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1.  A Meta-Analysis Identifies New Loci Associated with Body Mass index in Individuals of African Ancestry 
Monda, Keri L. | Chen, Gary K. | Taylor, Kira C. | Palmer, Cameron | Edwards, Todd L. | Lange, Leslie A. | Ng, Maggie C.Y. | Adeyemo, Adebowale A. | Allison, Matthew A. | Bielak, Lawrence F. | Chen, Guanji | Graff, Mariaelisa | Irvin, Marguerite R. | Rhie, Suhn K. | Li, Guo | Liu, Yongmei | Liu, Youfang | Lu, Yingchang | Nalls, Michael A. | Sun, Yan V. | Wojczynski, Mary K. | Yanek, Lisa R. | Aldrich, Melinda C. | Ademola, Adeyinka | Amos, Christopher I. | Bandera, Elisa V. | Bock, Cathryn H. | Britton, Angela | Broeckel, Ulrich | Cai, Quiyin | Caporaso, Neil E. | Carlson, Chris | Carpten, John | Casey, Graham | Chen, Wei-Min | Chen, Fang | Chen, Yii-Der I. | Chiang, Charleston W.K. | Coetzee, Gerhard A. | Demerath, Ellen | Deming-Halverson, Sandra L. | Driver, Ryan W. | Dubbert, Patricia | Feitosa, Mary F. | Freedman, Barry I. | Gillanders, Elizabeth M. | Gottesman, Omri | Guo, Xiuqing | Haritunians, Talin | Harris, Tamara | Harris, Curtis C. | Hennis, Anselm JM | Hernandez, Dena G. | McNeill, Lorna H. | Howard, Timothy D. | Howard, Barbara V. | Howard, Virginia J. | Johnson, Karen C. | Kang, Sun J. | Keating, Brendan J. | Kolb, Suzanne | Kuller, Lewis H. | Kutlar, Abdullah | Langefeld, Carl D. | Lettre, Guillaume | Lohman, Kurt | Lotay, Vaneet | Lyon, Helen | Manson, JoAnn E. | Maixner, William | Meng, Yan A. | Monroe, Kristine R. | Morhason-Bello, Imran | Murphy, Adam B. | Mychaleckyj, Josyf C. | Nadukuru, Rajiv | Nathanson, Katherine L. | Nayak, Uma | NDiaye, Amidou | Nemesure, Barbara | Wu, Suh-Yuh | Leske, M. Cristina | Neslund-Dudas, Christine | Neuhouser, Marian | Nyante, Sarah | Ochs-Balcom, Heather | Ogunniyi, Adesola | Ogundiran, Temidayo O. | Ojengbede, Oladosu | Olopade, Olufunmilayo I. | Palmer, Julie R. | Ruiz-Narvaez, Edward A. | Palmer, Nicholette D. | Press, Michael F. | Rampersaud, Evandine | Rasmussen-Torvik, Laura J. | Rodriguez-Gil, Jorge L. | Salako, Babatunde | Schadt, Eric E. | Schwartz, Ann G. | Shriner, Daniel A. | Siscovick, David | Smith, Shad B. | Wassertheil-Smoller, Sylvia | Speliotes, Elizabeth K. | Spitz, Margaret R. | Sucheston, Lara | Taylor, Herman | Tayo, Bamidele O. | Tucker, Margaret A. | Van Den Berg, David J. | Velez Edwards, Digna R. | Wang, Zhaoming | Wiencke, John K. | Winkler, Thomas W. | Witte, John S. | Wrensch, Margaret | Wu, Xifeng | Yang, James J. | Levin, Albert M. | Young, Taylor R. | Zakai, Neil A. | Cushman, Mary | Zanetti, Krista A. | Zhao, Jing Hua | Zhao, Wei | Zheng, Yonglan | Zhou, Jie | Ziegler, Regina G. | Zmuda, Joseph M. | Fernandes, Jyotika K. | Gilkeson, Gary S. | Kamen, Diane L. | Hunt, Kelly J. | Spruill, Ida J. | Ambrosone, Christine B. | Ambs, Stefan | Arnett, Donna K. | Atwood, Larry | Becker, Diane M. | Berndt, Sonja I. | Bernstein, Leslie | Blot, William J. | Borecki, Ingrid B. | Bottinger, Erwin P. | Bowden, Donald W. | Burke, Gregory | Chanock, Stephen J. | Cooper, Richard S. | Ding, Jingzhong | Duggan, David | Evans, Michele K. | Fox, Caroline | Garvey, W. Timothy | Bradfield, Jonathan P. | Hakonarson, Hakon | Grant, Struan F.A. | Hsing, Ann | Chu, Lisa | Hu, Jennifer J. | Huo, Dezheng | Ingles, Sue A. | John, Esther M. | Jordan, Joanne M. | Kabagambe, Edmond K. | Kardia, Sharon L.R. | Kittles, Rick A. | Goodman, Phyllis J. | Klein, Eric A. | Kolonel, Laurence N. | Le Marchand, Loic | Liu, Simin | McKnight, Barbara | Millikan, Robert C. | Mosley, Thomas H. | Padhukasahasram, Badri | Williams, L. Keoki | Patel, Sanjay R. | Peters, Ulrike | Pettaway, Curtis A. | Peyser, Patricia A. | Psaty, Bruce M. | Redline, Susan | Rotimi, Charles N. | Rybicki, Benjamin A. | Sale, Michèle M. | Schreiner, Pamela J. | Signorello, Lisa B. | Singleton, Andrew B. | Stanford, Janet L. | Strom, Sara S. | Thun, Michael J. | Vitolins, Mara | Zheng, Wei | Moore, Jason H. | Williams, Scott M. | Zhu, Xiaofeng | Zonderman, Alan B. | Kooperberg, Charles | Papanicolaou, George | Henderson, Brian E. | Reiner, Alex P. | Hirschhorn, Joel N. | Loos, Ruth JF | North, Kari E. | Haiman, Christopher A.
Nature genetics  2013;45(6):690-696.
Genome-wide association studies (GWAS) have identified 36 loci associated with body mass index (BMI), predominantly in populations of European ancestry. We conducted a meta-analysis to examine the association of >3.2 million SNPs with BMI in 39,144 men and women of African ancestry, and followed up the most significant associations in an additional 32,268 individuals of African ancestry. We identified one novel locus at 5q33 (GALNT10, rs7708584, p=3.4×10−11) and another at 7p15 when combined with data from the Giant consortium (MIR148A/NFE2L3, rs10261878, p=1.2×10−10). We also found suggestive evidence of an association at a third locus at 6q16 in the African ancestry sample (KLHL32, rs974417, p=6.9×10−8). Thirty-two of the 36 previously established BMI variants displayed directionally consistent effect estimates in our GWAS (binomial p=9.7×10−7), of which five reached genome-wide significance. These findings provide strong support for shared BMI loci across populations as well as for the utility of studying ancestrally diverse populations.
doi:10.1038/ng.2608
PMCID: PMC3694490  PMID: 23583978
2.  Correction: Identification, Replication, and Fine-Mapping of Loci Associated with Adult Height in Individuals of African Ancestry 
N'Diaye, Amidou | Chen, Gary K. | Palmer, Cameron D. | Ge, Bing | Tayo, Bamidele | Mathias, Rasika A. | Ding, Jingzhong | Nalls, Michael A. | Adeyemo, Adebowale | Adoue, Véronique | Ambrosone, Christine B. | Atwood, Larry | Bandera, Elisa V. | Becker, Lewis C. | Berndt, Sonja I. | Bernstein, Leslie | Blot, William J. | Boerwinkle, Eric | Britton, Angela | Casey, Graham | Chanock, Stephen J. | Demerath, Ellen | Deming, Sandra L. | Diver, W. Ryan | Fox, Caroline | Harris, Tamara B. | Hernandez, Dena G. | Hu, Jennifer J. | Ingles, Sue A. | John, Esther M. | Johnson, Craig | Keating, Brendan | Kittles, Rick A. | Kolonel, Laurence N. | Kritchevsky, Stephen B. | Le Marchand, Loic | Lohman, Kurt | Liu, Jiankang | Millikan, Robert C. | Murphy, Adam | Musani, Solomon | Neslund-Dudas, Christine | North, Kari E. | Nyante, Sarah | Ogunniyi, Adesola | Ostrander, Elaine A. | Papanicolaou, George | Patel, Sanjay | Pettaway, Curtis A. | Press, Michael F. | Redline, Susan | Rodriguez-Gil, Jorge L. | Rotimi, Charles | Rybicki, Benjamin A. | Salako, Babatunde | Schreiner, Pamela J. | Signorello, Lisa B. | Singleton, Andrew B. | Stanford, Janet L. | Stram, Alex H. | Stram, Daniel O. | Strom, Sara S. | Suktitipat, Bhoom | Thun, Michael J. | Witte, John S. | Yanek, Lisa R. | Ziegler, Regina G. | Zheng, Wei | Zhu, Xiaofeng | Zmuda, Joseph M. | Zonderman, Alan B. | Evans, Michele K. | Liu, Yongmei | Becker, Diane M. | Cooper, Richard S. | Pastinen, Tomi | Henderson, Brian E. | Hirschhorn, Joel N. | Lettre, Guillaume | Haiman, Christopher A.
