Beyond DNA: An Integrated and Functional Approach for Classifying Germline Variants in Breast Cancer Genes

International Journal of Breast Cancer

Volumn 2016, Issue , 2016, Pages

  Pesaran, T ^a   Karam, R ^a   Huether, R ^a   Li, S ^a   Farber Katz, S ^a   Chamberlin, A ^a   Chong, H ^a   Laduca, H ^a   Elliott, A ^a  

^a AMBRY GENETICS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MESSENGER RNA;

ALLELE; ALTERNATIVE RNA SPLICING; BREAST CANCER; CANCER GENETICS; CANCER RISK; CLINICAL ASSESSMENT; CLINICAL LABORATORY; DNA REPAIR; DNA STRAND BREAKAGE; FAMILIAL CANCER; GENE FREQUENCY; GENE FUNCTION; GENETIC SCREENING; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; HUMAN; NONSENSE MEDIATED MRNA DECAY; PERSONALIZED MEDICINE; PHENOTYPE; PROTEIN FUNCTION; REVIEW; RNA SPLICING; TRANSCRIPTION INITIATION; TUMOR GENE;

EID: 84994553142     PISSN: 20903170     EISSN: 20903189     Source Type: Journal    
DOI: 10.1155/2016/2469523     Document Type: Review

References (61)

