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1.  PGD for hereditary breast and ovarian cancer: the route to universal tests for BRCA1 and BRCA2 mutation carriers 
European Journal of Human Genetics  2013;21(12):1361-1368.
Preimplantation Genetic Diagnosis (PGD) is a method of testing in vitro embryos as an alternative to prenatal diagnosis with possible termination of pregnancy in case of an affected child. Recently, PGD for hereditary breast and ovarian cancer caused by BRCA1 and BRCA2 mutations has found its way in specialized labs. We describe the route to universal single-cell PGD tests for carriers of BRCA1/2 mutations. Originally, mutation-specific protocols with one or two markers were set up and changed when new couples were not informative. This route of changing protocols was finalized after 2 years with universal tests for both BRCA1 and BRCA2 mutation carriers based on haplotyping of, respectively, 6 (BRCA1) and 8 (BRCA2) microsatellite markers in a multiplex PCR. Using all protocols, 30 couples had a total of 47 PGD cycles performed. Eight cycles were cancelled upon IVF treatment due to hypostimulation. Of the remaining 39 cycles, a total of 261 embryos were biopsied and a genetic diagnosis was obtained in 244 (93%). In 34 of the 39 cycles (84.6%), an embryo transfer was possible and resulted in 8 pregnancies leading to a fetal heart beat per oocyte retrieval of 20.5% and a fetal heart beat per embryonic transfer of 23.5%. The preparation time and costs for set-up and validation of tests are minimized. The informativity of microsatellite markers used in the universal PGD-PCR tests is based on CEPH and deCODE pedigrees, making the tests applicable in 90% of couples coming from these populations.
doi:10.1038/ejhg.2013.50
PMCID: PMC3831069  PMID: 23531862
PGD; HBOC; BRCA1; BRCA2; microsatellites; mutation
2.  Common non-synonymous SNPs associated with breast cancer susceptibility: findings from the Breast Cancer Association Consortium 
Milne, Roger L. | Burwinkel, Barbara | Michailidou, Kyriaki | Arias-Perez, Jose-Ignacio | Zamora, M. Pilar | Menéndez-Rodríguez, Primitiva | Hardisson, David | Mendiola, Marta | González-Neira, Anna | Pita, Guillermo | Alonso, M. Rosario | Dennis, Joe | Wang, Qin | Bolla, Manjeet K. | Swerdlow, Anthony | Ashworth, Alan | Orr, Nick | Schoemaker, Minouk | Ko, Yon-Dschun | Brauch, Hiltrud | Hamann, Ute | Andrulis, Irene L. | Knight, Julia A. | Glendon, Gord | Tchatchou, Sandrine | Matsuo, Keitaro | Ito, Hidemi | Iwata, Hiroji | Tajima, Kazuo | Li, Jingmei | Brand, Judith S. | Brenner, Hermann | Dieffenbach, Aida Karina | Arndt, Volker | Stegmaier, Christa | Lambrechts, Diether | Peuteman, Gilian | Christiaens, Marie-Rose | Smeets, Ann | Jakubowska, Anna | Lubinski, Jan | Jaworska-Bieniek, Katarzyna | Durda, Katazyna | Hartman, Mikael | Hui, Miao | Yen Lim, Wei | Wan Chan, Ching | Marme, Federick | Yang, Rongxi | Bugert, Peter | Lindblom, Annika | Margolin, Sara | García-Closas, Montserrat | Chanock, Stephen J. | Lissowska, Jolanta | Figueroa, Jonine D. | Bojesen, Stig E. | Nordestgaard, Børge G. | Flyger, Henrik | Hooning, Maartje J. | Kriege, Mieke | van den Ouweland, Ans M.W. | Koppert, Linetta B. | Fletcher, Olivia | Johnson, Nichola | dos-Santos-Silva, Isabel | Peto, Julian | Zheng, Wei | Deming-Halverson, Sandra | Shrubsole, Martha J. | Long, Jirong | Chang-Claude, Jenny | Rudolph, Anja | Seibold, Petra | Flesch-Janys, Dieter | Winqvist, Robert | Pylkäs, Katri | Jukkola-Vuorinen, Arja | Grip, Mervi | Cox, Angela | Cross, Simon S. | Reed, Malcolm W.R. | Schmidt, Marjanka K. | Broeks, Annegien | Cornelissen, Sten | Braaf, Linde | Kang, Daehee | Choi, Ji-Yeob | Park, Sue K. | Noh, Dong-Young | Simard, Jacques | Dumont, Martine | Goldberg, Mark S. | Labrèche, France | Fasching, Peter A. | Hein, Alexander | Ekici, Arif B. | Beckmann, Matthias W. | Radice, Paolo | Peterlongo, Paolo | Azzollini, Jacopo | Barile, Monica | Sawyer, Elinor | Tomlinson, Ian | Kerin, Michael | Miller, Nicola | Hopper, John L. | Schmidt, Daniel F. | Makalic, Enes | Southey, Melissa C. | Hwang Teo, Soo | Har Yip, Cheng | Sivanandan, Kavitta | Tay, Wan-Ting | Shen, Chen-Yang | Hsiung, Chia-Ni | Yu, Jyh-Cherng | Hou, Ming-Feng | Guénel, Pascal | Truong, Therese | Sanchez, Marie | Mulot, Claire | Blot, William | Cai, Qiuyin | Nevanlinna, Heli | Muranen, Taru A. | Aittomäki, Kristiina | Blomqvist, Carl | Wu, Anna H. | Tseng, Chiu-Chen | Van Den Berg, David | Stram, Daniel O. | Bogdanova, Natalia | Dörk, Thilo | Muir, Kenneth | Lophatananon, Artitaya | Stewart-Brown, Sarah | Siriwanarangsan, Pornthep | Mannermaa, Arto | Kataja, Vesa | Kosma, Veli-Matti | Hartikainen, Jaana M. | Shu, Xiao-Ou | Lu, Wei | Gao, Yu-Tang | Zhang, Ben | Couch, Fergus J. | Toland, Amanda E. | Yannoukakos, Drakoulis | Sangrajrang, Suleeporn | McKay, James | Wang, Xianshu | Olson, Janet E. | Vachon, Celine | Purrington, Kristen | Severi, Gianluca | Baglietto, Laura | Haiman, Christopher A. | Henderson, Brian E. | Schumacher, Fredrick | Le Marchand, Loic | Devilee, Peter | Tollenaar, Robert A.E.M. | Seynaeve, Caroline | Czene, Kamila | Eriksson, Mikael | Humphreys, Keith | Darabi, Hatef | Ahmed, Shahana | Shah, Mitul | Pharoah, Paul D.P. | Hall, Per | Giles, Graham G. | Benítez, Javier | Dunning, Alison M. | Chenevix-Trench, Georgia | Easton, Douglas F. | Berchuck, Andrew | Eeles, Rosalind A. | Olama, Ali Amin Al | Kote-Jarai, Zsofia | Benlloch, Sara | Antoniou, Antonis | McGuffog, Lesley | Offit, Ken | Lee, Andrew | Dicks, Ed | Luccarini, Craig | Tessier, Daniel C. | Bacot, Francois | Vincent, Daniel | LaBoissière, Sylvie | Robidoux, Frederic | Nielsen, Sune F. | Cunningham, Julie M. | Windebank, Sharon A. | Hilker, Christopher A. | Meyer, Jeffrey | Angelakos, Maggie | Maskiell, Judi | van der Schoot, Ellen | Rutgers, Emiel | Verhoef, Senno | Hogervorst, Frans | Boonyawongviroj, Prat | Siriwanarungsan, Pornthep | Schrauder, Michael | Rübner, Matthias | Oeser, Sonja | Landrith, Silke | Williams, Eileen | Ryder-Mills, Elaine | Sargus, Kara | McInerney, Niall | Colleran, Gabrielle | Rowan, Andrew | Jones, Angela | Sohn, Christof | Schneeweiß, Andeas | Bugert, Peter | Álvarez, Núria | Lacey, James | Wang, Sophia | Ma, Huiyan | Lu, Yani | Deapen, Dennis | Pinder, Rich | Lee, Eunjung | Schumacher, Fred | Horn-Ross, Pam | Reynolds, Peggy | Nelson, David | Ziegler, Hartwig | Wolf, Sonja | Hermann, Volker | Lo, Wing-Yee | Justenhoven, Christina | Baisch, Christian | Fischer, Hans-Peter | Brüning, Thomas | Pesch, Beate | Rabstein, Sylvia | Lotz, Anne | Harth, Volker | Heikkinen, Tuomas | Erkkilä, Irja | Aaltonen, Kirsimari | von Smitten, Karl | Antonenkova, Natalia | Hillemanns, Peter | Christiansen, Hans | Myöhänen, Eija | Kemiläinen, Helena | Thorne, Heather | Niedermayr, Eveline | Bowtell, D | Chenevix-Trench, G | deFazio, A | Gertig, D | Green, A | Webb, P | Green, A. | Parsons, P. | Hayward, N. | Webb, P. | Whiteman, D. | Fung, Annie | Yashiki, June | Peuteman, Gilian | Smeets, Dominiek | Brussel, Thomas Van | Corthouts, Kathleen | Obi, Nadia | Heinz, Judith | Behrens, Sabine | Eilber, Ursula | Celik, Muhabbet | Olchers, Til | Manoukian, Siranoush | Peissel, Bernard | Scuvera, Giulietta | Zaffaroni, Daniela | Bonanni, Bernardo | Feroce, Irene | Maniscalco, Angela | Rossi, Alessandra | Bernard, Loris | Tranchant, Martine | Valois, Marie-France | Turgeon, Annie | Heguy, Lea | Sze Yee, Phuah | Kang, Peter | Nee, Kang In | Mariapun, Shivaani | Sook-Yee, Yoon | Lee, Daphne | Ching, Teh Yew | Taib, Nur Aishah Mohd | Otsukka, Meeri | Mononen, Kari | Selander, Teresa | Weerasooriya, Nayana | staff, OFBCR | Krol-Warmerdam, E. | Molenaar, J. | Blom, J. | Brinton, Louise | Szeszenia-Dabrowska, Neonila | Peplonska, Beata | Zatonski, Witold | Chao, Pei | Stagner, Michael | Bos, Petra | Blom, Jannet | Crepin, Ellen | Nieuwlaat, Anja | Heemskerk, Annette | Higham, Sue | Cross, Simon | Cramp, Helen | Connley, Dan | Balasubramanian, Sabapathy | Brock, Ian | Luccarini, Craig | Conroy, Don | Baynes, Caroline | Chua, Kimberley
Human Molecular Genetics  2014;23(22):6096-6111.
Candidate variant association studies have been largely unsuccessful in identifying common breast cancer susceptibility variants, although most studies have been underpowered to detect associations of a realistic magnitude. We assessed 41 common non-synonymous single-nucleotide polymorphisms (nsSNPs) for which evidence of association with breast cancer risk had been previously reported. Case-control data were combined from 38 studies of white European women (46 450 cases and 42 600 controls) and analyzed using unconditional logistic regression. Strong evidence of association was observed for three nsSNPs: ATXN7-K264R at 3p21 [rs1053338, per allele OR = 1.07, 95% confidence interval (CI) = 1.04–1.10, P = 2.9 × 10−6], AKAP9-M463I at 7q21 (rs6964587, OR = 1.05, 95% CI = 1.03–1.07, P = 1.7 × 10−6) and NEK10-L513S at 3p24 (rs10510592, OR = 1.10, 95% CI = 1.07–1.12, P = 5.1 × 10−17). The first two associations reached genome-wide statistical significance in a combined analysis of available data, including independent data from nine genome-wide association studies (GWASs): for ATXN7-K264R, OR = 1.07 (95% CI = 1.05–1.10, P = 1.0 × 10−8); for AKAP9-M463I, OR = 1.05 (95% CI = 1.04–1.07, P = 2.0 × 10−10). Further analysis of other common variants in these two regions suggested that intronic SNPs nearby are more strongly associated with disease risk. We have thus identified a novel susceptibility locus at 3p21, and confirmed previous suggestive evidence that rs6964587 at 7q21 is associated with risk. The third locus, rs10510592, is located in an established breast cancer susceptibility region; the association was substantially attenuated after adjustment for the known GWAS hit. Thus, each of the associated nsSNPs is likely to be a marker for another, non-coding, variant causally related to breast cancer risk. Further fine-mapping and functional studies are required to identify the underlying risk-modifying variants and the genes through which they act.
doi:10.1093/hmg/ddu311
PMCID: PMC4204770  PMID: 24943594
3.  The unfolding clinical spectrum of holoprosencephaly due to mutations in SHH, ZIC2, SIX3 and TGIF genes 
European Journal of Human Genetics  2010;18(9):999-1005.
