A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations

Fuyuki Miya, Mitsuhiro Kato, Tadashi Shiohama, Nobuhiko Okamoto, Shinji Saitoh, Mami Yamasaki, Daichi Shigemizu, Tetsuo Abe, Takashi Morizono, Keith A. Boroevich, Kenjiro Kosaki, Yonehiro Kanemura, Tatsuhiko Tsunoda

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Whole-exome sequencing (WES) is a useful method to identify disease-causing mutations, however, often no candidate mutations are identified using commonly available targeted probe sets. In a recent analysis, we also could not find candidate mutations for 20.9% (9/43) of our pedigrees with congenital neurological disorder using pre-designed capture probes (SureSelect V4 or V5). One possible cause for this lack of candidates is that standard WES cannot sequence all protein-coding sequences (CDS) due to capture probe design and regions of low coverage, which account for approximately 10% of all CDS regions. In this study, we combined a selective circularization-based target enrichment method (HaloPlex) with a hybrid capture method (SureSelect V5; WES), and achieved a more complete coverage of CDS regions (∼97% of all CDS). We applied this approach to 7 (SureSelect V5) out of 9 pedigrees with no candidates through standard WES analysis and identified novel pathogenic mutations in one pedigree. The application of this effective combination of targeted enrichment methodologies can be expected to aid in the identification of novel pathogenic mutations previously missed by standard WES analysis.

Original languageEnglish
Article number9331
JournalScientific Reports
Volume5
DOIs
Publication statusPublished - 2015 Mar 19

Fingerprint

Exome
Pedigree
Mutation
Congenital, Hereditary, and Neonatal Diseases and Abnormalities
Nervous System Diseases
Proteins

ASJC Scopus subject areas

  • General

Cite this

Miya, F., Kato, M., Shiohama, T., Okamoto, N., Saitoh, S., Yamasaki, M., ... Tsunoda, T. (2015). A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations. Scientific Reports, 5, [9331]. https://doi.org/10.1038/srep09331

A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations. / Miya, Fuyuki; Kato, Mitsuhiro; Shiohama, Tadashi; Okamoto, Nobuhiko; Saitoh, Shinji; Yamasaki, Mami; Shigemizu, Daichi; Abe, Tetsuo; Morizono, Takashi; Boroevich, Keith A.; Kosaki, Kenjiro; Kanemura, Yonehiro; Tsunoda, Tatsuhiko.

In: Scientific Reports, Vol. 5, 9331, 19.03.2015.

Research output: Contribution to journalArticle

Miya, F, Kato, M, Shiohama, T, Okamoto, N, Saitoh, S, Yamasaki, M, Shigemizu, D, Abe, T, Morizono, T, Boroevich, KA, Kosaki, K, Kanemura, Y & Tsunoda, T 2015, 'A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations', Scientific Reports, vol. 5, 9331. https://doi.org/10.1038/srep09331
Miya, Fuyuki ; Kato, Mitsuhiro ; Shiohama, Tadashi ; Okamoto, Nobuhiko ; Saitoh, Shinji ; Yamasaki, Mami ; Shigemizu, Daichi ; Abe, Tetsuo ; Morizono, Takashi ; Boroevich, Keith A. ; Kosaki, Kenjiro ; Kanemura, Yonehiro ; Tsunoda, Tatsuhiko. / A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations. In: Scientific Reports. 2015 ; Vol. 5.
@article{6bcb3d6fb39e4289a41c2bcb7e1b0199,
title = "A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations",
abstract = "Whole-exome sequencing (WES) is a useful method to identify disease-causing mutations, however, often no candidate mutations are identified using commonly available targeted probe sets. In a recent analysis, we also could not find candidate mutations for 20.9{\%} (9/43) of our pedigrees with congenital neurological disorder using pre-designed capture probes (SureSelect V4 or V5). One possible cause for this lack of candidates is that standard WES cannot sequence all protein-coding sequences (CDS) due to capture probe design and regions of low coverage, which account for approximately 10{\%} of all CDS regions. In this study, we combined a selective circularization-based target enrichment method (HaloPlex) with a hybrid capture method (SureSelect V5; WES), and achieved a more complete coverage of CDS regions (∼97{\%} of all CDS). We applied this approach to 7 (SureSelect V5) out of 9 pedigrees with no candidates through standard WES analysis and identified novel pathogenic mutations in one pedigree. The application of this effective combination of targeted enrichment methodologies can be expected to aid in the identification of novel pathogenic mutations previously missed by standard WES analysis.",
author = "Fuyuki Miya and Mitsuhiro Kato and Tadashi Shiohama and Nobuhiko Okamoto and Shinji Saitoh and Mami Yamasaki and Daichi Shigemizu and Tetsuo Abe and Takashi Morizono and Boroevich, {Keith A.} and Kenjiro Kosaki and Yonehiro Kanemura and Tatsuhiko Tsunoda",
year = "2015",
month = "3",
day = "19",
doi = "10.1038/srep09331",
language = "English",
volume = "5",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "Nature Publishing Group",

