Genome instability in blood cells of a BRCA1+ breast cancer family

BMC Cancer

Volumn 14, Issue 1, 2014, Pages

  Xiao, Fengxia ^a   Kim, Yeong C ^a   Snyder, Carrie ^b   Wen, Hongxiu ^a   Chen, Pei X ^b   Luo, Jiangtao ^c   Becirovic, Dina ^b   Downs, Bradley ^a   Cowan, Kenneth H ^c   Lynch, Henry ^b   Wang, San M ^a  

^a UNIVERSITY OF NEBRASKA MEDICAL CENTER   (United States)

^b CREIGHTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF NEBRASKA MEDICAL CENTER   (United States)

Author keywords

Bioinformatics; Exome sequencing; Familial breast cancer; Genome instability; Germline mutation

Indexed keywords

CELL NUCLEUS RECEPTOR; NUCLEAR RECEPTOR ACTIVATOR SRA1; PHOSPHORYLASE KINASE; PHOSPHORYLASE KINASE PHKG2; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR BPTF; TRANSCRIPTION FACTOR FOXP1; UBIQUITIN LIGASE CUL4B; UBIQUITIN PROTEIN LIGASE; UNCLASSIFIED DRUG; BRCA1 PROTEIN; BRCA1 PROTEIN, HUMAN; TUMOR MARKER;

ADULT; AGED; ARTICLE; BLOOD CELL; BREAST CANCER; BREAST CARCINOGENESIS; CLINICAL ARTICLE; CONTROLLED STUDY; EXOME; EXON; FEMALE; GENE DUPLICATION; GENE MUTATION; GENOMIC INSTABILITY; GERMLINE MUTATION; HUMAN; INHERITANCE; MALE; ONCOGENE; ONCOGENE BPTF; ONCOGENE CUL4B; ONCOGENE FOXP1; ONCOGENE PHKG2; ONCOGENE SRA1; SEQUENCE ANALYSIS; SOMATIC MUTATION; BLOOD; BREAST TUMOR; FOUNDER EFFECT; GENETIC PREDISPOSITION; GENETICS; HEREDITY; MIDDLE AGED; MOTHER; MUTATION; NUCLEAR FAMILY; NUCLEOTIDE SEQUENCE; PEDIGREE; PHENOTYPE;

ADULT; BRCA1 PROTEIN; BREAST NEOPLASMS; DNA MUTATIONAL ANALYSIS; EXONS; FEMALE; FOUNDER EFFECT; GENETIC PREDISPOSITION TO DISEASE; GENOMIC INSTABILITY; HEREDITY; HUMANS; MALE; MIDDLE AGED; MOTHERS; MUTATION; NUCLEAR FAMILY; PEDIGREE; PHENOTYPE; TUMOR MARKERS, BIOLOGICAL;

EID: 84901442182     PISSN: None     EISSN: 14712407     Source Type: Journal    
DOI: 10.1186/1471-2407-14-342     Document Type: Article

References (43)

