10−5). For three cis-eQTL associations (P<1.4×10−3, FDR<0.05) at 1p36 (CDC42), 1p34 (CDCA8) and 2q31 (HOXD9), we evaluate the functional role of each candidate by perturbing expression of each gene in HGSOC precursor cells. Overexpression of HOXD9 increases anchorage-independent growth, shortens population-doubling time and reduces contact inhibition. Chromosome conformation capture identifies an interaction between rs2857532 and the HOXD9 promoter, suggesting this SNP is a leading causal variant. Transcriptomic profiling after HOXD9 overexpression reveals enrichment of HGSOC risk variants within HOXD9 target genes (P=6×10−10 for risk variants (P<10−4) within 10kb of a HOXD9 target gene in ovarian cells), suggesting a broader role for this network in genetic susceptibility to HGSOC.
doi:10.1038/ncomms9234
PMCID: PMC4580986  PMID: 26391404
23.  Cis-eQTL analysis and functional validation of candidate susceptibility genes for high-grade serous ovarian cancer 
Lawrenson, Kate | Li, Qiyuan | Kar, Siddhartha | Seo, Ji-Heui | Tyrer, Jonathan | Spindler, Tassja J. | Lee, Janet | Chen, Yibu | Karst, Alison | Drapkin, Ronny | Aben, Katja K. H. | Anton-Culver, Hoda | Antonenkova, Natalia | Baker, Helen | Bandera, Elisa V. | Bean, Yukie | Beckmann, Matthias W. | Berchuck, Andrew | Bisogna, Maria | Bjorge, Line | Bogdanova, Natalia | Brinton, Louise A. | Brooks-Wilson, Angela | Bruinsma, Fiona | Butzow, Ralf | Campbell, Ian G. | Carty, Karen | Chang-Claude, Jenny | Chenevix-Trench, Georgia | Chen, Anne | Chen, Zhihua | Cook, Linda S. | Cramer, Daniel W. | Cunningham, Julie M. | Cybulski, Cezary | Dansonka-Mieszkowska, Agnieszka | Dennis, Joe | Dicks, Ed | Doherty, Jennifer A. | Dörk, Thilo | du Bois, Andreas | Dürst, Matthias | Eccles, Diana | Easton, Douglas T. | Edwards, Robert P. | Eilber, Ursula | Ekici, Arif B. | Fasching, Peter A. | Fridley, Brooke L. | Gao, Yu-Tang | Gentry-Maharaj, Aleksandra | Giles, Graham G. | Glasspool, Rosalind | Goode, Ellen L. | Goodman, Marc T. | Grownwald, Jacek | Harrington, Patricia | Harter, Philipp | Hasmad, Hanis Nazihah | Hein, Alexander | Heitz, Florian | Hildebrandt, Michelle A. T. | Hillemanns, Peter | Hogdall, Estrid | Hogdall, Claus | Hosono, Satoyo | Iversen, Edwin S. | Jakubowska, Anna | James, Paul | Jensen, Allan | Ji, Bu-Tian | Karlan, Beth Y. | Kruger Kjaer, Susanne | Kelemen, Linda E. | Kellar, Melissa | Kelley, Joseph L. | Kiemeney, Lambertus A. | Krakstad, Camilla | Kupryjanczyk, Jolanta | Lambrechts, Diether | Lambrechts, Sandrina | Le, Nhu D. | Lee, Alice W. | Lele, Shashi | Leminen, Arto | Lester, Jenny | Levine, Douglas A. | Liang, Dong | Lissowska, Jolanta | Lu, Karen | Lubinski, Jan | Lundvall, Lene | Massuger, Leon F. A. G. | Matsuo, Keitaro | McGuire, Valerie | McLaughlin, John R. | Nevanlinna, Heli | McNeish, Ian | Menon, Usha | Modugno, Francesmary | Moysich, Kirsten B. | Narod, Steven A. | Nedergaard, Lotte | Ness, Roberta B. | Azmi, Mat Adenan Noor | Odunsi, Kunle | Olson, Sara H. | Orlow, Irene | Orsulic, Sandra | Weber, Rachel Palmieri | Pearce, Celeste L. | Pejovic, Tanja | Pelttari, Liisa M. | Permuth-Wey, Jennifer | Phelan, Catherine M. | Pike, Malcolm C. | Poole, Elizabeth M. | Ramus, Susan J. | Risch, Harvey A. | Rosen, Barry | Rossing, Mary Anne | Rothstein, Joseph H. | Rudolph, Anja | Runnebaum, Ingo B. | Rzepecka, Iwona K. | Salvesen, Helga B. | Schildkraut, Joellen M. | Schwaab, Ira | Sellers, Thomas A. | Shu, Xiao-Ou | Shvetsov, Yurii B. | Siddiqui, Nadeem | Sieh, Weiva | Song, Honglin | Southey, Melissa C. | Sucheston, Lara | Tangen, Ingvild L. | Teo, Soo-Hwang | Terry, Kathryn L. | Thompson, Pamela J. | Timorek, Agnieszka | Tsai, Ya-Yu | Tworoger, Shelley S. | van Altena, Anne M. | Van Nieuwenhuysen, Els | Vergote, Ignace | Vierkant, Robert A. | Wang-Gohrke, Shan | Walsh, Christine | Wentzensen, Nicolas | Whittemore, Alice S. | Wicklund, Kristine G. | Wilkens, Lynne R. | Woo, Yin-Ling | Wu, Xifeng | Wu, Anna H. | Yang, Hannah | Zheng, Wei | Ziogas, Argyrios | Monteiro, Alvaro | Pharoah, Paul D. | Gayther, Simon A. | Freedman, Matthew L.
