PMID: 26776187Jan 19, 2016Paper

REPURPOSING GERMLINE EXOMES OF THE CANCER GENOME ATLAS DEMANDS A CAUTIOUS APPROACH AND SAMPLE-SPECIFIC VARIANT FILTERING

Pacific Symposium on Biocomputing
Amanda KoireOlivier Lichtarge

Abstract

When seeking to reproduce results derived from whole-exome or genome sequencing data that could advance precision medicine, the time and expense required to produce a patient cohort make data repurposing an attractive option. The first step in repurposing is setting some quality baseline for the data so that conclusions are not spurious. This is difficult because there can be variations in quality from center to center, clinic to clinic and even patient to patient. Here, we assessed the quality of the whole-exome germline mutations of TCGA cancer patients using patterns of nucleotide substitution and negative selection against impactful mutations. We estimated the fraction of false positive variant calls for each exome with respect to two gold standard germline exomes, and found large variability in the quality of SNV calls between samples, cancer subtypes, and institutions. We then demonstrated how variant features, such as the average base quality for reads supporting an allele, can be used to identify sample-specific filtering parameters to optimize the removal of false positive calls. We concluded that while these germlines have many potential applications to precision medicine, users should assess the quality of the availa...Continue Reading

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.