Clinical exome sequencing-Mistakes and caveats.
NGS data analysis
clinical exome
clinical variant interpretation
genetic diagnostics
next generation sequencing
whole exome sequencing
Journal
Human mutation
ISSN: 1098-1004
Titre abrégé: Hum Mutat
Pays: United States
ID NLM: 9215429
Informations de publication
Date de publication:
08 2022
08 2022
Historique:
revised:
11
01
2022
received:
10
07
2021
accepted:
18
02
2022
pubmed:
23
2
2022
medline:
20
7
2022
entrez:
22
2
2022
Statut:
ppublish
Résumé
Massive parallel sequencing technology has become the predominant technique for genetic diagnostics and research. Many genetic laboratories have wrestled with the challenges of setting up genetic testing workflows based on a completely new technology. The learning curve we went through as a laboratory was accompanied by growing pains while we gained new knowledge and expertise. Here we discuss some important mistakes that have been made in our laboratory through 10 years of clinical exome sequencing but that have given us important new insights on how to adapt our working methods. We provide these examples and the lessons that we learned to help other laboratories avoid to make the same mistakes.
Identifiants
pubmed: 35191116
doi: 10.1002/humu.24360
pmc: PMC9541396
doi:
Types de publication
Journal Article
Review
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1041-1055Informations de copyright
© 2022 The Authors. Human Mutation published by Wiley Periodicals LLC.
Références
Am J Med Genet A. 2018 Apr;176(4):862-876
pubmed: 29460469
J Mol Diagn. 2019 May;21(3):369-374
pubmed: 30605766
Bioinformatics. 2011 Oct 1;27(19):2648-54
pubmed: 21828086
Sci Rep. 2021 Feb 22;11(1):4325
pubmed: 33619287
Cell. 2010 Jun 25;141(7):1171-82
pubmed: 20602999
Neurology. 2012 Aug 21;79(8):777-84
pubmed: 22875091
Genomics. 2016 Jan;107(1):1-8
pubmed: 26554401
Am J Hum Genet. 2012 Oct 5;91(4):597-607
pubmed: 23040492
Hereditas. 2021 Feb 17;158(1):10
pubmed: 33597004
Am J Hum Genet. 2019 Nov 7;105(5):921-932
pubmed: 31607426
BMC Genomics. 2012 May 20;13:194
pubmed: 22607156
Eur J Pediatr. 2001 Aug;160(8):464-7
pubmed: 11548182
Genet Med. 2017 Oct;19(10):1151-1158
pubmed: 28518168
Hum Genet. 2013 Oct;132(10):1077-130
pubmed: 23820649
Genet Med. 2021 Oct;23(10):1818-1829
pubmed: 34131312
Nucleic Acids Res. 2015 Sep 3;43(15):7217-28
pubmed: 26130710
Comput Struct Biotechnol J. 2019 Nov 17;18:9-19
pubmed: 31890139
Bioinformatics. 2012 Nov 1;28(21):2747-54
pubmed: 22942019
Genome Res. 2017 Nov;27(11):1895-1903
pubmed: 28887402
Hum Mutat. 2015 Aug;36(8):815-22
pubmed: 25973577
Genet Med. 2020 Jul;22(7):1269-1275
pubmed: 32366967
Sci Rep. 2020 Feb 24;10(1):3235
pubmed: 32094380
Ann Hum Genet. 2020 May;84(3):214-220
pubmed: 32232836
Hum Mutat. 2022 Aug;43(8):1041-1055
pubmed: 35191116
Brief Bioinform. 2014 Nov;15(6):879-89
pubmed: 24067931
BMC Genomics. 2012 Nov 24;13:666
pubmed: 23176052
Genet Med. 2020 Jul;22(7):1235-1246
