Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel)

Human Mutation

Volumn 37, Issue 1, 2016, Pages 28-35

  Douville, Christopher ^a   Masica, David L ^a   Stenson, Peter D ^b   Cooper, David N ^b   Gygax, Derek M ^c   Kim, Rick ^c   Ryan, Michael ^c   Karchin, Rachel ^a,d  

^a Johns Hopkins University   (United States)

^b CARDIFF UNIVERSITY   (United Kingdom)

^c In Silico Solutions   (United States)

^d JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Bioinformatics pathogenicity predictor; In frame frameshift; Indel; Insertion deletion variant; Meta predictor

Indexed keywords

AMINO ACID SEQUENCE; AREA UNDER THE CURVE; ARTICLE; BIOINFORMATICS; EXON; FALSE POSITIVE RESULT; FRAMESHIFT MUTATION; GENE FREQUENCY; GENETIC ANALYSIS; HUMAN; INDEL MUTATION; MISSENSE MUTATION; NONHUMAN; PATHOGENICITY; PRIORITY JOURNAL; RECEIVER OPERATING CHARACTERISTIC; SENSITIVITY AND SPECIFICITY; SOMATIC MUTATION; VARIANT EFFECT SCORING TOOL; ALGORITHM; BIOLOGICAL MODEL; BIOLOGY; INFORMATION PROCESSING; PROCEDURES; REPRODUCIBILITY; SOFTWARE; WEB BROWSER;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATASETS AS TOPIC; HUMANS; INDEL MUTATION; MODELS, GENETIC; MUTATION, MISSENSE; REPRODUCIBILITY OF RESULTS; SOFTWARE; WEB BROWSER;

EID: 84954397194     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.22911     Document Type: Article

References (45)

