Technological advances in DNA sequence enrichment and sequencing for germline genetic diagnosis

Expert Review of Molecular Diagnostics

Volumn 12, Issue 2, 2012, Pages 159-173

  Ku, Chee Seng ^a   Wu, Mengchu ^a   Cooper, David N ^b   Naidoo, Nasheen ^c   Pawitan, Yudi ^d   Pang, Brendan ^e   Iacopetta, Barry ^f   Soong, Richie ^a,e  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b CARDIFF UNIVERSITY   (United Kingdom)

^c NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^d KAROLINSKA INSTITUTE   (Sweden)

^e NATIONAL UNIVERSITY HEALTH SYSTEM   (Singapore)

^f UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

diagnostic; exome; Mendelian disorder; next generation sequencing; sequence enrichment

Indexed keywords

DEOXYRIBONUCLEOSIDE TRIPHOSPHATE; REPETITIVE DNA; SMALL UNTRANSLATED RNA; X LINKED INHIBITOR OF APOPTOSIS;

ADENOMATOUS POLYP; ALPORT SYNDROME; AMPLICON; BECKER MUSCULAR DYSTROPHY; CHEMICAL ANALYSIS; CILIARY DYSKINESIA; CONGENITAL DISORDER OF GLYCOSYLATION; DNA HYBRIDIZATION; DNA SEQUENCE; DNA TEMPLATE; DUCHENNE MUSCULAR DYSTROPHY; EXOME; GENE DELETION; GENE DUPLICATION; GENE LOCUS; GENETIC DISORDER; GENETIC PROCEDURES; GENETIC SCREENING; HEART ATRIUM SEPTUM DEFECT; HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS; HEREDITARY ATAXIA; HEREDITARY BREAST AND OVARIAN CANCER SYNDROME; HEREDITARY MOTOR SENSORY NEUROPATHY; HIGH THROUGHPUT SEQUENCING; HUMAN; MULTIPLEX POLYMERASE CHAIN REACTION; MUTATIONAL ANALYSIS; NUCLEIC ACID PROBE; ONCOGENE; PIERRE ROBIN SYNDROME; POINT MUTATION; POLYMERASE CHAIN REACTION; PROTEIN DEFICIENCY; RETINITIS PIGMENTOSA; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; SUPERIOR CAVA VEIN SYNDROME; WHOLE EXOME SEQUENCING; WHOLE GENOME SEQUENCING; X CHROMOSOME LINKED DISORDER;

EXOME; GERM-LINE MUTATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; MULTIPLEX POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 84857955703     PISSN: 14737159     EISSN: 17448352     Source Type: Journal    
DOI: 10.1586/erm.11.95     Document Type: Review

References (77)