Holoprosencephaly is a severe malformation of the brain characterized by abnormal formation and separation of the developing central nervous system. The prevalence is 1:250 during early embryogenesis, the live-born prevalence is 1:16 000. The etiology of HPE is extremely heterogeneous and can be teratogenic or genetic. We screened four known HPE genes in a Dutch cohort of 86 non-syndromic HPE index cases, including 53 family members. We detected 21 mutations (24.4%), 3 in SHH, 9 in ZIC2 and 9 in SIX3. Eight mutations involved amino-acid substitutions, 7 ins/del mutations, 1 frame-shift, 3 identical poly-alanine tract expansions and 2 gene deletions. Pathogenicity of mutations was presumed based on de novo character, predicted non-functionality of mutated proteins, segregation of mutations with affected family-members or combinations of these features. Two mutations were reported previously. SNP array confirmed detected deletions; one spanning the ZIC2/ZIC5 genes (approx. 100 kb) the other a 1.45 Mb deletion including SIX2/SIX3 genes. The mutation percentage (24%) is comparable with previous reports, but we detected significantly less mutations in SHH: 3.5 vs 10.7% (P=0.043) and significantly more in SIX3: 10.5 vs 4.3% (P=0.018). For TGIF1 and ZIC2 mutation the rate was in conformity with earlier reports. About half of the mutations were de novo, one was a germ line mosaic. The familial mutations displayed extensive heterogeneity in clinical manifestation. Of seven familial index patients only two parental carriers showed minor HPE signs, five were completely asymptomatic. Therefore, each novel mutation should be considered as a risk factor for clinically manifest HPE, with the caveat of reduced clinical penetrance.
doi:10.1038/ejhg.2010.70
PMCID: PMC2987413  PMID: 20531442
Holoprosencephaly; SHH; SIX3; ZIC2; TGIF; genotype–phenotype
4.  Linkage analysis with chromosome 15q11-13 markers shows genomic imprinting in familial Angelman syndrome. 
Journal of Medical Genetics  1992;29(12):853-857.
Angelman syndrome (AS) and Prader-Willi syndrome (PWS) have become the classical examples of genomic imprinting in man, as completely different phenotypes are generated by the absence of maternal (AS) or paternal (PWS) contributions to the q11-13 region of chromosome 15 as a result of deletion or uniparental disomy. Apparently, most patients are sporadic cases. The genetic mechanism underlying familial AS has remained enigmatic for a long time. Recently, evidence has been emerging suggesting autosomal dominant inheritance of a detectable or undetectable defect in a gene or genes at 15q11-13, subject to genomic imprinting. The present report describes an unusually large pedigree with segregation of AS through maternal inheritance and apparent asymptomatic transmission through several male ancestors. Deletion and paternal disomy at 15q11-13 were excluded. However, the genetic defect is still located in this region, as we obtained a maximum lod score of 5.40 for linkage to the GABA receptor locus GABRB3 and the anonymous DNA marker D15S10, which have been mapped within or adjacent to the AS critical region at 15q11-13. The size of the pedigree allowed calculation of an odds ratio in favour of genomic imprinting of 9.25 x 10(5). This family illustrates the necessity of extensive pedigree analysis when considering recurrence risks for relatives of AS patients, those without detectable deletion or disomy in particular.
Images
PMCID: PMC1016200  PMID: 1362220
5.  Optimized 14 + 1 receive coil array and position system for 3D high-resolution MRI of dental and maxillomandibular structures 
Dentomaxillofacial Radiology  2015;45(1):20150177.
Objectives:
The purpose of this study was to design, build and test a multielement receive coil array and position system, which is optimized for three-dimensional (3D) high-resolution dental and maxillomandibular MRI with high patient comfort.
Methods:
A 14 + 1 coil array and positioning system, allowing easy handling by the technologists, reproducible positioning of the patients and high patient comfort, was tested with three healthy volunteers using a 3.0-T MRI machine (Siemens Skyra; Siemens Medical Solutions, Erlangen, Germany). High-resolution 3D T1 weighted, water excitation T1 weighted and fat-saturated T2 weighted imaging sequences were scanned, and 3D image data were reformatted in different orientations and curvatures to aid diagnosis.
Results:
The high number of receiving coils and the comfortable positioning of the coil array close to the patient's face provided a high signal-to-noise ratio and allowed high quality, high resolution, 3D image data to be acquired within reasonable scan times owing to the possibility of parallel image acquisition acceleration. Reformatting the isotropic 3D image data in different views is helpful for diagnosis, e.g. panoramic reconstruction. The visibility of soft tissues such as the mandibular canal, nutritive canals and periodontal ligaments was exquisite.
Conclusions:
The optimized MRI receive coil array and positioning system for dental and oral–maxillofacial imaging provides a valuable tool for detecting and diagnosing pathologies in dental and oral–maxillofacial structures while avoiding radiation dose. The high patient comfort, as achieved by our design, is very crucial, since image artefacts due to movement or failing to complete the examination jeopardize the diagnostic value of MRI examinations.
doi:10.1259/dmfr.20150177
PMCID: PMC5083890  PMID: 26371075
dental pulp; periodontal ligament; apical foramen; salivary glands
6.  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
7.  Neurophysiology versus clinical genetics in Rett syndrome: A multicenter study 
Many studies have attempted to establish the genotype–phenotype correlation in Rett syndrome (RTT). Cardiorespiratory measurements provide robust objective data, to correlate with each of the different clinical phenotypes. It has important implications for the management and treatment of this syndrome. The aim of this study was to correlate the genotype with the quantitative cardiorespiratory data obtained by neurophysiological measurement combined with a clinical severity score. This international multicenter study was conducted in four European countries from 1999 to 2012. The study cohort consisted of a group of 132 well‐defined RTT females aged between 2 and 43 years with extended clinical, molecular, and neurophysiological assessments. Diagnosis of RTT was based on the consensus criteria for RTT and molecular confirmation. Genotype–phenotype analyses of clinical features and cardiorespiratory data were performed after grouping mutations by the same type and localization or having the same putative biological effect on the MeCP2 protein, and subsequently on eight single recurrent mutations. A less severe phenotype was seen in females with CTS, p.R133C, and p.R294X mutations. Autonomic disturbances were present in all females, and not restricted to nor influenced by one specific group or any single recurrent mutation. The objective information from non‐invasive neurophysiological evaluation of the disturbed central autonomic control is of great importance in helping to organize the lifelong care for females with RTT. Further research is needed to provide insights into the pathogenesis of autonomic dysfunction, and to develop evidence‐based management in RTT. © 2016 The Authors. American Journal of Medical Genetics Part A published by Wiley Periodicals, Inc.
doi:10.1002/ajmg.a.37812
PMCID: PMC5157762  PMID: 27354166
Rett syndrome; neurophysiology; MECP2
8.  Discovery and structural characterisation of new fold type IV-transaminases exemplify the diversity of this enzyme fold 
Scientific Reports  2016;6:38183.
