Evaluation of CADD Scores in Curated Mismatch Repair Gene Variants Yields a Model for Clinical Validation and Prioritization

Human Mutation

Volumn 36, Issue 7, 2015, Pages 712-719

[No Author Info available]

Author keywords

Cumulative link model; Lynch syndrome; Pathogenicity prediction; Variant classification

Indexed keywords

MISMATCH REPAIR PROTEIN;

ARTICLE; CLINICAL ASSESSMENT TOOL; CLINICAL CLASSIFICATION; COMBINED ANNOTATION DEPENDENT DEPLETION SCORE; DISEASE ASSOCIATION; GENE FREQUENCY; GENE MUTATION; GENETIC VARIABILITY; HEREDITARY NONPOLYPOSIS COLORECTAL CANCER; HUMAN; INHERITANCE; PATHOGENICITY; PHENOTYPE; PRIORITY JOURNAL; PROTEIN FUNCTION; STOP CODON; BIOLOGY; CHEMICAL STRUCTURE; GENETIC ASSOCIATION STUDY; GENETIC VARIATION; GENETICS; HIGH THROUGHPUT SEQUENCING; MISMATCH REPAIR; SOFTWARE;

COLORECTAL NEOPLASMS, HEREDITARY NONPOLYPOSIS; COMPUTATIONAL BIOLOGY; DNA MISMATCH REPAIR; GENETIC ASSOCIATION STUDIES; GENETIC VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MODELS, MOLECULAR; SOFTWARE;

EID: 84931563993     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.22798     Document Type: Article

References (27)

1. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. 2010. A method and server for predicting damaging missense mutations. Nat Methods 7:248-249.
2. Agresti A. 2002. Categorical data analysis. New York: John Wiley & Sons. doi: 10.1002/0471249688
3. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. 2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, snpEff: SNPs in the genome of drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6:80-92.
4. Cooper GM, Shendure J. 2011. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat Rev Genet 12:628-640.
5. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, et al. 2011. The variant call format and VCFtools. Bioinformatics 27(15):2156-2158.
6. den Dunnen JT, Paalman MH. 2003. Standardizing mutation nomenclature: why bother? Hum Mutat 22:181-182.
7. Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J, Kaul R, Khatun J, Lajoie BR, et al. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74.
8. Gelman A, Rubin DB. 1992. Inference from iterative simulation using multiple sequences. Stat Sci 7:457-472.
9. Kampstra P. 2008. Beanplot: a boxplot alternative for visual comparison of distributions. J Stat Soft 28:1-9.
10. Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. 2014. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 46:310-315.
11. Kumar P, Henikoff S, Ng PC. 2009. Predicting the effects of coding non-synonymous variants on protein function using the sIFT algorithm. Nat Protoc 4:1073-1081.
12. Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, Maglott DR. 2013. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res 42:D980-D985.
13. Lipkin SM, Rozek LS, Rennert G, Yang W, Chen P-C, Hacia J, Hunt N, Shin B, Fodor S, Kokoris M, Greenson JK, Fearon E, et al. 2004. The mLH1 d132H variant is associated with susceptibility to sporadic colorectal cancer. Nat Genet 36:694-699.
14. Lohmann K, Klein C. 2014. Next generation sequencing and the future of genetic diagnosis. Neurotherapeutics 11:699-707.
15. McCullagh P. 1980. Regression models for ordinal data. J R Stat Soc Series B 42:109-142.
16. McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. 2010. Deriving the consequences of genomic variants with the ensembl aPI and sNP effect predictor. Bioinformatics 26:2069-2070.
17. Plon SE, Eccles DM, Easton D, Foulkes WD, Genuardi M, Greenblatt MS, Hogervorst FB, Hoogerbrugge N, Spurdle AB, Tavtigian SV. 2008. Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results. Hum Mutat 29:1282-1291.
18. Plummer M. 2003. JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling. Proceedings of the 3rd international workshop on distributed statistical computing (DSC). Vienna 124:125.
19. Plummer M, Best N, Cowles K, Vines K. 2006. CODA: convergence diagnosis and output analysis for mCMC. R News 6:7-11.
20. Saunders CJ, Miller NA, Soden SE, Dinwiddie DL, Noll A, Alnadi NA, Andraws N, Patterson ML, Krivohlavek LA, Fellis J, Humphray S, Saffrey P, et al. 2012. Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units. Sci Transl Med 4:154ra135-154ra135.
21. TGotN Consortium. 2014a. The genome of the Netherlands: design, and project goals. Eur J Hum Genet 22:221-227.
22. TGotN Consortium. 2014b. Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat Genet 46:818-825.
23. Thompson BA, Greenblatt MS, Vallee MP, Herkert JC, Tessereau C, Young EL, Adzhubey IA, Li B, Bell R, Feng B, Mooney SD, Radivojac P, et al. 2013a. Calibration of multiple in silico tools for predicting pathogenicity of mismatch repair gene missense substitutions. Hum Mutat 34:255-265.
24. Thompson BA, Spurdle AB, Plazzer J-P, Greenblatt MS, Akagi K, Al-Mulla F, Bapat B, Bernstein I, Capellá G, den Dunnen JT, du Sart D, Fabre A, et al. 2013b. Application of a 5-tiered scheme for standardized classification of 2360 unique mismatch repair gene variants in the inSiGHT locus-specific database. Nat Genet 46:107-115.
25. T1GP Consortium. 2012. An integrated map of genetic variation from 1092 human genomes. Nature 491:56-65.
26. Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, Klemm A, Flicek P, Manolio T, Hindorff L, Parkinson H. 2013. The NHGRI GWAS catalog, a curated resource of sNP-trait associations. Nucleic Acids Res 42 (Database issue):D1001-D1006.
27. Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, Braxton A, Beuten J, Xia F, Niu Z, Hardison M, Person R, et al. 2013. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med 369:1502-1511.