The impact of next generation sequencing technologies on haematological research - A review

Pathogenesis

Volumn 2, Issue 1-2, 2015, Pages 9-16

  Black, Jessica S ^a   Salto Tellez, Manuel ^a,b   Mills, Ken I ^a   Catherwood, Mark A ^a,b  

^a QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

^b ROYAL GROUP OF HOSPITALS TRUST   (United Kingdom)

Author keywords

Diagnostics; Haematological malignancies; Next generation sequencing

Indexed keywords

DNA METHYLTRANSFERASE 3A; ISOCITRATE DEHYDROGENASE 1; NOTCH1 RECEPTOR; NUCLEOPHOSMIN; SMALL NUCLEAR RIBONUCLEOPROTEIN; STAT3 PROTEIN;

ACUTE MYELOBLASTIC LEUKEMIA; ARTICLE; CANCER RESEARCH; CHROMOSOME TRANSLOCATION; CHRONIC LYMPHATIC LEUKEMIA; CHRONIC MYELOID LEUKEMIA; CLINICAL TRIAL (TOPIC); COST EFFECTIVENESS ANALYSIS; CYTOGENETICS; DNA SEQUENCE; FLOW CYTOMETRY; GENE MUTATION; HAIRY CELL LEUKEMIA; HEMATOLOGIC MALIGNANCY; HEMATOLOGICAL PROCEDURE; HIGH THROUGHPUT SEQUENCING; HUMAN; IMMUNOCYTOCHEMISTRY; LARGE CELL LYMPHOMA; LARGE GRANULAR LYMPHOCYTE LEUKEMIA; MEDICAL TECHNOLOGY; MINIMAL RESIDUAL DISEASE; MOLECULAR PATHOLOGY; MUTATIONAL ANALYSIS; MYELODYSPLASTIC SYNDROME; NEXT GENERATION SEQUENCING; OVERALL SURVIVAL; PROGRESSION FREE SURVIVAL; RNA SPLICING; TREATMENT RESPONSE; VALIDATION STUDY;

EID: 84931566186     PISSN: None     EISSN: 22146636     Source Type: Journal    
DOI: 10.1016/j.pathog.2015.05.004     Document Type: Review

References (76)

