Impact of DNA source on genetic variant detection from human whole-genome sequencing data.
J Med Genet
; 56(12): 809-817, 2019 12.
Article
em En
| MEDLINE
| ID: mdl-31515274
ABSTRACT
BACKGROUND:
Whole blood is currently the most common DNA source for whole-genome sequencing (WGS), but for studies requiring non-invasive collection, self-collection, greater sample stability or additional tissue references, saliva or buccal samples may be preferred. However, the relative quality of sequencing data and accuracy of genetic variant detection from blood-derived, saliva-derived and buccal-derived DNA need to be thoroughly investigated.METHODS:
Matched blood, saliva and buccal samples from four unrelated individuals were used to compare sequencing metrics and variant-detection accuracy among these DNA sources.RESULTS:
We observed significant differences among DNA sources for sequencing quality metrics such as percentage of reads aligned and mean read depth (p<0.05). Differences were negligible in the accuracy of detecting short insertions and deletions; however, the false positive rate for single nucleotide variation detection was slightly higher in some saliva and buccal samples. The sensitivity of copy number variant (CNV) detection was up to 25% higher in blood samples, depending on CNV size and type, and appeared to be worse in saliva and buccal samples with high bacterial concentration. We also show that methylation-based enrichment for eukaryotic DNA in saliva and buccal samples increased alignment rates but also reduced read-depth uniformity, hampering CNV detection.CONCLUSION:
For WGS, we recommend using DNA extracted from blood rather than saliva or buccal swabs; if saliva or buccal samples are used, we recommend against using methylation-based eukaryotic DNA enrichment. All data used in this study are available for further open-science investigation.Palavras-chave
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Bases de dados:
MEDLINE
Assunto principal:
DNA
/
Variações do Número de Cópias de DNA
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Sequenciamento Completo do Genoma
Tipo de estudo:
Diagnostic_studies
Limite:
Adult
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Female
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Humans
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Male
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Middle aged
Idioma:
En
Revista:
J Med Genet
Ano de publicação:
2019
Tipo de documento:
Article
País de afiliação:
Canadá