1. Welcsh PL, King MC. BRCA1 and BRCA2 and the genetics of breast and ovarian cancer. Hum Mol Genet 2001, 10:705-713. 10.1093/hmg/10.7.705, 11257103.
2. Hall JM, Lee MK, Newman B, Morrow JE, Anderson LA, Huey B, King MC. Linkage of early-onset familial breast cancer to chromosome 17q21. Science 1990, 250:1684-1689. 10.1126/science.2270482, 2270482.
3. Narod SA, Feunteun J, Lynch HT, Watson P, Conway T, Lynch J, Lenoir GM. Familial breast-ovarian cancer locus on chromosome 17q12-q23. Lancet 1991, 338:82-83. 10.1016/0140-6736(91)90076-2, 1676470.
4. Miki Y, Swensen J, Shattuck-Eidens D, Futreal PA, Harshman K, Tavtigian S, Liu Q, Cochran C, Bennett LM, Ding W, Bell R, Rosenthal J, Hussey C, Tran T, McClure M, Frye C, Hattier T, Phelps R, Haugen-Strano A, Katcher H, Yakumo K, Gholami Z, Shaffer D, Stone S, Bayer S, Wray C, Bogden R, Dayananth P, Ward J, Tonin P, Narod S. A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science 1994, 266:66-71. 10.1126/science.7545954, 7545954.
5. U.S. Preventive Services Task Force Genetic risk assessment and BRCA mutation testing for breast and ovarian cancer susceptibility: recommendation statement. Ann Intern Med 2005, 143:355-361. U.S. Preventive Services Task Force.
6. Venkitaraman AR. Cancer susceptibility and the functions of BRCA1 and BRCA2. Cell 2002, 108:171-182. 10.1016/S0092-8674(02)00615-3, 11832208.
7. Stratton MR, Rahman N. The emerging landscape of breast cancer susceptibility. Nat Genet 2008, 40:17-22. 10.1038/ng.2007.53, 18163131.
8. Tirkkonen M, Johannsson O, Agnarsson BA, Olsson H, Ingvarsson S, Karhu R, Tanner M, Isola J, Barkardottir RB, Borg A, Kallioniemi OP. Distinct somatic genetic changes associated with tumor progression in carriers of BRCA1 and BRCA2 germ-line mutations. Cancer Res 1997, 57:1222-1227.
9. Tomlinson GE, Chen TT, Stastny VA, Virmani AK, Spillman MA, Tonk V, Blum JL, Schneider NR, Wistuba II, Shay JW, Minna JD, Gazdar AF. Characterization of a breast cancer cell line derived from a germ-line BRCA1 mutation carrier. Cancer Res 1998, 58:3237-3242.
10. Weigman VJ, Chao HH, Shabalin AA, He X, Parker JS, Nordgard SH, Grushko T, Huo D, Nwachukwu C, Nobel A, Kristensen VN, Børresen-Dale AL, Olopade OI, Perou CM. Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival. Breast Cancer Res Treat 2012, 133:865-880. 10.1007/s10549-011-1846-y, 3387500, 22048815.
11. Popova T, Manié E, Rieunier G, Caux-Moncoutier V, Tirapo C, Dubois T, Delattre O, Sigal-Zafrani B, Bollet M, Longy M, Houdayer C, Sastre-Garau X, Vincent-Salomon A, Stoppa-Lyonnet D, Stern M. Ploidy and large-scale genomic instability consistently identify basal-like breast carcinomas with BRCA1/2 inactivation. Cancer Res 2012, 72:5454-5462. 10.1158/0008-5472.CAN-12-1470, 22933060.
12. Konishi H, Mohseni M, Tamaki A, Garay JP, Croessmann S, Karnan S, Ota A, Wong HY, Konishi Y, Karakas B, Tahir K, Abukhdeir AM, Gustin JP, Cidado J, Wang GM, Cosgrove D, Cochran R, Jelovac D, Higgins MJ, Arena S, Hawkins L, Lauring J, Gross AL, Heaphy CM, Hosokawa Y, Gabrielson E, Meeker AK, Visvanathan K, Argani P, Bachman KE, Park BH. Mutation of a single allele of the cancer susceptibility gene BRCA1 leads to genomic instability in human breast epithelial cells. Proc Natl Acad Sci U S A 2011, 108:17773-17778. 10.1073/pnas.1110969108, 3203756, 21987798.
13. Kwei KA, Kung Y, Salari K, Holcomb IN, Pollack JR. Genomic instability in breast cancer: pathogenesis and clinical implications. Mol Oncol 2010, 4:255-266. 10.1016/j.molonc.2010.04.001, 2904860, 20434415.
