Twist exome capture allows for lower average sequence coverage in clinical exome sequencing

[en] Background Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. Results We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. Conclusion We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques.

Research center :

- Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group)

Disciplines :

Genetics & genetic processes
Human health sciences: Multidisciplinary, general & others

Author, co-author :

Yaldiz, Burcu

Kucuk, Erdi

Hampstead, Juliet

Hofste, Tom

Pfundt, Rolph

Corominas Galbany, Jordi

Rinne, Tuula

Yntema, Helger G.

Hoischen, Alexander

Nelen, Marcel

More authors (295 more)

External co-authors :

yes

Language :

English

Title :

Twist exome capture allows for lower average sequence coverage in clinical exome sequencing

Publication date :

03 May 2023

Journal title :

Human Genomics

ISSN :

1479-7364

Publisher :

BioMed Central, United Kingdom

Volume :

Issue :

Pages :

Peer reviewed :

Peer Reviewed verified by ORBi

Additional URL :

https://humgenomics.biomedcentral.com/articles/10.1186/s40246-023-00485-5

Available on ORBilu :

since 07 May 2023

Statistics

Number of views

56 (1 by Unilu)

Number of downloads

15 (0 by Unilu)

More statistics

Scopus citations^®

Scopus citations^®
without self-citations

WoS citations^™

Bibliography

Corominas J, Smeekens SP, Nelen MR, Yntema HG, Kamsteeg EJ, Pfundt R, et al. Clinical exome sequencing—mistakes and caveats. Hum Mutat. 2022;43:1041. DOI: 10.1002/humu.24360
Hartman P, Beckman K, Silverstein K, Yohe S, Schomaker M, Henzler C, et al. Next generation sequencing for clinical diagnostics: five year experience of an academic laboratory. Mol Genet Metab Rep. 2019;19:100464. DOI: 10.1016/j.ymgmr.2019.100464
McNeill A. Exome sequencing-one test to rule them all? Eur J Hum Genet. 2022;30:869. DOI: 10.1038/s41431-022-01145-3
Arts P, Simons A, Alzahrani MS, Yilmaz E, Alidrissi E, Van Aerde KJ, et al. Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies. Genome Med. 2019;11:1–15. DOI: 10.1186/s13073-019-0649-3
Neveling K, Feenstra I, Gilissen C, Hoefsloot LH, Kamsteeg E-J, et al. A post-hoc comparison of the utility of sanger sequencing and exome sequencing for the diagnosis of heterogeneous diseases. Hum Mutat. 2013;34:1721–6. DOI: 10.1002/humu.22450
Rabbani B, Tekin M, Mahdieh N. The promise of whole-exome sequencing in medical genetics. J Hum Genet. 2014;59:5–15. DOI: 10.1038/jhg.2013.114
Parla JS, Iossifov I, Grabill I, Spector MS, Kramer M, Mccombie R. A comparative analysis of exome capture. Genome Biol. 2011;12:1–17. DOI: 10.1186/gb-2011-12-9-r97
Díaz-de Usera A, Lorenzo-Salazar JM, Rubio-Rodríguez LA, Muñoz-Barrera A, Guillen-Guio B, Marcelino-Rodríguez I, et al. Evaluation of whole-exome enrichment solutions: lessons from the high-end of the short-read sequencing scale. J Clin Med. 2020;9:3656. DOI: 10.3390/jcm9113656
Zhou J, Zhang M, Li X, Wang Z, Pan D, Shi Y. Performance comparison of four types of target enrichment baits for exome DNA sequencing. Hereditas. 2021;158:1–12. DOI: 10.1186/s41065-021-00171-3
