A comparative genomic hybridization approach to study gene copy number variations among chinese hamster cell lines

Nandita Vishwanathan; Arpan Bandyopadhyay; Hsu Yuan Fu; Kathryn C. Johnson; Nathan M. Springer; Wei Shou Hu

doi:10.1002/bit.26311

A comparative genomic hybridization approach to study gene copy number variations among chinese hamster cell lines

Nandita Vishwanathan, Arpan Bandyopadhyay, Hsu Yuan Fu, Kathryn C. Johnson, Nathan M. Springer, Wei Shou Hu

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

Abstract

Chinese Hamster Ovary (CHO) cells are aneuploid in nature. The genome of recombinant protein producing CHO cell lines continuously undergoes changes in its structure and organization. We analyzed nine cell lines, including parental cell lines, using a comparative genomic hybridization (CGH) array focused on gene-containing regions. The comparison of CGH with copy-number estimates from sequencing data showed good correlation. Hierarchical clustering of the gene copy number variation data from CGH data revealed the lineage relationships between the cell lines. On analyzing the clones of a clonal population, some regions with altered genomic copy number status were identified indicating genomic changes during passaging. A CGH array is thus an effective tool in quantifying genomic alterations in industrial cell lines and can provide insights into the changes in the genomic structure during cell line derivation and long term culture. Biotechnol. Bioeng. 2017;114: 1903–1908.

Original language	English (US)
Pages (from-to)	1903-1908
Number of pages	6
Journal	Biotechnology and bioengineering
Volume	114
Issue number	8
DOIs	https://doi.org/10.1002/bit.26311
State	Published - Aug 2017

Bibliographical note

Publisher Copyright:
© 2017 Wiley Periodicals, Inc.

Keywords

Chinese hamster ovary cell lines
comparative genomic hybridization
copy number variants
sequencing

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10.1002/bit.26311

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title = "A comparative genomic hybridization approach to study gene copy number variations among chinese hamster cell lines",

abstract = "Chinese Hamster Ovary (CHO) cells are aneuploid in nature. The genome of recombinant protein producing CHO cell lines continuously undergoes changes in its structure and organization. We analyzed nine cell lines, including parental cell lines, using a comparative genomic hybridization (CGH) array focused on gene-containing regions. The comparison of CGH with copy-number estimates from sequencing data showed good correlation. Hierarchical clustering of the gene copy number variation data from CGH data revealed the lineage relationships between the cell lines. On analyzing the clones of a clonal population, some regions with altered genomic copy number status were identified indicating genomic changes during passaging. A CGH array is thus an effective tool in quantifying genomic alterations in industrial cell lines and can provide insights into the changes in the genomic structure during cell line derivation and long term culture. Biotechnol. Bioeng. 2017;114: 1903–1908.",

keywords = "Chinese hamster ovary cell lines, comparative genomic hybridization, copy number variants, sequencing",

author = "Nandita Vishwanathan and Arpan Bandyopadhyay and Fu, {Hsu Yuan} and Johnson, {Kathryn C.} and Springer, {Nathan M.} and Hu, {Wei Shou}",

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T1 - A comparative genomic hybridization approach to study gene copy number variations among chinese hamster cell lines

AU - Vishwanathan, Nandita

AU - Bandyopadhyay, Arpan

AU - Fu, Hsu Yuan

AU - Johnson, Kathryn C.

AU - Springer, Nathan M.

AU - Hu, Wei Shou

PY - 2017/8

Y1 - 2017/8

N2 - Chinese Hamster Ovary (CHO) cells are aneuploid in nature. The genome of recombinant protein producing CHO cell lines continuously undergoes changes in its structure and organization. We analyzed nine cell lines, including parental cell lines, using a comparative genomic hybridization (CGH) array focused on gene-containing regions. The comparison of CGH with copy-number estimates from sequencing data showed good correlation. Hierarchical clustering of the gene copy number variation data from CGH data revealed the lineage relationships between the cell lines. On analyzing the clones of a clonal population, some regions with altered genomic copy number status were identified indicating genomic changes during passaging. A CGH array is thus an effective tool in quantifying genomic alterations in industrial cell lines and can provide insights into the changes in the genomic structure during cell line derivation and long term culture. Biotechnol. Bioeng. 2017;114: 1903–1908.

AB - Chinese Hamster Ovary (CHO) cells are aneuploid in nature. The genome of recombinant protein producing CHO cell lines continuously undergoes changes in its structure and organization. We analyzed nine cell lines, including parental cell lines, using a comparative genomic hybridization (CGH) array focused on gene-containing regions. The comparison of CGH with copy-number estimates from sequencing data showed good correlation. Hierarchical clustering of the gene copy number variation data from CGH data revealed the lineage relationships between the cell lines. On analyzing the clones of a clonal population, some regions with altered genomic copy number status were identified indicating genomic changes during passaging. A CGH array is thus an effective tool in quantifying genomic alterations in industrial cell lines and can provide insights into the changes in the genomic structure during cell line derivation and long term culture. Biotechnol. Bioeng. 2017;114: 1903–1908.

KW - Chinese hamster ovary cell lines

KW - comparative genomic hybridization

KW - copy number variants

KW - sequencing

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JO - Biotechnology and Bioengineering

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IS - 8

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A comparative genomic hybridization approach to study gene copy number variations among chinese hamster cell lines

Abstract

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