تفاصيل الوثيقة

نوع الوثيقة : مقال في مجلة دورية 
عنوان الوثيقة :
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
 
لغة الوثيقة : الانجليزية 
المستخلص : 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. 
ردمد : 2045-2322 
اسم الدورية : Scientific reports 
المجلد : 6 
العدد : 1 
سنة النشر : 1437 هـ
2016 م 
نوع المقالة : مقالة علمية 
تاريخ الاضافة على الموقع : Tuesday, July 18, 2017 

الباحثون

اسم الباحث (عربي)اسم الباحث (انجليزي)نوع الباحثالمرتبة العلميةالبريد الالكتروني
Lei CaiCai, Lei باحثدكتوراه 
Wei YuanYuan, Wei باحثدكتوراه 
Zhou ZhangZhang, Zhou باحثدكتوراه 
Lin HeHe, Lin باحثدكتوراه 
Kuo-Chen ChouChou, Kuo-Chen باحثدكتوراهlcai@sjtu.edu.cn

الملفات

اسم الملفالنوعالوصف
 42022.pdf pdf 

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