Belova V, Shmitko A, Pavlova A, Afasizhev R, Cheranev V, Tabanakova A, et al. Performance comparison of agilent new sureselect all exon v8 probes with v7 probes for exome sequencing. BMC Genom. 2022;23:1–8. 10.1186/s12864-022-08825-w. DOI: 10.1186/s12864-022-08825-w
Meienberg J, Zerjavic K, Keller I, Okoniewski M, Patrignani A, Ludin K, et al. New insights into the performance of human whole-exome capture platforms. Nucleic Acids Res. 2015;43:e76. DOI: 10.1093/nar/gkv216
Wang Q, Shashikant CS, Jensen M, Altman NS, Girirajan S. Novel metrics to measure coverage in whole exome sequencing datasets reveal local and global non-uniformity. Sci Rep. 2017;7:1–11. 10.1038/s41598-017-01005-x. DOI: 10.1038/s41598-017-01005-x
Clark MJ, Chen R, Lam HYK, Karczewski KJ, Chen R, Euskirchen G, et al. Performance comparison of exome DNA sequencing technologies. Nat Biotechnol. 2011;29:908–16. DOI: 10.1038/nbt.1975
Barbitoff YA, Polev DE, Glotov AS, Serebryakova EA, Shcherbakova IV, Kiselev AM, et al. Systematic dissection of biases in whole-exome and whole-genome sequencing reveals major determinants of coding sequence coverage. Sci Rep. 2020;10:1–13. DOI: 10.1038/s41598-020-59026-y
Royer-Bertrand B, Cisarova K, Niel-Butschi F, Mittaz-Crettol L, Fodstad H, Superti-Furga A. CNV detection from exome sequencing data in routine diagnostics of rare genetic disorders: opportunities and limitations. Genes. 2021;12:1427. DOI: 10.3390/genes12091427
Pfundt R, del Rosario M, Vissers L, Kwint MP, Janssen IM, de Leeuw N, et al. Detection of clinically relevant copy-number variants by exome sequencing in a large cohort of genetic disorders. Genet Med. 2017;19:667–75. DOI: 10.1038/gim.2016.163
Dong X, Liu B, Yang L, Wang H, Wu B, Chen X, et al. Clinical exome sequencing as the first-tier test for diagnosing developmental disorders covering both CNV and SNV: a Chinese cohort diagnostics. J Med Genet. 2020;57:558–66. DOI: 10.1136/jmedgenet-2019-106377
Martinez-Granero F, Blanco-Kelly F, Sanchez-Jimeno C, Avila-Fernandez A, Arteche A, Bustamante-Aragones A, et al. Comparison of the diagnostic yield of aCGH and genome-wide sequencing across different neurodevelopmental disorders. NPJ Genom Med. 2021;6:25. DOI: 10.1038/s41525-021-00188-7
Srivastava S, Love-Nichols JA, Dies KA, Ledbetter DH, Martin CL, Chung WK, et al. Meta-analysis and multidisciplinary consensus statement: exome sequencing is a first-tier clinical diagnostic test for individuals with neurodevelopmental disorders. Genet Med. 2019;21:2413–21. DOI: 10.1038/s41436-019-0554-6
Shakked BP, Barel O, Singer A, Regev M, Dayan EZ, Zeev B, et al. A single center experience with publicly funded clinical exome sequencing for neurodevelopmental disorders or multiple congenital anomalies. Sci Rep. 2021. 10.1038/s41598-021-98646-w. DOI: 10.1038/s41598-021-98646-w
Diaz-Horta O, Bademci G, Tokgoz-Yilmaz S, Guo S, Zafeer F, Sineni CJ, et al. Novel variant p.E269K confirms causative role of PLS1 mutations in autosomal dominant hearing loss. Clin Genet. 2019;96:575–8. DOI: 10.1111/cge.13626
Pauper M, Kucuk E, Wenger AM, Chakraborty S, Baybayan P, Kwint M, et al. Long-read trio sequencing of individuals with unsolved intellectual disability. Eur J Hum Genet. 2021;29:637–48. 10.1038/s41431-020-00770-0. DOI: 10.1038/s41431-020-00770-0
