Validation of whole genome sequencing from dried blood spots.
Dried blood spots
Population studies
Whole genome sequencing
Journal
BMC medical genomics
ISSN: 1755-8794
Titre abrégé: BMC Med Genomics
Pays: England
ID NLM: 101319628
Informations de publication
Date de publication:
20 04 2021
20 04 2021
Historique:
received:
22
12
2020
accepted:
23
03
2021
entrez:
21
4
2021
pubmed:
22
4
2021
medline:
21
1
2022
Statut:
epublish
Résumé
Dried blood spots (DBS) are a relatively inexpensive source of nucleic acids and are easy to collect, transport, and store in large-scale field surveys, especially in resource-limited settings. However, their performance in whole-genome sequencing (WGS) relative to that of venous blood DNA has not been analyzed for various downstream applications. This study compares the WGS performance of DBS paired with venous blood samples collected from 12 subjects. Results of standard quality checks of coverage, base quality, and mapping quality were found to be near identical between DBS and venous blood. Concordance for single-nucleotide variants, insertions and deletions, and copy number variants was high between these two sample types. Additionally, downstream analyses typical of population-based studies were performed, such as mitochondrial heteroplasmy detection, haplotype analysis, mitochondrial copy number changes, and determination of telomere lengths. The absolute mitochondrial copy number values were higher for DBS than for venous blood, though the trend in sample-to-sample variation was similar between DBS and blood. Telomere length estimates in most DBS samples were on par with those from venous blood. DBS samples can serve as a robust and feasible alternative to venous blood for studies requiring WGS analysis.
Sections du résumé
BACKGROUND
Dried blood spots (DBS) are a relatively inexpensive source of nucleic acids and are easy to collect, transport, and store in large-scale field surveys, especially in resource-limited settings. However, their performance in whole-genome sequencing (WGS) relative to that of venous blood DNA has not been analyzed for various downstream applications.
METHODS
This study compares the WGS performance of DBS paired with venous blood samples collected from 12 subjects.
RESULTS
Results of standard quality checks of coverage, base quality, and mapping quality were found to be near identical between DBS and venous blood. Concordance for single-nucleotide variants, insertions and deletions, and copy number variants was high between these two sample types. Additionally, downstream analyses typical of population-based studies were performed, such as mitochondrial heteroplasmy detection, haplotype analysis, mitochondrial copy number changes, and determination of telomere lengths. The absolute mitochondrial copy number values were higher for DBS than for venous blood, though the trend in sample-to-sample variation was similar between DBS and blood. Telomere length estimates in most DBS samples were on par with those from venous blood.
CONCLUSION
DBS samples can serve as a robust and feasible alternative to venous blood for studies requiring WGS analysis.
Identifiants
pubmed: 33879142
doi: 10.1186/s12920-021-00951-w
pii: 10.1186/s12920-021-00951-w
pmc: PMC8056537
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
110Subventions
Organisme : NIA NIH HHS
ID : P30 AG024409
Pays : United States
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