ArticlePLoS genetics2010
Allelic selection of amplicons in glioblastoma revealed by combining somatic and germline analysis.
Article in PLoS genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
22 citing papers in PubMed.
- Elevated DOCK4 expression correlates with favorable prognosis and immune infiltration in clear cell renal cell carcinoma.Annals of medicine · 2026Article
- Pathological Features of Tumors of the Nervous System in Hereditary Cancer Predisposition Syndromes: A Review.Neurosurgery · 2021Review
- [An improved association analysis pipeline for tumor susceptibility variant in haplotype amplification area].Nan fang yi ke da xue xue bao = Journal of Southern Medical University · 2020Article
- Germline Variants Impact Somatic Events during Tumorigenesis.Trends in genetics : TIG · 2019Review
- GOG 8020/210: Risk stratification of lymph node metastasis, disease progression and survival using single nucleotide polymorphisms in endometrial cancer: An NRG oncology/gynecologic oncology group study.Gynecologic oncology · 2019Article
- Article
- Concordance between somatic copy number loss and down-regulated expression: A pan-cancer study of cancer predisposition genes.Scientific reports · 2016Article
- dbCPG: A web resource for cancer predisposition genes.Oncotarget · 2016Article
- Patterns and functional implications of rare germline variants across 12 cancer types.Nature communications · 2015Article
- Identification of regulatory SNPs associated with genetic modifications in lung adenocarcinoma.BMC research notes · 2015Article
- Article
- The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge.Contemporary oncology (Poznan, Poland) · 2015Review
- Approaches to integrating germline and tumor genomic data in cancer research.Carcinogenesis · 2014Review
- The transcriptional regulatory network of proneural glioma determines the genetic alterations selected during tumor progression.Cancer research · 2014Article
- Detecting statistical interaction between somatic mutational events and germline variation from next-generation sequence data.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2014Article
- Cancer genomic research at the crossroads: realizing the changing genetic landscape as intratumoral spatial and temporal heterogeneity becomes a confounding factor.Cancer cell international · 2014Article
- Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue.Genome biology · 2013Article
- Calling amplified haplotypes in next generation tumor sequence data.Genome research · 2012Article
- Evaluation of allele-specific somatic changes of genome-wide association study susceptibility alleles in human colorectal cancers.PloS one · 2012Article
- Identity by descent mapping of founder mutations in cancer using high-resolution tumor SNP data.PloS one · 2012Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Cancer is a disease driven by a combination of inherited risk alleles coupled with the acquisition of somatic mutations, including amplification and deletion of genomic DNA. Potential relationships between the inherited and somatic aspects of the disease have only rarely been examined on a genome-wide level. Applying a novel integrative analysis of SNP and copy number measurements, we queried the tumor and normal-tissue genomes of 178 glioblastoma patients from the Cancer Genome Atlas project for preferentially amplified alleles, under the hypothesis that oncogenic germline variants will be selectively amplified in the tumor environment. Selected alleles are revealed by allelic imbalance in amplification across samples. This general approach is based on genetic principles and provides a method for identifying important tumor-related alleles. We find that SNP alleles that are most significantly overrepresented in amplicons tend to occur in genes involved with regulation of kinase and transferase activity, and many of these genes are known contributors to gliomagenesis. The analysis also implicates variants in synapse genes. By incorporating gene expression data, we demonstrate synergy between preferential allelic amplification and expression in DOCK4 and EGFR. Our results support the notion that combining germline and tumor genetic data can identify regions relevant to cancer biology.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.