Integrated sequence analysis pipeline provides one-stop solution for identifying disease-causing mutations

Human Mutation

Volumn 35, Issue 12, 2014, Pages 1427-1435

  Hu, Hao ^a   Wienker, Thomas F ^a   Musante, Luciana ^a   Kalscheuer, Vera M ^a   Kahrizi, Kimia ^b   Najmabadi, Hossein ^b   Ropers, H Hilger ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^b UNIVERSITY OF SOCIAL WELFARE AND REHABILITATION SCIENCES   (Iran)

Author keywords

Indels; Intellectual disability; Logistic model; Next generation sequencing

Indexed keywords

DISEASES; GENETICS; HUMAN; MUTATION; PROCEDURES; SEQUENCE ANALYSIS;

DISEASE; HUMANS; MUTATION; SEQUENCE ANALYSIS;

EID: 84911445906     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.22695     Document Type: Article

References (53)

1. Abyzov A, Urban AE, Snyder M, Gerstein M. 2011. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res 21:974-984.
2. 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.
3. The 1000 Genomes Project Consortium. 2012. An integrated map of genetic variation from 1, 092 human genomes. Nature 491:56-65.
4. Bainbridge MN, Hu H, Muzny DM, Musante L, Lupski JR, Graham BH, Chen W, Gripp KW, Jenny K, Wienker TF, Yang Y, Sutton VR, Gibbs RA, Ropers HH. 2013. De novo truncating mutations in ASXL3 are associated with a novel clinical phenotype with similarities to Bohring-Opitz syndrome. Genome Med 5:11.
5. Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J. 2011. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet 12:745-755.
6. Belet S, Fieremans N, Yuan X, Van Esch H, Verbeeck J, Ye Z, Cheng L, Brodsky BR, Hu H, Kalscheuer VM, Brodsky RA, Froyen G. 2014. Early frameshift mutation in PIGA identified in a large XLID family without neonatal lethality. Hum Mutat 35:350-355.
7. Bell CJ, Dinwiddie DL, Miller NA, Hateley SL, Ganusova EE, Mudge J, Langley RJ, Zhang L, Lee CC, Schilkey FD, Sheth V, Woodward JE, et al. 2011. Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med 3:65ra4.
8. Boycott KM, Vanstone MR, Bulman DE, MacKenzie AE. 2013. Rare-disease genetics in the era of next-generation sequencing: discovery to translation. Nat Rev Genet 14:681-691.
9. Calabrese R, Capriotti E, Fariselli P, Martelli PL, Casadio R. 2009. Functional annotations improve the predictive score of human disease-related mutations in proteins. Hum Mutat 30:1237-1244.
10. Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM. 2010. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 38:1767-1771.
11. Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. 2010. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol 6:e1001025.
12. de Brouwer AP, Nabuurs SB, Verhaart IE, Oudakker AR, Hordijk R, Yntema HG, Hordijk-Hos JM, Voesenek K, de Vries BB, van Essen T, Chen W, Hu H, et al. 2014. A 3-base pair deletion, c.9711_9713del, in DMD results in intellectual disability without muscular dystrophy. Eur J Hum Genet 22:480-485.
13. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, et al. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491-498.
14. Dreha-Kulaczewski S, Kalscheuer V, Tzschach A, Hu H, Helms G, Brockmann K, Weddige A, Dechent P, Schluter G, Kratzner R, Ropers HH, Gartner J, Zirn B. 2013. A novel SLC6A8 mutation in a large family with X-linked intellectual disability: clinical and proton magnetic resonance spectroscopy data of both hemizygous males and heterozygous females. JIMD Rep 13:91-99.
15. Ewing B, Green P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186-194.
16. 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 102:223-238.
17. Fu W, O'Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Rieder MJ, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ; NHLBI Exome Sequencing Project, Akey JM. 2013. Analysis of 6, 515 exomes reveals the recent origin of most human protein-coding variants. Nature 493:216-220.