14. Xu X, Wagner KU, Larson D, Weaver Z, Li C, Ried T, Hennighausen L, Wynshaw-Boris A, Deng CX. Conditional mutation of Brca1 in mammary epithelial cells results in blunted ductal morphogenesis and tumour formation. Nat Genet 1999, 22:37-43. 10.1038/8743, 10319859.
15. Shen SX, Weaver Z, Xu X, Li C, Weinstein M, Chen L, Guan XY, Ried T, Deng CX. A targeted disruption of the murine Brca1 gene causes gamma-irradiation hypersensitivity and genetic instability. Oncogene 1998, 17:3115-3124. 10.1038/sj.onc.1202243, 9872327.
16. Brodie SG, Xu X, Qiao W, Li WM, Cao L, Deng CX. Multiple genetic changes are associated with mammary tumorigenesis in Brca1 conditional knockout mice. Oncogene 2001, 20:7514-7523. 10.1038/sj.onc.1204929, 11709723.
17. Puget N, Sinilnikova OM, Stoppa-Lyonnet D, Audoynaud C, Pagès S, Lynch HT, Goldgar D, Lenoir GM, Mazoyer S. An Alu-mediated 6-kb duplication in the BRCA1 gene: a new founder mutation?. Am J Hum Genet 1999, 64:300-302. 10.1086/302211, 1377730, 9915971.
18. The BRCA1 Exon 13 Duplication Screening Group The exon 13 duplication in the BRCA1 gene is a founder mutation present in geographically diverse populations. Am J Hum Genet 2000, 67:207-212. 10.1086/302974, 1287079, 10827109, The BRCA1 Exon 13 Duplication Screening Group.
19. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie2. Nat Methods 2012, 9:357-359. 10.1038/nmeth.1923, 3322381, 22388286.
20. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 2012, 22:568-576. 10.1101/gr.129684.111, 3290792, 22300766.
21. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010, 20:1297-1303. 10.1101/gr.107524.110, 2928508, 20644199.
22. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, . 1000 Genome Project Data The sequence alignment/map (SAM) format and SAMtools. Bioinformatics 2009, 25:2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943, 1000 Genome Project Data.
23. The 1000 Genomes Project Consortium An integrated map of genetic variation from 1,092 human genomes. Nature 2012, 491:56-65. 10.1038/nature11632, 3498066, 23128226, The 1000 Genomes Project Consortium.
24. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods 2010, 7:248-249. 10.1038/nmeth0410-248, 2855889, 20354512.
25. Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 2009, 4:1073-1081. 10.1038/nprot.2009.86, 19561590.
26. Wang K, Li M, Hakonarson H. ANNOVAR: Functional annotation of genetic variants from next-generation sequencing data. Nucleic Acids Res 2010, 38:e164. 10.1093/nar/gkq603, 2938201, 20601685.
27. Fungtammasan A, Walsh E, Chiaromonte F, Eckert KA, Makova KD. A genome-wide analysis of common fragile sites: what features determine chromosomal instability in the human genome?. Genome Res 2012, 22:993-1005. 10.1101/gr.134395.111, 3371707, 22456607.
28. Ruthenburg AJ, Li H, Milne TA, Dewell S, McGinty RK, Yuen M, Ueberheide B, Dou Y, Muir TW, Patel DJ, Allis CD. Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions. Cell 2011, 145:692-706. 10.1016/j.cell.2011.03.053, 3135172, 21596426.
29. Buganim Y, Goldstein I, Lipson D, Milyavsky M, Polak-Charcon S, Mardoukh C, Solomon H, Kalo E, Madar S, Brosh R, Perelman M, Navon R, Goldfinger N, Barshack I, Yakhini Z, Rotter V. A novel translocation breakpoint within the BPTF gene is associated with a pre-malignant phenotype. PLoS One 2010, 5:e9657. 10.1371/journal.pone.0009657, 2836376, 20300178.
