کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
11007670 | 1545069 | 2018 | 23 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
SEG - A Software Program for Finding Somatic Copy Number Alterations in Whole Genome Sequencing Data of Cancer
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کلمات کلیدی
موضوعات مرتبط
علوم زیستی و بیوفناوری
بیوشیمی، ژنتیک و زیست شناسی مولکولی
بیوتکنولوژی یا زیستفناوری
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چکیده انگلیسی
As next-generation sequencing technology advances and the cost decreases, whole genome sequencing (WGS) has become the preferred platform for the identification of somatic copy number alteration (CNA) events in cancer genomes. To more effectively decipher these massive sequencing data, we developed a software program named SEG, shortened from the word “segment”. SEG utilizes mapped read or fragment density for CNA discovery. To reduce CNA artifacts arisen from sequencing and mapping biases, SEG first normalizes the data by taking the log2-ratio of each tumor density against its matching normal density. SEG then uses dynamic programming to find change-points among a contiguous log2-ratio data series along a chromosome, dividing the chromosome into different segments. SEG finally identifies those segments having CNA. Our analyses with both simulated and real sequencing data indicate that SEG finds more small CNAs than other published software tools.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Computational and Structural Biotechnology Journal - Volume 16, 2018, Pages 335-341
Journal: Computational and Structural Biotechnology Journal - Volume 16, 2018, Pages 335-341
نویسندگان
Mucheng Zhang, Deli Liu, Jie Tang, Yuan Feng, Tianfang Wang, Kevin K. Dobbin, Paul Schliekelman, Shaying Zhao,