Comprehensive Genomic Alterations in Common Cancer Cell Lines Revealed by Exome Sequencing

2013 ◽  
pp. 165-182
Author(s):  
Han Chang ◽  
Donald G. Jackson ◽  
Paul S. Kayne ◽  
Petra B. Ross-Macdonald ◽  
Rolf-Peter Ryseck ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Cell Lines ◽  
Cancer Cell ◽  
Cancer Cell Lines ◽  
Genomic Alterations ◽  
Common Cancer

scholarly journals Exome Sequencing Reveals Comprehensive Genomic Alterations across Eight Cancer Cell Lines

PLoS ONE ◽  
2011 ◽  
Vol 6 (6) ◽  
pp. e21097 ◽  
Author(s):  
Han Chang ◽  
Donald G. Jackson ◽  
Paul S. Kayne ◽  
Petra B. Ross-Macdonald ◽  
Rolf-Peter Ryseck ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Cell Lines ◽  
Cancer Cell ◽  
Cancer Cell Lines ◽  
Genomic Alterations

scholarly journals Ru(II)-based antineoplastic: A “wingtip” N-heterocyclic carbene facilitates access to a new class of organometallics that are cytotoxic to common cancer cell lines

2018 ◽  
Vol 33 (1) ◽  
pp. e4692 ◽  
Author(s):  
Ambarish Mondal ◽  
Rajat K. Tripathy ◽  
Parul Dutta ◽  
Manas Kumar Santra ◽  
Anvarhusein A. Isab ◽  
...  
Keyword(s):  
Cell Lines ◽  
Cancer Cell ◽  
Cancer Cell Lines ◽  
New Class ◽  
Common Cancer

Abstract 743: Fusion gene identification from common cancer cell lines and comparison to primary tumors

2019 ◽  
Author(s):  
Neetha Nanoth Vellichirammal ◽  
Abrar Albahrani ◽  
Jasjit K. Banwait ◽  
You Li ◽  
Babu Guda
Keyword(s):  
Cell Lines ◽  
Cancer Cell ◽  
Fusion Gene ◽  
Cancer Cell Lines ◽  
Gene Identification ◽  
Primary Tumors ◽  
Common Cancer

Abstract 743: Fusion gene identification from common cancer cell lines and comparison to primary tumors

2019 ◽  
Author(s):  
Neetha Nanoth Vellichirammal ◽  
Abrar Albahrani ◽  
Jasjit K. Banwait ◽  
You Li ◽  
Babu Guda
Keyword(s):  
Cell Lines ◽  
Cancer Cell ◽  
Fusion Gene ◽  
Cancer Cell Lines ◽  
Gene Identification ◽  
Primary Tumors ◽  
Common Cancer

Subtle genomic alterations and genomic instability revealed in diploid cancer cell lines

2008 ◽  
Vol 267 (1) ◽  
pp. 49-54 ◽  
Author(s):  
Xueying Mao ◽  
Bryan D. Young ◽  
Tracy Chaplin ◽  
Janet Shipley ◽  
Yong-Jie Lu
Keyword(s):  
Genomic Instability ◽  
Cell Lines ◽  
Cancer Cell ◽  
Cancer Cell Lines ◽  
Genomic Alterations

scholarly journals Deep sequencing of 3 cancer cell lines on 2 sequencing platforms

2019 ◽  
Author(s):  
Kanika Arora ◽  
Minita Shah ◽  
Molly Johnson ◽  
Rashesh Sanghvi ◽  
Jennifer Shelton ◽  
...  
Keyword(s):  
Cell Lines ◽  
Cancer Cell ◽  
Deep Sequencing ◽  
Normal Cell ◽  
Cancer Genomics ◽  
Cancer Cell Lines ◽  
High Confidence ◽  
Sequencing Platform ◽  
Common Cancer ◽  
Sequencing Platforms

AbstractTo 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.

scholarly journals Deep whole genome sequencing identifies recurrent genomic alterations in commonly-used breast cancer cell lines and patient derived xenograft models

2021 ◽  
Author(s):  
Niantao Deng ◽  
Andre Minoche ◽  
Kate Harvey ◽  
Andrei Goga ◽  
Alex Swarbrick
Keyword(s):  
Breast Cancer ◽  
Whole Genome Sequencing ◽  
Cell Lines ◽  
Cancer Cell ◽  
Genome Sequencing ◽  
Cancer Cell Lines ◽  
Whole Genome ◽  
Breast Cancers ◽  
Genomic Alterations ◽  
Pdx Models

Abstract BackgroundBreast cancer cell lines (BCCLs) and patient-derived xenografts (PDX) are the most frequently used models in breast cancer research. Despite their widespread usage, genome sequencing of these models is incomplete, with previous studies only focusing on targeted gene panels, whole exome or shallow whole genome sequencing. Deep whole genome sequencing is the most sensitive and accurate method to detect single nucleotide variants and indels, gene copy number and structural events such as gene fusions. ResultsHere we describe deep whole genome sequencing (WGS) of commonly used BCCL and PDX models using the Illumina X10 platform with an average ~ 60x coverage. We identify novel genomic alterations, including point mutations and genomic rearrangements at base-pair resolution, compared to previously available sequencing data. Through integrative analysis with publicly available functional screening data, we annotate new genomic features likely to be of biological significance. CSMD1 , previously identified as a tumor suppressor gene in various cancer types, including head and neck, lung and breast cancers, has been identified with deletion in 50% of our PDX models, suggesting an important role in aggressive breast cancers. ConclusionsOur WGS data provides a comprehensive genome sequencing resource of these models.

Abstract 4742: Using 1ng of DNA to detect haplotype phasing and gene fusions from whole exome sequencing of cancer cell lines

2015 ◽  
Author(s):  
Mirna Jarosz ◽  
Michael Schnall-Levin ◽  
Grace X. Y. Zheng ◽  
Patrick Marks ◽  
Sofia Kyriazopoulou-Panagiotopoulou ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Cell Lines ◽  
Cancer Cell ◽  
Cancer Cell Lines ◽  
Gene Fusions ◽  
Haplotype Phasing ◽  
Whole Exome

scholarly journals Identifying Candidate Druggable Targets in Canine Cancer Cell Lines Using Whole-Exome Sequencing

2019 ◽  
Vol 18 (8) ◽  
pp. 1460-1471 ◽  
Author(s):  
Sunetra Das ◽  
Rupa Idate ◽  
Kathryn E. Cronise ◽  
Daniel L. Gustafson ◽  
Dawn L. Duval
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Cell Lines ◽  
Cancer Cell ◽  
Cancer Cell Lines ◽  
Whole Exome ◽  
Canine Cancer ◽  
Druggable Targets
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