Transaminases are useful biocatalysts for the production of amino acids and chiral amines as intermediates for a broad range of drugs and fine chemicals. Here, we describe the discovery and characterisation of new transaminases from microorganisms which were enriched in selective media containing (R)-amines as sole nitrogen source. While most of the candidate proteins were clearly assigned to known subgroups of the fold IV family of PLP-dependent enzymes by sequence analysis and characterisation of their substrate specificity, some of them did not fit to any of these groups. The structure of one of these enzymes from Curtobacterium pusillum, which can convert d-amino acids and various (R)-amines with high enantioselectivity, was solved at a resolution of 2.4 Å. It shows significant differences especially in the active site compared to other transaminases of the fold IV family and thus indicates the existence of a new subgroup within this family. Although the discovered transaminases were not able to convert ketones in a reasonable time frame, overall, the enrichment-based approach was successful, as we identified two amine transaminases, which convert (R)-amines with high enantioselectivity, and can be used for a kinetic resolution of 1-phenylethylamine and analogues to obtain the (S)-amines with e.e.s >99%.
doi:10.1038/srep38183
PMCID: PMC5131300  PMID: 27905516
9.  Temporally stable adaptation is robust, incomplete and specific 
The European Journal of Neuroscience  2016;44(9):2708-2715.
Abstract
Sensorimotor adaptation, the process that reduces movement errors by learning from sensory feedback, is often studied within a session of about half an hour. Within such a single session, adaptation generally reaches plateau before errors are completely removed. However, adaptation may complete on longer timescales: the slow components of error‐based adaptation are associated with good retention. In this study, we tested how adaptation evolves over time by asking participants to perform six adaptation sessions on different days. In these sessions, participants performed a three‐dimensional reaching task while visual feedback about endpoint errors was rotated around the cyclopean eye. In addition, context specificity of the adaptation was addressed by measuring inter‐limb transfer and transfer to visual and proprioceptive perceptual tasks. We show that from the second session on, the adaptation was retained almost completely across sessions. However, after six learning sessions, adaptation still reached plateau before errors were completely removed. The adaptation was specific: the adaptation did neither transfer to the other hand, nor to the visual, and only marginally to the proprioceptive perceptual estimates. We conclude that motor adaptation is robust, specific and incomplete.
doi:10.1111/ejn.13355
PMCID: PMC5129530  PMID: 27469297
retention; sensory realignment; training; visuomotor adaptation
10.  Stress, stress‐induced cortisol responses, and eyewitness identification performance 
Behavioral Sciences & the Law  2016;34(4):580-594.
Abstract
In the eyewitness identification literature, stress and arousal at the time of encoding are considered to adversely influence identification performance. This assumption is in contrast with findings from the neurobiology field of learning and memory, showing that stress and stress hormones are critically involved in forming enduring memories. This discrepancy may be related to methodological differences between the two fields of research, such as the tendency for immediate testing or the use of very short (1–2 hours) retention intervals in eyewitness research, while neurobiology studies insert at least 24 hours. Other differences refer to the extent to which stress‐responsive systems (i.e., the hypothalamic–pituitary–adrenal axis) are stimulated effectively under laboratory conditions. The aim of the current study was to conduct an experiment that accounts for the contemporary state of knowledge in both fields. In all, 123 participants witnessed a live staged theft while being exposed to a laboratory stressor that reliably elicits autonomic and glucocorticoid stress responses or while performing a control task. Salivary cortisol levels were measured to control for the effectiveness of the stress induction. One week later, participants attempted to identify the thief from target‐present and target‐absent line‐ups. According to regression and receiver operating characteristic analyses, stress did not have robust detrimental effects on identification performance. Copyright © 2016 John Wiley & Sons, Ltd. © 2016 The Authors Behavioral Sciences & the Law Published by John Wiley & Sons Ltd
doi:10.1002/bsl.2249
PMCID: PMC5129533  PMID: 27417874
Stress; stress‐induced cortisol responses; and eyewitness identification performance
11.  Improving care for heart failure patients in primary care, GPs' perceptions: a qualitative evidence synthesis 
BMJ Open  2016;6(11):e013459.
Objectives
General practitioners (GPs) play a key role in heart failure (HF) management. Despite multiple guidelines, the management of patients with HF in primary care is suboptimal. Therefore, all the qualitative evidence concerning GPs’ perceptions of managing HF in primary care was synthesised to identify barriers and facilitators for optimal care, and ideas for improvement.
Design
Qualitative evidence synthesis.
Methods
Searches of MEDLINE, EMBASE, Web of Science and CINAHL databases up to 20/12/2015 were conducted. The Critical Appraisal Skills Programme's checklist for qualitative research was used for quality assessment. Thematic analysis was used as method of analysis.
Results
Of 5427 articles, 18 qualitative articles were included. Findings were organised in HF-specific factors, patient factors, physician factors and contextual factors. GPs’ uncertainty in all areas of HF management was highlighted. HF management started with an uncertain diagnosis, leading to difficulties with communication, treatment and advance care planning. Lack of access to specialised care and lack of knowledge were identified as important contributors to this uncertainty. In an effort to overcome this, strategies bringing evidence into practice should be promoted. GPs expressed the need for a multidisciplinary chronic care approach for HF. However, mixed experiences were noted with regard to interprofessional collaboration.
