Classifying variants of undetermined significance in BRCA2 with protein likelihood ratios

Cancer Informatics

Volumn 6, Issue , 2008, Pages 203-216

  Karchin, Rachel ^a,f   Agarwal, Mukesh ^b   Sali, Andrej ^c   Couch, Fergus ^b   Beattie, Mary S ^d,e  

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b MAYO CLINIC   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f Johns Hopkins University   (United States)

Author keywords

Bioinformatics and computational biology; Breast cancer; Cancer susceptibility genes; Missense variants; Mutagenesis; Risk assessment

Indexed keywords

ACID PROTEIN; BRCA2 PROTEIN; PROTEIN DSS1; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; BREAST CANCER; CANCER SUSCEPTIBILITY; CRYSTAL STRUCTURE; GENETIC ANALYSIS; GENETIC VARIABILITY; HIGH RISK POPULATION; MISSENSE MUTATION; NUCLEOTIDE SEQUENCE; OVARY CANCER; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN STRUCTURE; SUPPORT VECTOR MACHINE; TUMOR SUPPRESSOR GENE; BIOTECHNOLOGY; GENETIC SCREENING; PROTEIN BINDING;

EID: 49649087897     PISSN: 11769351     EISSN: 11769351     Source Type: Journal    
DOI: 10.4137/cin.s618     Document Type: Article

References (42)

