Exome sequencing in a breast cancer family without BRCA mutation.
作者： Jae Myoung Noh , Jihun Kim , Dae Yeon Cho , Doo Ho Choi , Won Park
DOI: 10.3857/ROJ.2015.33.2.149
关键词:
摘要: Purpose We performed exome sequencing in a breast cancer family without BRCA mutations. Materials and methods A that three sisters have history of was selected for analysis. There were no members with the previous generation. Genetic testing mutation negative, even by multiplex ligation-dependent probe amplification method. Two as affected members, while mother non-affected member. Whole on HiSeq 2000 platform paired-end reads 101 bp members. Results identified 19,436, 19,468, 19,345 single-nucleotide polymorphisms (SNPs) coding regions. Among them, 8,759, 8,789, 8,772 non-synonymous SNPs, respectively. After filtering out 12,843 synonymous variations 12,105 known indels found dbSNP135 or 1000 Genomes Project database, we 73 samples from did not occur sample unaffected mother. Using Sorting Intolerant From Tolerant (SIFT), PolyPhen-2, MutationTaster algorithms to predict amino acid substitutions, XCR1, DLL1, TH, ACCS, SPPL3, CCNF, SRL genes risky among all algorithms, definite candidate could be conclusively determined. Conclusion sequencing, 7 variants evidence disease association should confirmed future studies.
e-roj.org参考文章(25)
Christian Gilissen, Alexander Hoischen, Han G Brunner, Joris A Veltman, Disease gene identification strategies for exome sequencing European Journal of Human Genetics. ,vol. 20, pp. 490- 497 ,(2012) , 10.1038/EJHG.2011.258
Katie Snape, Elise Ruark, Patrick Tarpey, Anthony Renwick, Clare Turnbull, Sheila Seal, Anne Murray, Sandra Hanks, Jenny Douglas, Michael R. Stratton, Nazneen Rahman, Predisposition gene identification in common cancers by exome sequencing: insights from familial breast cancer. Breast Cancer Research and Treatment. ,vol. 134, pp. 429- 433 ,(2012) , 10.1007/S10549-012-2057-X
Yu Lei, Yousuke Takahama, XCL1 and XCR1 in the immune system. Microbes and Infection. ,vol. 14, pp. 262- 267 ,(2012) , 10.1016/J.MICINF.2011.10.003
Henry Lynch, Hongxiu Wen, Yeong C. Kim, Carrie Snyder, Yulia Kinarsky, Pei Xian Chen, Fengxia Xiao, David Goldgar, Kenneth H. Cowan, San Ming Wang, Can Unknown Predisposition in Familial Breast Cancer be Family-Specific? Breast Journal. ,vol. 19, pp. 520- 528 ,(2013) , 10.1111/TBJ.12145
K. Wang, M. Li, H. Hakonarson, ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data Nucleic Acids Research. ,vol. 38, ,(2010) , 10.1093/NAR/GKQ603
Haeyoung Kim, , Dae-Yeon Cho, Doo Ho Choi, Su-Youn Choi, Inkyung Shin, Won Park, Seung Jae Huh, Sung-Hee Han, Min Hyuk Lee, Sei Hyun Ahn, Byung Ho Son, Sung-Won Kim, Bruce G. Haffty, Characteristics and spectrum of BRCA1 and BRCA2 mutations in 3,922 Korean patients with breast and ovarian cancer Breast Cancer Research and Treatment. ,vol. 134, pp. 1315- 1326 ,(2012) , 10.1007/S10549-012-2159-5