Conclusions
The main challenges identified in this synthesis were how to deal with GPs’ uncertainty about clinical practice, how to bring evidence into practice and how to work together as a multiprofessional team. These barriers were situated predominantly on the physician and contextual level. Targets to improve GPs’ HF care were identified.
doi:10.1136/bmjopen-2016-013459
PMCID: PMC5168518  PMID: 27903565
PRIMARY CARE; QUALITATIVE RESEARCH
12.  Rett syndrome – biological pathways leading from MECP2 to disorder phenotypes 
Rett syndrome (RTT) is a rare disease but still one of the most abundant causes for intellectual disability in females. Typical symptoms are onset at month 6–18 after normal pre- and postnatal development, loss of acquired skills and severe intellectual disability. The type and severity of symptoms are individually highly different. A single mutation in one gene, coding for methyl-CpG-binding protein 2 (MECP2), is responsible for the disease. The most important action of MECP2 is regulating epigenetic imprinting and chromatin condensation, but MECP2 influences many different biological pathways on multiple levels although the molecular pathways from gene to phenotype are currently not fully understood. In this review the known changes in metabolite levels, gene expression and biological pathways in RTT are summarized, discussed how they are leading to some characteristic RTT phenotypes and therefore the gaps of knowledge are identified. Namely, which phenotypes have currently no mechanistic explanation leading back to MECP2 related pathways? As a result of this review the visualization of the biologic pathways showing MECP2 up- and downstream regulation was developed and published on WikiPathways which will serve as template for future omics data driven research. This pathway driven approach may serve as a use case for other rare diseases, too.
doi:10.1186/s13023-016-0545-5
PMCID: PMC5123333  PMID: 27884167
Rett syndrome; MECP2; Systems biology; Bioinformatics; Data integration; DNA methylation; Epigenetics
13.  Specific MRI Abnormalities Reveal Severe Perrault Syndrome due to CLPP Defects 
In establishing a genetic diagnosis in heterogeneous neurological disease, clinical characterization and whole exome sequencing (WES) go hand-in-hand. Clinical data are essential, not only to guide WES variant selection and define the clinical severity of a genetic defect but also to identify other patients with defects in the same gene. In an infant patient with sensorineural hearing loss, psychomotor retardation, and epilepsy, WES resulted in identification of a novel homozygous CLPP frameshift mutation (c.21delA). Based on the gene defect and clinical symptoms, the diagnosis Perrault syndrome type 3 (PRLTS3) was established. The patient’s brain-MRI revealed specific abnormalities of the subcortical and deep cerebral white matter and the middle blade of the corpus callosum, which was used to identify similar patients in the Amsterdam brain-MRI database, containing over 3000 unclassified leukoencephalopathy cases. In three unrelated patients with similar MRI abnormalities the CLPP gene was sequenced, and in two of them novel missense mutations were identified together with a large deletion that covered part of the CLPP gene on the other allele. The severe neurological and MRI abnormalities in these young patients were due to the drastic impact of the CLPP mutations, correlating with the variation in clinical manifestations among previously reported patients. Our data show that similarity in brain-MRI patterns can be used to identify novel PRLTS3 patients, especially during early disease stages, when only part of the disease manifestations are present. This seems especially applicable to the severely affected cases in which CLPP function is drastically affected and MRI abnormalities are pronounced.
doi:10.3389/fneur.2016.00203
PMCID: PMC5110515  PMID: 27899912
genetic diagnosis; brain-MRI; Perrault syndrome type 3; Perrault syndrome; CLPP
14.  Proprioceptive Localization of the Hand Changes When Skin Stretch around the Elbow Is Manipulated 
Frontiers in Psychology  2016;7:1620.
Cutaneous information has been shown to influence proprioceptive position sense when subjects had to judge or match the posture of their limbs. In the present study, we tested whether cutaneous information also affects proprioceptive localization of the hand when moving it to a target. In an explorative study, we manipulated the skin stretch around the elbow by attaching elastic sports tape to one side of the arm. Subjects were asked to move the unseen manipulated arm to visually presented targets. We found that the tape induced a significant shift of the end-points of these hand movements. Surprisingly, this shift corresponded with an increase in elbow extension, irrespective of the side of the arm that was taped. A control experiment showed that this cannot be explained by how the skin stretches, because the skin near the elbow stretches to a similar extent on the inside and outside of the arm when the elbow angle increases and decreases, respectively. A second control experiment reproduced and extended the results of the main experiment for tape on the inside of the arm, and showed that the asymmetry was not just a consequence of the tape originally being applied slightly differently to the outside of the arm. However, the way in which the tape was applied does appear to matter, because applying the tape in the same way to the outside of the arm as to the inside of the arm influenced different subjects quite differently, suggesting that the relationship between skin stretch and sensed limb posture is quite complex. We conclude that the way the skin is stretched during a goal-directed movement provides information that helps guide the hand toward the target.
doi:10.3389/fpsyg.2016.01620
PMCID: PMC5073131  PMID: 27818638
skin stretch; proprioception; hand localization
15.  Reliability of measuring regional callosal atrophy in neurodegenerative diseases 
NeuroImage : Clinical  2016;12:825-831.
The Corpus Callosum (CC) is an important structure connecting the two brain hemispheres. As several neurodegenerative diseases are known to alter its shape, it is an interesting structure to assess as biomarker. Yet, currently, the CC-segmentation is often performed manually and is consequently an error prone and time-demanding procedure. In this paper, we present an accurate and automated method for corpus callosum segmentation based on T1-weighted MRI images.
After the initial construction of a CC atlas based on healthy controls, a new image is subjected to a mid-sagittal plane (MSP) detection algorithm and a 3D affine registration in order to initialise the CC within the extracted MSP. Next, an active shape model is run to extract the CC. We calculated the reliability of most popular CC features (area, circularity, corpus callosum index and thickness profile) in healthy controls, Alzheimer's Disease patients and Multiple Sclerosis patients. Importantly, we also provide inter-scanner reliability estimates.
We obtained an intra-class correlation coefficient (ICC) of over 0.95 for most features and most datasets. The inter-scanner reliability assessed on the MS patients was remarkably well and ranged from 0.77 to 0.97.
In summary, we have constructed an algorithm that reliably detects the CC in 3D T1 images in a fully automated way in healthy controls and different neurodegenerative diseases. Although the CC area and the circularity are the most reliable features (ICC > 0.97); the reliability of the thickness profile (ICC > 0.90; excluding the tip) is sufficient to warrant its inclusion in future clinical studies.
