PCR-free whole exome sequencing: Cost-effective and efficient in detecting rare mutations
Autoři:
Izumi Yamaguchi aff001; Takashi Watanabe aff001; Osamu Ohara aff001; Yoshinori Hasegawa aff001
Působiště autorů:
Laboratory of Clinical Omics Research, Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
aff001
Vyšlo v časopise:
PLoS ONE 14(9)
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pone.0222562
Souhrn
In this study, we describe the development of a PCR-free whole exome sequencing method. Using this method, 2 μg DNA was sufficient for library preparation for whole exome sequencing. Furthermore, the method is simple and makes use of a commercial kit, with additional step of concentrating the captured library by ethanol precipitation. The accuracy of the PCR-free method was found to be equivalent to that of unique molecular identifier-corrected analysis method, which is the commonly used method to detect rare mutations. Thus, the PCR-free whole exome sequencing method is cost-effective as well as efficient in detecting rare mutations.
Klíčová slova:
Biology and life sciences – Genetics – DNA – DNA libraries – DNA electrophoresis – Gene identification and analysis – Mutation detection – Genomics – Genome analysis – Transcriptome analysis – Biochemistry – Nucleic acids – Molecular biology – Molecular biology techniques – Artificial gene amplification and extension – Polymerase chain reaction – DNA construction – DNA manipulations – DNA fragment ligation – Molecular probe techniques – Probe hybridization – Computational biology – Research and analysis methods – DNA hybridization – Sequencing techniques – DNA sequencing – Next-generation sequencing – Specimen preparation and treatment – Mechanical treatment of specimens – Sonication – Ultrasonication – Electrophoretic techniques
Zdroje
1. Warr A, Robert C, Hume D, Archibald A, Deeb N, Watson M. Exome sequencing: current and future perspectives. G3 (Bethesda). 2015;5(8): 1543–1550. doi: 10.1534/g3.115.018564 26139844
2. Wang R, Yoshida K, Toki T, Sawada T, Uechi T, Okuno Y, et al. Loss of function mutations in RPL27 and RPS27 identified by whole-exome sequencing in Diamond-Blackfan anaemia. Br J Haematol. 2015;168(6): 854–864. doi: 10.1111/bjh.13229 25424902
3. Ikeda F, Yoshida K, Toki T, Uechi T, Ishida S, Nakajima Y, et al. Exome sequencing identified RPS15A as a novel causative gene for Diamond-Blackfan anemia. Haematologica. 2017;102(3): e93–e96. doi: 10.3324/haematol.2016.153932 27909223
4. Karasaki T, Nagayama K, Kuwano H, Nitadori JI, Sato M, Anraku M, et al. Prediction and prioritization of neoantigens: integration of RNA sequencing data with whole-exome sequencing. Cancer Sci. 2017;108(2): 170–177. doi: 10.1111/cas.13131 27960040
5. Petljak M, Alexandrov LB, Brammeld JS, Price S, Wedge DC, Grossmann S, et al. Characterizing mutational signatures in human cancer cell lines reveals episodic APOBEC mutagenesis. Cell. 2019;176(6): 1282–1294.e20. doi: 10.1016/j.cell.2019.02.012 30849372
6. Sahraeian SME, Liu R, Lau B, Podesta K, Mohiyuddin M, Lam HYK. Deep convolutional neural networks for accurate somatic mutation detection. Nat Commun. 2019;10(1): 1041. doi: 10.1038/s41467-019-09027-x 30833567
7. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 2008;36(16):e105. doi: 10.1093/nar/gkn425 18660515
8. Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, et al. Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods. 2010;7(1):47–49. doi: 10.1038/nmeth.1404 19946276
9. Aird D, Ross MG, Chen WS, Danielsson M, Fennell T, Russ C, et al. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 2011;12(2):R18. doi: 10.1186/gb-2011-12-2-r18 21338519
10. Gundry M, Vijg J. Direct mutation analysis by high-throughput sequencing: from germline to low-abundant, somatic variants. Mutat Res. 2012;729(1–2):1–15. doi: 10.1016/mrfmmm.2011.10.001 22016070
11. Kinde I, Wu J, Papadopoulos N, Kinzler KW, Vogelstein B. Detection and quantification of rare mutations with massively parallel sequencing. Proc Natl Acad Sci U S A. 2011;108(23): 9530–9535. doi: 10.1073/pnas.1105422108 21586637
12. Schmitt MW, Kennedy SR, Salk JJ, Fox EJ, Hiatt JB, Loeb LA. Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci U S A. 2012;109(36): 14508–14513. doi: 10.1073/pnas.1208715109 22853953
13. Ahn EH, Hirohata K, Kohrn BF, Fox EJ, Chang CC, Loeb LA. Detection of ultra-rare mitochondrial mutations in breast stem cells by duplex sequencing. PLoS One. 2015;10(8): e0136216. doi: 10.1371/journal.pone.0136216 26305705
14. Kou R, Lam H, Duan H, Ye L, Jongkam N, Chen W, et al. Benefits and challenges with applying unique molecular identifiers in next generation sequencing to detect low frequency mutations. PLoS One. 2016;11(1): e0146638. doi: 10.1371/journal.pone.0146638 26752634
15. Dolzhenko E, van Vugt JJFA, Shaw RJ, Bekritsky MA, van Blitterswijk M, Narzisi G, et al. Detection of long repeat expansions from PCR-free whole-genome sequence data. Genome Res. 2017;27(11): 1895–1903. doi: 10.1101/gr.225672.117 28887402
16. Kennedy SR, Schmitt MW, Fox EJ, Kohrn BF, Salk JJ, Ahn EH, et al. Detecting ultralow-frequency mutations by Duplex Sequencing. Nat Protoc. 2014;9(11): 2586–2606. doi: 10.1038/nprot.2014.170 25299156
Článek vyšel v časopise
PLOS One
2019 Číslo 9
- S diagnostikou Parkinsonovy nemoci může nově pomoci AI nástroj pro hodnocení mrkacího reflexu
- Je libo čepici místo mozkového implantátu?
- Pomůže v budoucnu s triáží na pohotovostech umělá inteligence?
- AI může chirurgům poskytnout cenná data i zpětnou vazbu v reálném čase
- Nová metoda odlišení nádorové tkáně může zpřesnit resekci glioblastomů
Nejčtenější v tomto čísle
- Graviola (Annona muricata) attenuates behavioural alterations and testicular oxidative stress induced by streptozotocin in diabetic rats
- CH(II), a cerebroprotein hydrolysate, exhibits potential neuro-protective effect on Alzheimer’s disease
- Comparison between Aptima Assays (Hologic) and the Allplex STI Essential Assay (Seegene) for the diagnosis of Sexually transmitted infections
- Assessment of glucose-6-phosphate dehydrogenase activity using CareStart G6PD rapid diagnostic test and associated genetic variants in Plasmodium vivax malaria endemic setting in Mauritania
Zvyšte si kvalifikaci online z pohodlí domova
Všechny kurzy