Predicting Mendelian Disease-Causing Non-Synonymous Single Nucleotide Variants in Exome Sequencing Studies

PLoS Genetics

Volumn 9, Issue 1, 2013, Pages

  Li, Miao Xin ^a   Kwan, Johnny S H ^a   Bao, Su Ying ^a   Yang, Wanling ^a   Ho, Shu Leong ^a   Song, Yong Qiang ^a   Sham, Pak C ^a,b  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ANALYTIC METHOD; ARTICLE; AUTOSOMAL DOMINANT DISORDER; AUTOSOMAL RECESSIVE DISORDER; CONSANGUINEOUS MARRIAGE; EXOME; GENE FREQUENCY; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC DISORDER; GENETIC VARIABILITY; HETEROZYGOTE; HUMAN; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; MENDELIAN DISEASE; MUTATIONAL ANALYSIS; PREDICTION; PREDICTIVE VALUE; PROBABILITY; PURIFYING SELECTION; RISK ASSESSMENT; SCORING SYSTEM; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL;

AMINO ACID SUBSTITUTION; CONSANGUINITY; EXOME; GENE FREQUENCY; GENES, RECESSIVE; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MODELS, GENETIC; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84873486397     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003143     Document Type: Article

References (43)

1. Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, et al. (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461: 272-U153.
2. Stenson PD, Mort M, Ball EV, Howells K, Phillips AD, et al. (2009) The Human Gene Mutation Database: 2008 update. Genome Med 1: 13.
3. Li MX, Gui HS, Kwan JS, Bao SY, Sham PC, (2012) A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases. Nucleic Acids Res 40: e53.
4. Ge D, Ruzzo EK, Shianna KV, He M, Pelak K, et al. (2011) SVA: software for annotating and visualizing sequenced human genomes. Bioinformatics 27: 1998-2000.
5. Wang K, Li M, Hakonarson H, (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38: e164.
6. Ng PC, Henikoff S, (2006) Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet 7: 61-80.
7. 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 Genet 88: 440-449.
8. Lopes MC, Joyce C, Ritchie GR, John SL, Cunningham F, et al. (2012) A combined functional annotation score for non-synonymous variants. Hum Hered 73: 47-51.
9. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, et al. (2010) A method and server for predicting damaging missense mutations. Nat Methods 7: 248-249.
10. Kryukov GV, Pennacchio LA, Sunyaev SR, (2007) Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. American journal of human genetics 80: 727-739.
11. Sim NL, Kumar P, Hu J, Henikoff S, Schneider G, et al. (2012) SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res.
12. Chun S, Fay JC, (2009) Identification of deleterious mutations within three human genomes. Genome Res 19: 1553-1561.
13. Schwarz JM, Rodelsperger C, Schuelke M, Seelow D, (2010) MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods 7: 575-576.
14. Cooper GM, Stone EA, Asimenos G, Program NCS, Green ED, et al. (2005) Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 15: 901-913.
15. Matthews BW, (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta 405: 442-451.
16. Kwan S, Purcell S, Sham P, (2007) Introduction to biometrical genetics. Statistical.
17. Scheidel W, (1997) Brother-sister marriage in Roman Egypt. J Biosoc Sci 29: 361-371.
18. Leutenegger AL, Prum B, Genin E, Verny C, Lemainque A, et al. (2003) Estimation of the inbreeding coefficient through use of genomic data. Am J Hum Genet 73: 516-523.
19. Li M, Pang S, Song Y, Kung M, Ho SL, et al. (2012) Whole exome sequencing identifies a novel mutation in the transglutaminase 6 gene for spinocerebellar ataxia in a Chinese family. Clin Genet.
20. Mao H, Yang W, Lee PP, Ho MH, Yang J, et al. (2012) Exome sequencing identifies novel compound heterozygous mutations of IL-10 receptor 1 in neonatal-onset Crohn's disease. Genes Immun.
21. Furney SJ, Alba MM, Lopez-Bigas N, (2006) Differences in the evolutionary history of disease genes affected by dominant or recessive mutations. BMC Genomics 7: 165.
22. Jimenez-Sanchez G, Childs B, Valle D, (2001) Human disease genes. Nature 409: 853-855.
23. Lopez-Bigas N, Blencowe BJ, Ouzounis CA, (2006) Highly consistent patterns for inherited human diseases at the molecular level. Bioinformatics 22: 269-277.
24. Papp B, Pal C, Hurst LD, (2003) Dosage sensitivity and the evolution of gene families in yeast. Nature 424: 194-197.
25. Strachan T, Read AP (1999) Human Molecular Genetics; edition. n, editor. New York: Wiley-Liss.
26. Crow JF, Kimura M, (1970) An introduction to population genetics theory. An introduction to population genetics theory.
27. Sutter J, Tabah L, (1952) Effets de la consanguinité et de l'endogamie. Une enquête en Morbihan et Loir-et-Cher. Population (French Edition) pp. 249-266.
28. Slatis HM, (1954) A method of estimating the frequency of abnormal autosomal recessive genes in man. American journal of human genetics 6: 412.
29. Slatis HM, Reis RH, Hoene RE, (1958) Consanguineous marriages in the Chicago region. American journal of human genetics 10: 446.
30. Scott-Emuakpor AB, (1974) The mutation load in an African population. I. An analysis of consanguineous marriages in Nigeria. American journal of human genetics 26: 674.
31. Morton NE, Crow JF, Muller H, (1956) An estimate of the mutational damage in man from data on consanguineous marriages. Proceedings of the National Academy of Sciences of the United States of America 42: 855.
32. Bittles AH, Neel JV, (1994) The costs of human inbreeding and their implications for variations at the DNA level. Nature genetics 8: 117-121.
33. Kondrashov AS, (1995) Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over? Journal of theoretical biology 175: 583-594.
34. Riazuddin S, Castelein CM, Ahmed ZM, Lalwani AK, Mastroianni MA, et al. (2000) Dominant modifier DFNM1 suppresses recessive deafness DFNB26. Nature genetics 26: 431-434.
35. Oprea GE, Kröber S, McWhorter ML, Rossoll W, Müller S, et al. (2008) Plastin 3 is a protective modifier of autosomal recessive spinal muscular atrophy. Science 320: 524-527.
36. Kaplan BS, Kaplan P, de Chadarevian JP, Jequier S, O'Regan S, et al. (1988) Variable expression of autosomal recessive polycystic kidney disease and congenital hepatic fibrosis within a family. American journal of medical genetics 29: 639-647.
37. MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, et al. (2012) A systematic survey of loss-of-function variants in human protein-coding genes. Science 335: 823-828.
38. Goecks J, Nekrutenko A, Taylor J, Galaxy T, (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11: R86.
39. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res 15: 1451-1455.
40. Liu X, Jian X, Boerwinkle E, (2011) dbNSFP: A lightweight database of human nonsynonymous SNPs and their functional predictions. Human mutation 32: 894-899.
41. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
42. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297-1303.
43. Davis J, Goadrich M (2006) The Relationship Between Precision-Recall and ROC Curves. 23rd International Conference on Machine Learning (ICML). Pittsburgh, PA, USA.