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Updated: Apr 22, 2026

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

Estimating genotype error rates from high-coverage next-generation sequence data.

Jeffrey D Wall¹, Ling Fung Tang², Brandon Zerbe³

¹Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California 94143, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, California 94143, USA; wallj@humgen.ucsf.edu.

Genome Research

|October 12, 2014

Summary

This summary is machine-generated.

Next-generation sequencing (NGS) platforms like Complete Genomics and Illumina HiSeq have variable genotype call accuracy. Error rates for whole-genome and whole-exome sequencing range from 0.1% to 0.6%, increasing for rare variants.

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Exome and whole-genome sequencing are increasingly utilized in research.
Accuracy of genotype calls from common sequencing platforms is not well-established.

Purpose of the Study:

To estimate genotype error rates for Complete Genomics and Illumina HiSeq platforms.
To evaluate factors influencing sequencing accuracy, including sample type, platform, coverage depth, and variant rarity.

Main Methods:

Replicate high-coverage sequencing of blood and saliva DNA from four individuals.
Analysis of genotype calls from Complete Genomics and Illumina HiSeq whole-genome and whole-exome sequencing data.
Estimation of error rates for nonreference genotype calls.

Main Results:

Nonreference genotype error rates ranged from 0.1% to 0.6%.
Complete Genomics exhibited higher error rates than Illumina.
Error rates increased for rare/unique variants (up to 6%) and with greater depth of coverage on Illumina.
No significant difference in error rates between blood and saliva samples.

Conclusions:

Caution is advised when interpreting results from next-generation sequencing association studies.
Clinical application of NGS requires validation due to potential inaccuracies, especially for rare variants.
Genotype quality scores may not accurately reflect error rates at higher values for Illumina data.