}

TY - JOUR

T1 - A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations

AU - Miya, Fuyuki

AU - Kato, Mitsuhiro

AU - Shiohama, Tadashi

AU - Okamoto, Nobuhiko

AU - Saitoh, Shinji

AU - Yamasaki, Mami

AU - Shigemizu, Daichi

AU - Abe, Tetsuo

AU - Morizono, Takashi

AU - Boroevich, Keith A.

AU - Kosaki, Kenjiro

AU - Kanemura, Yonehiro

AU - Tsunoda, Tatsuhiko

PY - 2015/3/19

Y1 - 2015/3/19

N2 - Whole-exome sequencing (WES) is a useful method to identify disease-causing mutations, however, often no candidate mutations are identified using commonly available targeted probe sets. In a recent analysis, we also could not find candidate mutations for 20.9% (9/43) of our pedigrees with congenital neurological disorder using pre-designed capture probes (SureSelect V4 or V5). One possible cause for this lack of candidates is that standard WES cannot sequence all protein-coding sequences (CDS) due to capture probe design and regions of low coverage, which account for approximately 10% of all CDS regions. In this study, we combined a selective circularization-based target enrichment method (HaloPlex) with a hybrid capture method (SureSelect V5; WES), and achieved a more complete coverage of CDS regions (∼97% of all CDS). We applied this approach to 7 (SureSelect V5) out of 9 pedigrees with no candidates through standard WES analysis and identified novel pathogenic mutations in one pedigree. The application of this effective combination of targeted enrichment methodologies can be expected to aid in the identification of novel pathogenic mutations previously missed by standard WES analysis.

AB - Whole-exome sequencing (WES) is a useful method to identify disease-causing mutations, however, often no candidate mutations are identified using commonly available targeted probe sets. In a recent analysis, we also could not find candidate mutations for 20.9% (9/43) of our pedigrees with congenital neurological disorder using pre-designed capture probes (SureSelect V4 or V5). One possible cause for this lack of candidates is that standard WES cannot sequence all protein-coding sequences (CDS) due to capture probe design and regions of low coverage, which account for approximately 10% of all CDS regions. In this study, we combined a selective circularization-based target enrichment method (HaloPlex) with a hybrid capture method (SureSelect V5; WES), and achieved a more complete coverage of CDS regions (∼97% of all CDS). We applied this approach to 7 (SureSelect V5) out of 9 pedigrees with no candidates through standard WES analysis and identified novel pathogenic mutations in one pedigree. The application of this effective combination of targeted enrichment methodologies can be expected to aid in the identification of novel pathogenic mutations previously missed by standard WES analysis.

UR - http://www.scopus.com/inward/record.url?scp=84925250471&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84925250471&partnerID=8YFLogxK

U2 - 10.1038/srep09331

DO - 10.1038/srep09331

M3 - Article

VL - 5

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

M1 - 9331

ER -