Nature Communications  2015;6:8234.
Genome-wide association studies have reported 11 regions conferring risk of high-grade serous epithelial ovarian cancer (HGSOC). Expression quantitative trait locus (eQTL) analyses can identify candidate susceptibility genes at risk loci. Here we evaluate cis-eQTL associations at 47 regions associated with HGSOC risk (P≤10−5). For three cis-eQTL associations (P<1.4 × 10−3, FDR<0.05) at 1p36 (CDC42), 1p34 (CDCA8) and 2q31 (HOXD9), we evaluate the functional role of each candidate by perturbing expression of each gene in HGSOC precursor cells. Overexpression of HOXD9 increases anchorage-independent growth, shortens population-doubling time and reduces contact inhibition. Chromosome conformation capture identifies an interaction between rs2857532 and the HOXD9 promoter, suggesting this SNP is a leading causal variant. Transcriptomic profiling after HOXD9 overexpression reveals enrichment of HGSOC risk variants within HOXD9 target genes (P=6 × 10−10 for risk variants (P<10−4) within 10 kb of a HOXD9 target gene in ovarian cells), suggesting a broader role for this network in genetic susceptibility to HGSOC.
Genome-wide association studies have identified regions which confer risk of high-grade serous epithelial ovarian cancer. Here the authors use expression quantitative train locus analysis to identify candidate genes and functionally characterise them, identifying a role for HOXD9 in ovarian cancer.
doi:10.1038/ncomms9234
PMCID: PMC4580986  PMID: 26391404
24.  Gender differences in the aerobic fitness levels of young African-American adults. 
This study examines gender differences in the aerobic fitness levels of young African-American adults. Two hundred twelve African-American college freshmen (79 men, 133 women) completed the Houston Non-Exercise Test-Body Mass Index Model (HNET-BMI) questionnaire, a questionnaire designed to estimate maximum oxygen consumption (VO2max, mL kg-1 min-1) in adults. Using a three-point scoring system (below average, average, and above average), 100% of the men and 80% of the women were classified as having average or above average levels of VO2max. Statistical analysis revealed that more women than men had average or below average levels of aerobic fitness (chi 2 = 54.5; P = .0001). The results of this study suggest that a larger percentage of African-American women have lower levels of aerobic fitness compared with African-American men.
PMCID: PMC2608467  PMID: 10643210
25.  Evaluation of Placental and Fetal Tissue Specimens for Zika Virus Infection — 50 States and District of Columbia, January–December, 2016 
Reagan-Steiner, Sarah | Simeone, Regina | Simon, Elizabeth | Bhatnagar, Julu | Oduyebo, Titilope | Free, Rebecca | Denison, Amy M. | Rabeneck, Demi B. | Ellington, Sascha | Petersen, Emily | Gary, Joy | Hale, Gillian | Keating, M. Kelly | Martines, Roosecelis B. | Muehlenbachs, Atis | Ritter, Jana | Lee, Ellen | Davidson, Alexander | Conners, Erin | Scotland, Sarah | Sandhu, Kayleigh | Bingham, Andrea | Kassens, Elizabeth | Smith, Lou | St. George, Kirsten | Ahmad, Nina | Tanner, Mary | Beavers, Suzanne | Miers, Brooke | VanMaldeghem, Kelley | Khan, Sumaiya | Rabe, Ingrid | Gould, Carolyn | Meaney-Delman, Dana | Honein, Margaret A. | Shieh, Wun-Ju | Jamieson, Denise J. | Fischer, Marc | Zaki, Sherif R. | Kretschmer, Melissa | Tarter, Kara | Yaglom, Hayley | Alhajmohammad, Shoruq | Chhabra, Dildeep | Jilek, Wendy | Madala, Meghana | Messenger, Sharon | Porse, Charsey Cole | Salas, Maria | Singh, Diana | Skallet, Sarah | Sowunmi, Similoluwa | Marzec, Natalie S. | Davis, Karin | Esponda-Morrison, Brenda | Fraser, M. Zachariah | O'Connor, Colleen Ann | Chung, Wendy M. | Richardson, Folasuyi | Stocks, Meredith E. | Bundek, Amanda Marie | Zambri, Jennifer L. | Allen, Ashley | Etienne, Marie Ketty | Jackson, Jennifer | Landis, Vanessa | Logue, Teresa | Muse, Nicole | Prieto, Juliana | Rojas, Mercedes | Feldpausch, Amanda | Graham, Teri | Mann, Sylvia | Park, Sarah Y. | Freeman, Debbie | Potts, Emily J. | Stevens, Taryn | Simonson, Sean | Tonzel, Julius L. | Davis, Shari | Robinson, Sara | Hyun, Judie K. | Jenkins, Erin Maureen | Brown, Catherine | Soliva, Susan | Schiffman, Elizabeth | Byers, Paul | Hand, Sheryl | Mulgrew, Christine L. | Hamik, Jeff | Koirala, Samir | Ludwig, Elizabeth | Fredette, Carolyn R. | Mathewson, Abigail A. | Garafalo, Kristin | Worthington, Karen | Ropri, Abubakar | Bloch, Danielle | Clark, Sandhya | Cooper, Hannah | Fine, Annie D. | Hrusa, Gili | Iwamoto, Martha | Kubinson, Hannah | Lee, Christopher T. | Slavinski, Sally | Wilson, Eliza | Winters, Ann | Yang, David Yi | Ade, Julius N. | Alaali, Zahra | Alvarez, Kimberly | Backenson, P. Bryon | Blog, Debra | Dean, Amy | Dufort, Elizabeth | Furuya, Andrea Marias | Fuschino, Meghan | Hull, Rene | Kleabonas, Matthew | Kulas, Karen | Kurpiel, Philip | Lance, Lou Ann | Leak, Emaly | Limberger, Ronald J. | Ostrowski, Stephanie | Polfleit, MaryJo | Robbins, Amy | Rowlands, Jemma V. | Sohi, Inderbir | Sommer, Jamie N. | White, Jennifer | Wiley, Dorothy | Zeng, Li | Chan, Ronna L. | MacFarquhar, Jennifer | Cronquist, Laura | Lind, Leah | Nalluswami, Kumar | Perella, Dana | Brady, Diane S. | Gosciminski, Michael | McAuley, Patricia | Teevan, Bridget E. | Drociuk, Daniel | Leedom, Vinita | Witrick, Brian | Bollock, Jan | Kightlinger, Lon | Hartel, Marie Bottomley | Lucinski, Loraine Swanson | McDonald, Morgan | Miller, Angela M. | Ponson, Tori Armand | Price, Laura | Broussard, Kelly | Nance, Amy E. | Peterson, Dallin | Martin, Brennan | Browne, Shea | Griffin-Thomas, LaToya A. | Macdonald, Jennifer O. | Neary, Jillian | Oltean, Hanna | Adamski, Alys | Baez-Santiago, Madelyn | Bollweg, Brigid C. | Cragan, Janet D. | Ermias, Yokabed | Estetter, Lindsey B. C. | Fleck-Derderian, Shannon | Goldsmith, Cynthia S. | Groenewold, Matthew R. | Hayes, Heather | Igbinosa, Irogue | Jenkinson, Tiffany Gayle | Jones, Abbey M. | Lewis, Amanda | Moore, Cynthia A. | Newsome, Kimberly B. | Parihar, Vaunita | Patel, Mitesh M. | Paulino, Anna | Rasmussen, Sonja A. | Raycraft, Meghan | Reynolds, Megan R | Rollin, Dominique C. | Sanders, Jeanine H. | Shapiro-Mendoza, Carrie | Silva-Flannery, Luciana | Spivey, Pamela | Tshiwala, Alphonse K. | Williams, Tonya R. | Bower, William A. | Davlantes, Elizabeth | Forward, Terra R. | Fukunaga, Rena | Hines, Jonas | Hu, Shaohua Sean | Leung, Jessica | Lewis, Lillianne | Martin, Stacey | McNamara, Lucy | Omura, John D. | Robinson, Candice L. | Schmit, Kristine | Self, Julie L. | Shah, Minesh | Straily, Anne | Van Dyne, Elizabeth A. | Vu, Milan | Williams, Charnetta
doi:10.15585/mmwr.mm6624a3
PMCID: PMC5657799  PMID: 28640798

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