1. H. LaDuca, A. J. Stuenkel, J. S. Dolinsky et al., "Utilization of multigene panels in hereditary cancer predisposition testing: analysis of more than 2,000 patients," Genetics in Medicine, vol. 16, no. 11, pp. 830-837, 2014.
2. M. B. Daly, J. E. Axilbund, S. Buys et al., "Genetic/familial highrisk assessment: breast and ovarian," The National Comprehensive Cancer Network, vol. 8, pp. 562-594, 2010.
3. "National Comprehensive Cancer Network Genetic/Familial High-Risk Assessment: Breast and Ovarian (Version 2.2016)," 2016, https://www.nccn.org/professionals/physician gls/pdf/ genetics screening.pdf.
4. M. Magrane and UniProt Consortium, "UniProt knowledgebase: a hub of integrated protein data," Database, vol. 2011, Article ID bar009, 2011.
5. H. M. Berman, J.Westbrook, Z. Feng et al., "The protein data bank," Nucleic Acids Research, vol. 28, no. 1, pp. 235-242, 2000.
6. W. C. Lau, Y. Li, Z. Liu, Y. Gao, Q. Zhang, and M. S. Huen, "Structure of the human dimeric ATM kinase," Cell Cycle, vol. 15, no. 8, pp. 1117-1124, 2016.
7. S. Richards, N. Aziz, S. Bale et al., "Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology," Genetics in Medicine, vol. 17, no. 5, pp. 405-424, 2015.
8. C. S. Richards, S. Bale, D. B. Bellissimo et al., "ACMG recommendations for standards for interpretation and reporting of sequence variations: revisions 2007," Genetics in Medicine, vol. 10, no. 4, pp. 294-300, 2008.
9. S. V. Tavtigian, M. S. Greenblatt,D. E. Goldgar, and P. Boffetta, "Assessing pathogenicity: overview of results from the IARC unclassified genetic variants working group," HumanMutation, vol. 29, no. 11, pp. 1261-1264, 2008.
10. K. N. Maxwell, S. N. Hart, J. Vijai et al., "Evaluation of ACMGguideline-based variant classification of cancer susceptibility and non-cancer-associated genes in families affected by breast cancer,"The American Journal of Human Genetics, vol. 98, no. 5, pp. 801-817, 2016.
11. K. D. Gonzalez, C. H. Buzin, K. A. Noltner et al., "High frequency of de novo mutations in Li-Fraumeni syndrome," Journal of Medical Genetics, vol. 46, no. 10, pp. 689-693, 2009.
12. J. Mester and C. Eng, "Estimate of de novo mutation frequency in probands with PTEN hamartoma tumor syndrome," Genetics in Medicine, vol. 14, no. 9, pp. 819-822, 2012.
13. D. R. Walker, J. P. Bond, R. E. Tarone et al., "Evolutionary conservation and somatic mutation hotspot maps of p53: correlation with p53 protein structural and functional features," Oncogene, vol. 18, no. 1, pp. 211-218, 1999.
14. M. Lek, K. J. Karczewski, E. V. Minikel et al., "Analysis of protein-coding genetic variation in 60,706 humans," Nature, vol. 536, no. 7616, pp. 285-291, 2016.
15. F. P. Li, J. F. Fraumeni Jr., J. J. Mulvihill et al., "A cancer family syndrome in twenty-four kindreds," Cancer Research, vol. 48, no. 18, pp. 5358-5362, 1988.
16. D. Pruss, B. Morris, E. Hughes et al., "Development and validation of a new algorithm for the reclassification of genetic variants identified in the BRCA1 and BRCA2 genes," Breast Cancer Research and Treatment, vol. 147, no. 1, pp. 119-132, 2014.
17. L. Guidugli, V. S. Pankratz, N. Singh et al., "A classification model for BRCA2 DNA binding domain missense variants based on homology-directed repair activity," Cancer Research, vol. 73, no. 1, pp. 265-275, 2013.
18. R. Karam, J. Wengrod, L. B. Gardner, and M. F. Wilkinson, "Regulation of nonsense-mediated mRNA decay: implications for physiology and disease," Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, vol. 1829, no. 6-7, pp. 624-633, 2013.
19. O. Anczuków, M. D. Ware, M. Buisson et al., "Does the nonsense-mediated mRNA decay mechanism prevent the synthesis of truncated BRCA1, CHK2, and p53 proteins?" Human Mutation, vol. 29, no. 1, pp. 65-73, 2008.
20. X. Jian, E. Boerwinkle, and X. Liu, "In silico tools for splicing defect prediction: a survey from the viewpoint of end users," Genetics in Medicine, vol. 16, no. 7, pp. 497-503, 2014.
21. C. Houdayer, V. Caux-Moncoutier, S. Krieger et al., "Guidelines for splicing analysis inmolecular diagnosis derived from a set of 327 combined in silico/in vitro studies on BRCA1 and BRCA2 variants," Human Mutation, vol. 33, no. 8, pp. 1228-1238, 2012.
