Whole exome and whole genome sequencing

Current Opinion in Pediatrics

Volumn 23, Issue 6, 2011, Pages 594-600

  Bick, David ^a   Dimmock, David ^a  

^a MEDICAL COLLEGE OF WISCONSIN   (United States)

Author keywords

DNA; exome; genome; next generation; sequencing

Indexed keywords

CANCER CHEMOTHERAPY; CANCER GENETICS; DIAGNOSTIC PROCEDURE; DNA SEQUENCE; EXOME; GENE MUTATION; GENETIC COUNSELING; GENETIC DISORDER; GENETIC VARIABILITY; HEALTH CARE COST; HUMAN; HUMAN GENOME; MEDICAL INSTRUMENTATION; NEXT GENERATION SEQUENCING; PRIORITY JOURNAL; REVIEW;

EXOME; GENOME, HUMAN; GENOMICS; HUMANS; SEQUENCE ANALYSIS, DNA;

EID: 80955144198     PISSN: 10408703     EISSN: 1531698X     Source Type: Journal    
DOI: 10.1097/MOP.0b013e32834b20ec     Document Type: Review

References (78)

1. von Bubnoff A. Next-generation sequencing: the race is on. Cell 2008; 132:721-723.
2. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci 1977; 74:5463-5467.
3. Maxam AM, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci USA 1977; 74:560-564. (Pubitemid 8038842)
4. Illumina Individual Genome Sequencing. http://www.everygenome.com/?utm- campaign=consumer-genetics-conference-pr&utm-medium=pr&utm-sour ce=various&utm-content=everygenome.com/cgcA. [Accessed 26 July 2011]
5. Teer JK, Mullikin JC. Exome sequencing: the sweet spot before whole genomes. Hum Mol Genet 2010; 19 (R2):R145-R151.
6. Zhang J, Chiodini R, Badr A, Zhang G. The impact of next-generation sequencing on genomics. J Genet Genomics 2011; 38:95-109.
7. Bao S, Jiang R, Kwan W, et al. Evaluation of next-generation sequencing software in mapping and assembly. J Hum Genet 2011; 56:406-414.
8. Moore B, Hu H, Singleton M, et al. Global analysis of disease-related DNA sequence variation in 10 healthy individuals: implications for whole genome-based clinical diagnostics. Genet Med 2011; 13:210-217.
9. NCBI Human Genome Resources. http://www.ncbi.nlm.nih.gov/genome/guide/ human/. [Accessed 26 July 2011]
10. Richards CS, Bale S, Bellissimo DB, et al. ACMG recommendations for standards for interpretation and reporting of sequence variations: revisions 2007; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee. Genet Med 2008; 10:294-300. (Pubitemid 351544132)
11. Galperin MY, Cochrane GR. The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. Nucleic Acids Res 2011; 39(Database issue): D1-6.
12. Worthey EA, Mayer AN, Syverson GD, et al. Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet Med 2011; 13:255-262.
13. Altshuler D, Durbin RM, Abecasis GR, et al. A map of human genome variation from population-scale sequencing. 1000 Genomes Project Consortium. Nature 2010; 467:1061-1073.
14. Human genome: genomes by the thousand. Nature 2010; 467:1026-1027.
15. Online Mendelian Inheritance in Man, OMIM. McKusick-Nathans Institute of Genetic Medicine. Johns Hopkins University (Baltimore, MD). http://www.ncbi.nlm. nih.gov.proxy.lib.mcw.edu/omim. [Accessed 26 July 2011]
16. Bolze A, Byun M, McDonald D, et al. Whole-exome-sequencing-based discovery of human FADD deficiency. Am J Hum Genet 2010; 87:873-881.
17. Byun M, Abhyankar A, Lelarge V, et al. Whole-exome sequencing-based discovery of STIM1 deficiency in a child with fatal classic Kaposi sarcoma. J Exp Med 2010; 207:2307-2312.
18. Çalskan M, Chong JX, Uricchio L, et al. Exome sequencing reveals a novel mutation for autosomal recessive nonsyndromic mental retardation in the TECR gene on chromosome 19p13. Hum Mol Genet 2011; 20:1285-1289.
19. Abou Jamra R, Philippe O, Raas-Rothschild A, et al. Adaptor protein complex 4 deficiency causes severe autosomal-recessive intellectual disability, progressive spastic paraplegia, shy character, and short stature. Am J Hum Genet 2011; 88:788-795.
20. Shoubridge C, Tarpey PS, Abidi F, et al. Mutations in the guanine nucleotide exchange factor gene IQSEC2 cause nonsyndromic intellectual disability. Nat Genet 2010; 42:486-488.
21. Link DC, Schuettpelz LG, Shen D, et al. Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML. JAMA 2011; 305:1568-1576.
22. O'Roak BJ, Deriziotis P, Lee C, et al. Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat Genet 2011; 43:585-589.
