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Deep sequencing of 3 cancer cell lines on 2 sequencing platforms

Kanika Arora, Minita Shah, Molly Johnson, Rashesh Sanghvi, Jennifer Shelton, Kshithija Nagulapalli, Dayna M. Oschwald, Michael C. Zody, Soren Germer, Vaidehi Jobanputra, Jade Carter, View ORCID ProfileNicolas Robine
doi: https://doi.org/10.1101/623702
Kanika Arora
New York Genome Center
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Minita Shah
New York Genome Center
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Molly Johnson
New York Genome Center
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Rashesh Sanghvi
New York Genome Center
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Jennifer Shelton
New York Genome Center
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Kshithija Nagulapalli
New York Genome Center
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Dayna M. Oschwald
New York Genome Center
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Michael C. Zody
New York Genome Center
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Soren Germer
New York Genome Center
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Vaidehi Jobanputra
New York Genome Center
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Jade Carter
New York Genome Center
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Nicolas Robine
New York Genome Center
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  • ORCID record for Nicolas Robine
  • For correspondence: nrobine@nygenome.org
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Abstract

To test the performance of a new sequencing platform, develop an updated somatic calling pipeline and establish a reference for future benchmarking experiments, we sequenced 3 common cancer cell lines along with their matched normal cell lines to great sequencing depths (up to 278X coverage) on both Illumina HiSeqX and NovaSeq sequencing instruments. Somatic calling was generally consistent between the two platforms despite minor differences at the read level. We designed and implemented a novel pipeline for the analysis of tumor-normal samples, using multiple variant callers. We show that coupled with a high-confidence filtering strategy, it improves the accuracy of somatic calls. We also demonstrate the utility of the dataset by creating an artificial purity ladder to evaluate the somatic pipeline and benchmark methods for estimating purity and ploidy from tumor-normal pairs. The data and results of the pipeline are made accessible to the cancer genomics community.

Footnotes

  • https://www.nygenome.org/bioinformatics/3-cancer-cell-lines-on-2-sequencers/

  • ↵8 https://www.nygenome.org/bioinformatics/3-cancer-cell-lines-on-2-sequencers/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted April 30, 2019.
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Deep sequencing of 3 cancer cell lines on 2 sequencing platforms
Kanika Arora, Minita Shah, Molly Johnson, Rashesh Sanghvi, Jennifer Shelton, Kshithija Nagulapalli, Dayna M. Oschwald, Michael C. Zody, Soren Germer, Vaidehi Jobanputra, Jade Carter, Nicolas Robine
bioRxiv 623702; doi: https://doi.org/10.1101/623702
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Deep sequencing of 3 cancer cell lines on 2 sequencing platforms
Kanika Arora, Minita Shah, Molly Johnson, Rashesh Sanghvi, Jennifer Shelton, Kshithija Nagulapalli, Dayna M. Oschwald, Michael C. Zody, Soren Germer, Vaidehi Jobanputra, Jade Carter, Nicolas Robine
bioRxiv 623702; doi: https://doi.org/10.1101/623702

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