In Phase HLA Genotyping by Next Generation Sequencing — A Comparison Between Two Massively Parallel Sequencing Bench-Top Systems, the Roche GS Junior and Ion Torrent PGM

Jerzy Kulski; Shingo Suzuki; Y. Ozaki; S. Mitsunaga; Hidetoshi Inoko; Takashi Shiina

doi:10.5772/57556

In Phase HLA Genotyping by Next Generation Sequencing — A Comparison Between Two Massively Parallel Sequencing Bench-Top Systems, the Roche GS Junior and Ion Torrent PGM

Jerzy Kulski, Shingo Suzuki, Y. Ozaki, S. Mitsunaga, Hidetoshi Inoko, Takashi Shiina

Research output: Chapter in Book/Conference paper › Chapter › peer-review

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Abstract

We have developed procedures for massively parallel sequencing of multiplex products that can be used for several benchtop sequencing platforms. We have obtained sequences of sufficient high quality to permit accurate HLA in phase genotypes across the full-length gene from the 5’ promoter/enhancer region to the 3’ UTR for most of the classical class I and class II genes. The use of sample tags or barcodes allows for optimization of second generation sequencing technologies by pooling samples and sequencing multiple samples in parallel for time- and cost-efficient workflows. We are currently working towards optimizing the Ion PGM/SS-SBT method for HLA in phase genotyping for both the clinical diagnostic and research laboratories.

Original language	English
Title of host publication	HLA and Associated Important Diseases
Editors	Yongzhi Xi
Place of Publication	Croatia
Publisher	InTech
Pages	141-181
Number of pages	41
ISBN (Print)	978-953-51-1230-3
DOIs	https://doi.org/10.5772/57556
Publication status	Published - 19 Mar 2014

Publication series

Name	Immunology, Allergology and Rheumatology

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Kulski, J., Suzuki, S., Ozaki, Y., Mitsunaga, S., Inoko, H., & Shiina, T. (2014). In Phase HLA Genotyping by Next Generation Sequencing — A Comparison Between Two Massively Parallel Sequencing Bench-Top Systems, the Roche GS Junior and Ion Torrent PGM. In Y. Xi (Ed.), HLA and Associated Important Diseases (pp. 141-181). (Immunology, Allergology and Rheumatology). InTech. https://doi.org/10.5772/57556

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abstract = "We have developed procedures for massively parallel sequencing of multiplex products that can be used for several benchtop sequencing platforms. We have obtained sequences of sufficient high quality to permit accurate HLA in phase genotypes across the full-length gene from the 5{\textquoteright} promoter/enhancer region to the 3{\textquoteright} UTR for most of the classical class I and class II genes. The use of sample tags or barcodes allows for optimization of second generation sequencing technologies by pooling samples and sequencing multiple samples in parallel for time- and cost-efficient workflows. We are currently working towards optimizing the Ion PGM/SS-SBT method for HLA in phase genotyping for both the clinical diagnostic and research laboratories.",

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author = "Jerzy Kulski and Shingo Suzuki and Y. Ozaki and S. Mitsunaga and Hidetoshi Inoko and Takashi Shiina",

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Kulski, J, Suzuki, S, Ozaki, Y, Mitsunaga, S, Inoko, H & Shiina, T 2014, In Phase HLA Genotyping by Next Generation Sequencing — A Comparison Between Two Massively Parallel Sequencing Bench-Top Systems, the Roche GS Junior and Ion Torrent PGM. in Y Xi (ed.), HLA and Associated Important Diseases. Immunology, Allergology and Rheumatology, InTech, Croatia, pp. 141-181. https://doi.org/10.5772/57556

In Phase HLA Genotyping by Next Generation Sequencing — A Comparison Between Two Massively Parallel Sequencing Bench-Top Systems, the Roche GS Junior and Ion Torrent PGM. / Kulski, Jerzy; Suzuki, Shingo; Ozaki, Y. et al.
HLA and Associated Important Diseases. ed. / Yongzhi Xi. Croatia: InTech, 2014. p. 141-181 (Immunology, Allergology and Rheumatology).

Research output: Chapter in Book/Conference paper › Chapter › peer-review

TY - CHAP

T1 - In Phase HLA Genotyping by Next Generation Sequencing — A Comparison Between Two Massively Parallel Sequencing Bench-Top Systems, the Roche GS Junior and Ion Torrent PGM

AU - Kulski, Jerzy

AU - Suzuki, Shingo

AU - Ozaki, Y.

AU - Mitsunaga, S.

AU - Inoko, Hidetoshi

AU - Shiina, Takashi

PY - 2014/3/19

Y1 - 2014/3/19

N2 - We have developed procedures for massively parallel sequencing of multiplex products that can be used for several benchtop sequencing platforms. We have obtained sequences of sufficient high quality to permit accurate HLA in phase genotypes across the full-length gene from the 5’ promoter/enhancer region to the 3’ UTR for most of the classical class I and class II genes. The use of sample tags or barcodes allows for optimization of second generation sequencing technologies by pooling samples and sequencing multiple samples in parallel for time- and cost-efficient workflows. We are currently working towards optimizing the Ion PGM/SS-SBT method for HLA in phase genotyping for both the clinical diagnostic and research laboratories.

AB - We have developed procedures for massively parallel sequencing of multiplex products that can be used for several benchtop sequencing platforms. We have obtained sequences of sufficient high quality to permit accurate HLA in phase genotypes across the full-length gene from the 5’ promoter/enhancer region to the 3’ UTR for most of the classical class I and class II genes. The use of sample tags or barcodes allows for optimization of second generation sequencing technologies by pooling samples and sequencing multiple samples in parallel for time- and cost-efficient workflows. We are currently working towards optimizing the Ion PGM/SS-SBT method for HLA in phase genotyping for both the clinical diagnostic and research laboratories.

KW - sequencing, hla, m/c, polymorphism, next generation sequencing

UR - https://www.intechopen.com/books/hla-and-associated-important-diseases

U2 - 10.5772/57556

DO - 10.5772/57556

M3 - Chapter

SN - 978-953-51-1230-3

T3 - Immunology, Allergology and Rheumatology

SP - 141

EP - 181

BT - HLA and Associated Important Diseases

A2 - Xi, Yongzhi

PB - InTech

CY - Croatia

ER -

Kulski J, Suzuki S, Ozaki Y, Mitsunaga S, Inoko H, Shiina T. In Phase HLA Genotyping by Next Generation Sequencing — A Comparison Between Two Massively Parallel Sequencing Bench-Top Systems, the Roche GS Junior and Ion Torrent PGM. In Xi Y, editor, HLA and Associated Important Diseases. Croatia: InTech. 2014. p. 141-181. (Immunology, Allergology and Rheumatology). doi: 10.5772/57556

In Phase HLA Genotyping by Next Generation Sequencing — A Comparison Between Two Massively Parallel Sequencing Bench-Top Systems, the Roche GS Junior and Ion Torrent PGM

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