1. International Human Genome Sequencing Consortium Finishing the euchromatic sequence of the human genome. Nature 2004, 431:931-945.
2. Stein D.S. Human Genome: end of the beginning. Nature 2004, 431:915-916.
3. Venter T.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., et al. The sequence of the human genome. Science 2001, 291(5507):1304-1351.
4. Collins F.S., Green E.D., Guttmacher A.E., Guyer M.S. A vision for the future of genomics research. Nature 2003, 422:835-847.
5. Sanger F., Nicklen S., Coulson A.R. DNA Sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 1977, 74(12):5463-5467.
6. Chaisson M., Pevzner P., Tang H. Fragment assembly with short reads. Bioinformatics 2004, 20(13):2067-2074.
7. Martinez D.A., Nelson M.A. The next generation becomes the now generations. PLoS Genet 2010, 6(4):e10000906.
8. Bains W., Smith G.C. A novel method for nucleic acid sequence determination. J Theor Biol 1988, 135(3):303-307.
9. Brenner S., Williams S.R., Vermaas E.H., Storck T., Moon K., McCollum C., et al. In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differently expressed cDNAs. Proc Natl Acad Sci 2000, 97:1665-1670.
10. Ronaghi M., Karamohamed S., Pettersson B., Uhlen M., Nyren P. Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem 1996, 242:84-89.
11. Liu L., Yinhu L., Siliang L., Hu N., He Y., Pong R., et al. Comparison of next-generation sequencing systems. J Biomedicine Biotechnol 2012, [Article ID 251364].
12. http://www.illumina.com/systems/miseq/performance:specifications.ilmn.
13. http://www.lifetechnologies.com/uk/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrentnext-generation-sequencing-run-sequence/ion-pgm-system-for-next-generation-sequencing.html.
14. Quail M.A., Smith M., Coupland P., Otto T.D., Harris S.R., Connor T.R., et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosystems and Illumina MiSeq Sequencers. BMC Genomics 2012, 13:341.
15. Loman N.J., Misra R.V., Dallman T.J., Constantinidou C., Gharbia S.E., Wain J., et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 2012, 30:434-439.
16. http://allseq.com/knowledgebank/sequencing-platforms/roche-454.
17. Braggio E., Egan J.B., Fonseca R., Stewart A.K. Lessons from next-generation sequencing analysis in haematological malignancies. Blood Cancer J 2013, 3:e127.
18. Kohlmann A., Grossmann V., Nadarahjah N., Haferlach T. Next generation sequencing - feasibility and practicality in hematology. BJH 2013, 160(6):736-753.
19. Metzker M.L. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11:31-46.
20. Cullum R., Alder O., Hoodless P.A. The next generation: using new sequencing technologies to analyse gene regulation. Respirology 2010, 16:210-222.
21. http://454.com/downloads/GSJuniorSystem_Brochure.pdf.
22. http://res.illumina.com/documents/systems/hiseq/datasheet_hiseq_systems.pdf.
23. http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf.
24. https://tools.lifetechnologies.com/content/sfs/brochures/PGM-Specification-Sheet.pdf.
25. Ley T.J., Ding L., Walter M.J., McLellan M.D., Lamprecht T., Larson D.E., et al. DNMT3A mutations in acute myeloid leukemia. N Eng J Med 2010, 363:2424-2433.
26. Ley T.J., Mardis E.R., Ding L., Fulton B., McLellan M.D., Chen K., et al. DNA sequencing of a cytogenetically normal acute myeloid leukemia genome. Nature 2008, 456:66-72.
27. The ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74.
28. Mamanova L., Coffey A.J., Scott C.E., Kozarewa I., Turner E.H., Kumar A., et al. Target-enrichment strategies for next-generation sequencing. Nat Methods 2010, 7:111-118.
29. Rowley J.D. A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinaerine fluorescence and Giemsa staining. Nature 1973, 243(5405):290-293.
30. Rowley J.D., Golomb H.M., Dougherty C. 15/17 translocation: a consistent chromosomal change in acute promyelocytic leukaemia. Lancet 1977, 309(8010):549-550.
31. Rudkin G.T., Hungerford D.A., Nowell P.C. DNA contents of chromosome Ph1 and chromosome 21 in human chronic granulocytic leukemia. Science 1964, 144(3623):1229-1232.