Highlights
•A completely automated segmentation of the Corpus Callosum•Both traditional features and the thickness profile using Laplace's equation are calculated.•Excellent reproducibility and accuracy in healthy controls•Excellent reproducibility and accuracy in Alzheimer's Dementia and Multiple Sclerosis patients•Excellent inter-scanner reliability enabling the pooling of multi-center data
doi:10.1016/j.nicl.2016.10.012
PMCID: PMC5094205  PMID: 27830115
Corpus callosum segmentation; Biomarker; Repeatability; Reproducibility; Multiple sclerosis; Alzheimer's disease; Corpus callosum thickness profile
16.  Diagnostic rules and algorithms for the diagnosis of non-acute heart failure in patients 80 years of age and older: a diagnostic accuracy and validation study 
BMJ Open  2016;6(10):e012888.
Objectives
Different diagnostic algorithms for non-acute heart failure (HF) exist. Our aim was to compare the ability of these algorithms to identify HF in symptomatic patients aged 80 years and older and identify those patients at highest risk for mortality.
Design
Diagnostic accuracy and validation study.
Setting
General practice, Belgium.
Participants
365 patients with HF symptoms aged 80 years and older (BELFRAIL cohort). Participants underwent a full clinical assessment, including a detailed echocardiographic examination at home.
Outcome measures
The diagnostic accuracy of 4 different algorithms was compared using an intention-to-diagnose analysis. The European Society of Cardiology (ESC) definition of HF was used as the reference standard for HF diagnosis. Kaplan-Meier curves for 5-year all-cause mortality were plotted and HRs and corresponding 95% CIs were calculated to compare the mortality risk predicting abilities of the different algorithms. Net reclassification improvement (NRI) was calculated.
Results
The prevalence of HF was 20% (n=74). The 2012 ESC algorithm yielded the highest sensitivity (92%, 95% CI 83% to 97%) as well as the highest referral rate (71%, n=259), whereas the Oudejans algorithm yielded the highest specificity (73%, 95% CI 68% to 78%) and the lowest referral rate (36%, n=133). These differences could be ascribed to differences in N-terminal probrain natriuretic peptide cut-off values (125 vs 400 pg/mL). The Kelder and Oudejans algorithms exhibited NRIs of 12% (95% CI 0.7% to 22%, p=0.04) and 22% (95% CI 9% to 32%, p<0.001), respectively, compared with the ESC algorithm. All algorithms detected patients at high risk for mortality (HR 1.9, 95% CI 1.4 to 2.5; Kelder) to 2.3 (95% CI 1.7 to 3.1; Oudejans). No significant differences were observed among the algorithms with respect to mortality risk predicting abilities.
Conclusions
Choosing a diagnostic algorithm for non-acute HF in elderly patients represents a trade-off between sensitivity and specificity, mainly depending on differences between cut-off values for natriuretic peptides.
doi:10.1136/bmjopen-2016-012888
PMCID: PMC5073666  PMID: 27855108
GERIATRIC MEDICINE; PRIMARY CARE
17.  Immersed Boundary Models for Quantifying Flow-Induced Mechanical Stimuli on Stem Cells Seeded on 3D Scaffolds in Perfusion Bioreactors 
PLoS Computational Biology  2016;12(9):e1005108.
Perfusion bioreactors regulate flow conditions in order to provide cells with oxygen, nutrients and flow-associated mechanical stimuli. Locally, these flow conditions can vary depending on the scaffold geometry, cellular confluency and amount of extra cellular matrix deposition. In this study, a novel application of the immersed boundary method was introduced in order to represent a detailed deformable cell attached to a 3D scaffold inside a perfusion bioreactor and exposed to microscopic flow. The immersed boundary model permits the prediction of mechanical effects of the local flow conditions on the cell. Incorporating stiffness values measured with atomic force microscopy and micro-flow boundary conditions obtained from computational fluid dynamics simulations on the entire scaffold, we compared cell deformation, cortical tension, normal and shear pressure between different cell shapes and locations. We observed a large effect of the precise cell location on the local shear stress and we predicted flow-induced cortical tensions in the order of 5 pN/μm, at the lower end of the range reported in literature. The proposed method provides an interesting tool to study perfusion bioreactors processes down to the level of the individual cell’s micro-environment, which can further aid in the achievement of robust bioprocess control for regenerative medicine applications.
Author Summary
Tissue Engineering involves the combination of cells, growth factors and biomaterials into artificial constructs which, upon implantation, can improve the healing capacity of the human body. A remaining challenge involves providing physical stimuli to individual cells, thereby guiding them towards the properties of the desired tissue type. Perfusion bioreactors try to control the local concentration of oxygen, nutrients and growth factors and mechanical stresses by varying the fluid flow. In this work, we predict the shear stress that individual cells experience at the microscopic scale, as a function of the bioreactor inlet flow velocity, by making use of the immersed boundary method. This method combines an Eulerian grid (fixed in space) with a Lagrangian grid (moving with the flow) to model the deformation of cells due to flow inside a scaffold pore. Our simulations show that the local shear stress levels on specific, realistic cell geometries are different from the shear stress levels on empty scaffolds, which are often still used as a reference. Finally, we predict and discuss the additional effect of realistic flow on other mechanical cell properties, such as its deformation and its cortical tension.
doi:10.1371/journal.pcbi.1005108
PMCID: PMC5033382  PMID: 27658116
18.  How Heavy Is an Illusory Length? 
i-Perception  2016;7(5):2041669516669155.
The perception of object properties, such as size and weight, can be subject to illusions. Could a visual size illusion influence perceived weight? Here, we tested whether the size-weight illusion occurs when lifting two physically identical but perceptually different objects, by using an illusion of size. Participants judged the weight and length of 11 to 17 cm brass bars with equal density to which cardboard arrowheads were attached to create a Müller–Lyer illusion. We found that these stimuli induced an illusion in which the bar that was visually perceived as being shorter was also perceived as feeling heavier. In fact, a 5-mm increase in illusory length corresponded to a decrease in illusory weight of 15 g.
doi:10.1177/2041669516669155
PMCID: PMC5034333  PMID: 27708753
heaviness perception; size-weight illusion; Müller–Lyer illusion; multisensory perception
20.  Further delineation of the KBG syndrome phenotype caused by ANKRD11 aberrations 
European Journal of Human Genetics  2014;23(9):1176-1185.