30. Nakagawa T, Xiong Y. X-linked mental retardation gene CUL4B targets ubiquitylation of H3K4 methyltransferase component WDR5 and regulates neuronal gene expression. Mol Cell 2011, 43:381-391. 10.1016/j.molcel.2011.05.033, 3230935, 21816345.
31. Shigekawa T, Ijichi N, Ikeda K, Horie-Inoue K, Shimizu C, Saji S, Aogi K, Tsuda H, Osaki A, Saeki T, Inoue S. FOXP1, an estrogen-inducible transcription factor, modulates cell proliferation in breast cancer cells and 5-year recurrence-free survival of patients with tamoxifen-treated breast cancer. Horm Cancer 2011, 2:286-297. 10.1007/s12672-011-0082-6, 21901488.
32. Robinson A, Huttley GA, Booth HS, Board PG. Modelling and bioinformatics studies of the human Kappa-class glutathione transferase predict a novel third glutathione transferase family with similarity to prokaryotic 2-hydroxychromene-2-carboxylate isomerases. Biochem J 2004, 379(Pt3):541-552. 1224102, 14709161.
33. Porter D, Weremowicz S, Chin K, Seth P, Keshaviah A, Lahti-Domenici J, Bae YK, Monitto CL, Merlos-Suarez A, Chan J, Hulette CM, Richardson A, Morton CC, Marks J, Duyao M, Hruban R, Gabrielson E, Gelman R, Polyak K. A neural survival factor is a candidate oncogene in breast cancer. Proc Natl Acad Sci U S A 2003, 100:10931-10936. 10.1073/pnas.1932980100, 196905, 12953101.
34. Burwinkel B, Rootwelt T, Kvittingen EA, Chakraborty PK, Kilimann MW. Severe phenotype of phosphorylase kinase-deficient liver glycogenosis with mutations in PHKG2 gene. Pediatr Res 2003, 54:834-839. 10.1203/01.PDR.0000088069.09275.10, 12930917.
35. Chooniedass-Kothari S, Vincett D, Yan Y, Cooper C, Hamedani MK, Myal Y, Leygue E. The protein encoded by the functional steroid receptor RNA activator is a new modulator of ER alpha transcriptional activity. FEBS Lett 2010, 584:1174-1180. 10.1016/j.febslet.2010.02.024, 20153324.
36. Cancer Genome Atlas Network Comprehensive molecular portraits of human breast tumours. Nature 2012, 490:61-70. 10.1038/nature11412, 3465532, 23000897, Cancer Genome Atlas Network.
37. Ijichi N, Shigekawa T, Ikeda K, Horie-Inoue K, Shimizu C, Saji S, Aogi K, Tsuda H, Osaki A, Saeki T, Inoue S, Inoue S. Association of double-positive FOXA1 and FOXP1 immunoreactivities with favorable prognosis of tamoxifen-treated breast cancer patients. Horm Cancer 2012, 3:147-159. 10.1007/s12672-012-0111-0, 22476979.
38. Hahn WC, Weinberg RA. Rules for making human tumor cells. N Engl J Med 2002, 347:1593-1603. 10.1056/NEJMra021902, 12432047.
39. Rubin AF, Green P. Mutation patterns in cancer genomes. Proc Natl Acad Sci U S A 2009, 106(51):21766-21870. 10.1073/pnas.0912499106, 2799788, 19995982.
40. Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA, Kinzler KW. Cancer genome landscapes. Science 2013, 339(6127):1546-1558. 10.1126/science.1235122, 3749880, 23539594.
41. Garraway LA, Lander ES. Lessons from the cancer genome. Cell 2013, 153(1):17-37. 10.1016/j.cell.2013.03.002, 23540688.
42. Shlien A, Tabori U, Marshall CR, Pienkowska M, Feuk L, Novokmet A, Nanda S, Druker H, Scherer SW, Malkin D. Excessive genomic DNA copy number variation in the Li-Fraumeni cancer predisposition syndrome. Proc Natl Acad Sci U S A 2008, 105:11264-11269. 10.1073/pnas.0802970105, 2516272, 18685109.
43. MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T. A systematic survey of loss-of-function variants in human protein-coding genes. Science 2012, 335(6070):823-828. 10.1126/science.1215040, 3299548, 22344438.