SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach
| العنوان: | SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach |
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| المؤلفون: | Mingyi Wang, Bin Zhu, Russell Williams, Kristine Jones, Meredith Yeager, Belynda Hicks, Herbert Higson, Wen Luo, Dongjing Wu, Xiaopeng Bian |
| المصدر: | Scientific Reports, Vol 10, Iss 1, Pp 1-16 (2020) Scientific Reports |
| بيانات النشر: | Nature Publishing Group, 2020. |
| سنة النشر: | 2020 |
| مصطلحات موضوعية: | Somatic cell, Computer science, lcsh:Medicine, Machine learning, computer.software_genre, Tumor heterogeneity, Polymorphism, Single Nucleotide, Article, Neoplasms, Humans, Exome, lcsh:Science, Allele frequency, Cancer, Multidisciplinary, business.industry, lcsh:R, Computational Biology, High-Throughput Nucleotide Sequencing, Computational biology and bioinformatics, Nucleic acid, lcsh:Q, Artificial intelligence, business, Databases, Nucleic Acid, computer, Algorithms, Software |
| الوصف: | It is challenging to identify somatic variants from high-throughput sequence reads due to tumor heterogeneity, sub-clonality, and sequencing artifacts. In this study, we evaluated the performance of eight primary somatic variant callers and multiple ensemble methods using both real and synthetic whole-genome sequencing, whole-exome sequencing, and deep targeted sequencing datasets with the NA12878 cell line. The test results showed that a simple consensus approach can significantly improve performance even with a limited number of callers and is more robust and stable than machine learning based ensemble approaches. To fully exploit the multi-callers, we also developed a software package, SomaticCombiner, that can combine multiple callers and integrates a new variant allelic frequency (VAF) adaptive majority voting approach, which can maintain sensitive detection for variants with low VAFs. |
| اللغة: | English |
| تدمد: | 2045-2322 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::97b0dffee9ed4d9eac60126714a30466 http://link.springer.com/article/10.1038/s41598-020-69772-8 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....97b0dffee9ed4d9eac60126714a30466 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 20452322 |
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