1. Metzker ML. Sequencing technologies - the next generation. Nat. Rev. Genet. 11(1), 31-46 (2010).
2. Mardis ER. A decade's perspective on DNA sequencing technology. Nature 470(7333), 198-203 (2011).
3. Choi M, Scholl UI, Ji W et al. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc. Natl Acad. Sci. USA 106(45), 19096-19101 (2009).
4. Majewski J, Wang Z, Lopez I et al. A new ocular phenotype associated with an unexpected but known systemic disorder and mutation: novel use of genomic diagnostics and exome sequencing. J. Med. Genet. 48(9), 593-596 (2011).
5. Cullinane AR, Vilboux T, O'Brien K et al. Homozygosity mapping and whole-exome sequencing to detect SLC45A2 and G6PC3 mutations in a single patient with oculocutaneous albinism and neutropenia. J. Invest. Dermatol. 131(10), 2017-2025 (2011).
6. Clark MJ, Chen R, Lam HY et al. Performance comparison of exome DNA sequencing technologies. Nat. Biotechnol. 29, 908-914 (2011).
7. Ng SB, Turner EH, Robertson PD et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461(7261), 272-276 (2009).
8. Ng SB, Buckingham KJ, Lee C et al. Exome sequencing identifies the cause of a mendelian disorder. Nat. Genet. 42(1), 30-35 (2010).
9. Turner EH, Ng SB, Nickerson DA, Shendure J. Methods for genomic partitioning. Annu. Rev. Genomics Hum. Genet. 10, 263-284 (2009).
10. Mamanova L, Coffey AJ, Scott CE et al. Target-enrichment strategies for next-generation sequencing. Nat. Methods 7(2), 111-118 (2010).
11. Kuhlenbaumer G, Hullmann J, Appenzeller S. Novel genomic techniques open new avenues in the analysis of monogenic disorders. Hum. Mutat. 32(2), 144-151 (2011).
12. Berg JS, Evans JP, Leigh MW et al. Next generation massively parallel sequencing of targeted exomes to identify genetic mutations in primary ciliary dyskinesia: implications for application to clinical testing. Genet. Med. 13(3), 218-229 (2011).
13. Jones MA, Bhide S, Chin E et al. Targeted polymerase chain reaction-based enrichment and next generation sequencing for diagnostic testing of congenital disorders of glycosylation. Genet. Med. 13(11), 921-932 (2011).
14. Goossens D, Moens LN, Nelis E et al. Simultaneous mutation and copy number variation (CNV) detection by multiplex PCR-based GS-FLX sequencing. Hum. Mutat. 30(3), 472-476 (2009).
15. Jiang Q, Turner T, Sosa MX, Rakha A, Arnold S, Chakravarti A. Rapid and efficient human mutation detection using a bench-top next-generation DNA sequencer. Hum. Mutat. 33(1), 281-289 (2012).
16. Hoischen A, Gilissen C, Arts P et al. Massively parallel sequencing of ataxia genes after array-based enrichment. Hum. Mutat. 31(4), 494-499 (2010).
17. Shearer AE, DeLuca AP, Hildebrand MS et al. Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing. Proc. Natl Acad. Sci. USA 107(49), 21104-21109 (2010).
18. Hopp K, Heyer CM, Hommerding CJ et al. B9D1 is revealed as a novel Meckel syndrome (MKS) gene by targeted exon-enriched next-generation sequencing and deletion analysis. Hum. Mol. Genet. 20(13), 2524-2534 (2011).
19. Tewhey R, Warner JB, Nakano M et al. Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat. Biotechnol. 27(11), 1025-1031 (2009).
20. Walsh T, Lee MK, Casadei S et al. Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc. Natl Acad. Sci. USA 107(28), 12629-12633 (2010).
21. Jasperson KW, Tuohy TM, Neklason DW, Burt RW. Hereditary and familial colon cancer. Gastroenterology 138(6), 2044-2058 (2010).
22. Artuso R, Fallerini C, Dosa L et al. Advances in Alport syndrome diagnosis using next-generation sequencing. Eur. J. Hum. Genet. 20(1), 50-57 (2012).
23. Rothberg JM, Hinz W, Rearick TM et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475(7356), 348-352 (2011).
24. Montenegro G, Powell E, Huang J et al. Exome sequencing allows for rapid gene identification in a Charcot-Marie-Tooth family. Ann. Neurol. 69(3), 464-470 (2011).
