Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: A case study in lung cancer.
Whole exome sequencing (WES) and RNA sequencing (RNA-Seq) are two main platforms used for next-generation sequencing (NGS). While WES is primarily for DNA variant discovery and RNA-Seq is mainly for measurement of gene expression, both can be used for detection of genetic variants, especially single nucleotide variants (SNVs). How consistently variants can be detected from WES and RNA-Seq has not been systematically evaluated. In this study, we examined the technical and biological inconsistencies in SNV detection using WES and RNA-Seq data from 27 pairs of tumor and matched normal samples. We analyzed SNVs in three categories: WES unique - those only detected in WES, RNA-Seq unique - those only detected in RNA-Seq, and shared - those detected in both. We found a small overlap (average ∼14%) between the SNVs called in WES and RNA-Seq. The WES unique SNVs were mainly due to low coverage, low expression, or their location on the non-transcribed strand in RNA-Seq data, while the RNA-Seq unique SNVs were primarily due to their location out of the WES-capture boundary regions (accounting ∼71%), as well as low coverage of the regions, low coverage of the mutant alleles or RNA-editing. The shared SNVs had high locus-specific coverage in both WES and RNA-Seq and high gene expression levels. Additionally, WES unique and RNA-Seq unique SNVs showed different nucleotide substitution patterns, e.g., ∼55% of RNA-Seq unique variants were A:T→G:C, a hallmark of RNA editing. This study provides an important evaluation on the inconsistencies of somatic SNVs called in WES and RNA-Seq data.
Center for Human Genetics Research, Vanderbilt University School of Medicine, Nashville, TN 37232, United States; Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, United States. Electronic address: timothy.obrien@vanderbilt.edu.
Timothy D
TD
O'Brien
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, United States. Electronic address: peilin.jia@vanderbilt.edu.
Peilin
P
Jia
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, United States. Electronic address: jfxia@ahu.edu.cn.
Junfeng
J
Xia
Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, United States. Electronic address: stqa8350@gmail.com.
Uma
U
Saxena
Department of Medicine/Division of Hematology-Oncology, Vanderbilt University School of Medicine, Nashville, TN 37232, United States. Electronic address: hailing.jin@Vanderbilt.Edu.
Hailing
H
Jin
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, United States. Electronic address: huy.vuong@gmail.com.
Huy
H
Vuong
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, United States. Electronic address: pora.kim@vanderbilt.edu.
Pora
P
Kim
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, United States. Electronic address: josephw10000@gmail.com.
Qingguo
Q
Wang
Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, United States. Electronic address: Aryee.Martin@mgh.harvard.edu.
Martin J
MJ
Aryee
Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, United States. Electronic address: MMINOKENUDSON@partners.org.
Mari
M
Mino-Kenudson
Department of Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA 02114, United States. Electronic address: JENGELMAN@partners.org.
Jeffrey A
JA
Engelman
Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, United States. Electronic address: LPLE@partners.org.
Long P
LP
Le
Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, United States. Electronic address: AIAFRATE@partners.org.
A John
AJ
Iafrate
Department of Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA 02114, United States. Electronic address: RHEIST@partners.org.
Rebecca S
RS
Heist
Department of Medicine/Division of Hematology-Oncology, Vanderbilt University School of Medicine, Nashville, TN 37232, United States. Electronic address: william.pao@Vanderbilt.Edu.
William
W
Pao
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, United States; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232, United States; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, United States. Electronic address: zhongming.zhao@vanderbilt.edu.
Zhongming
Z
Zhao
D059472:Exome / Q000235:genetics*; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*
Allele frequency; RNA editing; RNA-Seq; Single nucleotide variants; Somatic mutations; Whole exome sequencing