Long-read sequencing for molecular diagnostics in constitutional genetic disorders.
Oxford Nanopore
PacBio
constitutional disorders
long-read sequencing
molecular diagnostics
Journal
Human mutation
ISSN: 1098-1004
Titre abrégé: Hum Mutat
Pays: United States
ID NLM: 9215429
Informations de publication
Date de publication:
11 2022
11 2022
Historique:
revised:
03
09
2022
received:
23
06
2022
accepted:
06
09
2022
pubmed:
11
9
2022
medline:
14
10
2022
entrez:
10
9
2022
Statut:
ppublish
Résumé
Long-read sequencing (LRS) has been around for more than a decade, but widespread adoption of the technology has been slow due to the perceived high error rates and high sequencing cost. This is changing due to the recent advancements to produce highly accurate sequences and the reducing costs. LRS promises significant improvement over short read sequencing in four major areas: (1) better detection of structural variation (2) better resolution of highly repetitive or nonunique regions (3) accurate long-range haplotype phasing and (4) the detection of base modifications natively from the sequencing data. Several successful applications of LRS have demonstrated its ability to resolve molecular diagnoses where short-read sequencing fails to identify a cause. However, the argument for increased diagnostic yield from LRS remains to be validated. Larger cohort studies may be required to establish the realistic boundaries of LRS's clinical utility and analytical validity, as well as the development of standards for clinical applications. We discuss the limitations of the current standard of care, and contrast with the applications and advantages of two major LRS platforms, PacBio and Oxford Nanopore, for molecular diagnostics of constitutional disorders, and present a critical argument about the potential of LRS in diagnostic settings.
Identifiants
pubmed: 36086952
doi: 10.1002/humu.24465
pmc: PMC9561063
mid: NIHMS1835394
doi:
Types de publication
Journal Article
Review
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
1531-1544Subventions
Organisme : NHGRI NIH HHS
ID : R01 HG009708
Pays : United States
Informations de copyright
© 2022 Wiley Periodicals LLC.
Références
JAMA Pediatr. 2020 Sep 1;174(9):821-822
pubmed: 32597967
Mol Neurodegener. 2018 Aug 21;13(1):46
pubmed: 30126445
Nat Biotechnol. 2022 Jul;40(7):1035-1041
pubmed: 35347328
Genome Res. 2017 Nov;27(11):1895-1903
pubmed: 28887402
HGG Adv. 2021 Apr 8;2(2):
pubmed: 33937879
Genet Med. 2020 Mar;22(3):490-499
pubmed: 31607746
Nat Biotechnol. 2021 Nov;39(11):1348-1365
pubmed: 34750572
Am J Hum Genet. 2019 Apr 4;104(4):685-700
pubmed: 30929737
N Engl J Med. 2018 Oct 04;379(14):1353-1362
pubmed: 30281996
Genome Med. 2020 Jan 30;12(1):14
pubmed: 32000839
Genet Med. 2020 May;22(5):945-953
pubmed: 32066871
Genome Res. 2013 Jan;23(1):121-8
pubmed: 23064752
Genet Med. 2018 Dec;20(12):1600-1608
pubmed: 29595809
Genome Med. 2022 Apr 5;14(1):38
pubmed: 35379322
Mol Ther Methods Clin Dev. 2020 Sep 11;19:162-173
pubmed: 33209959
Cell. 2018 Feb 22;172(5):897-909.e21
pubmed: 29474918
Nucleic Acids Res. 2018 Mar 16;46(5):2159-2168
pubmed: 29401301
Genet Med. 2020 May;22(5):927-936
pubmed: 31911672
Pharmacogenomics J. 2021 Apr;21(2):251-261
pubmed: 33462347
Int J Mol Sci. 2020 Dec 01;21(23):
pubmed: 33271988
Nat Rev Genet. 2001 Oct;2(10):791-800
pubmed: 11584295
Genome Biol. 2020 Feb 7;21(1):30
pubmed: 32033565
Nat Methods. 2021 Nov;18(11):1322-1332
pubmed: 34725481
J Med Genet. 2022 May 9;:
pubmed: 35534204
J Mol Diagn. 2018 Mar;20(2):195-202
pubmed: 29269280
Genet Med. 2016 Dec;18(12):1282-1289
pubmed: 27228465
Genet Med. 2022 Jun;24(6):1336-1348
pubmed: 35305867
Hum Mutat. 2017 Jul;38(7):870-879
pubmed: 28378423
Genet Med. 2022 Jan;24(1):130-145
pubmed: 34906502
Am J Hum Genet. 2010 May 14;86(5):749-64
pubmed: 20466091
J Comput Biol. 2015 Jun;22(6):498-509
pubmed: 25658651
Nat Commun. 2018 May 25;9(1):2064
pubmed: 29802345
Nat Commun. 2017 Nov 6;8(1):1326
pubmed: 29109544
NPJ Parkinsons Dis. 2017 Sep 5;3:27
pubmed: 28890930
Nat Rev Genet. 2016 May 17;17(6):333-51
pubmed: 27184599
Sci Transl Med. 2017 Apr 19;9(386):
pubmed: 28424332
Am J Hum Genet. 2019 Oct 3;105(4):719-733
pubmed: 31564432
Nat Biotechnol. 2019 Oct;37(10):1155-1162
pubmed: 31406327
Genet Med. 2020 Oct;22(10):1731-1732
pubmed: 32728138
PLoS One. 2019 Jul 5;14(7):e0219446
pubmed: 31276570
Hereditas. 2018 Sep 28;155:32
pubmed: 30279644
Sci Transl Med. 2020 Jan 1;12(524):
pubmed: 31894106
Mutat Res Rev Mutat Res. 2022 Jul 27;790:108428
pubmed: 35905832
Am J Hum Genet. 2020 Oct 1;107(4):654-669
pubmed: 32937144
Hum Mutat. 2022 Feb;43(2):189-199
pubmed: 34859533
Lancet Neurol. 2022 Mar;21(3):234-245
pubmed: 35182509
Genet Med. 2021 Nov;23(11):2029-2037
pubmed: 34211152
PLoS One. 2015 Aug 21;10(8):e0135906
pubmed: 26295943
Nucleic Acids Res. 2018 Nov 16;46(20):e120
pubmed: 30169659
Trends Genet. 2001 Nov;17(11):661-9
pubmed: 11672867
Am J Hum Genet. 2021 Aug 5;108(8):1436-1449
pubmed: 34216551
Bioinformatics. 2013 Jan 1;29(1):84-91
pubmed: 23093610
Prenat Diagn. 2022 May;42(6):662-685
pubmed: 35170059
J Mol Diagn. 2020 Aug;22(8):1087-1095
pubmed: 32473995
Sci Adv. 2022 Mar 4;8(9):eabm5386
pubmed: 35245110
Nat Rev Clin Oncol. 2020 Apr;17(4):196
pubmed: 31980806
Mov Disord. 2019 Oct;34(10):1571-1576
pubmed: 31483537
JAMA Netw Open. 2020 Sep 1;3(9):e2018109
pubmed: 32960281
Bioinformatics. 2019 Jul 1;35(13):2193-2198
pubmed: 30462145
Genome Biol. 2019 Jun 3;20(1):117
pubmed: 31159850
N Engl J Med. 2022 Feb 17;386(7):700-702
pubmed: 35020984
Hum Mutat. 2018 Sep;39(9):1262-1272
pubmed: 29932473
Bioinformatics. 2019 Nov 1;35(22):4754-4756
pubmed: 31134279