Douglas F Easton, Karen A Pooley, Alison M Dunning, Paul DP Pharoah, Deborah Thompson, Dennis G Ballinger, Jeffery P Struewing, Jonathan Morrison, Helen Field, Robert Luben, Nicholas Wareham, Shahana Ahmed, Catherine S Healey, Richard Bowman, SEARCH collaborators Luccarini Craig 61 Conroy Don 61 Shah Mitul 61 Munday Hannah 61 Jordan Clare 61 Perkins Barbara 61 West Judy 61 Redman Karen 61 Driver Kristy 61, Kerstin B Meyer, Christopher A Haiman, Laurence K Kolonel, Brian E Henderson, Loic Le Marchand, Paul Brennan, Suleeporn Sangrajrang, Valerie Gaborieau, Fabrice Odefrey, Chen-Yang Shen, Pei-Ei Wu, Hui-Chun Wang, Diana Eccles, D Gareth Evans, Julian Peto, Olivia Fletcher, Nichola Johnson, Sheila Seal, Michael R Stratton, Nazneen Rahman, Georgia Chenevix-Trench, Stig E Bojesen, Børge G Nordestgaard, Christen K Axelsson, Montserrat Garcia-Closas, Louise Brinton, Stephen Chanock, Jolanta Lissowska, Beata Peplonska, Heli Nevanlinna, Rainer Fagerholm, Hannaleena Eerola, Daehee Kang, Keun-Young Yoo, Dong-Young Noh, Sei-Hyun Ahn, David J Hunter, Susan E Hankinson, David G Cox, Per Hall, Sara Wedren, Jianjun Liu, Yen-Ling Low, Natalia Bogdanova, Peter Schürmann, Thilo Dörk, Rob AEM Tollenaar, Catharina E Jacobi, Peter Devilee, Jan GM Klijn, Alice J Sigurdson, Michele M Doody, Bruce H Alexander, Jinghui Zhang, Angela Cox, Ian W Brock, Gordon MacPherson, Malcolm WR Reed, Fergus J Couch, Ellen L Goode, Janet E Olson, Hanne Meijers-Heijboer, Ans van den Ouweland, André Uitterlinden, Fernando Rivadeneira, Roger L Milne, Gloria Ribas, Anna Gonzalez-Neira, Javier Benitez, John L Hopper, Margaret McCredie, Melissa Southey, Graham G Giles, Chris Schroen, Christina Justenhoven, Hiltrud Brauch, Ute Hamann, Yon-Dschun Ko, Amanda B Spurdle, Jonathan Beesley, Xiaoqing Chen, AOCS Management Group Bowtell David 146 Green Adele 82 deFazio Anna 147 Chenevix-Trench Georgia 82 Gertig Dorota 111 Webb Penny 82, Arto Mannermaa, Veli-Matti Kosma, Vesa Kataja, Jaana Hartikainen, Nicholas E Day, David R Cox, Bruce AJ Ponder, None, Genome-wide association study identifies novel breast cancer susceptibility loci Nature. ,vol. 447, pp. 1087- 1093 ,(2007) , 10.1038/NATURE05887
Sei Hyun Ahn, Keun Young Yoo, Korean Breast Cancer Society, None, Chronological changes of clinical characteristics in 31,115 new breast cancer patients among Koreans during 1996-2004. Breast Cancer Research and Treatment. ,vol. 99, pp. 209- 214 ,(2006) , 10.1007/S10549-006-9188-X
Francisco Javier Gracia-Aznarez, Victoria Fernandez, Guillermo Pita, Paolo Peterlongo, Orlando Dominguez, Miguel de la Hoya, Mercedes Duran, Ana Osorio, Leticia Moreno, Anna Gonzalez-Neira, Juan Manuel Rosa-Rosa, Olga Sinilnikova, Sylvie Mazoyer, John Hopper, Conchi Lazaro, Melissa Southey, Fabrice Odefrey, Siranoush Manoukian, Irene Catucci, Trinidad Caldes, Henry T Lynch, Florentine SM Hilbers, Christi J van Asperen, Hans FA Vasen, David Goldgar, Paolo Radice, Peter Devilee, Javier Benitez, None, Whole Exome Sequencing Suggests Much of Non-BRCA1/BRCA2 Familial Breast Cancer Is Due to Moderate and Low Penetrance Susceptibility Alleles PLoS ONE. ,vol. 8, pp. e55681- ,(2013) , 10.1371/JOURNAL.PONE.0055681
Vincenzo D’Angiolella, Valerio Donato, Sangeetha Vijayakumar, Anita Saraf, Laurence Florens, Michael P. Washburn, Brian Dynlacht, Michele Pagano, SCF Cyclin F controls centrosome homeostasis and mitotic fidelity through CP110 degradation Nature. ,vol. 466, pp. 138- 142 ,(2010) , 10.1038/NATURE09140