25. Watkins D, Schwartzentruber JA, Ganesh J et al. Novel inborn error of folate metabolism: identification by exome capture and sequencing of mutations in the MTHFD1 gene in a single proband. J. Med. Genet. 48(9), 590-592 (2011).
26. 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. 13(3), 255-262 (2011).
27. Bonnefond A, Durand E, Sand O et al. Molecular diagnosis of neonatal diabetes mellitus using next-generation sequencing of the whole exome. PLoS One 5(10), e13630 (2010).
28. Schrader KA, Heravi-Moussavi A, Waters PJ et al. Using next-generation sequencing for the diagnosis of rare disorders: a family with retinitis pigmentosa and skeletal abnormalities. J. Pathol. 225(1), 12-18 (2011).
29. Al-Romaih KI, Genovese G, Al-Mojalli H et al. Genetic diagnosis in consanguineous families with kidney disease by homozygosity mapping coupled with whole-exome sequencing. Am. J. Kidney Dis. 58(2), 186-195 (2011).
30. Simpson DA, Clark GR, Alexander S, Silvestri G, Willoughby CE. Molecular diagnosis for heterogeneous genetic diseases with targeted high-throughput DNA sequencing applied to retinitis pigmentosa. J. Med. Genet. 48(3), 145-151 (2011).
31. 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(13), 1181-1191 (2010).
32. Rios J, Stein E, Shendure J, Hobbs HH, Cohen JC. Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia. Hum. Mol. Genet. 19(22), 4313-4318 (2010).
33. 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. 6(6), e1000991 (2010).
34. Ng SB, Nickerson DA, Bamshad MJ, Shendure J. Massively parallel sequencing and rare disease. Hum. Mol. Genet. 19(R2), R119-R124 (2010).
35. Ku CS, Naidoo N, Pawitan Y. Revisiting Mendelian disorders through exome sequencing. Hum. Genet. 129(4), 351-370 (2011).
36. Teer JK, Mullikin JC. Exome sequencing: the sweet spot before whole genomes. Hum. Mol. Genet. 19(R2), R145-R151 (2010).
37. Bick D, Dimmock D. Whole exome and whole genome sequencing. Curr. Opin. Pediatr. 23(6), 594-600 (2011).
38. Zuchner S, Dallman J, Wen R et al. Whole-exome sequencing links a variant in DHDDS to retinitis pigmentosa. Am. J. Hum. Genet. 88(2), 201-206 (2011).
39. Huentelman MJ. Targeted next-generation sequencing: microdroplet PCR approach for variant detection in research and clinical samples. Expert Rev. Mol. Diagn. 11(4), 347-349 (2011).
40. Okou DT, Steinberg KM, Middle C, Cutler DJ, Albert TJ, Zwick ME. Microarray-based genomic selection for high-throughput resequencing. Nat. Methods 4(11), 907-909 (2007). (Pubitemid 350042376)
41. Albert TJ, Molla MN, Muzny DM et al. Direct selection of human genomic loci by microarray hybridization. Nat. Methods 4(11), 903-905 (2007). (Pubitemid 350042375)
42. Gnirke A, Melnikov A, Maguire J et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27(2), 182-189 (2009).
43. Mertes F, Elsharawy A, Sauer S et al. Targeted enrichment of genomic DNA regions for next-generation sequencing. Brief Funct. Genomics 10(6), 374-386 (2011).
44. Parla JS, Iossifov I, Grabill I, Spector MS, Kramer M, McCombie WR. A comparative analysis of exome capture. Genome Biol. 12(9), R97 (2011).
45. Sulonen AM, Ellonen P, Almusa H et al. Comparison of solution-based exome capture methods for next generation sequencing. Genome Biol. 12(9), R94 (2011).
46. Mondal K, Shetty AC, Patel V, Cutler DJ, Zwick ME. Targeted sequencing of the human X chromosome exome. Genomics 98(4), 260-265 (2011).
47. Tarpey PS, Smith R, Pleasance E et al. A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation. Nat. Genet. 41(5), 535-543 (2009).
48. Johnston JJ, Teer JK, Cherukuri PF et al. Massively parallel sequencing of exons on the X chromosome identifies RBM10 as the gene that causes a syndromic form of cleft palate. Am. J. Hum. Genet. 86(5), 743-748 (2010).