Loss-of-function variants in ANKRD11 were identified as the cause of KBG syndrome, an autosomal dominant syndrome with specific dental, neurobehavioural, craniofacial and skeletal anomalies. We present the largest cohort of KBG syndrome cases confirmed by ANKRD11 variants reported so far, consisting of 20 patients from 13 families. Sixteen patients were molecularly diagnosed by Sanger sequencing of ANKRD11, one familial case and three sporadic patients were diagnosed through whole-exome sequencing and one patient was identified through genomewide array analysis. All patients were evaluated by a clinical geneticist. Detailed orofacial phenotyping, including orthodontic evaluation, intra-oral photographs and orthopantomograms, was performed in 10 patients and revealed besides the hallmark feature of macrodontia of central upper incisors, several additional dental anomalies as oligodontia, talon cusps and macrodontia of other teeth. Three-dimensional (3D) stereophotogrammetry was performed in 14 patients and 3D analysis of patients compared with controls showed consistent facial dysmorphisms comprising a bulbous nasal tip, upturned nose with a broad base and a round or triangular face. Many patients exhibited neurobehavioural problems, such as autism spectrum disorder or hyperactivity. One-third of patients presented with (conductive) hearing loss. Congenital heart defects, velopharyngeal insufficiency and hip anomalies were less frequent. On the basis of our observations, we recommend cardiac assessment in children and regular hearing tests in all individuals with a molecular diagnosis of KBG syndrome. As ANKRD11 is a relatively common gene in which sequence variants have been identified in individuals with neurodevelopmental disorders, it seems an important contributor to the aetiology of both sporadic and familial cases.
doi:10.1038/ejhg.2014.253
PMCID: PMC4538199  PMID: 25424714
21.  Fine-Mapping of the 1p11.2 Breast Cancer Susceptibility Locus 
Horne, Hisani N. | Chung, Charles C. | Zhang, Han | Yu, Kai | Prokunina-Olsson, Ludmila | Michailidou, Kyriaki | Bolla, Manjeet K. | Wang, Qin | Dennis, Joe | Hopper, John L. | Southey, Melissa C. | Schmidt, Marjanka K. | Broeks, Annegien | Muir, Kenneth | Lophatananon, Artitaya | Fasching, Peter A. | Beckmann, Matthias W. | Fletcher, Olivia | Johnson, Nichola | Sawyer, Elinor J. | Tomlinson, Ian | Burwinkel, Barbara | Marme, Frederik | Guénel, Pascal | Truong, Thérèse | Bojesen, Stig E. | Flyger, Henrik | Benitez, Javier | González-Neira, Anna | Anton-Culver, Hoda | Neuhausen, Susan L. | Brenner, Hermann | Arndt, Volker | Meindl, Alfons | Schmutzler, Rita K. | Brauch, Hiltrud | Hamann, Ute | Nevanlinna, Heli | Khan, Sofia | Matsuo, Keitaro | Iwata, Hiroji | Dörk, Thilo | Bogdanova, Natalia V. | Lindblom, Annika | Margolin, Sara | Mannermaa, Arto | Kosma, Veli-Matti | Chenevix-Trench, Georgia | Wu, Anna H. | ven den Berg, David | Smeets, Ann | Zhao, Hui | Chang-Claude, Jenny | Rudolph, Anja | Radice, Paolo | Barile, Monica | Couch, Fergus J. | Vachon, Celine | Giles, Graham G. | Milne, Roger L. | Haiman, Christopher A. | Marchand, Loic Le | Goldberg, Mark S. | Teo, Soo H. | Taib, Nur A. M. | Kristensen, Vessela | Borresen-Dale, Anne-Lise | Zheng, Wei | Shrubsole, Martha | Winqvist, Robert | Jukkola-Vuorinen, Arja | Andrulis, Irene L. | Knight, Julia A. | Devilee, Peter | Seynaeve, Caroline | García-Closas, Montserrat | Czene, Kamila | Darabi, Hatef | Hollestelle, Antoinette | Martens, John W. M. | Li, Jingmei | Lu, Wei | Shu, Xiao-Ou | Cox, Angela | Cross, Simon S. | Blot, William | Cai, Qiuyin | Shah, Mitul | Luccarini, Craig | Baynes, Caroline | Harrington, Patricia | Kang, Daehee | Choi, Ji-Yeob | Hartman, Mikael | Chia, Kee Seng | Kabisch, Maria | Torres, Diana | Jakubowska, Anna | Lubinski, Jan | Sangrajrang, Suleeporn | Brennan, Paul | Slager, Susan | Yannoukakos, Drakoulis | Shen, Chen-Yang | Hou, Ming-Feng | Swerdlow, Anthony | Orr, Nick | Simard, Jacques | Hall, Per | Pharoah, Paul D. P. | Easton, Douglas F. | Chanock, Stephen J. | Dunning, Alison M. | Figueroa, Jonine D.
PLoS ONE  2016;11(8):e0160316.
The Cancer Genetic Markers of Susceptibility genome-wide association study (GWAS) originally identified a single nucleotide polymorphism (SNP) rs11249433 at 1p11.2 associated with breast cancer risk. To fine-map this locus, we genotyped 92 SNPs in a 900kb region (120,505,799–121,481,132) flanking rs11249433 in 45,276 breast cancer cases and 48,998 controls of European, Asian and African ancestry from 50 studies in the Breast Cancer Association Consortium. Genotyping was done using iCOGS, a custom-built array. Due to the complicated nature of the region on chr1p11.2: 120,300,000–120,505,798, that lies near the centromere and contains seven duplicated genomic segments, we restricted analyses to 429 SNPs excluding the duplicated regions (42 genotyped and 387 imputed). Per-allelic associations with breast cancer risk were estimated using logistic regression models adjusting for study and ancestry-specific principal components. The strongest association observed was with the original identified index SNP rs11249433 (minor allele frequency (MAF) 0.402; per-allele odds ratio (OR) = 1.10, 95% confidence interval (CI) 1.08–1.13, P = 1.49 x 10-21). The association for rs11249433 was limited to ER-positive breast cancers (test for heterogeneity P≤8.41 x 10-5). Additional analyses by other tumor characteristics showed stronger associations with moderately/well differentiated tumors and tumors of lobular histology. Although no significant eQTL associations were observed, in silico analyses showed that rs11249433 was located in a region that is likely a weak enhancer/promoter. Fine-mapping analysis of the 1p11.2 breast cancer susceptibility locus confirms this region to be limited to risk to cancers that are ER-positive.