1. Easton, D.F. et al. 2007. A Systematic Genetic Assessment of 1,433 Sequence Variants of Unknown Clinical Significance in the BRCA1 and BRCA2 Breast Cancer Predisposition Genes. American Journal of Human Genetics, 81 (5):873-83.
2. Chenevix-Trench, G. et al. 2006. Genetic and histopathologic evaluation of BRCA1 and BRCA2 DNA sequence variants of unknown clinical significance. Cancer Res., 66(4):2019-27.
3. Petrucelli, N. et al. 2002. Clinical interpretation and recommendations for patients with a variant of uncertain significance in BRCA1 or BRCA2: a survey of genetic counseling practice. Genet. Test, 6(2):107-13.
4. Ford, D. et al. 1998. Genetic heterogeneity and penetrance analysis of the BRCA1 and BRCA2 genes in breast cancer families. The Breast Cancer Linkage Consortium. Am. J. Hum. Genet., 62(3):676-89.
5. Antoniou, A. et al. 2003. Average risks of breast and ovarian cancer associated with BRCA1 or BRCA2 mutations detected in case Series unselected for family history: a combined a nalysis of 22 studies. Am. J. Hum. Genet., 72(5):1117-30.
6. King, M.C., Marks, J.H. and Mandell, J.B. 2003. Breast and ovarian cancer risks due to inherited mutations in BRCA1 and BRCA2. Science, 302(5645):643-6.
7. Narod, S.A. and Foulkes, W.D. 2004. BRCA1 and BRCA2: 1994 and beyond. Nat. Rev. Cancer, 4(9):665-76.
8. Goldgar, D.E. et al. 2004. Integrated evaluation of DNA sequence variants of unknown clinical significance: application to BRCA1 and BRCA2. American Journal of Human Genetics, 75(4):535-44.
9. Tavtigian, S.V. et al. 2006. Comprehensive statistical study of 452 BRCA1 missense substitutions with classification of eight recurrent substitutions as neutral. J. Med. Genet., 43(4):295-305.
10. Malone, K.E. et al. 2006. Prevalence and Predictors of BRCA1 and BRCA2 Mutations in a Population-Based Study of Breast Cancer in White and Black American Women Ages 35 to 64 Years. Cancer Res., 66(16):8297-308.
11. Risch, H.A. et al. 2006. Population BRCA1 and BRCA2 mutation frequencies and cancer penetrances: a kin-cohort study in Ontario, Canada. J. Natl. Cancer Inst., 98(23):1694-706.
12. Cancer risks in BRCA2 mutation carriers. 1999. The Breast Cancer Linkage Consortium. J. Natl. Cancer Inst., 91(15):1310-6.
13. Carvalho, M.A. et al. 2007. Determination of cancer risk associated with germline BRCA1 missense variants by functional analysis. Cancer Research, 67(4):1494-501.
14. Vapnik, V. 1995. The Nature of Statistical Learning TheoryNew York: Springer-Verlag.
15. Cristianini, N. and Shawe-Taylor, J. An introduction to support vector machines. 2000, Cambridge, U.K.: Cambridge University Press.
16. Jakel, F., Scholkopf, B. and Wichmann, F.A. 2007. A tutorial on kernel methods for categorization. Journal of Mathematical Psychology, 51(6):343-58.
17. Team, R.D.C. R.: A language and environment for statistical computing. 2005, R. Foundation for Statistical Computing: Vienna, Austria.
18. Karchin, R. et al. 2007. Functional impact of missense mutants in BRCA1 predicted by supervised learning. PLoS. Comp. Biol., 3(2):e26.
19. Kato, S. et al. U.S.A., 2003. Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis. Proc. Natl. Acad. Sci., 100(14):8424-9.
20. Yang, H.J. et al. 2002. BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure. Science, 297(5588):1837-48.
21. Gudmundsdottir, K. et al. 2004. DSS1 is required for RAD51 focus formation and genomic stability in mammalian cells. EMBO Rep., 5(10):989-93.
22. Marston, N.J. et al. 1999. Interaction between the product of the breast cancer susceptibility gene BRCA2 and DSS1, a protein functionally conserved from yeast to mammals. Molecular and Cellular Biology, 19(7):4633-42.
23. Berman, H.M. et al. 2000. The Protein Data Bank. Nucleic Acids Res., 28(1):235-42.
24. Joo, W.S. et al. 2002. Structure of the 53BP1 BRCT region bound to p53 and its comparison to the Brca1 BRCT structure. Genes and Development, 16(5):583-93.
25. Sali, A. and Blundell, T.L. 1993. Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology, 234(3):779-815.
26. Shen, M.Y. and Sali, A. 2006. Statistical potential for assessment and prediction of protein structures. Protein Sci., 15(11):2507-24.
27. Wu, C.H. et al. 2006. The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res., 34(Database issue):D187-91.
28. Karplus, K. et al. 2001. What is the value added by human intervention in protein structure prediction? Proteins, (Suppl 5):86-91.
29. DeGroot, M. and Fienberg, S. 1983. The Comparison and Evaluation of Forecasters. The Statistician, 32:12-22.
30. Harrell, F.E., Jr et al. 1982. Evaluating the yield of medical tests. Jama, 247(18):2543-6.
31. Ng, P.C. and Henikoff, S. 2001. Predicting deleterious amino acid substitutions. Genome Res., 11(5):863-74.
32. Ramensky, V., Bork, P. and Sunyaev, S. 2002. Human non-synonymous SNPs: server and survey. Nucleic Acids Res., 30(17):3894-900.
33. Ferrer-Costa, C., Orozco, M. and de la Cruz, X. 2002. Characterization of disease-associated single amino acid polymorphisms in terms of sequence and structure properties. Journal of Molecular Biology, 315(4):771-86.
34. Hofmann, W. et al. 2003. The BRCA2 variant 8204G > A is a splicing mutation and results in an in frame deletion of the gene. J. Med. Genet., 40(3):e23.
35. Kojic, M. et al. 2003. The BRCA2-interacting protein DSS1 is vital for DNA repair, recombination, and genome stability in Ustilago maydis. Mol. Cell., 12(4):1043-9.
36. Li, J. et al. 2006. DSS1 is required for the stability of BRCA2. Oncogene, 25(8):1186-94.
37. Chenevix-Trench, G. et al. 2006. Genetic and Histopathologic Evaluation of BRCA1 and BRCA2 DNA Sequence Variants of Unknown Clinical Significance. Cancer Research, 66(4):2019-27.
38. Williams, R.S. et al. 2003. Detection of protein folding defects caused by BRCA1-BRCT truncation and missense mutations. Journal of Biological Chemistry, 278(52):53007-16.
39. Mirkovic, N. et al. 2004. Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition. Cancer Res., 64(11):3790-7.
40. Couch, F.J. 2007. Unpublished results.
41. Wu, K. et al. 2005. Functional evaluation and cancer risk assessment of BRCA2 unclassified variants. Cancer Res., 65(2):417-26.
42. American Society of Clinical Oncology policy statement update: genetic testing for cancer susceptibility. 2003. J. Clin. Oncol., 21(12):2397-406.