18. 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.
19. Grantham R. 1974. Amino acid difference formula to help explain protein evolution. Science 185:862-864.
20. Hirata H, Nanda I, van Riesen A, McMichael G, Hu H, Hambrock M, Papon MA, Fischer U, Marouillat S, Ding C, Alirol S, Bienek M, et al. 2013. ZC4H2 mutations are associated with arthrogryposis multiplex congenita and intellectual disability through impairment of central and peripheral synaptic plasticity. Am J Hum Genet 92:681-695.
21. Hu H, Eggers K, Chen W, Garshasbi M, Motazacker MM, Wrogemann K, Kahrizi K, Tzschach A, Hosseini M, Bahman I, Hucho T, Muhlenhoff M, et al. 2011. ST3GAL3 mutations impair the development of higher cognitive functions. Am J Hum Genet 89:407-414.
22. Hu H, Wrogemann K, Kalscheuer V, Tzschach A, Richard H, Haas SA, Menzel C, Bienek M, Froyen G, Raynaud M, Bokhoven HV, Chelly J, Ropers H, Chen W. 2009. Mutation screening in 86 known X-linked mental retardation genes by droplet-based multiplex PCR and massive parallel sequencing. Hugo J 3:41-49.
23. Huang L, Jolly LA, Willis-Owen S, Gardner A, Kumar R, Douglas E, Shoubridge C, Wieczorek D, Tzschach A, Cohen M, Hackett A, Field M, et al. 2012. A noncoding, regulatory mutation implicates HCFC1 in nonsyndromic intellectual disability. Am J Hum Genet 91:694-702.
24. Kahrizi K, Hu CH, Garshasbi M, Abedini SS, Ghadami S, Kariminejad R, Ullmann R, Chen W, Ropers HH, Kuss AW, Najmabadi H, Tzschach A. 2011. Next generation sequencing in a family with autosomal recessive Kahrizi syndrome (OMIM 612713) reveals a homozygous frameshift mutation in SRD5A3. Eur J Hum Genet 19:115-117.
25. 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.
26. Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L. 2009. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25:2283-2285.
27. Larti F, Kahrizi K, Musante L, Hu H, Papari E, Fattahi Z, Bazazzadegan N, Liu Z, Banan M, Garshasbi M, Wienker TF, Ropers HH, Galjart N, Najmabadi H. 2014. A defect in the CLIP1 gene (CLIP-170) can cause autosomal recessive intellectual disability. Eur J Hum Genet.[Epub ahead of print]
28. Lesca G, Moizard MP, Bussy G, Boggio D, Hu H, Haas SA, Ropers HH, Kalscheuer VM, Des Portes V, Labalme A, Sanlaville D, Edery P, Raynaud M, Lespinasse J. 2013. Clinical and neurocognitive characterization of a family with a novel MED12 gene frameshift mutation. Am J Med Genet A 161A:3063-3071.
29. Li B, Krishnan VG, Mort ME, Xin F, Kamati KK, Cooper DN, Mooney SD, Radivojac P. 2009a. Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics 25:2744-2750.
30. Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. 2009b. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25:1966-1967.
31. Lopes MC, Joyce C, Ritchie GR, John SL, Cunningham F, Asimit J, Zeggini E. 2012. A combined functional annotation score for non-synonymous variants. Hum Hered 73:47-51.
32. Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J, Turner DJ. 2010. Target-enrichment strategies for next-generation sequencing. Nat Methods 7:111-118.
33. Masurel-Paulet A, Kalscheuer VM, Lebrun N, Hu H, Levy F, Thauvin-Robinet C, Darmency-Stamboul V, El Chehadeh S, Thevenon J, Chancenotte S, Ruffier-Bourdet M, Bonnet M, et al. 2014. Expanding the clinical phenotype of patients with a ZDHHC9 mutation. Am J Med Genet A 164A:789-795.
34. Najmabadi H, Hu H, Garshasbi M, Zemojtel T, Abedini SS, Chen W, Hosseini M, Behjati F, Haas S, Jamali P, Zecha A, Mohseni M, et al. 2011. Deep sequencing reveals 50 novel genes for recessive cognitive disorders. Nature 478:57-63.
35. Ng PC, Henikoff S. 2003. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res 31:3812-3814.
36. O'Rawe J, Jiang T, Sun G, Wu Y, Wang W, Hu J, Bodily P, Tian L, Hakonarson H, Johnson WE, Wei Z, Wang K, Lyon GJ. 2013. Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med 5:28.