22. M. P. G. Vreeswijk, J. N. Kraan, H. M. van der Klift et al., "Intronic variants in BRCA1 and BRCA2 that affect RNA splicing can be reliably selected by splice-site prediction programs," Human Mutation, vol. 30, no. 1, pp. 107-114, 2009.
23. P. J. Whiley, M. de la Hoya, M. Thomassen et al., "Comparison of mRNA splicing assay protocols across multiple laboratories: recommendations for best practice in standardized clinical testing," Clinical Chemistry, vol. 60, no. 2, pp. 341-352, 2014.
24. G. A. Millot, M. A. Carvalho, S. M. Caputo et al., "A guide for functional analysis of BRCA1 variants of uncertain significance," Human Mutation, vol. 33, no. 11, pp. 1526-1537, 2012.
25. D. J. R. Ransburgh, N. Chiba, C. Ishioka, A. E. Toland, and J. D. Parvin, "Identification of breast tumor mutations in BRCA1 that abolish its function in homologous DNA recombination," Cancer Research, vol. 70, no. 3, pp. 988-995, 2010.
26. C. Lu, M. Xie, M. C. Wendl et al., "Patterns and functional implications of rare germline variants across 12 cancer types," Nature Communications, vol. 6, Article ID10086, 2015.
27. R. Scully, S. Ganesan, K. Vlasakova, J. Chen, M. Socolovsky, and D.M. Livingston, "Genetic analysis of BRCA1 function in a defined tumor cell line," Molecular Cell, vol. 4, no. 6, pp. 1093-1099, 1999.
28. W.W.Y.AuandB. R.Henderson, "TheBRCA1 RINGandBRCT domains cooperate in targeting BRCA1 to ionizing radiationinduced nuclear foci,"The Journal of Biological Chemistry, vol. 280, no. 8, pp. 6993-7001, 2005.
29. J. A. Rodriguez,W.W.Y.Au, and B. R.Henderson, "Cytoplasmic mislocalization of BRCA1 caused by cancer-associated mutations in the BRCTdomain," ExperimentalCell Research, vol. 293, no. 1, pp. 14-21, 2004.
30. R. Drost, P. Bouwman, S. Rottenberg et al., "BRCA1 RING function is essential for tumor suppression but dispensable for therapy resistance," Cancer Cell, vol. 20, no. 6, pp. 797-809, 2011.
31. K.A.T.Naipal, N. S. Verkaik, N. Ameziane et al., "FunctionalEx vivo assay to select homologous recombination-deficient breast tumors for PARP inhibitor treatment," Clinical Cancer Research, vol. 20, no. 18, pp. 4816-4826, 2014.
32. A. N. A. Monteiro, A. August, and H. Hanafusa, "Evidence for a transcriptional activation function of BRCA1 C-terminal region," Proceedings of the National Academy of Sciences of the United States of America, vol. 93, no. 24, pp. 13595-13599, 1996.
33. J. Vallon-Christersson, C. Cayanan, K.Haraldsson et al., "Functional analysis of BRCA1 C-terminal missense mutations identified in breast and ovarian cancer families," Human Molecular Genetics, vol. 10, no. 4, pp. 353-360, 2001.
34. C. M. Phelan, V. Dapic, B. Tice et al., "Classification of BRCA1 missense variants of unknown clinical significance," Journal of Medical Genetics, vol. 42, no. 2, pp. 138-146, 2005.
35. M. A. Carvalho, S. M. Marsillac, R. Karchin et al., "Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis," Cancer Research, vol. 67, no. 4, pp. 1494-1501, 2007.
36. P. S. Brzovic, J. R. Keeffe, H. Nishikawa et al., "Binding and recognition in the assembly of an active BRCA1/BARD1 ubiquitin-ligase complex," Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 10, pp. 5646-5651, 2003.
37. J. R.Morris, L. Pangon, C. Boutell, T. Katagiri,N.H. Keep, and E. Solomon, "Genetic analysis of BRCA1 ubiquitin ligase activity and its relationship to breast cancer susceptibility," Human Molecular Genetics, vol. 15, no. 4, pp. 599-606, 2006.
38. S. T. South, C. Lee, A. N. Lamb et al., "ACMG standards and guidelines for constitutional cytogenomic microarray analysis, including postnatal and prenatal applications: revision 2013," Genetics in Medicine, vol. 15, no. 11, pp. 901-909, 2013.
39. M. S. Lee, R. Green, S. M. Marsillac et al., "Comprehensive analysis of missense variations in the BRCT domain of BRCA1 by structural and functional assays," Cancer Research, vol. 70, no. 12, pp. 4880-4890, 2010.
40. A. Kallioniemi, O.-P. Kallioniemi, D. Sudar et al., "Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors," Science, vol. 258, no. 5083, pp. 818-821, 1992.
41. D. Pinkel and D. G. Albertson, "Array comparative genomic hybridization and its applications in cancer," Nature Genetics, vol. 37, no. 6, supplement, pp. S11-S17, 2005.