1. Altschul SF, Madden TL, Schaeffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
2. Boutet E, Lieberherr D, Tognolli M, Schneider M, Bairoch A. 2007. Uniprotkb/Swiss-Prot. Plant Bioinformatics: Springer. p 89-112.
3. Breiman L. 2001. Random forests. Mach Learn 45:5-32.
4. Capriotti E, Altman RB. 2011. A new disease-specific machine learning approach for the prediction of cancer-causing missense variants. Genomics 98:310.
5. Capriotti E, Nehrt NL, Kann MG, Bromberg Y. 2012. Bioinformatics for personal genome interpretation. Brief Bioinform 13:495-512.
6. Carter H, Douville C, Stenson PD, Cooper DN, Karchin R. 2013. Identifying Mendelian disease genes with the variant effect scoring tool. BMC Genomics 14(Suppl 3):S3.
7. Chan PA, Duraisamy S, Miller PJ, Newell JA, McBride C, Bond JP, Raevaara T, Ollila S, Nyström M, Grimm AJ, Christodoulou J, Oetting WS, Greenblatt MS. 2007. Interpreting missense variants: comparing computational methods in human disease genes CDKN2A, MLH1, MSH2, MECP2, and tyrosinase (TYR). Hum Mutat 28:683-693.
8. Choi Y, Sims GE, Murphy S, Miller JR, Chan AP. 2012. Predicting the functional effect of amino acid substitutions and indels. PloS ONE 7:e46688.
9. Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M. 2012. The 1000 Genomes Project: data management and community access. Nat Methods 9:459-462.
10. Consortium GP. 2010. A map of human genome variation from population-scale sequencing. Nature 467:1061-1073.
11. Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S. 2015. Ensembl 2015. Nucleic Acids Res 43:D662-D669.
12. Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R. 2013. CRAVAT: cancer-related analysis of variants toolkit. Bioinformatics 29:647-648.
13. Fawcett T. 2004. ROC graphs: notes and practical considerations for researchers. Mach Learn 31:1-38.
14. Folkman L, Yang Y, Li Z, Stantic B, Sattar A, Mort M, Cooper DN, Liu Y, Zhou Y. 2015. DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels. Bioinformatics 31:1599-1606.
15. Frousios K, Iliopoulos CS, Schlitt T, Simpson MA. 2013. Predicting the functional consequences of non-synonymous DNA sequence variants-Evaluation of bioinformatics tools and development of a consensus strategy. Genomics 102:223-228.
16. Fu W, O'Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Rieder MJ, Altshuler D, Shendure J. 2013. Analysis of 6, 515 exomes reveals the recent origin of most human protein-coding variants. Nature 493:216-220.
17. Gonzalez-Perez A, Lopez-Bigas N. 2011. Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. Am J Hum Genetics 88:440-449.
18. Hall M, Frank E, Holmes G, Pfahringer B, Reutemann P, Witten IH. 2009. The WEKA data mining software: an update. ACM SIGKDD Explor Newslett 11:10-18.
19. Hicks S, Wheeler DA, Plon SE, Kimmel M. 2011. Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed. Hum Mutat 32:661-668.
20. Hu J, Ng PC. 2012. Predicting the effects of frameshifting indels. Genome Biol 13:R9.
21. Hu J, Ng PC. 2013. SIFT Indel: predictions for the functional effects of amino acid insertions/deletions in proteins. PloS ONE 8:e77940.
22. Hudson RR. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18:337-338.
23. Karchin R, Kelly L, Sali A. Improving functional annotation of non-synonomous SNPs with information theory; 2005.
24. 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.
25. Knijnenburg TA, Wessels LF, Reinders MJ, Shmulevich I. 2009. Fewer permutations, more accurate P-values. Bioinformatics 25:i161-i168.
26. 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(Database Issue):D980-985.
27. Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ, Sunyaev SR, Nielsen R. 2008. Proportionally more deleterious genetic variation in European than in African populations. Nature 451:994-997.
28. MacArthur DG, Tyler-Smith C. 2010. Loss-of-function variants in the genomes of healthy humans. Hum Mol Genet 19(R2):R125-R130.
29. Martelotto LG, Ng CK, De Filippo MR, Zhang Y, Piscuoglio S, Lim R, Shen R, Norton L, Reis-Filho JS, Weigelt B. 2014. Benchmarking mutation effect prediction algorithms using functionally validated cancer-related missense mutations. Genome Biol 15:484.
30. Masica DL, Karchin R. 2011. Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival. Cancer Res 71:4550-4561.
31. Ng PC, Levy S, Huang J, Stockwell TB, Walenz BP, Li K, Axelrod N, Busam DA, Strausberg RL, Venter JC. 2008. Genetic variation in an individual human exome. PLoS Genet 4:e1000160.
32. Pfeifer B, Wittelsburger U, Onsins SER, Lercher MJ. 2014. PopGenome: an efficient Swiss army knife for population genomic analyses in R. Mol Biol Evol 31:1929-1936.
33. Pickands III J. 1975. Statistical inference using extreme order statistics. Ann Stat 3:119-131.
34. Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. 2010. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res 20:110-121.
35. Pruitt KD, Tatusova T, Maglott DR. 2007. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35(Suppl 1):D61-D65.
36. Schuler GD, Epstein JA, Ohkawa H, Kans JA. 1996. Entrez: molecular biology database and retrieval system. Methods Enzymol 266:141.
37. Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GL, Edwards KJ, Day IN, Gaunt TR. 2013. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum Mutat 34:57-65.
38. Stenson PD, Mort M, Ball EV, Shaw K, Phillips AD, Cooper DN. 2014. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Hum Genet 133:1-9.
39. Steward RE, MacArthur MW, Laskowski RA, Thornton JM. 2003. Molecular basis of inherited diseases: a structural perspective. Trends Genet 19:505-513.
40. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
41. Tennessen JA, Madeoy J, Akey JM. 2010. Signatures of positive selection apparent in a small sample of human exomes. Genome Res 20:1327-1334.
42. Thusberg J, Olatubosun A, Vihinen M. 2011. Performance of mutation pathogenicity prediction methods on missense variants. Hum Mutat 32:358-368.
43. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S. 2007. Database resources of the national center for biotechnology information. Nucleic Acids Res 35(Suppl 1):D5-D12.
44. Wong WC, Kim D, Carter H, Diekhans M, Ryan MC, Karchin R. 2011. CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. Bioinformatics 27:2147-2148.
45. Zhao H, Yang Y, Lin H, Zhang X, Mort M, Cooper DN, Liu Y, Zhou Y. 2013. DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels. Genome Biol 14:R23.