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CHOPPI: a web tool for the analysis of immunogenicity risk from host cell proteins in CHO-based protein production.

Bailey-Kellogg C, Gutiérrez AH, Moise L, Terry F, Martin WD, De Groot AS - Biotechnol. Bioeng. (2014)

Bottom Line: Even at low levels, residual HCPs can induce a detrimental immune response compromising the safety and efficacy of a biologic.Biotechnol.Bioeng. 2014;111: 2170-2182. © 2014 Wiley Periodicals, Inc.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Dartmouth College, Hanover, New Hampshire.

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Filtering the CHO genome. CHOPPI enables selection of CHO protein subsets by homology matching with a CHO transcriptome, a human proteome, a mouse secretome, and the human genome, along with testing for the presence of a predicted signal peptide.
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fig02: Filtering the CHO genome. CHOPPI enables selection of CHO protein subsets by homology matching with a CHO transcriptome, a human proteome, a mouse secretome, and the human genome, along with testing for the presence of a predicted signal peptide.

Mentions: The “genome filter” usage (Fig. 1a and c) starts with a specified CHO genome and filters it according to user-specified criteria evaluating potential for expression and secretion, along with similarity to human proteins. The possible filters (Fig. 2) include matching to a CHO transcriptome, CHO proteome, mouse secretome, and human genome, and testing for a predicted signal peptide. Homology matching is based on results from BLAST according to user-specified sequence identity and coverage thresholds. Note that, except for the transcriptome, all sequences are amino acid sequences, previously translated and annotated from the relevant genomic data. This application of CHOPPI enables the identification of potentially immunogenic proteins that might be suitable for targeted downregulation in CHO protein production, if reduced immunogenicity is a desired outcome. See below for further illustration of the genome filter tool.


CHOPPI: a web tool for the analysis of immunogenicity risk from host cell proteins in CHO-based protein production.

Bailey-Kellogg C, Gutiérrez AH, Moise L, Terry F, Martin WD, De Groot AS - Biotechnol. Bioeng. (2014)

Filtering the CHO genome. CHOPPI enables selection of CHO protein subsets by homology matching with a CHO transcriptome, a human proteome, a mouse secretome, and the human genome, along with testing for the presence of a predicted signal peptide.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4282101&req=5

fig02: Filtering the CHO genome. CHOPPI enables selection of CHO protein subsets by homology matching with a CHO transcriptome, a human proteome, a mouse secretome, and the human genome, along with testing for the presence of a predicted signal peptide.
Mentions: The “genome filter” usage (Fig. 1a and c) starts with a specified CHO genome and filters it according to user-specified criteria evaluating potential for expression and secretion, along with similarity to human proteins. The possible filters (Fig. 2) include matching to a CHO transcriptome, CHO proteome, mouse secretome, and human genome, and testing for a predicted signal peptide. Homology matching is based on results from BLAST according to user-specified sequence identity and coverage thresholds. Note that, except for the transcriptome, all sequences are amino acid sequences, previously translated and annotated from the relevant genomic data. This application of CHOPPI enables the identification of potentially immunogenic proteins that might be suitable for targeted downregulation in CHO protein production, if reduced immunogenicity is a desired outcome. See below for further illustration of the genome filter tool.

Bottom Line: Even at low levels, residual HCPs can induce a detrimental immune response compromising the safety and efficacy of a biologic.Biotechnol.Bioeng. 2014;111: 2170-2182. © 2014 Wiley Periodicals, Inc.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Dartmouth College, Hanover, New Hampshire.

Show MeSH