37. Pak C, Garshasbi M, Kahrizi K, Gross C, Apponi LH, Noto JJ, Kelly SM, Leung SW, Tzschach A, Behjati F, Abedini SS, Mohseni M, et al. 2011. Mutation of the conserved polyadenosine RNA binding protein, ZC3H14/dNab2, impairs neural function in Drosophila and humans. Proc Natl Acad Sci USA 108:12390-12395.
38. Philips AK, Siren A, Avela K, Somer M, Peippo M, Ahvenainen M, Doagu F, Arvio M, Kaariainen H, Van Esch H, Froyen G, Haas SA, Hu H, Kalscheuer VM, Jarvela I. 2014. X-exome sequencing in Finnish families with intellectual disability-four novel mutations and two novel syndromic phenotypes. Orphanet J Rare Dis 9:49.
39. Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. 2010. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res 20:110-121.
40. Puttmann L, Stehr H, Garshasbi M, Hu H, Kahrizi K, Lipkowitz B, Jamali P, Tzschach A, Najmabadi H, Ropers HH, Musante L, Kuss AW. 2013. A novel ALDH5A1 mutation is associated with succinic semialdehyde dehydrogenase deficiency and severe intellectual disability in an Iranian family. Am J Med Genet A 161A:1915-1922.
41. Rafiq MA, Kuss AW, Puettmann L, Noor A, Ramiah A, Ali G, Hu H, Kerio NA, Xiang Y, Garshasbi M, Khan MA, Ishak GE, et al. 2011. Mutations in the alpha 1, 2-mannosidase gene, MAN1B1, cause autosomal-recessive intellectual disability. Am J Hum Genet 89:176-182.
42. Rauch A, Wieczorek D, Graf E, Wieland T, Endele S, Schwarzmayr T, Albrecht B, Bartholdi D, Beygo J, Di Donato N, Dufke A, Cremer K, et al. 2012. Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet 380:1674-1682.
43. Ropers F, Derivery E, Hu H, Garshasbi M, Karbasiyan M, Herold M, Nurnberg G, Ullmann R, Gautreau A, Sperling K, Varon R, Rajab A. 2011. Identification of a novel candidate gene for non-syndromic autosomal recessive intellectual disability: the WASH complex member SWIP. Hum Mol Genet 20:2585-3590.
44. Ropers HH. 2010. Genetics of early onset cognitive impairment. Annu Rev Genomics Hum Genet 11:161-187.
45. Schraders M, Haas SA, Weegerink NJ, Oostrik J, Hu H, Hoefsloot LH, Kannan S, Huygen PL, Pennings RJ, Admiraal RJ, Kalscheuer VM, Kunst HP, Kremer H. 2011. Next-generation sequencing identifies mutations of SMPX, which encodes the small muscle protein, X-linked, as a cause of progressive hearing impairment. Am J Hum Genet 88:628-634.
46. Schwarz JM, Rodelsperger C, Schuelke M, Seelow D. 2010. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods 7:575-576.
47. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. 2001. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29:308-311.
48. Sifrim A, Popovic D, Tranchevent LC, Ardeshirdavani A, Sakai R, Konings P, Vermeesch JR, Aerts J, De Moor B, Moreau Y. 2013. eXtasy: variant prioritization by genomic data fusion. Nat Methods 10:1083-1084.
49. Strobl-Wildemann G, Kalscheuer VM, Hu H, Wrogemann K, Ropers HH, Tzschach A. 2011. Novel GDI1 mutation in a large family with nonsyndromic X-linked intellectual disability. Am J Med Genet A 155A:3067-3070.
50. Vissers LE, de Ligt J, Gilissen C, Janssen I, Steehouwer M, de Vries P, van Lier B, Arts P, Wieskamp N, del Rosario M, van Bon BW, Hoischen A, de Vries BB, Brunner HG, Veltman JA. 2010. A de novo paradigm for mental retardation. Nat Genet 42:1109-1112.
51. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. 2009. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25:2865-2871.
52. Yu TW, Chahrour MH, Coulter ME, Jiralerspong S, Okamura-Ikeda K, Ataman B, Schmitz-Abe K, Harmin DA, Adli M, Malik AN, D'Gama AM, Lim ET, et al. 2013. Using whole-exome sequencing to identify inherited causes of autism. Neuron 77:259-273.
53. Zanni G, Cali T, Kalscheuer VM, Ottolini D, Barresi S, Lebrun N, Montecchi-Palazzi L, Hu H, Chelly J, Bertini E, Brini M, Carafoli E. 2012. Mutation of plasma membrane Ca2 +ATPase isoform 3 in a family with X-linked congenital cerebellar ataxia impairs Ca2 +homeostasis. Proc Natl Acad Sci USA 109:14514-14519.