تفاصيل الوثيقة
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نوع الوثيقة |
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مقال في مجلة دورية |
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عنوان الوثيقة |
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In-depth comparison of somatic point mutation callers based on different tumor next-generation sequencing depth data In-depth comparison of somatic point mutation callers based on different tumor next-generation sequencing depth data |
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لغة الوثيقة |
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الانجليزية |
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المستخلص |
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Four popular somatic single nucleotide variant (SNV) calling methods (Varscan, SomaticSniper, Strelka
and MuTect2) were carefully evaluated on the real whole exome sequencing (WES, depth of ~50X)
and ultra-deep targeted sequencing (UDT-Seq, depth of ~370X) data. The four tools returned poor
consensus on candidates (only 20% of calls were with multiple hits by the callers). For both WES and
UDT-Seq, MuTect2 and Strelka obtained the largest proportion of COSMIC entries as well as the lowest
rate of dbSNP presence and high-alternative-alleles-in-control calls, demonstrating their superior
sensitivity and accuracy. Combining different callers does increase reliability of candidates, but narrows
the list down to very limited range of tumor read depth and variant allele frequency. Calling SNV on
UDT-Seq data, which were of much higher read-depth, discovered additional true-positive variations,
despite an even more tremendous growth in false positive predictions. Our findings not only provide
valuable benchmark for state-of-the-art SNV calling methods, but also shed light on the access to more
accurate SNV identification in the future. |
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ردمد |
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2045-2322 |
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اسم الدورية |
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Scientific reports |
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المجلد |
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6 |
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العدد |
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1 |
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سنة النشر |
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1437 هـ
2016 م |
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نوع المقالة |
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مقالة علمية |
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تاريخ الاضافة على الموقع |
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Tuesday, July 18, 2017 |
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الباحثون
| Lei Cai | Cai, Lei | باحث | دكتوراه | |
| Wei Yuan | Yuan, Wei | باحث | دكتوراه | |
| Zhou Zhang | Zhang, Zhou | باحث | دكتوراه | |
| Lin He | He, Lin | باحث | دكتوراه | |
| Kuo-Chen Chou | Chou, Kuo-Chen | باحث | دكتوراه | lcai@sjtu.edu.cn |
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الرجوع إلى صفحة الأبحاث
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