32. Mardis E.R., Ding L., Dooling D.J., Larson D.E., McLellan M.D., Chen K., et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med 2009, 361:1058-1066.
33. Kang M.R., Kin M.S., Oh J.E., Kim Y.R., Song S.Y., Seo S.I., et al. Mutational analysis of IDH1 codon 132 in glioblastomas and other common cancers. Int J Cancer 2009, 125:353-355.
34. Zhao S., Lin Y., Xu W., Jiang W., Zha Z., Wang P., et al. Glioma-derived mutation in IDH1 domain inhibit IDH1 catalytic activity and in HIF-1alpha. Science 2009, 324:261-265.
35. Paschka P., Schlenk R.F., Gaidzik V.I., Habdank M., Kronke J., Bullinger L., et al. IDH1 and IDH2 mutations are frequent genetic alterations in acute myeloid leukemia and confer adverse prognosis in cytogenetically normal acute myeloid leukemia with NPM1 mutation without FLT3 internal tandem duplications. J Clin Oncol 2010, 28:3636-3643.
36. Welch J.S., Ley T.J., Link D.C., Millar C.A., Larson D.E., Koboldt D.C., et al. The origin and evolution of mutations in acute myeloid leukemia. Cell 2012, 150(2):264-278.
37. Ding L., Ley T.J., Larson D.E., Millar C.A., Koboldt D.C., Welch J.S., et al. Clonal evolution in relapsed acute myeloid leukemia revealed by whole genome sequencing. Nature 2012, 481:506-510.
38. Yoshida K., Sonada M., Shiraishi K., Nowak D., Nagata Y., Yamamoto R., et al. Frequent pathway mutations of splicing machinery in myelodysplasia. Nature 2011, 478:64-69.
39. Visconte V., Makishima H., Jankowska A., Szpurka H., Traina F., Jerez A., et al. SF3B1; a splicing factor is frequently mutated in refractory anaemia with ring sideroblasts. Leukemia 2012, 26:542-545.
40. Papaemmanuil E., Cazzola M., Boultwood J., Malcovatil L., Vyas P., Bowen D., et al. Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts. N Engl J Med 2011, 305:1384-1395.
41. Fabbri G., Rasi S., Rossi D., Trifonov V., Khiabanian H., Ma J., et al. Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation. JEM 2011, 208(7):1389-1401.
42. Sportoletti P., Baldoni S., Cavalli L., Del Papa B., Bonifacio E., Ciurnelli R., et al. NOTCH1 PEST domain mutation is adverse prognostic factor in B-CLL. Br J Haematol 2010, 151:404-406.
43. Puente X.S., Pinyol M., Quesada V., Conde L., Ordonez G.R., Villamor N., et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 2011, 475:101-105.
44. Ngo V.N., Young R.M., Schmitz R., Jhavar S., Xiao S., Lim K., et al. Oncogenically active MYD88 mutations in human lymphoma. Nature 2011, 470:115-119.
45. Quesada V., Conde L., Villamor N., Ordonez G.R., Jares P., Bassaganyas L., et al. Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nat Gen 2012, 44:47-52.
46. Quesada V., Ramsay A.J. Chronic lymphocytic leukemia with SF3B1 mutation. N Engl J Med 2012, 366:2530.
47. Wang L., Lawrence M.S., Wan Y., Stojanov P., Sougnez C., Stevenson K., et al. SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med 2011, 365:2497-2506.
48. Oscier D.G., Rose-Zerilli M.J.J., Winkelmann N., Je Castro G.D., Gomez B., Forster J., et al. The clinical significance of NOTCH1 and SF3B1 mutations in UK LRF CLL4 trial. Blood 2013, 121:468-475.
49. Gonzalez D., Martinez P., Wade R., Hockley S., Oscier D., Matutes E., et al. Mutational status of the TP53 gene as a predictor of response and survival in patients with chronic lymphocytic leukemia: results from the LRF CLL4 trial. J Clin Oncol 2011, 29(16):2223-2229.
50. Mullighan G.C., Phillips L.A., Su X., Ma J., Miller C.B., Shurtleff S.A., et al. Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia. Science 2008, 322(5906):1377-1380.
51. Zuna J., Ford A.M., Peham M., Patel N., Saha V., Eckert C., et al. TEL deletion analysis supports a novel view of relapse in childhood acute lymphoblastic leukemia. Clin Cancer Res 2004, 10:5355-5360.
52. Pasqualucci L., Trifonov V., Fabbri G., Ma J., Rossi D., Chiarenza A., et al. Analysis of the coding genome of diffuse large B-cell lymphoma. Nat Genet 2011, 43:830-837.
53. Krivtsov A.V., Armstran S.A. MLL translocations, histone modifications and leukaemia stem-cell development. Nat Rev Cancer 2007, 7:823-833.
