Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

The Middle Ground: Midline Catheter use and Trainee Involvement in US Critical Care Fellowships.

Journal of intensive care medicine·2026

Same author

Carboplatin May Be an Effective and Tolerable Treatment Option for Platinum-Sensitive Pancreatic Cancer Patients With Pre-existing Neuropathy.

Cureus·2026

Same author

Hundreds of cardiac MRI traits derived using 3D diffusion autoencoders share a common genetic architecture.

Nature communications·2026

Same author

The Biobank Rare Variant consortium powers the discovery of rare genetic associations through global collaboration.

medRxiv : the preprint server for health sciences·2026

Same author

Cohort profile: Creation of an e-cohort to Address the Evaluation of Population Secondary Prevention Quality and Outcomes Post-Stroke (ESP-QOPS) in Wales.

International journal of population data science·2026

Same author

Mechanism of age-related accumulation of mtDNA mutations in human blood.

Nature·2026

Same journal

A human-specific genetic modifier reconfigures large-scale cortical network dynamics underlying behavioral performance.

bioRxiv : the preprint server for biology·2026

Same journal

<i>Staphylococcus aureus</i> uses a eukaryotic-like uridyltransferase to make UDP-GlcNAc for cell wall synthesis.

bioRxiv : the preprint server for biology·2026

Same journal

Dynamic redistribution of eIF4F controls cap-dependent translation initiation.

bioRxiv : the preprint server for biology·2026

Same journal

When does additional information improve accuracy of RNA secondary structure prediction?

bioRxiv : the preprint server for biology·2026

Same journal

Normative brain-state trajectories reveal deviation from healthy aging in Alzheimer's disease.

bioRxiv : the preprint server for biology·2026

Same journal

Noradrenergic infraslow rhythm during sleep is the critical link between heart-rate dynamics and memory consolidation.

bioRxiv : the preprint server for biology·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jul 24, 2025

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

CHARR efficiently estimates contamination from DNA sequencing data.

Wenhan Lu^1,2,3, Laura D Gauthier^1,4, Timothy Poterba^1,2,3

¹Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.

Biorxiv : the Preprint Server for Biology

|July 10, 2023

Summary

This summary is machine-generated.

DNA sample contamination in whole genome and exome sequencing can cause genotyping errors. A new metric, CHARR, estimates contamination using variant data, reducing costs and improving accuracy for large datasets.

More Related Videos

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

Published on: April 14, 2016

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Published on: June 3, 2017

Related Experiment Videos

Last Updated: Jul 24, 2025

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

Published on: April 14, 2016

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Published on: June 3, 2017

Area of Science:

Genomics
Bioinformatics

Background:

DNA sample contamination is a significant challenge in clinical and research whole genome and exome sequencing.
Contamination can lead to substantial reductions in variant call quality and widespread genotyping errors.
Existing contamination estimation tools rely on short-read data (BAM/CRAM), which are costly to store and often not retained.

Approach:

Propose CHARR (Contamination from Homozygous Alternate Reference Reads), a novel metric for estimating DNA sample contamination.
CHARR leverages reference reads within homozygous alternate variant calls.
Utilizes variant-level genotype information, computable from gVCFs, VCF/BCF callsets, or Hail VDS format.

Key Points:

CHARR accurately estimates contamination levels, comparable to existing methods.
Requires only a small fraction of variant-level genotype data.
Offers substantial cost savings in data storage and manipulation compared to BAM/CRAM-based tools.

Conclusions:

CHARR provides an accurate and cost-effective solution for estimating DNA sample contamination.
Improves the accuracy and efficiency of downstream analyses for large-scale sequencing datasets.
Facilitates more reliable variant calling and genotyping in genomic studies.