Single nucleotide variant sequencing errors in whole exome sequencing using the Ion Proton System

Fujita,Shiro; Masago,Katsuhiro; Okuda,Chiyuki; Hata,Akito; Kaji,Reiko; Katakami,Nobuyuki; Hirata,Yukio

doi:10.3892/br.2017.911

July-2017 Volume 7 Issue 1

Full Size Image

Journals

International Journal of Molecular Medicine

International Journal of Molecular Medicine is an international journal devoted to molecular mechanisms of human disease.

International Journal of Oncology

International Journal of Oncology is an international journal devoted to oncology research and cancer treatment.

Molecular Medicine Reports

Covers molecular medicine topics such as pharmacology, pathology, genetics, neuroscience, infectious diseases, molecular cardiology, and molecular surgery.

Oncology Reports

Oncology Reports is an international journal devoted to fundamental and applied research in Oncology.

Experimental and Therapeutic Medicine

Experimental and Therapeutic Medicine is an international journal devoted to laboratory and clinical medicine.

Oncology Letters

Oncology Letters is an international journal devoted to Experimental and Clinical Oncology.

Biomedical Reports

Explores a wide range of biological and medical fields, including pharmacology, genetics, microbiology, neuroscience, and molecular cardiology.

Molecular and Clinical Oncology

International journal addressing all aspects of oncology research, from tumorigenesis and oncogenes to chemotherapy and metastasis.

World Academy of Sciences Journal

Multidisciplinary open-access journal spanning biochemistry, genetics, neuroscience, environmental health, and synthetic biology.

International Journal of Functional Nutrition

Open-access journal combining biochemistry, pharmacology, immunology, and genetics to advance health through functional nutrition.

International Journal of Epigenetics

Publishes open-access research on using epigenetics to advance understanding and treatment of human disease.

Medicine International

An International Open Access Journal Devoted to General Medicine.

July-2017 Volume 7 Issue 1

Full Size Image

Article Open Access

Single nucleotide variant sequencing errors in whole exome sequencing using the Ion Proton System

Authors:
- Shiro Fujita
- Katsuhiro Masago
- Chiyuki Okuda
- Akito Hata
- Reiko Kaji
- Nobuyuki Katakami
- Yukio Hirata
View Affiliations / Copyright

Affiliations: Division of Integrated Oncology, Institute of Biomedical Research and Innovation, Chuo-ku, Kobe 650-0047, Japan

Copyright: © Fujita et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
Pages: 17-20
|
Published online on: May 17, 2017

https://doi.org/10.3892/br.2017.911
Expand metrics +

Abstract

Errors in sequencing are a major obstacle in the interpretation of next-generation sequencing (NGS) results. In the present study, sequencing errors identified from analysis of single nucleotide variants (SNVs) identified during exome sequencing of human germline DNA were studied using the Thermo Fisher Ion Proton System. Two consanguineous cases were selected for sequencing using the AmpliSeq Exome capture kit, and SNVs found in both cases were validated using Sanger sequencing. A total of 98 SNVs detected by NGS were randomly selected for further analysis. Nine of the analyzed SNVs were shown to be false positives when confirmed by Sanger sequencing. All but one SNV were considered to be homopolymer regions, mainly through the insertion or deletion of nucleotides. The remaining error was considered to be related to the primer. The present results revealed that the majority of the SNV sequencing errors originated from homopolymer insertion/deletion errors, which are commonly observed when using the Ion Torrent system.

View Figures

View References

1	Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin ML, Ordóñez GR, Bignell GR, et al: A comprehensive catalogue of somatic mutations from a human cancer genome. Nature. 463:191–196. 2010. View Article : Google Scholar : PubMed/NCBI
2	Horak P, Frohling S and Glimm H: Integrating next-generation sequencing into clinical oncology: strategies, promises and pitfalls. ESMO Open. 1:e0000942016. View Article : Google Scholar : PubMed/NCBI
3	Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA, et al: Exome sequencing identifies the cause of a mendelian disorder. Nat Genet. 42:30–35. 2010. View Article : Google Scholar : PubMed/NCBI
4	Bonnefond A, Durand E, Sand O, De Graeve F, Gallina S, Busiah K, Lobbens S, Simon A, Bellanné-Chantelot C, Létourneau L, et al: Molecular diagnosis of neonatal diabetes mellitus using next-generation sequencing of the whole exome. PLoS One. 5:e136302010. View Article : Google Scholar : PubMed/NCBI
5	Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, et al: An integrated semiconductor device enabling non-optical genome sequencing. Nature. 475:348–352. 2011. View Article : Google Scholar : PubMed/NCBI
6	Boland JF, Chung CC, Roberson D, Mitchell J, Zhang X, Im KM, He J, Chanock SJ, Yeager M and Dean M: The new sequencer on the block: Comparison of Life Technology's Proton sequencer to an Illumina HiSeq for whole-exome sequencing. Human genetics. 132:1153–1163. 2013. View Article : Google Scholar : PubMed/NCBI
7	Zhang G, Wang J, Yang J, Li W, Deng Y, Li J, Huang J, Hu S and Zhang B: Comparison and evaluation of two exome capture kits and sequencing platforms for variant calling. BMC genomics. 16:5812015. View Article : Google Scholar : PubMed/NCBI
8	Damiati E, Borsani G and Giacopuzzi E: Amplicon-based semiconductor sequencing of human exomes: performance evaluation and optimization strategies. Human genetics. 135:499–511. 2016. View Article : Google Scholar : PubMed/NCBI
9	McCall CM, Mosier S, Thiess M, Debeljak M, Pallavajjala A, Beierl K, Deak KL, Datto MB, Gocke CD, Lin MT and Eshleman JR: False positives in multiplex PCR-based next-generation sequencing have unique signatures. JMD. 16:541–549. 2014.PubMed/NCBI
10	Thermo Fisher Scientific, Ion Torrent. https://www.thermofisher.com/jp/en/home/brands/ion-torrent.htmlApril 10–2017
11	Garrison E and Marth G: Haplotype-based variant detection from short-read sequencing. arXiv.org>q-bio>arXiv:1207.3907. 2012

Journals

International Journal of Molecular Medicine

International Journal of Oncology

Molecular Medicine Reports

Oncology Reports

Experimental and Therapeutic Medicine

Oncology Letters

Biomedical Reports

Molecular and Clinical Oncology

World Academy of Sciences Journal

International Journal of Functional Nutrition

International Journal of Epigenetics

Medicine International

Single nucleotide variant sequencing errors in whole exome sequencing using the Ion Proton System

This article is mentioned in:

Abstract

Figure 1

Figure 2

Figure 3

Figure 4

Related Articles