دورية أكاديمية
SMaSH: Sample matching using SNPs in humans
| العنوان: | SMaSH: Sample matching using SNPs in humans |
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| المؤلفون: | Maximillian Westphal, David Frankhouser, Carmine Sonzone, Peter G. Shields, Pearlly Yan, Ralf Bundschuh |
| المصدر: | BMC Genomics, Vol 20, Iss S12, Pp 1-10 (2019) |
| بيانات النشر: | BMC, 2019. |
| سنة النشر: | 2019 |
| المجموعة: | LCC:Biotechnology LCC:Genetics |
| مصطلحات موضوعية: | Sample swap, Next generation sequencing data, Identity matching, Biotechnology, TP248.13-248.65, Genetics, QH426-470 |
| الوصف: | Abstract Background Inadvertent sample swaps are a real threat to data quality in any medium to large scale omics studies. While matches between samples from the same individual can in principle be identified from a few well characterized single nucleotide polymorphisms (SNPs), omics data types often only provide low to moderate coverage, thus requiring integration of evidence from a large number of SNPs to determine if two samples derive from the same individual or not. Methods We select about six thousand SNPs in the human genome and develop a Bayesian framework that is able to robustly identify sample matches between next generation sequencing data sets. Results We validate our approach on a variety of data sets. Most importantly, we show that our approach can establish identity between different omics data types such as Exome, RNA-Seq, and MethylCap-Seq. We demonstrate how identity detection degrades with sample quality and read coverage, but show that twenty million reads of a fairly low quality RNA-Seq sample are still sufficient for reliable sample identification. Conclusion Our tool, SMASH, is able to identify sample mismatches in next generation sequencing data sets between different sequencing modalities and for low quality sequencing data. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 1471-2164 |
| العلاقة: | https://doaj.org/toc/1471-2164Test |
| DOI: | 10.1186/s12864-019-6332-7 |
| الوصول الحر: | https://doaj.org/article/07fe8bcd6f2d4e1195e0d10126a435a7Test |
| رقم الانضمام: | edsdoj.07fe8bcd6f2d4e1195e0d10126a435a7 |
| قاعدة البيانات: | Directory of Open Access Journals |
Full Text Finder | تدمد: | 14712164 |
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| DOI: | 10.1186/s12864-019-6332-7 |