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Now showing items 31-40 of 43
Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer.
(NATURE PUBLISHING GROUP, 2018-10-01)
Efforts are being directed to systematically analyze the non-coding regions of the genome for cancer-driving mutations1-6. cis-regulatory elements (CREs) represent a highly enriched subset of the non-coding regions of the ...
Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data.
(PUBLIC LIBRARY SCIENCE, 2017-09-25)
A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA) in human cancer. Our study employs Whole Genome DNA Sequence (WGS) data from tumor samples (n = 103) to comprehensively ...
Identification of neutral tumor evolution across cancer types.
(NATURE PUBLISHING GROUP, 2016-03-01)
Despite extraordinary efforts to profile cancer genomes, interpreting the vast amount of genomic data in the light of cancer evolution remains challenging. Here we demonstrate that neutral tumor evolution results in a ...
CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting.
(BMC, 2015-07-28)
BACKGROUND: Next-generation sequencing (NGS) offers unprecedented opportunities to expand clinical genomics. It also presents challenges with respect to integration with data from other sequencing methods and historical ...
Gene Copy Number Estimation from Targeted Next-Generation Sequencing of Prostate Cancer Biopsies: Analytic Validation and Clinical Qualification.
(AMER ASSOC CANCER RESEARCH, 2017-10-15)
Purpose: Precise detection of copy number aberrations (CNA) from tumor biopsies is critically important to the treatment of metastatic prostate cancer. The use of targeted panel next-generation sequencing (NGS) is inexpensive, ...
Search for rare protein altering variants influencing susceptibility to multiple myeloma.
(IMPACT JOURNALS LLC, 2017-05-30)
The genetic basis underlying the inherited risk of developing multiple myeloma (MM) is largely unknown. To examine the impact of rare protein altering variants on the risk of developing MM we analyzed high-coverage exome ...
Post hoc Analysis for Detecting Individual Rare Variant Risk Associations Using Probit Regression Bayesian Variable Selection Methods in Case-Control Sequencing Studies.
(WILEY, 2016-09-01)
Rare variants (RVs) have been shown to be significant contributors to complex disease risk. By definition, these variants have very low minor allele frequencies and traditional single-marker methods for statistical analysis ...
Comparison of tumor-informed and tumor-naïve sequencing assays for ctDNA detection in breast cancer.
(WILEY, 2023-06-07)
Analysis of circulating tumor DNA (ctDNA) to monitor cancer dynamics and detect minimal residual disease has been an area of increasing interest. Multiple methods have been proposed but few studies have compared the ...
Representative Sequencing: Unbiased Sampling of Solid Tumor Tissue.
(CELL PRESS, 2020-05-05)
Although thousands of solid tumors have been sequenced to date, a fundamental under-sampling bias is inherent in current methodologies. This is caused by a tissue sample input of fixed dimensions (e.g., 6 mm biopsy), which ...
Signatures of positive selection reveal a universal role of chromatin modifiers as cancer driver genes.
(NATURE PORTFOLIO, 2017-10-13)
Tumors are composed of an evolving population of cells subjected to tissue-specific selection, which fuels tumor heterogeneity and ultimately complicates cancer driver gene identification. Here, we integrate cancer cell ...