Evaluation of Whole-Exome Enrichment Solutions: Lessons from the High-End of the Short-Read Sequencing Scale

Journal of Clinical Medicine
Ana Díaz-de UseraCarlos Flores

Abstract

Whole-exome sequencing has become a popular technique in research and clinical settings, assisting in disease diagnosis and increasing the understanding of disease pathogenesis. In this study, we aimed to compare common enrichment capture solutions available in the market. Peripheral blood-purified DNA samples were enriched with SureSelectQXT V6 (Agilent) and various Illumina solutions: TruSeq DNA Nano, TruSeq DNA Exome, Nextera DNA Exome, and Illumina DNA Prep with Enrichment, and sequenced on a HiSeq 4000. We found that their percentage of duplicate reads was as much as 2 times higher than previously reported values for the previous HiSeq series. SureSelectQXT and Illumina DNA Prep with Enrichment showed the best average on-target coverage, which improved when off-target regions were included. At high coverage levels and in shared bases, these two solutions and TruSeq DNA Exome provided three of the best performances. With respect to the number of small variants detected, SureSelectQXT presented the lowest number of detected variants in target regions. When off-target regions were considered, its ability equalized to other solutions. Our results show SureSelectQXT and Illumina DNA Prep with Enrichment to be the best enrichmen...Continue Reading

References

Nov 10, 2000·Nucleic Acids Research·M D KaneS J Madore
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Feb 6, 2007·Seminars in Cell & Developmental Biology·Axel ViselLen A Pennacchio
Oct 15, 2008·Human Molecular Genetics·Alexandra C Nica, Emmanouil T Dermitzakis
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 25, 2009·Bioinformatics·Nava WhitefordClive Brown
Jul 1, 2009·Cell·Jennifer E Phillips, Victor G Corces
Sep 11, 2009·Nature·Axel ViselLen A Pennacchio
Oct 29, 2009·Proceedings of the National Academy of Sciences of the United States of America·Murim ChoiRichard P Lifton
Jan 30, 2010·Nature Methods·Lira MamanovaDaniel J Turner
Jun 3, 2010·Nature Reviews. Genetics·Jonathan Marchini, Bryan Howie
Sep 14, 2010·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Noboru J Sakabe, Marcelo A Nobrega
Dec 7, 2010·Developmental Biology·Maximilian Haeussler, Jean-Stéphane Joly
Dec 22, 2010·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Elizabeth A WortheyDavid P Dimmock
Feb 23, 2011·Genome Biology·Daniel AirdAndreas Gnirke
Sep 17, 2011·Nature Reviews. Genetics·Sharon R Browning, Brian L Browning
Sep 29, 2011·Nature Biotechnology·Michael J ClarkMichael Snyder
Oct 1, 2011·Genome Biology·Anna-Maija SulonenJanna Saarela
Oct 25, 2011·Nature Genetics·Soumya RaychaudhuriJohanna M Seddon
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Oct 5, 2012·The New England Journal of Medicine·Joep de LigtLisenka E L M Vissers
Aug 10, 2013·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Vandana ShashiDavid G Goldstein
Oct 4, 2013·The New England Journal of Medicine·Yaping YangChristine M Eng
Feb 8, 2014·BioTechniques·Steven R HeadPhillip Ordoukhanian
Aug 19, 2014·Annals of Neurology·Siddharth SrivastavaAli Fatemi
Oct 19, 2014·JAMA : the Journal of the American Medical Association·Yaping YangChristine M Eng
Oct 19, 2014·JAMA : the Journal of the American Medical Association·Hane LeeStanley F Nelson
Mar 31, 2015·Nucleic Acids Research·Janine MeienbergGabor Matyas
Aug 4, 2015·Scientific Reports·Daichi ShigemizuTatsuhiko Tsunoda
Oct 3, 2015·Bioinformatics·Konstantin OkonechnikovFernando García-Alcalde
Dec 15, 2015·Briefings in Functional Genomics·Eleanor G SeabySarah Ennis
Apr 20, 2016·Proceedings of the National Academy of Sciences of the United States of America·Carl W FullerJingyue Ju
May 18, 2016·Nature Reviews. Genetics·Sara GoodwinW Richard McCombie
Aug 30, 2016·Nature Genetics·Sayantan DasChristian Fuchsberger
Oct 30, 2016·Clinical Chemistry·Kirsten J M van NimwegenJanneke P C Grutters
Oct 31, 2016·Genomics, Proteomics & Bioinformatics·Hengyun LuZemin Ning
Mar 24, 2017·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Lisenka E L M VissersMichèl A A P Willemsen

❮ Previous
Next ❯

Citations

Jul 3, 2021·International Journal of Molecular Sciences·Eva Suarez-PajesCarlos Flores

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR
Assay
exome sequencing
genotyping

Software Mentioned

Michigan Imputation Server
Qualimap
MEM
GATK Quality Score Recalibration ( VQSR
SureSelect QXT
GATK HaplotypeCaller
seqtk
SureSelect
BWA
Nextera Flex

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.