Impact of DNA source on genetic variant detection from human whole-genome sequencing data
| العنوان: | Impact of DNA source on genetic variant detection from human whole-genome sequencing data |
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| المؤلفون: | Charly L Phillips, Sergio L. Pereira, Wilson W L Sung, Syed A Haider, Stephen W. Scherer, Christian R. Marshall, Susan Walker, Charlotte Nguyen, Lisa J. Strug, Akshaya Raajkumar, Edward J Higginbotham, Michael J. Szego, Brett Trost |
| المصدر: | Journal of Medical Genetics |
| بيانات النشر: | BMJ, 2019. |
| سنة النشر: | 2019 |
| مصطلحات موضوعية: | Adult, Male, 0301 basic medicine, Saliva, DNA Copy Number Variations, Genotype, Buccal swab, Eukaryotic DNA replication, Computational biology, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, stomatognathic system, blood, buccal, Methods, Genetics, Humans, Genetics (clinical), Whole blood, Whole genome sequencing, saliva, Whole Genome Sequencing, Mouth Mucosa, DNA, Sequence Analysis, DNA, Buccal administration, Methylation, DNA Methylation, Middle Aged, dna source, stomatognathic diseases, 030104 developmental biology, chemistry, whole-genome sequencing, 030220 oncology & carcinogenesis, Female |
| الوصف: | BackgroundWhole 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.MethodsMatched blood, saliva and buccal samples from four unrelated individuals were used to compare sequencing metrics and variant-detection accuracy among these DNA sources.ResultsWe observed significant differences among DNA sources for sequencing quality metrics such as percentage of reads aligned and mean read depth (pConclusionFor 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. |
| تدمد: | 1468-6244 0022-2593 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5925735759d5ad0daff0d94d72837292 https://doi.org/10.1136/jmedgenet-2019-106281 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....5925735759d5ad0daff0d94d72837292 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 14686244 00222593 |
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