23. Otto EA, Hurd TW, Airik R, et al. Candidate exome capture identifies mutation of SDCCAG8 as the cause of a retinal-renal ciliopathy. Nat Genet 2010; 42:840-850.
24. Barak T, Kwan KY, Louvi A, et al. Recessive LAMC3 mutations cause malformations of occipital cortical development. Nat Genet 2011; 43:590-594.
25. Walsh T, Shahin H, Elkan-Miller T, et al. Whole exome sequencing and homozygosity mapping identify mutation in the cell polarity protein GPSM2 as the cause of nonsyndromic hearing loss DFNB82. Am J Hum Genet 2010; 87:90-94.
26. Becker J, Semler O, Gilissen C, et al. Exome sequencing identifies truncating mutations in human SERPINF1 in autosomal-recessive osteogenesis imper-fecta. Am J Hum Genet 2011; 88:362-371.
27. O'Sullivan J, Bitu CC, Daly SB, et al. Whole-Exome sequencing identifies FAM20A mutations as a cause of amelogenesis imperfecta and gingival hyperplasia syndrome. Am J Hum Genet 2011; 88:616-620.
28. Züchner S, Dallman J, Wen R, et al. Whole-exome sequencing links a variant in DHDDS to retinitis pigmentosa. Am J Hum Genet 2011; 88:201-206.
29. Lupski JR, Reid JG, Gonzaga-Jauregui C, et al. Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N Engl J Med 2010; 362:1181-1191.
30. Wang JL, Yang X, Xia K, et al. TGM6 identified as a novel causative gene of spinocerebellar ataxias using exome sequencing. Brain 2010; 133:3510-3518.
31. Gilissen C, Arts HH, Hoischen A, et al. Exome sequencing identifies WDR35 variants involved in Sensenbrenner syndrome. Am J Hum Genet 2010; 87:418-423.
32. Bilgüvar K, Oztürk AK, Louvi A, et al. Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations. Nature 2010; 467:207-210.
33. Haack TB, Danhauser K, Haberberger B, et al. Exome sequencing identifies ACAD9 mutations as a cause of complex I deficiency. Nat Genet 2010; 42:1131-1134.
34. Musunuru K, Pirruccello JP, Do R, et al. Exome sequencing, ANGPTL3 mutations, and familial combined hypolipidemia. N Engl J Med 2010; 363:2220-2227.
35. Ng SB, Buckingham KJ, Lee C, et al. Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 2010; 42:30-35.
36. Ng SB, Bigham AW, Buckingham KJ, et al. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet 2010; 42:790-793.
37. Pierce SB, Walsh T, Chisholm KM, et al. Mutations in the DBP-deficiency protein HSD17B4 cause ovarian dysgenesis, hearing loss, and ataxia of Perrault Syndrome. Am J Hum Genet 2010; 87:282-288.
38. Sirmaci A, Walsh T, Akay H, et al. MASP1 mutations in patients with facial, umbilical, coccygeal, and auditory findings of Carnevale, Malpuech, OSA, and Michels syndromes. Am J Hum Genet 2010; 87:679-686.
39. Kalay E, Yigit G, Aslan Y, et al. CEP152 is a genome maintenance protein disrupted in Seckel syndrome. Nat Genet 2011; 43:23-26.
40. Krawitz PM, Schweiger MR, Rö delsperger C, et al. Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphos-phatasia mental retardation syndrome. Nat Genet 2010; 42:827-829.
41. Puente XS, Quesada V, Osorio FG, et al. Exome sequencing and functional analysis identifies BANF1 mutation as the cause of a hereditary progeroid syndrome. Am J Hum Genet 2011; 88:650-656.
42. Simpson MA, Irving MD, Asilmaz E, et al. Mutations in NOTCH2 cause Hajdu-Cheney syndrome, a disorder of severe and progressive bone loss. Nat Genet 2011; 43:303-305.
43. Sun Y, Almomani R, Aten E, et al. Terminal osseous dysplasia is caused by a single recurrent mutation in the FLNA gene. Am J Hum Genet 2010; 87:146-153.
44. Yariz KO, Walsh T, Uzak A, et al. Inherited mutation of the luteinizing hormone/choriogonadotropin receptor (LHCGR) in empty follicle syndrome. Fertil Steril 2011; 96:e125-e130.
45. Sobreira NL, Cirulli ET, Avramopoulos D, et al. Whole-genome sequencing of a single proband together with linkage analysis identifies a Mendelian disease gene. PLoS Genet 2010; 6:e1000991.
46. Holm H, Gudbjartsson DF, Sulem P, et al.Arare variant in MYH6 is associated with high risk of sick sinus syndrome. Nat Genet 2011; 43:316-320.
47. Rios J, Stein E, Shendure J, et al. Identification by whole-genome resequen-cing of gene defect responsible for severe hypercholesterolemia. Hum Mol Genet 2010; 19:4313-4318.
48. Rios J, Stein E, Shendure J, et al. Exome sequencing reveals VCP mutations as a cause of familial ALS. Neuron 2010; 68:857-864.