42. Y. Saillour, M. Cossée, F. Leturcq et al., "Detection of exonic copy-number changes using a highly efficient oligonucleotidebased comparative genomic hybridization-array method," Human Mutation, vol. 29, no. 9, pp. 1083-1090, 2008.
43. J. Staaf, T. Törngren, E. Rambech et al., "Detection and precise mapping of germline rearrangements in BRCA1, BRCA2, MSH2, and MLH1 using zoom-in array comparative genomic hybridization (aCGH)," Human Mutation, vol. 29, no. 4, pp. 555-564, 2008.
44. T. A. Peterson, E.Doughty, and M. G. Kann, "Towards precision medicine: advances in computational approaches for the analysis of human variants," Journal of Molecular Biology, vol. 425, no. 21, pp. 4047-4063, 2013.
45. Y. Choi, G. E. Sims, S. Murphy, J. R. Miller, and A. P. Chan, "Predicting the functional effect of amino acid substitutions and indels," PLoS ONE, vol. 7, no. 10, Article IDe46688, 2012.
46. S. Stefl, H. Nishi, M. Petukh, A. R. Panchenko, and E. Alexov, "Molecular mechanisms of disease-causing missense mutations," Journal of Molecular Biology, vol. 425, no. 21, pp. 3919-3936, 2013.
47. T. G. Kucukkal, Y. Yang, S. C. Chapman, W. Cao, and E. Alexov, "Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics," International Journal ofMolecular Sciences, vol. 15, no. 6, pp. 9670-9717, 2014.
48. B. M. Kroncke, C. G. Vanoye, J. Meiler, A. L. George Jr., and C. R. Sanders, "Personalized biochemistry and biophysics," Biochemistry, vol. 54, no. 16, pp. 2551-2559, 2015.
49. J. Reumers, J. Schymkowitz, and F. Rousseau, "Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations," BMC Bioinformatics, vol. 10, supplement 8, article S9, 2009.
50. R. Casadio, M. Vassura, S. Tiwari, P. Fariselli, and P. Luigi Martelli, "Correlating disease-related mutations to their effect on protein stability: a large-scale analysis of the human proteome," Human Mutation, vol. 32, no. 10, pp. 1161-1170, 2011.
51. D. E.V. Pires, J.Chen, T. L. Blundell, andD. B. Ascher, "In silico functional dissection of saturation mutagenesis: interpreting the relationship between phenotypes and changes in protein stability, interactions and activity," Scientific Reports, vol. 6, Article ID 19848, 2016.
52. R. Karchin, M. Agarwal, A. Sali, F. Couch, and M. S. Beattie, "Classifying variants of undetermined significance in BRCA2 with protein likelihood ratios," Cancer Informatics, vol. 6, pp. 203-216, 2008.
53. A. A. Yee, A. Savchenko, A. Ignachenko et al., "NMR and X-ray crystallography, complementary tools in structural proteomics of small proteins," Journal of the American Chemical Society, vol. 127, no. 47, pp. 16512-16517, 2005.
54. R. D. Finn, P. Coggill, R. Y. Eberhardt et al., "The Pfam protein families database: towards a more sustainable future," Nucleic Acids Research, vol. 44, no. 1, pp.D279-D285, 2016.
55. S. Hunter, R. Apweiler, T. K. Attwood et al., "InterPro: the integrative protein signature database," Nucleic Acids Research, vol. 37, no. 1, pp. D211-D215, 2009.
56. J. A. Clapperton, I. A. Manke, D. M. Lowery et al., "Structure and mechanism of BRCA1 BRCT domain recognition of phosphorylated BACH1 with implications for cancer," Nature Structural & Molecular Biology, vol. 11, no. 6, pp. 512-518, 2004.
57. S. L. Clark, A. M. Rodriguez, R. R. Snyder, G. D. V. Hankins, and D. Boehning, "Structure-function of the tumor suppressor BRCA1," Computational and Structural Biotechnology Journal, vol. 1, no. 1, pp. 1-8, 2012.
58. R. S.Williams, R. Green, and J. N. M. Glover, "Crystal structure of the BRCT repeat region from the breast cancer-associated protein BRCA1," Nature Structural Biology, vol. 8, no. 10, pp. 838-842, 2001.
59. R. S. Williams, M. S. Lee, D. D. Hau, and J. N. M. Glover, "Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1," Nature Structural & Molecular Biology, vol. 11, no. 6, pp. 519-525, 2004.
60. P. J. E. Rowling, R. Cook, and L. S. Itzhaki, "Toward classification of BRCA1missense variants using a biophysical approach," The Journal of Biological Chemistry, vol. 285, no. 26, pp. 20080-20087, 2010.
61. J. N. M. Glover, "Insights into the molecular basis of human hereditary breast cancer from studies of the BRCA1 BRCT domain," Familial Cancer, vol. 5, no. 1, pp. 89-93, 2006.