A new massively parallel nanoball sequencing platform for whole exome research.
BGISEQ-500
Variation detection
Whole exome sequencing
Journal
BMC bioinformatics
ISSN: 1471-2105
Titre abrégé: BMC Bioinformatics
Pays: England
ID NLM: 100965194
Informations de publication
Date de publication:
25 Mar 2019
25 Mar 2019
Historique:
received:
02
11
2018
accepted:
19
03
2019
entrez:
27
3
2019
pubmed:
27
3
2019
medline:
17
4
2019
Statut:
epublish
Résumé
Whole exome sequencing (WES) has been widely used in human genetics research. BGISEQ-500 is a recently established next-generation sequencing platform. However, the performance of BGISEQ-500 on WES is not well studied. In this study, we evaluated the performance of BGISEQ-500 on WES by side-to-side comparison with Hiseq4000, on well-characterized human sample NA12878. BGISEQ demonstrated similarly high reproducibility as Hiseq for variation detection. Also, the SNVs from BGISEQ data is highly consistent with Hiseq results (concordance 96.5%~ 97%). Variation detection accuracy was subsequently evaluated with data from the genome in a bottle project as the benchmark. Both platforms showed similar sensitivity and precision in SNV detection. While in indel detection, BGISEQ showed slightly higher sensitivity and lower precision. The impact of sequence depth and read length on variation detection accuracy was further analyzed, and showed that variation detection sensitivity still increasing when the sequence depth is larger than 100x, and the impact of read length is minor when using 100x data. This study suggested that BGISEQ-500 is a qualified sequencing platform for WES.
Sections du résumé
BACKGROUND
BACKGROUND
Whole exome sequencing (WES) has been widely used in human genetics research. BGISEQ-500 is a recently established next-generation sequencing platform. However, the performance of BGISEQ-500 on WES is not well studied. In this study, we evaluated the performance of BGISEQ-500 on WES by side-to-side comparison with Hiseq4000, on well-characterized human sample NA12878.
RESULTS
RESULTS
BGISEQ demonstrated similarly high reproducibility as Hiseq for variation detection. Also, the SNVs from BGISEQ data is highly consistent with Hiseq results (concordance 96.5%~ 97%). Variation detection accuracy was subsequently evaluated with data from the genome in a bottle project as the benchmark. Both platforms showed similar sensitivity and precision in SNV detection. While in indel detection, BGISEQ showed slightly higher sensitivity and lower precision. The impact of sequence depth and read length on variation detection accuracy was further analyzed, and showed that variation detection sensitivity still increasing when the sequence depth is larger than 100x, and the impact of read length is minor when using 100x data.
CONCLUSIONS
CONCLUSIONS
This study suggested that BGISEQ-500 is a qualified sequencing platform for WES.
Identifiants
pubmed: 30909888
doi: 10.1186/s12859-019-2751-3
pii: 10.1186/s12859-019-2751-3
pmc: PMC6434795
doi:
Types de publication
Evaluation Study
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
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