Great expectations: using massively parallel sequencing to solve inherited disorders

References

• Metzker ML. Sequencing technologies – the next generation. Nat. Rev. Genet.11, 31–46 (2010).
   PubMed Web of Science ®Google Scholar
• Cooper DN, Chen J, Ball EV et al. Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics. Hum. Mutat.31, 631–655 (2010).
   PubMed Web of Science ®Google Scholar
• Choi M, Scholl UI, Ji W et al. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc. Natl Acad. Sci. USA106, 19096–19101 (2009).
   PubMed Web of Science ®Google Scholar
• Ng SB, Buckingham KJ, Lee C et al. Exome sequencing identifies the cause of a Mendelian disorder. Nat. Genet.42, 30–35 (2010).
   PubMed Web of Science ®Google Scholar
• Roach JC, Glusman G, Smit AFA et al. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science328, 636–639 (2010).
   PubMed Web of Science ®Google Scholar
• Herman DS, Hovingh GK, Iartchouk O et al. Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection. Nat. Methods6, 507–510 (2009).
   PubMedGoogle Scholar
• Iskow RC, McCabe MT, Mills RE et al. Natural mutagenesis of human genomes by endogenous retrotransposons. Cell141, 1253–1261 (2010).
   PubMed Web of Science ®Google Scholar
• Huang CRL, Schneider AM, Lu Y et al. Mobile interspersed repeats are major structural variants in the human genome. Cell141, 1171–1182 (2010).
   PubMedGoogle Scholar
• Alkan C, Kidd JM, Marques-Bonet T et al. Personalized copy number and segmental duplication maps using next-generation sequencing. Nat. Genet.41, 1061–1067 (2009).
   PubMed Web of Science ®Google Scholar
• Lupski JR, Reid JG, Gonzaga-Jauregui C et al. Whole-genome sequencing in a patient with Charcot–Marie–Tooth neuropathy. N. Engl. J. Med.362, 1181–1191 (2010).
   PubMed Web of Science ®Google Scholar
• Ng SB, Turner EH, Robertson PD et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature461, 272–276 (2009).
   PubMed Web of Science ®Google Scholar
• Schuster SC, Miller W, Ratan A et al. Complete Khoisan and Bantu genomes from southern Africa. Nature463, 943–947 (2010).
   PubMed Web of Science ®Google Scholar
• Bentley DR, Balasubramanian S, Swerdlow HP et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature456, 53–59 (2008).
   PubMed Web of Science ®Google Scholar
• Sobreira NLM, Cirulli ET, Avramopoulos D et al. Whole-genome sequencing of a single proband together with linkage analysis identifies a Mendelian disease gene. PLoS Genet.6, e1000991 (2010).
   PubMedGoogle Scholar
• Hoischen A, Gilissen C, Arts P et al. Massively parallel sequencing of ataxia genes after array-based enrichment. Hum. Mutat.31, 494–499 (2010).
   PubMed Web of Science ®Google Scholar
• Reversade B, Escande-Beillard N, Dimopoulou A et al. Mutations in PYCR1 cause cutis laxa with progeroid features. Nat. Genet.41, 1016–1021 (2009).
   PubMedGoogle Scholar
• Volpi L, Roversi G, Colombo EA et al. Targeted next-generation sequencing appoints C16orf57 as Clericuzio-type poikiloderma with neutropenia gene. Am. J. Hum. Genet.86, 72–76 (2010).
   PubMed Web of Science ®Google Scholar
• Corbett MA, Bahlo M, Jolly L et al. A focal epilepsy and intellectual disability syndrome is due to a mutation in TBC1D24. Am. J. Hum. Genet.87, 371–375 (2010).
   PubMedGoogle Scholar
• Albert TJ, Molla MN, Muzny DM et al. Direct selection of human genomic loci by microarray hybridization. Nat. Methods4, 903–905 (2007).
   PubMed Web of Science ®Google Scholar
• Gnirke A, Melnikov A, Maguire J et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol.27, 182–189 (2009).
   PubMed Web of Science ®Google Scholar
• Tewhey R, Warner JB, Nakano M et al. Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat. Biotechnol.27, 1025–1031 (2009).
   PubMed Web of Science ®Google Scholar
• Van Vlierberghe P, Palomero T, Khiabanian H et al.PHF6 mutations in T-cell acute lymphoblastic leukemia. Nat. Genet.42, 338–342 (2010).
   PubMed Web of Science ®Google Scholar
• Conrad DF, Bird C, Blackburne B et al. Mutation spectrum revealed by breakpoint sequencing of human germline CNVs. Nat. Genet.42, 385–391 (2010).
   PubMed Web of Science ®Google Scholar
• Heinzen EL, Radtke RA, Urban TJ et al. Rare deletions at 16p13.11 predispose to a diverse spectrum of sporadic epilepsy syndromes. Am. J. Hum. Genet.86, 707–718 (2010).
   PubMedGoogle Scholar
• Hodges E, Smith AD, Kendall J et al. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res.19, 1593–1605 (2009).
   PubMed Web of Science ®Google Scholar
• Mitchell AA, Zwick ME, Chakravarti A Cutler DJ. Discrepancies in dbSNP confirmation rates and allele frequency distributions from varying genotyping error rates and patterns. Bioinformatics20, 1022–1032 (2004).
   PubMedGoogle Scholar
• Musumeci L, Arthur JW, Cheung FSG et al. Single nucleotide differences (SNDs) in the dbSNP database may lead to errors in genotyping and haplotyping studies. Hum. Mutat.31, 67–73 (2010).
   PubMedGoogle Scholar
• Baranzini SE, Mudge J, Van Velkinburgh JC et al. Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature464, 1351–1356 (2010).
   PubMed Web of Science ®Google Scholar
• Tarpey P, Smith R, Pleasance E et al. A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation. Nat. Genet.41, 535–543 (2009).
   PubMed Web of Science ®Google Scholar
• Tucker T, Marra M, Friedman JM. Massively parallel sequencing: the next big thing in genetic medicine. Am. J. Hum. Genet.85, 142–154 (2009).
   PubMed Web of Science ®Google Scholar
• Ferrer-Costa C, Gelpi JL, Zamakola L et al. PMUT: a web-based tool for the annotation of pathological mutations on proteins. Bioinformatics21, 3176–3178 (2005).
   PubMed Web of Science ®Google Scholar
• Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc.4, 1073–1081 (2009).
   PubMed Web of Science ®Google Scholar
• Sunyaev S, Ramensky V, Koch I et al. Prediction of deleterious human alleles. Hum. Mol. Genet.10, 591–597 (2001).
   PubMed Web of Science ®Google Scholar