PLoS Genetics  2011;7(11):10.1371/annotation/58c67154-3f10-4155-9085-dcd6e3689008.
doi:10.1371/annotation/58c67154-3f10-4155-9085-dcd6e3689008
PMCID: PMC3227698
3.  Identification, Replication, and Fine-Mapping of Loci Associated with Adult Height in Individuals of African Ancestry 
N'Diaye, Amidou | Chen, Gary K. | Palmer, Cameron D. | Ge, Bing | Tayo, Bamidele | Mathias, Rasika A. | Ding, Jingzhong | Nalls, Michael A. | Adeyemo, Adebowale | Adoue, Véronique | Ambrosone, Christine B. | Atwood, Larry | Bandera, Elisa V. | Becker, Lewis C. | Berndt, Sonja I. | Bernstein, Leslie | Blot, William J. | Boerwinkle, Eric | Britton, Angela | Casey, Graham | Chanock, Stephen J. | Demerath, Ellen | Deming, Sandra L. | Diver, W. Ryan | Fox, Caroline | Harris, Tamara B. | Hernandez, Dena G. | Hu, Jennifer J. | Ingles, Sue A. | John, Esther M. | Johnson, Craig | Keating, Brendan | Kittles, Rick A. | Kolonel, Laurence N. | Kritchevsky, Stephen B. | Le Marchand, Loic | Lohman, Kurt | Liu, Jiankang | Millikan, Robert C. | Murphy, Adam | Musani, Solomon | Neslund-Dudas, Christine | North, Kari E. | Nyante, Sarah | Ogunniyi, Adesola | Ostrander, Elaine A. | Papanicolaou, George | Patel, Sanjay | Pettaway, Curtis A. | Press, Michael F. | Redline, Susan | Rodriguez-Gil, Jorge L. | Rotimi, Charles | Rybicki, Benjamin A. | Salako, Babatunde | Schreiner, Pamela J. | Signorello, Lisa B. | Singleton, Andrew B. | Stanford, Janet L. | Stram, Alex H. | Stram, Daniel O. | Strom, Sara S. | Suktitipat, Bhoom | Thun, Michael J. | Witte, John S. | Yanek, Lisa R. | Ziegler, Regina G. | Zheng, Wei | Zhu, Xiaofeng | Zmuda, Joseph M. | Zonderman, Alan B. | Evans, Michele K. | Liu, Yongmei | Becker, Diane M. | Cooper, Richard S. | Pastinen, Tomi | Henderson, Brian E. | Hirschhorn, Joel N. | Lettre, Guillaume | Haiman, Christopher A.
PLoS Genetics  2011;7(10):e1002298.
