Screening the human exome: a comparison of whole genome and whole transcriptome sequencing.
Abstract
BACKGROUND: There is considerable interest in the development of methods to efficiently
identify all coding variants present in large sample sets of humans. There are three
approaches possible: whole-genome sequencing, whole-exome sequencing using exon capture
methods, and RNA-Seq. While whole-genome sequencing is the most complete, it remains
sufficiently expensive that cost effective alternatives are important. RESULTS: Here
we provide a systematic exploration of how well RNA-Seq can identify human coding
variants by comparing variants identified through high coverage whole-genome sequencing
to those identified by high coverage RNA-Seq in the same individual. This comparison
allowed us to directly evaluate the sensitivity and specificity of RNA-Seq in identifying
coding variants, and to evaluate how key parameters such as the degree of coverage
and the expression levels of genes interact to influence performance. We find that
although only 40% of exonic variants identified by whole genome sequencing were captured
using RNA-Seq; this number rose to 81% when concentrating on genes known to be well-expressed
in the source tissue. We also find that a high false positive rate can be problematic
when working with RNA-Seq data, especially at higher levels of coverage. CONCLUSIONS:
We conclude that as long as a tissue relevant to the trait under study is available
and suitable quality control screens are implemented, RNA-Seq is a fast and inexpensive
alternative approach for finding coding variants in genes with sufficiently high expression
levels.
Type
Journal articleSubject
Base SequenceDatabases, Genetic
Exons
Gene Expression Profiling
Gene Expression Regulation
Genome, Human
Humans
Leukocytes, Mononuclear
Polymorphism, Single Nucleotide
Sequence Alignment
Sequence Analysis, DNA
Sequence Homology, Nucleic Acid
Permalink
https://hdl.handle.net/10161/4395Published Version (Please cite this version)
10.1186/gb-2010-11-5-r57Publication Info
Cirulli, Elizabeth T; Singh, Abanish; Shianna, Kevin V; Ge, Dongliang; Smith, Jason
P; Maia, Jessica M; ... Center for HIV/AIDS Vaccine Immunology (CHAVI) (2010). Screening the human exome: a comparison of whole genome and whole transcriptome sequencing.
Genome Biol, 11(5). pp. R57. 10.1186/gb-2010-11-5-r57. Retrieved from https://hdl.handle.net/10161/4395.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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Show full item recordScholars@Duke
David Benjamin Goldstein
Adjunct Professor in the Department of Molecular Genetics and Microbiology
Abanish Singh
Assistant Professor of Psychiatry and Behavioral Sciences
With a unique skill set resulting from outstanding training, my sole aim was to help
improve human health through cutting-edge translational research. Specifically, I
have been interested in illuminating the mechanisms responsible for the causes and
progression of the leading public health conditions, which may help with the development
and enhancement of precision medicine. As part of this endeavor, I also became interested
in studying the measurement of biobehavioral risk factors and
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