Genomic sequencing and analysis of a Chinese hamster ovary cell line using Illumina sequencing technology.
BACKGROUND
Chinese hamster ovary (CHO) cells are among the most widely used hosts for therapeutic protein production. Yet few genomic resources are available to aid in engineering high-producing cell lines.


RESULTS
High-throughput Illumina sequencing was used to generate a 1x genomic coverage of an engineered CHO cell line expressing secreted alkaline phosphatase (SEAP). Reference-guided alignment and assembly produced 3.57 million contigs and CHO-specific sequence information for ~ 18,000 mouse and ~ 19,000 rat orthologous genes. The majority of these genes are involved in metabolic processes, cellular signaling, and transport and represent attractive targets for cell line engineering.


CONCLUSIONS
This demonstrates the applicability of next-generation sequencing technology and comparative genomic analysis in the development of CHO genomic resources.
Department of Chemical Engineering, University of Delaware, Newark, DE 19711, USA.
Stephanie
S
Hammond
Jeffrey C
JC
Swanberg
Mihailo
M
Kaplarevic
Kelvin H
KH
Lee
D000469:Alkaline Phosphatase / Q000235:genetics; D000818:Animals; D016466:CHO Cells / Q000378:metabolism*; D019295:Computational Biology; D006224:Cricetinae; D003412:Cricetulus; D051379:Mice; D008969:Molecular Sequence Data; D051381:Rats; D017422:Sequence Analysis, DNA / Q000379:methods*
D000469:Alkaline Phosphatase
Genome Biol. 2009;10(9):R98
19761611
Nat Rev Genet. 2010 Jan;11(1):31-46
19997069
Nucleic Acids Res. 2010 Jul;38(12):3999-4010
20194116
Nat Methods. 2009 Nov;6(11 Suppl):S13-20
19844226
Biotechnol J. 2006 Jun;1(6):639-50
16892312
BMC Bioinformatics. 2009 Dec 15;10:421
20003500
BMC Genomics. 2009 Oct 16;10:479
19835600
Mol Cell Biol. 1990 Jun;10(6):3056-66
2188107
Genome Biol. 2001;2(6):REVIEWS0005
11423011
J Biosci Bioeng. 2010 May;109(5):504-11
20347775
Biotechnol Bioeng. 2009 Dec 1;104(5):1041-6
19557832
Biotechnol Bioeng. 2009 Dec 1;104(5):986-94
19575438
Biotechnol Bioeng. 2010 Apr 1;105(5):1002-9
19882695
Biotechnol Bioeng. 2009 Jan 1;102(1):246-63
18726962
PLoS One. 2010 Jun 29;5(6):e11370
20614011
Genome Biol. 2009;10(8):R88
19712469
Nat Biotechnol. 2004 Nov;22(11):1393-8
15529164
Genome Res. 2009 Sep;19(9):1586-92
19657104
Nat Biotechnol. 2008 Oct;26(10):1135-45
18846087
Biotechnol Adv. 2009 Nov-Dec;27(6):1028-1035
19470403
BMC Genomics. 2009 Aug 18;10:382
19689807
Cytotechnology. 2007 Apr;53(1-3):3-22
19003186
Mol Biotechnol. 2006 Oct;34(2):125-40
17172658
Nature. 2005 Sep 15;437(7057):376-80
16056220
Biotechnol Bioeng. 2005 Sep 5;91(5):592-606
16003777
Biochem Biophys Res Commun. 2006 Feb 24;340(4):1069-77
16403443
Biotechnol Bioeng. 2008 Dec 15;101(6):1359-65
18814282
Biotechnol Bioeng. 2005 May 5;90(3):354-64
15772946
Biotechnol Bioeng. 2007 Oct 1;98(2):391-410
17461427
Genome Res. 2008 Nov;18(11):1851-8
18714091
Genome Res. 2002 Apr;12(4):656-64
11932250
Nature. 2004 Apr 1;428(6982):493-521
15057822
BMC Genomics. 2005 May 10;6:70
15885146
Genome Res. 1998 Oct;8(10):1074-84
9799794
Science. 2003 Sep 26;301(5641):1898-903
14512627
BMC Genomics. 2008 Aug 28;9:404
18755037
Biologicals. 1994 Jun;22(2):95-102
7917238
Bioinformatics. 2009 Jun 15;25(12):1554-5
19369497
Bioinformatics. 2009 Nov 1;25(21):2878-81
19542148
Biotechnol Bioeng. 2007 Oct 1;98(2):429-39
17390381
Nature. 2002 Dec 5;420(6915):520-62
12466850