Identification of immunoglobulin gene sequences from a small read number of mRNA-seq using hybridomas

Yuki Kuniyoshi, Kazumitsu Maehara, Takeshi Iwasaki, Masayasu Hayashi, Yuichiro Semba, Masatoshi Fujita, Yuko Sato, Hiroshi Kimura, Akihito Harada, Yasuyuki Ohkawa

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Identification of immunoglobulin genes in hybridomas is essential for producing antibodies for research and clinical applications. A couple of methods such as RACE and degenerative PCR have been developed for determination of the Igh and Igl/Igk coding sequences (CDSs) but it has been difficult to process a number of hybridomas both with accuracy and rapidness. Here, we propose a new strategy for antibody sequence determination by mRNA-seq of hybridomas. We demonstrated that hybridomas highly expressed the Igh and Igl/Igk genes and that de novo transcriptome assembly using mRNA-seq data enabled identification of the CDS of both Igh and Igl/Igk accurately. Furthermore, we estimated that only 30,000 sequenced reads are required to identify immunoglobulin sequences from four different hybridoma clones. Thus, our approach would facilitate determining variable CDSs drastically.

Original languageEnglish
Article numbere0165473
JournalPloS one
Volume11
Issue number10
DOIs
Publication statusPublished - Oct 1 2016

Fingerprint

immunoglobulin genes
Immunoglobulin Genes
hybridomas
Hybridomas
Immunoglobulins
Genes
nucleotide sequences
Messenger RNA
Antibodies
antibodies
Transcriptome
transcriptome
immunoglobulins
Sequence Analysis
sequence analysis
Clone Cells
clones
Polymerase Chain Reaction
Research
genes

All Science Journal Classification (ASJC) codes

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Identification of immunoglobulin gene sequences from a small read number of mRNA-seq using hybridomas. / Kuniyoshi, Yuki; Maehara, Kazumitsu; Iwasaki, Takeshi; Hayashi, Masayasu; Semba, Yuichiro; Fujita, Masatoshi; Sato, Yuko; Kimura, Hiroshi; Harada, Akihito; Ohkawa, Yasuyuki.

In: PloS one, Vol. 11, No. 10, e0165473, 01.10.2016.

Research output: Contribution to journalArticle

Kuniyoshi, Yuki ; Maehara, Kazumitsu ; Iwasaki, Takeshi ; Hayashi, Masayasu ; Semba, Yuichiro ; Fujita, Masatoshi ; Sato, Yuko ; Kimura, Hiroshi ; Harada, Akihito ; Ohkawa, Yasuyuki. / Identification of immunoglobulin gene sequences from a small read number of mRNA-seq using hybridomas. In: PloS one. 2016 ; Vol. 11, No. 10.
@article{1f545ab353004d6db02d457bce1d1b71,
title = "Identification of immunoglobulin gene sequences from a small read number of mRNA-seq using hybridomas",
abstract = "Identification of immunoglobulin genes in hybridomas is essential for producing antibodies for research and clinical applications. A couple of methods such as RACE and degenerative PCR have been developed for determination of the Igh and Igl/Igk coding sequences (CDSs) but it has been difficult to process a number of hybridomas both with accuracy and rapidness. Here, we propose a new strategy for antibody sequence determination by mRNA-seq of hybridomas. We demonstrated that hybridomas highly expressed the Igh and Igl/Igk genes and that de novo transcriptome assembly using mRNA-seq data enabled identification of the CDS of both Igh and Igl/Igk accurately. Furthermore, we estimated that only 30,000 sequenced reads are required to identify immunoglobulin sequences from four different hybridoma clones. Thus, our approach would facilitate determining variable CDSs drastically.",
author = "Yuki Kuniyoshi and Kazumitsu Maehara and Takeshi Iwasaki and Masayasu Hayashi and Yuichiro Semba and Masatoshi Fujita and Yuko Sato and Hiroshi Kimura and Akihito Harada and Yasuyuki Ohkawa",
year = "2016",
month = "10",
day = "1",
doi = "10.1371/journal.pone.0165473",
language = "English",
volume = "11",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "10",

}

TY - JOUR

T1 - Identification of immunoglobulin gene sequences from a small read number of mRNA-seq using hybridomas

AU - Kuniyoshi, Yuki

AU - Maehara, Kazumitsu

AU - Iwasaki, Takeshi

AU - Hayashi, Masayasu

AU - Semba, Yuichiro

AU - Fujita, Masatoshi

AU - Sato, Yuko

AU - Kimura, Hiroshi

AU - Harada, Akihito

AU - Ohkawa, Yasuyuki

PY - 2016/10/1

Y1 - 2016/10/1

N2 - Identification of immunoglobulin genes in hybridomas is essential for producing antibodies for research and clinical applications. A couple of methods such as RACE and degenerative PCR have been developed for determination of the Igh and Igl/Igk coding sequences (CDSs) but it has been difficult to process a number of hybridomas both with accuracy and rapidness. Here, we propose a new strategy for antibody sequence determination by mRNA-seq of hybridomas. We demonstrated that hybridomas highly expressed the Igh and Igl/Igk genes and that de novo transcriptome assembly using mRNA-seq data enabled identification of the CDS of both Igh and Igl/Igk accurately. Furthermore, we estimated that only 30,000 sequenced reads are required to identify immunoglobulin sequences from four different hybridoma clones. Thus, our approach would facilitate determining variable CDSs drastically.

AB - Identification of immunoglobulin genes in hybridomas is essential for producing antibodies for research and clinical applications. A couple of methods such as RACE and degenerative PCR have been developed for determination of the Igh and Igl/Igk coding sequences (CDSs) but it has been difficult to process a number of hybridomas both with accuracy and rapidness. Here, we propose a new strategy for antibody sequence determination by mRNA-seq of hybridomas. We demonstrated that hybridomas highly expressed the Igh and Igl/Igk genes and that de novo transcriptome assembly using mRNA-seq data enabled identification of the CDS of both Igh and Igl/Igk accurately. Furthermore, we estimated that only 30,000 sequenced reads are required to identify immunoglobulin sequences from four different hybridoma clones. Thus, our approach would facilitate determining variable CDSs drastically.

UR - http://www.scopus.com/inward/record.url?scp=84992697230&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84992697230&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0165473

DO - 10.1371/journal.pone.0165473

M3 - Article

VL - 11

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 10

M1 - e0165473

ER -