Comparative study of whole exome sequencing-based copy number variation detection tools

BMC Bioinformatics
Lanling ZhaoJunbo Duan

Abstract

With the rapid development of whole exome sequencing (WES), an increasing number of tools are being proposed for copy number variation (CNV) detection based on this technique. However, no comprehensive guide is available for the use of these tools in clinical settings, which renders them inapplicable in practice. To resolve this problem, in this study, we evaluated the performances of four WES-based CNV tools, and established a guideline for the recommendation of a suitable tool according to the application requirements. In this study, first, we selected four WES-based CNV detection tools: CoNIFER, cn.MOPS, CNVkit and exomeCopy. Then, we evaluated their performances in terms of three aspects: sensitivity and specificity, overlapping consistency and computational costs. From this evaluation, we obtained four main results: (1) The sensitivity increases and subsequently stabilizes as the coverage or CNV size increases, while the specificity decreases. (2) CoNIFER performs better for CNV insertions than for CNV deletions, while the remaining tools exhibit the opposite trend. (3) CoNIFER, cn.MOPS and CNVkit realize satisfactory overlapping consistency, which indicates their results are trustworthy. (4) CoNIFER has the best space com...Continue Reading

References

Jul 1, 2006·Genome Research·Jennifer L FreemanCharles Lee
Feb 10, 2007·Science·Barbara E StrangerEmmanouil T Dermitzakis
Mar 28, 2007·Annual Review of Genomics and Human Genetics·Bernard Conrad, Stylianos E Antonarakis
Sep 5, 2007·Nature Genetics·Steven A McCarroll, David M Altshuler
Jul 15, 2009·Nature Reviews. Genetics·P J HastingsGrzegorz Ira
Nov 17, 2009·Nature Genetics·Sarah B NgMichael J Bamshad
Aug 11, 2011·Bioinformatics·Jarupon Fah SathirapongsasutiStanley F Nelson
May 16, 2012·Genome Research·Niklas KrummEvan E Eichler
Jan 1, 2011·Statistical Applications in Genetics and Molecular Biology·Michael I LoveStefan A Haas
Apr 16, 2014·BMC Bioinformatics·Heng WangKai Ying
Aug 12, 2014·BMC Genomics·Pubudu Saneth SamarakoonRobert Lyle
Apr 23, 2016·PLoS Computational Biology·Eric TalevichBoris C Bastian
Jul 22, 2018·Developmental Neurobiology·Suzanne RohrbackJerold Chun
Nov 30, 2018·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Xiguo YuanMeihong Gao

❮ Previous
Next ❯

Methods Mentioned

BETA
exome sequencing

Software Mentioned

exomeCopy
CNVkit
cn
MOPS
ExCopyDepth
GRange
bowtie2
CoNIFER
samtools

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.