ArticleGenome biology2010
Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing.
Article in Genome biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it.
- DNA methylation screening identifies driver epigenetic events of cancer cell survival.Cancer cell · 2012Pooled it
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- R-Loops and Its Chro-Mates: The Strange Case of Dr. Jekyll and Mr. Hyde.International journal of molecular sciences · 2021Review
- Hypoxia-induced SETX links replication stress with the unfolded protein response.Nature communications · 2021Article
- Establishment and characterization of novel human primary endometrial cancer cell line (ZJB-ENC1) and its genomic characteristic.Journal of Cancer · 2019Article
- Evaluation genotypes of cancer cell lines HCC1954 and SiHa by short tandem repeat (STR) analysis and DNA sequencing.Molecular biology reports · 2018Article
- Dormant origins and fork protection mechanisms rescue sister forks arrested by transcription.Nucleic acids research · 2018Article
- Integrated analysis of whole-exome sequencing and transcriptome profiling in males with autism spectrum disorders.Molecular autism · 2015Article
- Inositol pyrophosphates mediate the DNA-PK/ATM-p53 cell death pathway by regulating CK2 phosphorylation of Tti1/Tel2.Molecular cell · 2014Article
- G-protein-coupled receptor GPR161 is overexpressed in breast cancer and is a promoter of cell proliferation and invasion.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Harnessing the genome for characterization of G-protein coupled receptors in cancer pathogenesis.The FEBS journal · 2013Review
- eQTL Mapping Using RNA-seq Data.Statistics in biosciences · 2013Article
- nFuse: discovery of complex genomic rearrangements in cancer using high-throughput sequencing.Genome research · 2012Article
- Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer.Genome research · 2012Article
- Exome sequencing and the genetic basis of complex traits.Nature genetics · 2012Article
- Genomic sequencing in clinical trials.Journal of translational medicine · 2011Review
- Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual.Nucleic acids research · 2011Article
- SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data.BMC bioinformatics · 2011Article
Corrections and comments
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Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTo identify potential tumor suppressor genes, genome-wide data from exome and transcriptome sequencing were combined to search for genes with loss of heterozygosity and allele-specific expression. The analysis was conducted on the breast cancer cell line HCC1954, and a lymphoblast cell line from the same individual, HCC1954BL.
resultsBy comparing exome sequences from the two cell lines, we identified loss of heterozygosity events at 403 genes in HCC1954 and at one gene in HCC1954BL. The combination of exome and transcriptome sequence data also revealed 86 and 50 genes with allele specific expression events in HCC1954 and HCC1954BL, which comprise 5.4% and 2.6% of genes surveyed, respectively. Many of these genes identified by loss of heterozygosity and allele-specific expression are known or putative tumor suppressor genes, such as BRCA1, MSH3 and SETX, which participate in DNA repair pathways.
conclusionsOur results demonstrate that the combined application of high throughput sequencing to exome and allele-specific transcriptome analysis can reveal genes with known tumor suppressor characteristics, and a shortlist of novel candidates for the study of tumor suppressor activities.
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