49. Meder B, Haas J, Keller A et al. Targeted next-generation sequencing for the molecular genetic diagnostics of cardiomyopathies. Circ. Cardiovasc. Genet. 4(2), 110-122 (2011).
50. Shendure J, Ji H. Next-generation DNA sequencing. Nat. Biotechnol. 26(10), 1135-1145 (2008).
51. Droege M, Hill B. The genome sequencer FLX system - longer reads, more applications, straight forward bioinformatics and more complete data sets. J. Biotechnol. 136(1-2), 3-10 (2008).
52. Rothberg JM, Leamon JH. The development and impact of 454 sequencing. Nat. Biotechnol. 26(10), 1117-1124 (2008).
53. Bentley DR, Balasubramanian S, Swerdlow HP et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456(7218), 53-59 (2008).
54. Li Y, Wang J. Faster human genome sequencing. Nat. Biotechnol. 27(9), 820-821 (2009).
55. Lim BC, Lee S, Shin JY et al. Genetic diagnosis of Duchenne and Becker muscular dystrophy using next-generation sequencing technology: comprehensive mutational search in a single platform. J. Med. Genet. 48(11), 731-736 (2011).
56. Sathirapongsasuti JF, Lee H, Horst BA et al. Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics 27(19), 2648-2654 (2011).
57. Xie C, Tammi MT. CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 10, 80 (2009).
58. Medvedev P, Stanciu M, Brudno M. Computational methods for discovering structural variation with next-generation sequencing. Nat. Methods 6(Suppl. 11), S13-S20 (2009).
59. Medvedev P, Fiume M, Dzamba M, Smith T, Brudno M. Detecting copy number variation with mated short reads. Genome Res. 20(11), 1613-1622 (2010).
60. Meyerson M, Gabriel S, Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nat. Rev. Genet. 11(10), 685-696 (2010).
61. Robison K. Application of second-generation sequencing to cancer genomics. Brief Bioinform. 11(5), 524-534 (2010).
62. Ding L, Getz G, Wheeler DA et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 455(7216), 1069-1075 (2008).
63. Dalgliesh GL, Furge K, Greenman C et al. Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes. Nature 463(7279), 360-363 (2010).
64. Lee W, Jiang Z, Liu J et al. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 465(7297), 473-477 (2010).
65. 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. 13(6), 499-504 (2011).
66. Ingsmore SF, Saunders CJ. Deep sequencing of patient genomes for disease diagnosis: when will it become routine? Sci. Transl. Med. 3(87), 87ps23 (2011).
67. Sharp RR. Downsizing genomic medicine: approaching the ethical complexity of whole-genome sequencing by starting small. Genet. Med. 13(3), 191-194 (2011).
68. Mardis ER. The 1,000 genome, the 100,000 analysis? Genome Med. 2(11), 84 (2010).
69. Sboner A, Mu XJ, Greenbaum D, Auerbach RK, Gerstein MB. The real cost of sequencing: higher than you think! Genome Biol. 12(8), 125 (2011).
70. Manolio TA, Collins FS, Cox NJ et al. Finding the missing heritability of complex diseases. Nature 461(7265), 747-753 (2009).
71. Cooper DN, Chen JM, Ball EV et al. Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics. Hum. Mutat. 31(6), 631-655 (2010).
72. Genin E, Feingold J, Clerget-Darpoux F. Identifying modifier genes of monogenic disease: strategies and difficulties. Hum. Genet. 124(4), 357-368 (2008).
73. Bainbridge MN, Wang M, Wu Y et al. Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities. Genome Biol. 12(7), R68 (2011).
74. Coffey AJ, Kokocinski F, Calafato MS et al. The GENCODE exome: sequencing the complete human exome. Eur. J. Hum. Genet. 19(7), 827-831 (2011).
75. Drmanac R, Sparks AB, Callow MJ et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327(5961), 78-81 (2010).
76. Koboldt DC, Ding L, Mardis ER, Wilson RK. Challenges of sequencing human genomes. Brief Bioinform. 11(5), 484-498 (2010).
77. Haas J, Katus HA, Meder B. Next-generation sequencing entering the clinical arena. Mol. Cell Probes 25, 206-211 (2011).