Next generation sequencing for clinical diagnostics-principles and application to targeted resequencing for hypertrophic cardiomyopathy: a paper from the 2009 William Beaumont Hospital Symposium on Molecular Pathology.
During the past five years, new high-throughput DNA sequencing technologies have emerged; these technologies are collectively referred to as next generation sequencing (NGS). By virtue of sequencing clonally amplified DNA templates or single DNA molecules in a massively parallel fashion in a flow cell, NGS provides both qualitative and quantitative sequence data. This combination of information has made NGS the technology of choice for complex genetic analyses that were previously either technically infeasible or cost prohibitive. As a result, NGS has had a fundamental and broad impact on many facets of biomedical research. In contrast, the dissemination of NGS into the clinical diagnostic realm is in its early stages. Though NGS is powerful and can be envisioned to have multiple applications in clinical diagnostics, the technology is currently complex. Successful adoption of NGS into the clinical laboratory will require expertise in both molecular biology techniques and bioinformatics. The current report presents principles that underlie NGS including sequencing library preparation, sequencing chemistries, and an introduction to NGS data analysis. These concepts are subsequently further illustrated by showing representative results from a case study using NGS for targeted resequencing of genes implicated in hypertrophic cardiomyopathy.
Voelkerding
Karl V
KV
Department of Pathology, University of Utah, Salt Lake City, Utah, USA. voelkek@aruplab.com
Dames
Shale
S
Durtschi
Jacob D
JD
D002312:Cardiomyopathy, Hypertrophic / Q000175:diagnosis / Q000235:genetics*; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*
Nat Biotechnol. 2009 Nov;27(11):1013-23
19898456
Genome Res. 2007 Aug;17(8):1195-201
17600086
Nat Methods. 2008 Dec;5(12):1005-10
19034268
Nat Rev Genet. 2010 Jan;11(1):31-46
19997069
Genome Res. 2008 Oct;18(10):1638-42
18775913
Nature. 2009 Jan 22;457(7228):480-4
19043404
Nat Biotechnol. 2009 Nov;27(11):1025-31
19881494
Expert Rev Mol Diagn. 2009 Oct;9(7):659-66
19817551
PLoS One. 2008 Jun 25;3(6):e2527
18575584
Science. 2009 Jan 2;323(5910):133-8
19023044
Nat Methods. 2007 Nov;4(11):931-6
17934468
Genome Res. 2009 Sep;19(9):1527-41
19546169
Anal Bioanal Chem. 2009 Jan;393(1):171-5
18958448
Genome Res. 2009 Sep;19(9):1616-21
19638418
Nature. 2008 Apr 17;452(7189):872-6
18421352
Clin Chem. 2010 Mar;56(3):339-41
20040618
Nat Genet. 2007 Dec;39(12):1522-7
17982454
Genome Res. 2009 Oct;19(10):1843-8
19635845
Nat Methods. 2007 Nov;4(11):903-5
17934467
J Biomol Tech. 2010 Jul;21(2):73-80
20592870
Trends Genet. 2008 Mar;24(3):133-41
18262675
Nat Methods. 2007 Nov;4(11):907-9
17934469
Genomics. 2009 Dec;94(6):363-8
19720138
Nature. 2009 Oct 8;461(7265):814-8
19776739
Nucleosides Nucleotides Nucleic Acids. 2008 Sep;27(9):1072-83
18711669
J Am Coll Cardiol. 2009 Jul 14;54(3):201-11
19589432
Am J Hum Genet. 2009 Aug;85(2):142-54
19679224
J Dent Res. 2008 Nov;87(11):1016-20
18946007
Nat Rev Genet. 2009 Oct;10(10):669-80
19736561
Brief Bioinform. 2010 Mar;11(2):181-97
19864250
Annu Rev Genomics Hum Genet. 2008;9:387-402
18576944
J Clin Pathol. 2009 Mar;62(3):226-35
18930982
Nucleic Acids Res. 2005 Apr 28;33(8):e71
15860768
Trends Genet. 2008 May;24(5):231-7
18325624
Nature. 2008 Oct 23;455(7216):1069-75
18948947
Nat Biotechnol. 2008 Oct;26(10):1101-4
18846081
Clin Chem. 2008 Apr;54(4):682-7
18258667
Curr Opin Cardiol. 2005 May;20(3):175-81
15861004
Clin Biochem. 2009 Jun;42(9):755-65
19318019
Hum Mutat. 2008 Jun;29(6):879-85
18409188
Nat Methods. 2008 Oct;5(10):887-93
18794863
Clin Chem. 2009 Apr;55(4):641-58
19246620
Nat Genet. 2009 May;41(5):535-43
19377476
Proc Natl Acad Sci U S A. 2007 May 29;104(22):9387-92
17517648
J Am Coll Cardiol. 2007 Aug 21;50(8):727-37
17707176
Genome Res. 2009 Sep;19(9):1606-15
19525355
PLoS One. 2007 Feb 14;2(2):e197
17299583
Nat Biotechnol. 2009 Feb;27(2):182-9
19182786
Expert Rev Mol Diagn. 2004 Jan;4(1):99-113
14711353
Nat Rev Genet. 2009 Jan;10(1):57-63
19015660
Nat Methods. 2009 Nov;6(11 Suppl):S6-S12
19844229
Genome Biol. 2009;10(3):R32
19327155
Hum Genet. 2008 Sep;124(2):161-70
18704501
Nature. 2005 Sep 15;437(7057):376-80
16056220
Nature. 2008 Nov 6;456(7218):53-9
18987734
Genome Med. 2009 Oct 23;1(10):100
19852779
Hum Mutat. 2009 Mar;30(3):363-70
19035361
Science. 2008 Apr 4;320(5872):106-9
18388294
Nat Biotechnol. 2009 Nov;27(11):998-9
19898452
Proc Natl Acad Sci U S A. 2008 Jan 29;105(4):1176-81
18216253
Genome Res. 2009 Jun;19(6):1124-32
19420381
JAMA. 2009 Dec 9;302(22):2471-6
19996403
Nat Methods. 2010 Jan;7(1):47-9
19946276
Circ Cardiovasc Genet. 2009 Oct;2(5):436-41
20031618
Nat Methods. 2010 Feb;7(2):111-8
20111037