Adult height is a classic polygenic trait of high heritability (h2 ∼0.8). More than 180 single nucleotide polymorphisms (SNPs), identified mostly in populations of European descent, are associated with height. These variants convey modest effects and explain ∼10% of the variance in height. Discovery efforts in other populations, while limited, have revealed loci for height not previously implicated in individuals of European ancestry. Here, we performed a meta-analysis of genome-wide association (GWA) results for adult height in 20,427 individuals of African ancestry with replication in up to 16,436 African Americans. We found two novel height loci (Xp22-rs12393627, P = 3.4×10−12 and 2p14-rs4315565, P = 1.2×10−8). As a group, height associations discovered in European-ancestry samples replicate in individuals of African ancestry (P = 1.7×10−4 for overall replication). Fine-mapping of the European height loci in African-ancestry individuals showed an enrichment of SNPs that are associated with expression of nearby genes when compared to the index European height SNPs (P<0.01). Our results highlight the utility of genetic studies in non-European populations to understand the etiology of complex human diseases and traits.
Author Summary
Adult height is an ideal phenotype to improve our understanding of the genetic architecture of complex diseases and traits: it is easily measured and usually available in large cohorts, relatively stable, and mostly influenced by genetics (narrow-sense heritability of height h2∼0.8). Genome-wide association (GWA) studies in individuals of European ancestry have identified >180 single nucleotide polymorphisms (SNPs) associated with height. In the current study, we continued to use height as a model polygenic trait and explored the genetic influence in populations of African ancestry through a meta-analysis of GWA height results from 20,809 individuals of African descent. We identified two novel height loci not previously found in Europeans. We also replicated the European height signals, suggesting that many of the genetic variants that are associated with height are shared between individuals of European and African descent. Finally, in fine-mapping the European height loci in African-ancestry individuals, we found SNPs more likely to be associated with the expression of nearby genes than the SNPs originally found in Europeans. Thus, our results support the utility of performing genetic studies in non-European populations to gain insights into complex human diseases and traits.
doi:10.1371/journal.pgen.1002298
PMCID: PMC3188544  PMID: 21998595
4.  Patterns of sequence polymorphism in the fleshless berry locus in cultivated and wild Vitis vinifera accessions 
BMC Plant Biology  2010;10:284.
Background
Unlike in tomato, little is known about the genetic and molecular control of fleshy fruit development of perennial fruit trees like grapevine (Vitis vinifera L.). Here we present the study of the sequence polymorphism in a 1 Mb grapevine genome region at the top of chromosome 18 carrying the fleshless berry mutation (flb) in order, first to identify SNP markers closely linked to the gene and second to search for possible signatures of domestication.
Results
In total, 62 regions (17 SSR, 3 SNP, 1 CAPS and 41 re-sequenced gene fragments) were scanned for polymorphism along a 3.4 Mb interval (85,127-3,506,060 bp) at the top of the chromosome 18, in both V. vinifera cv. Chardonnay and a genotype carrying the flb mutation, V. vinifera cv. Ugni Blanc mutant. A nearly complete homozygosity in Ugni Blanc (wild and mutant forms) and an expected high level of heterozygosity in Chardonnay were revealed. Experiments using qPCR and BAC FISH confirmed the observed homozygosity. Under the assumption that flb could be one of the genes involved into the domestication syndrome of grapevine, we sequenced 69 gene fragments, spread over the flb region, representing 48,874 bp in a highly diverse set of cultivated and wild V. vinifera genotypes, to identify possible signatures of domestication in the cultivated V. vinifera compartment. We identified eight gene fragments presenting a significant deviation from neutrality of the Tajima's D parameter in the cultivated pool. One of these also showed higher nucleotide diversity in the wild compartments than in the cultivated compartments. In addition, SNPs significantly associated to berry weight variation were identified in the flb region.
Conclusions
We observed the occurrence of a large homozygous region in a non-repetitive region of the grapevine otherwise highly-heterozygous genome and propose a hypothesis for its formation. We demonstrated the feasibility to apply BAC FISH on the very small grapevine chromosomes and provided a specific probe for the identification of chromosome 18 on a cytogenetic map. We evidenced genes showing putative signatures of selection and SNPs significantly associated with berry weight variation in the flb region. In addition, we provided to the community 554 SNPs at the top of chromosome 18 for the development of a genotyping chip for future fine mapping of the flb gene in a F2 population when available.
doi:10.1186/1471-2229-10-284
PMCID: PMC3022909  PMID: 21176183

Results 1-4 (4)