pubmed: 32307445
Am J Hum Genet. 2019 May 2;104(5):925-935
pubmed: 30982609
Nature. 2020 May;581(7809):434-443
pubmed: 32461654
Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63
pubmed: 24259432
N Engl J Med. 2015 Jun 4;372(23):2235-42
pubmed: 26014595
Bioinformatics. 2012 Oct 15;28(20):2678-9
pubmed: 22914218
Genet Med. 2017 Nov;19(11):1285-1286
pubmed: 28640240
Hum Genet. 2016 Jun;135(6):603-14
pubmed: 27075447
Blood. 2018 Feb 1;131(5):496-504
pubmed: 29141946
Am J Hum Genet. 2017 Jul 6;101(1):50-64
pubmed: 28669404
Am J Hum Genet. 2021 Jun 3;108(6):1053-1068
pubmed: 33909990
Brain. 2017 Jun 1;140(6):1561-1578
pubmed: 28459997
Genet Med. 2016 Dec;18(12):1282-1289
pubmed: 27228465
Genet Med. 2021 Aug;23(8):1569-1573
pubmed: 33846582
Biochem J. 1992 Jul 1;285 ( Pt 1):65-9
pubmed: 1379041
Eur J Hum Genet. 2012 May;20(5):490-7
pubmed: 22258526
Genet Med. 2020 May;22(5):974-978
pubmed: 31965078
Eur J Hum Genet. 2019 Jan;27(1):1-16
pubmed: 30275486
J Mol Diagn. 2018 Jan;20(1):4-27
pubmed: 29154853
BMC Genomics. 2021 Jan 19;22(1):62
pubmed: 33468057
Genome Biol. 2014 Mar 25;15(3):R53
pubmed: 24667040
BMC Genomics. 2015;16 Suppl 8:S2
pubmed: 26110515
NPJ Genom Med. 2020 Sep 10;5(1):37
pubmed: 32963807
Clin Genet. 2012 Jan;81(1):82-7
pubmed: 21175598
N Engl J Med. 2019 Jun 20;380(25):2478-2480
pubmed: 31216405
Nat Rev Genet. 2019 Apr;20(4):235-248
pubmed: 30647469
Eur J Hum Genet. 2016 Oct;24(10):1515
pubmed: 27628564
Bioinformatics. 2014 Oct 15;30(20):2852-9
pubmed: 24966365
PLoS One. 2013 Aug 05;8(8):e70151
pubmed: 23940540
Sci Rep. 2020 Feb 6;10(1):2057
pubmed: 32029882
Genet Med. 2015 May;17(5):405-24
pubmed: 25741868
Hum Mutat. 2017 May;38(5):517-523
pubmed: 28229513
Nat Genet. 2012 Feb 26;44(4):435-9, S1-2
pubmed: 22366785
PLoS One. 2018 Dec 17;13(12):e0209185
pubmed: 30557390
Genome Res. 2012 Aug;22(8):1525-32
pubmed: 22585873
Eur J Hum Genet. 2004 Sep;12(9):744-51
pubmed: 15266303
Genome Res. 2012 Sep;22(9):1760-74
pubmed: 22955987
J Mol Diagn. 2014 Nov;16(6):639-47
pubmed: 25157971
Neurobiol Dis. 2008 Oct;32(1):10-5
pubmed: 18606230
Genet Med. 2021 Aug;23(8):1391-1398
pubmed: 34012069
Nat Biotechnol. 2011 Jan;29(1):24-6
pubmed: 21221095
Nat Biotechnol. 2019 May;37(5):561-566
pubmed: 30936564
Eur J Hum Genet. 2021 Sep;29(9):1325-1331
pubmed: 34075208
Eur J Hum Genet. 2014 Feb;22(2):160-70
pubmed: 23942201
NPJ Genom Med. 2020 Oct 23;5:47
pubmed: 33110627
Mol Genet Metab Rep. 2019 Mar 01;19:100464
pubmed: 30891420
Nature. 2014 Apr 24;508(7497):469-76
pubmed: 24759409
Genet Med. 2017 Jun;19(6):667-675
pubmed: 28574513
Arch Pathol Lab Med. 2017 Jun;141(6):787-797
pubmed: 28322587
Genet Med. 2020 Apr;22(4):803-808
pubmed: 31767986
Genet Med. 2021 Nov;23(11):2229
pubmed: 33941885
J Mol Diagn. 2016 May;18(3):446-453
pubmed: 26944031
BMC Bioinformatics. 2019 Jun 17;20(1):342
pubmed: 31208315
Genome Med. 2016 Aug 08;8(1):82
pubmed: 27503473
Genet Med. 2018 Apr;20(4):403-410
pubmed: 28837158