doi:10.1371/journal.pone.0160316
PMCID: PMC4996485  PMID: 27556229
22.  Use of the PREPARE (PREhabilitation, Physical Activity and exeRcisE) program to improve outcomes after lumbar fusion surgery for severe low back pain: a study protocol of a person-centred randomised controlled trial 
Background
Following lumbar fusion surgery, a successful outcome is empirically linked to effective rehabilitation. While rehabilitation is typically postoperative, the phase before surgery – termed prehabilitation – is reportedly an ideal time to prepare the patient. There are presently no guidelines for prehabilitation before lumbar fusion surgery. Physical activity has well-known health benefits, and staying physically active despite pain is a major principle in non-pharmacological chronic low back pain treatment. Psychological factors such as fear of movement, pain catastrophizing and low self-efficacy are known to be barriers to staying active. No studies have investigated prehabilitation protocols that promote physical activity and target psychological risk factors before lumbar fusion surgery. The aim of our proposed randomised controlled trial is to investigate whether patients who undergo lumbar fusion surgery for degenerative disc disease experience better functioning with a physiotherapeutic prehabilitation program (PREPARE) based on a cognitive behavioural approach compared to conventional care.
Methods/Design
We will recruit 110 patients between 18–70 years of age with degenerative disc disease who are waiting for lumbar fusion surgery. These patients will be randomly assigned to receive either PREPARE or conventional care. PREPARE uses a person-centred perspective and focuses on promoting physical activity and targeting psychological risk factors before surgery. The primary outcome will be disability measured using the Oswestry Disability Index 2.0. Secondary outcomes will include functioning (patient-reported and performance-based), physical activity (accelerometer), health-related quality of life, back and leg pain intensity, pain catastrophizing, kinesiophobia, self-efficacy, depression, anxiety, satisfaction with treatment results and health economic factors. Data will be collected at baseline (preoperatively) after the intervention (preoperatively), 3 and 8 weeks, 3, 6, 12, 24 and 60 months postoperatively.
Discussion
We hypothesise that the focus on promoting physical activity and targeting psychological risk factors before surgery will decrease disability and help the patients to be more active despite pain both before and after surgery. We will use a combination of outcome measures both patient-reported and performance-based, as well as accelerometer data. This will provide a more comprehensive picture of the patient’s functioning than just patient-reported outcomes alone.
Trial registration
Current Controlled Trials ISCRTN17115599, Retrospectively Registered 18 May 2015.
doi:10.1186/s12891-016-1203-8
PMCID: PMC4991107  PMID: 27538757
Prehabilitation; Rehabilitation; Spinal fusion surgery; Physiotherapy; Cognitive behavioural approach; Person-centred; Chronic low back pain; Physical activity
23.  New insights in Rett syndrome using pathway analysis for transcriptomics data 
Summary
The analysis of transcriptomics data is able to give an overview of cellular processes, but requires sophisticated bioinformatics tools and methods to identify the changes. Pathway analysis software, like PathVisio, captures the information about biological pathways from databases and brings this together with the experimental data to enable visualization and understanding of the underlying processes. Rett syndrome is a rare disease, but still one of the most abundant causes of intellectual disability in females. Cause of this neurological disorder is mutation of one single gene, the methyl-CpG-binding protein 2 (MECP2) gene. This gene is responsible for many steps in neuronal development and function. Although the genetic mutation and the clinical phenotype are well described, the molecular pathways linking them are not yet fully elucidated. In this study we demonstrate a workflow for the analysis of transcriptomics data to identify biological pathways and processes which are changed in a Mecp2-/y mouse model.
Electronic supplementary material
The online version of this article (doi: 10.1007/s10354-016-0488-4) contains supplementary material, which is available to authorized users.
doi:10.1007/s10354-016-0488-4
PMCID: PMC5005393  PMID: 27517371
Rett syndrome; Rare disease; Systems biology; Pathway analysis; Bioinformatics; Rett-Syndrom; Seltene Krankheit; Systembiologie; Pathway-Analyse; Bioinformatik
24.  The feasibility of immediately loading dental implants in edentulous jaws 
Purpose
Immediate loading of dental implants has been proved to be feasible in partially edentulous jaws. The purpose of this retrospective investigation was to assess the feasibility of immediately loading dental implants in fully edentulous jaws.
Methods
A total of 24 patients aged between 53 and 89 years received a total of 154 implants in their edentulous maxillae or mandibles. Among the implants, 45 were set in fresh extracted sockets and 109 in consolidated alveolar bones. The implants were provisionally managed with chair-side made provisional resin bridges and exposed to immediate loading. Implants were followed up for 1–8 years, including radiographic imaging. Marginal bone levels were evaluated based on radiographic imaging.
Results
A total of 148 out of the 154 implants survived over the follow-up period of 1 to 8 years, giving a survival rate of 96%. The time or region of the implantation, the pre-implant augmentation, and the length and diameter of the implants had no statistically significant influence on the survival or the success rate. The marginal bone level remained stable with only minimal loss of 0.3 mm after 60 months of loading.
Conclusions
Within the limitations of this study, immediate loading is feasible for dental implants in edentulous jaws.
Graphical Abstract
doi:10.5051/jpis.2016.46.4.234
PMCID: PMC5005811  PMID: 27588213
Dental implants; Immediate dental implant loading; Jaw, edentulous
25.  Approaches to Peripheral Nerve Repair: Generations of Biomaterial Conduits Yielding to Replacing Autologous Nerve Grafts in Craniomaxillofacial Surgery 
BioMed Research International  2016;2016:3856262.
Peripheral nerve injury is a common clinical entity, which may arise due to traumatic, tumorous, or even iatrogenic injury in craniomaxillofacial surgery. Despite advances in biomaterials and techniques over the past several decades, reconstruction of nerve gaps remains a challenge. Autografts are the gold standard for nerve reconstruction. Using autografts, there is donor site morbidity, subsequent sensory deficit, and potential for neuroma development and infection. Moreover, the need for a second surgical site and limited availability of donor nerves remain a challenge. Thus, increasing efforts have been directed to develop artificial nerve guidance conduits (ANCs) as new methods to replace autografts in the future. Various synthetic conduit materials have been tested in vitro and in vivo, and several first- and second-generation conduits are FDA approved and available for purchase, while third-generation conduits still remain in experimental stages. This paper reviews the current treatment options, summarizes the published literature, and assesses future prospects for the repair of peripheral nerve injury in craniomaxillofacial surgery with a particular focus on facial nerve regeneration.
doi:10.1155/2016/3856262
PMCID: PMC4983313  PMID: 27556032

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