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Comparison of Varia...
Comparison of Variant Calls from Whole Genome and Whole Exome Sequencing Data Using Matched Samples
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- Björn, Niclas (författare)
- Linköpings universitet,Avdelningen för läkemedelsforskning,Medicinska fakulteten
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- Pradhananga, Sailendra (författare)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Division of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
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- Sigurgeirsson, Benjamin (författare)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Division of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden; School of Engineering and Natural Sciences, University of Iceland, Reykjavík, Iceland
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- Lundeberg, Joakim (författare)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Division of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
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- Green, Henrik, 1975- (författare)
- Linköpings universitet,Avdelningen för läkemedelsforskning,Medicinska fakulteten,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Division of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
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- Sahlén, Pelin (författare)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Division of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
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(creator_code:org_t)
- 2018
- 2018
- Engelska.
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Ingår i: Journal of Next Generation Sequencing & Applications. - 2469-9853. ; 5:1, s. 1-8
- Relaterad länk:
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https://doi.org/10.4...
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https://www.longdom....
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https://kth.diva-por... (primary) (Raw object)
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https://liu.diva-por... (primary) (Raw object)
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https://urn.kb.se/re...
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https://urn.kb.se/re...
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Abstract
Ämnesord
Stäng
- Whole exome sequencing (WES) has been extensively used in genomic research. As sequencing costs decline it is being replaced by whole genome sequencing (WGS) in large-scale genomic studies, but more comparative information on WES and WGS datasets would be valuable. Thus, we have extensively compared variant calls obtained from WGS and WES of matched germline DNA samples from 96 lung cancer patients. WGS provided more homogeneous coverage with higher genotyping quality, and identified more variants, than WES, regardless of exome coverage depth. It also called more reference variants, reflecting its power to call rare variants, and more heterozygous variants that met applied quality criteria, indicating that WGS is less prone to allelic drop outs. However, increasing WES coverage reduced the discrepancy between the WES and WGS results. We believe that as sequencing costs further decline WGS will become the method of choice even for research confined to the exome.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinsk bioteknologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Medical Biotechnology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
Nyckelord
- Whole genome sequencing; Whole exome sequencing; Coverage; Depth; Genotyping quality; Discordant; Concordant; Variant calls; Single-nucleotide variants
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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