EVA: Exome Variation Analyzer, an efficient and versatile tool for filtering strategies in medical genomics

BMC Bioinformatics

Volumn 13, Issue SUPPL 1, 2012, Pages

  Coutant, Sophie ^a,b   Cabot, Chloé ^a,b   Lefebvre, Arnaud ^a,b   Léonard, Martine ^a,b   Prieur Gaston, Elise ^a,b   Campion, Dominique ^a,b   Lecroq, Thierry ^a,b   Dauchel, Hélène ^a,b  

^a UNIVERSITÉ DE ROUEN   (France)

^b UNIVERSITY OF ROUEN   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CLINICAL DIAGNOSTICS; FILTERING CRITERIA; FILTERING STRATEGIES; FUNDAMENTAL RESEARCH; GRAPHICAL VISUALIZATION; INTERACTIVE TABLES; PERSONAL STRATEGIES; PERSONALIZED MEDICINES;

ALGORITHMS; GENES; PATHOLOGY; RESEARCH; WORLD WIDE WEB;

DIAGNOSIS;

ALGORITHM; ALZHEIMER DISEASE; ARTICLE; COMPUTER PROGRAM; DNA SEQUENCE; EXOME; GENETIC DATABASE; GENETICS; HUMAN; INSTRUMENTATION; METHODOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; ALZHEIMER DISEASE; DATABASES, GENETIC; EXOME; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84875069273     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-S14-S9     Document Type: Article

References (40)

1. Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 2008, 9:387-402. 10.1146/annurev.genom.9.081307.164359, 18576944.
2. Mardis ER. The impact of next-generation sequencing technology on genetics. Trends in Genetics 2008, 24(3):133-141. 10.1016/j.tig.2007.12.007, 18262675.
3. Mardis ER. A decade's perspective on DNA sequencing technology. Nature 2011, 470(7333):198-203. 10.1038/nature09796, 21307932.
4. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11(1):31-46. 10.1038/nrg2626, 19997069.
5. Zhang J, Chiodini R, Badr A, Zhang G. The impact of next-generation sequencing on genomics. J Genet Genomics 2011, 38:95-109. 10.1016/j.jgg.2011.02.003, 3076108, 21477781.
6. Voelkerding K, Dames S, Durtschi J. Next-generation sequencing: from basic research to diagnostics. Clin Chem 2009, 55:641-58. 10.1373/clinchem.2008.112789, 19246620.
7. Shendure J, Ji H. Next-generation DNA sequencing. Nature Biotechnology 2008, 26:135-1145.
8. Koboldt DC, Ding L, Mardis ER, Wilson RK. Challenges of sequencing human genomes. Brief Bioinform 2010, 11(5):484-98. 10.1093/bib/bbq016, 2980933, 20519329.
9. Cooper GM, Shendure J. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat Rev Genet 2011, 12(9):628-40. 10.1038/nrg3046, 21850043.
10. 1000 Genomes Project Consortium A map of human genome variation from population-scale sequencing. Nature 2010, 467(7319):1061-73. 10.1038/nature09534, 3042601, 20981092, 1000 Genomes Project Consortium.
11. Sherry S, Ward M, Kholodov M, Baker J, Phan L, Smigielski E, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001, 29:308-311. 10.1093/nar/29.1.308, 29783, 11125122.
12. Majewski J, Schwartzentruber J, Lalonde E, Montpetit A, Jabado N. What can exome sequencing do for you?. J Med Genet 2011, 48(9):580-9. 10.1136/jmedgenet-2011-100223, 21730106.
13. Ng SB, Turner E, Robertson P, Flygare S, Bigham A, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler E, et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 2009, 461:272-276. 10.1038/nature08250, 2844771, 19684571.
14. Ku C-S, Naidoo N, Pawitan Y. Revisiting Mendelian disorders through exome sequencing. Hum Genet 2011, 129:351-370. 10.1007/s00439-011-0964-2, 21331778.
15. Exome sequencing special issue. Genome Biology 2011, 12(9). Garvey C, Cosgrove A, Attar N, Bilsborough G, Creavin T, Shendure J.
16. Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet 2011, 12(11):745-55. 10.1038/nrg3031, 21946919.
17. Singleton AB. Exome sequencing: a transformative technology. Lancet Neurol 2011, 10(10):942-6. 10.1016/S1474-4422(11)70196-X, 3302356, 21939903.
18. Online Mendelian Inheritance in Man. http://omim.org/
19. Stitziel NO, Kiezun A, Sunyaev S. Computational and statistical approaches to analysing variants identified by exome sequencing. Genome Biology 2011, 12(9):227-237. 10.1186/gb-2011-12-9-227, 3308043, 21920052.
20. Rovelet-Lecrux A, Legallic S, Wallon D, Flaman JM, Martinaud O, Bombois S, Rollin-Sillaire A, Michon A, Le Ber I, Pariente J, et al. A genome-wide study reveals rare CNVs exclusive to extreme phenotypes of Alzheimer disease. Eur J Hum Genet 2011, doi: 10.1038/ejhg.2011.225.
21. Fernald GH, Capriotti E, Daneshjou R, Karczewski KJ, Altman RB. Bioinformatics challenges for personalized medicine. Bioinformatics 2011, 27(13):1741-8. 10.1093/bioinformatics/btr295, 3117361, 21596790.
22. Van Oeveren J, Janssen A. Mining SNPs from DNA sequence data. computational approaches to SNP discovery and analysis. Methods Mol Biol 2009, 578:73-91. 10.1007/978-1-60327-411-1_4, 19768587.
23. Nielsen R, Paul JS, Albrechtsen A, Song YS. Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 2011, 12(6):443-51. 10.1038/nrg2986, 21587300.
24. Ku CS, Cooper DN, Polychronakos C, Naidoo N, Wu M, Soong R. Exome sequencing: dual role as a discovery and diagnostic tool. Ann Neurol 2012, 71(1):5-14. 10.1002/ana.22647, 22275248.
25. Pottier C, Hannequin D, Coutant S, Rovelet-Lecrux A, Wallon D, Rousseau S, Legallic S, Paquet C, Bombois S, Pariente J, et al. High frequency of potentially pathogenic SORL1 mutations in autosomal dominant early-onset Alzheimer disease. Mol Psychiatry 2012, AOP, 3 April 2012. doi:10.1038/mp.2012.15.
26. IntegraGen company. http://www.integragen.fr
27. The International HapMap Consortium The International HapMap Project. Nature 2003, 426:789-796. 10.1038/nature02168, 14685227, The International HapMap Consortium.
28. Pruitt KD, Tatusova T, Klimke W, Maglott DR. NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res 2009, (37 Database):D32-6.
29. Complete genomics. http://www.completegenomics.com
30. Exome Variant Server, NHLBI Exome Sequencing Project (ESP), Seattle, WA. http://evs.gs.washington.edu/EVS/
31. Riva A, Kohane IS. SNPper: retrieval and analysis of human SNPs. Bioinformatics 2002, 8:1681-1685.
32. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods 2010, 7:248-249. 10.1038/nmeth0410-248, 2855889, 20354512.
33. Schwarz JM, Rodelsperger C, Schuelke M, Seelow D. MutationTaster evaluates disease causing potential of sequence alterations. Nat Methods 2010, 7:575-576. 10.1038/nmeth0810-575, 20676075.
34. Schaefer C, Meier A, Rost B, Bromberg Y. SNPdbe: constructing an nsSNP functional impacts database. Bioinformatics 2012, 28:601-602. 10.1093/bioinformatics/btr705, 3278761, 22210871.
35. Reva B, Antipin Y, Sander C. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res 2011, 39:e118. 10.1093/nar/gkr407, 3177186, 21727090.
36. Ge D, Ruzzo EK, Shianna KV, He M, Pelak K, Heinzen EL, Need AC, Cirulli ET, Maia JM, Dickson SP, Zhu M, Singh A, Allen AS, Goldstein DB. SVA: software for annotating and visualizing sequenced human genomes. Bioinformatics 2011, 27:1998-2000. 10.1093/bioinformatics/btr317, 3129530, 21624899.
37. Teer JK, Green ED, Mullikin JC, Biesecker LG. VarSifter: visualizing and analyzing exome-scale sequence variation data on a desktop computer. Bioinformatics 2012, 28:599-600. 10.1093/bioinformatics/btr711, 22210868.
38. Sincan M, Simeonov DR, Adams D, Markello TC, Pierson TM, Toro C, Gahl WA, Boerkoel C. VAR-MD: A tool to analyze whole exome-genome variants in small human pedigrees with mendelian inheritance. Hum Mutat 2012, 33:593-598. 10.1002/humu.22034, 22290570.
39. Wang K, Li M, Hakonarson H. ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 2010, 38(16):e164. 10.1093/nar/gkq603, 2938201, 20601685.
40. McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 2010, 26(16):2069-70. 10.1093/bioinformatics/btq330, 2916720, 20562413.