49. Talkowski ME, Ernst C, Heilbut A, et al. Next-generation sequencing strategies enable routine detection of balanced chromosome rearrangements for clinical diagnostics and genetic research. Am J Hum Genet 2011; 88:469-481.
50. Meyerson M, Gabriel S, Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 2010; 11:685-696.
51. International Cancer Genome Consortium. http://www.icgc.org/content/icgc- home. [Accessed 26 July 2011]
52. Puente XS, Pinyol M, Quesada V, et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 2011; 475:101-105.
53. Yan XJ, Xu J, Gu ZH, et al. Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia. Nat Genet 2011; 43:309-315.
54. Welch JS, Westervelt P, Ding L, et al. Use of whole-genome sequencing to diagnose a cryptic fusion oncogene. JAMA 2011; 305:1577-1584.
55. Jones SJ, Laskin J, Li YY, et al. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol 2010; 11:R82.
56. Hegde M. Personal communication. http://genetics.emory.edu/egl/tests/? testid=1001. [Accessed 26 July 2011]
57. Funke B. Personal communication. http://pcpgm.partners.org/lmm. [Accessed 26 July 2011]
58. Kaski JP, Syrris P, Esteban MT, et al. Prevalence of sarcomere protein gene mutations in preadolescent children with hypertrophic cardiomyopathy. Circ Cardiovasc Genet 2009; 2:436-441.
59. Goh V, Helbling D, Biank V, et al. Next generation sequencing facilitates the diagnosis in a child with twinkle mutations causing cholestatic liver failure. J Pediatr Gastroenterol Nutr 2011. [Epub ahead of print]
60. Berg JS, Khoury MJ, Evans JP. Deploying whole genome sequencing in clinical practice and public health: meeting the challenge one bin at a time. Genet Med 2011; 13:499-504.
61. Miller DT, Adam MP, Aradhya S, et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet 2010; 86:749-764.
62. Kyoto Encyclopedia of Genes and Genomes. http://www.genome.jp/kegg/kegg1. html. [Accessed 26 July 2011]
63. Prevention Genetics. http://www.preventiongenetics.com/ClinicalTesting/ ClinicalPriceListByDisease.pdf. [Accessed 26 July 2011]
64. Bell CJ, Dinwiddie DL, Miller NA, et al. Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med 2011; 3:65-4.
65. Kudtarkar P, Deluca TF, Fusaro VA, et al. Cost-effective cloud computing: a case study using the comparative genomics tool, roundup. Evol Bioinform Online 2010; 6:197-203.
66. Stein LD. The case for cloud computing in genome informatics. Genome Biol 2010; 11:207.
67. Neill NJ, Torchia BS, Bejjani BA, et al. Comparative analysis of copy number detection by whole-genome BAC and oligonucleotide array CGH. Mol Cytogenet 2010; 3:11.
68. Bunnik EM, Schermer MH, Janssens AC. Personal genome testing: Test characteristics to clarify the discourse on ethical, legal and societal issues. BMC Med Ethics 2011; 12:11.
69. Gargis AS, Kalman L, Berry M, et al. Next generation sequencing: approaches to quality assurance and complying with regulatory and professional standards (in press).
70. Nothnagel M, Herrmann A, Wolf A, et al. Technology-specific error signatures in the 1000 Genomes Project data. Hum Genet 2011. [Epub ahead of print]
71. Nakamura K, Oshima T, Morimoto T, et al. Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res 2011; 39:e90.
72. Cook-Deegan R, Heaney C. Patents in genomics and human genetics. Annu Rev Genomics Hum Genet 2010; 11:383-425.
73. Feng H, Shuda M, Chang Y, Moore PS. Merkel cell polyomavirus in a rare human skin cancer. Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 2008; 319:1096-1100. (Pubitemid 351300792)
74. Arumugam M, Raes J, Pelletier E, et al. Enterotypes of the human gut microbiome. Nature 2011; 473:174-180.
75. Kelsey G. Epigenetics and the brain: transcriptome sequencing reveals new depths to genomic imprinting. Bioessays 2011; 33:362-367.
76. Ashley EA, Butte AJ, Wheeler MT, et al. Clinical assessment incorporating a personal genome. Lancet 2010; 375:1525-1535.
77. Matthews LJ, Butler PM. Novelty-seeking: DRD4 polymorphisms are associated with human migration distance out-of-Africa after controlling for neutral population gene structure. Am J Phys Anthropol 2011; 145:382-389.
78. http://www.youtube.com/watch?v¼a9HM-iu92Ac. [Accessed 26 July 2011]