54. Parsons D.W., Meng L., Zhang X., Jones S., Leary R.J., Lin J.C., et al. The genetic landscape of the childhood cancer medulloblastoma. Science 2011, 331:435-439.
55. Dalgliesh G.L., Furge K., Greenman C., Chen L., Bignell G., Butler A., et al. Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes. Nature 2010, 463:360-363.
56. Tiacci E., Trifonav V., Schiavoni G., Holmes A., Kern W., Martelli M.P., et al. BRAF mutations in hairy-cell leukemia. N Engl J Med 2011, 463:2305-2315.
57. Dietrich S., Glimm H., Andrulis M. BRAF inhibition in refractory hairy-cell leukemia. N Engl J Med 2012, 366:2038-2040.
58. Koskella H.L., Eldfors S., Ellonen P., van Adrichem A.J., Kuusanmaki H., Andersson E.I., et al. Somatic STAT3 mutations in large granular lymphocytic leukemia. N Engl J Med 2012, 366:1905-1913.
59. Morgan G.J., Pratt G. Modern molecular diagnostics and the management of haematological malignancies. Clin Lab Haem 1998, 20:135-141.
60. Godley L.A. Profiles in leukemia. N Engl J Med 2012, 366(12):1152-1153.
61. McCourt C.M., McArt D.G., Maxwell P., Catherwood M.A., Mills K.I., Waugh D.J., et al. Validation of next-generation sequencing technologies in comparison to current diagnostic gold standards for BRAF, EGFR and KRAS mutational analysis. PLoS One 2013, 8:e69604.
62. Voelkerding K., Dames S.A., Durtschi J.D. Next generation sequencing: from basic research to diagnostics. Clin Chem 2009, 55(4):641-658.
63. Patel J.P., Gonen M., Figueroa M.E., Fernandez H., Sun Z., Racevskis J., et al. Prognostic relevance of integrated genetic profiling in acute myeloid leukemia. N Engl J Med 2012, 366:1079-1089.
64. Grossman V., Kohlmann A., Klein H.U., Schindela S., Schnittger S., Dicker F., et al. Targeted next-generation sequencing detects point mutations, insertions, deletions and balanced chromosomal rearrangements as well as identifies novel leukemia-specific fusion genes in a single procedure. Leukemia 2011, 25:671-680.
65. Bouamar H., Abbas S., Lin A.P., Wang L., Jiang D., Holder K.N. A capture-sequencing strategy identifies IRF8, EBF1, APRIL as Nov IGH fusion partners in B-cell lymphoma 2013, 122:726-733.
66. Querings S., Altmuller J., Ansen S., Zander T., Seidel D., Gabler F., et al. Benchmarking of mutation diagnostics in clinical lung cancer specimens. PLoS One 2011, 6(5):e19601.
67. Jadersten M., Saft L., Smith A., Kulasekararaj A., Pomplun S., Gohring G., et al. TP53 mutations in low risk myleodysplastic syndromes with del(5g) predict disease progression. J Clin Oncol 2011, 29(15):1971-1979.
68. Kohlmann A., Grossman V., Haferlach T. Integration of next-generation sequencing into clinical practice: are we there yet?. Seminars Oncol 2012, 39(1):26-36.
69. Bosch J.R., Grody W.W. Keeping up with the next generation: massively parallel sequencing in clinical diagnostics. J Mol Diagnostics 2008, 10(6):484-492.
70. Onsong G., Erdmann J., Spears M.D., Chilton J., Beckman K.B., Hauge A., et al. Implementation of cloud based next generation sequencing data analysis in a clinical laboratory. BMC Res Notes 2012, 7:314.
71. Desai A.N., Jere A. Next-generation sequencing: ready for the clinics?. Clin Genet 2012, 81(6):503-510.
72. Lyon G.J., Jiang T., Van Wijk R., Wang W., Bodily P.M., Xing J., et al. Exome sequencing and unrelated findings in the context of complex disease research: ethical and clinical implications. Discov Med 2011, 12(62):41-55.
73. McGuire A.L., Lupski J.R. Personal genome research: what should the participants be told?. Trends Genet 2010, 26(5):199-201.
74. Salto-Tellez M., Gonzalez de Casto D. Next-generation sequencing: a change of paradigm in molecular diagnostic validation. J Pathology 2014, 234(1):5-10.
75. Schloss J.A. Hot to get genomes at one ten-thousandth the cost. Nat Biotech 2008, 26:1113-1115.
76. Briggs A.W., Good J.M., Green R.E., Krause J., Marieic T., Stenzel U., et al. Targeted Q4 retrieval and analysis of five Neanderthal mtDNA genomes. Science 2009, 325(5938):318-321.