Meienberg J, Bruggmann R, Oexle K, Matyas G. Clinical sequencing: Is WGS the better WES? Hum Genet. 2016;135:359–62. DOI: 10.1007/s00439-015-1631-9
Sekhar C, Chilamakuri R, Lorenz S, Madoui M-A, Vodák D, Sun J, et al. Performance comparison of four exome capture systems for deep sequencing. BMC Genom. 2014;15:1–13.
Shigemizu D, Momozawa Y, Abe T, Morizono T, Boroevich KA, Takata S, et al. Performance comparison of four commercial human whole-exome capture platforms. Sci Rep. 2015;5:1–8. DOI: 10.1038/srep12742
Lelieveld SH, Spielmann M, Mundlos S, Veltman JA, Gilissen C. Comparison of exome and genome sequencing technologies for the complete capture of protein-coding regions. Hum Mutat. 2015;36:815–22. DOI: 10.1002/humu.22813
Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009;25:1754–60. DOI: 10.1093/bioinformatics/btp324
Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014;42:756–63. DOI: 10.1093/nar/gkt1114
Cunningham F, Achuthan P, Akanni W, Allen J, Amode MR, Armean IM, et al. Ensembl 2019. Nucleic Acids Res. 2019;47:D745–51. DOI: 10.1093/nar/gky1113
Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, et al. The UCSC table browser data retrieval tool. Nucleic Acids Res. 2004;32:D493–6. DOI: 10.1093/nar/gkh103
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–2. 10.1093/bioinformatics/btq033. DOI: 10.1093/bioinformatics/btq033
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9. 10.1093/bioinformatics/btp352. DOI: 10.1093/bioinformatics/btp352
Mokry M, Feitsma H, Nijman IJ, de Bruijn E, van der Zaag PJ, Guryev V, et al. Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries. Nucleic Acids Res. 2010;38:e116. DOI: 10.1093/nar/gkq072
der Auwera GA, O’Connor BD. Genomics in the cloud: using Docker, GATK, and WDL in Terra [Internet]. O’Reilly Media; 2020. Available from: https://books.google.nl/books?id=vsXaDwAAQBAJ.
Mandelker D, Schmidt RJ, Ankala A, McDonald Gibson K, Bowser M, Sharma H, et al. Navigating highly homologous genes in a molecular diagnostic setting: a resource for clinical next-generation. Genet Med. 2016;18:1282–9. DOI: 10.1038/gim.2016.58
Kong SW, Lee IH, Liu X, Hirschhorn JN, Mandl KD. Measuring coverage and accuracy of whole-exome sequencing in clinical context. Genet Med. 2018;20:1617–26. 10.1038/gim.2018.51. DOI: 10.1038/gim.2018.51
Iadarola B, Xumerle L, Lavezzari D, Paterno M, Marcolungo L, Beltrami C, et al. Shedding light on dark genes: enhanced targeted resequencing by optimizing the combination of enrichment technology and DnA fragment length. Sci Rep. 2020;10:9424. DOI: 10.1038/s41598-020-66331-z
Jamal SM, Yu J-H, Chong JX, Dent KM, Conta JH, Tabor HK, et al. Practices and policies of clinical exome sequencing providers: analysis and implications. Am J Med Genet Part A. 2013;161:935–50. 10.1002/ajmg.a.35942. DOI: 10.1002/ajmg.a.35942
Acuna-Hidalgo R, Bo T, Kwint MP, Van De Vorst M, Pinelli M, Veltman JA, et al. Post-zygotic point mutations are an underrecognized source of de novo genomic variation. Am J Hum Genet. 2015;97:67–74. 10.1016/j.ajhg.2015.05.008. DOI: 10.1016/j.ajhg.2015.05.008
Pauper M, Kucuk E, Wenger AM, Chakraborty S, Baybayan P, Kwint M, et al. Long-read trio sequencing of individuals with unsolved intellectual disability. Eur J Hum Genet. 2020;29:637–48. DOI: 10.1038/s41431-020-00770-0