A machine-learning approach for accurate detection of copy number variants from exome sequencing
نویسندگان
چکیده
منابع مشابه
Enhanced copy number variants detection from whole-exome sequencing data using EXCAVATOR2
Copy Number Variants (CNVs) are structural rearrangements contributing to phenotypic variation that have been proved to be associated with many disease states. Over the last years, the identification of CNVs from whole-exome sequencing (WES) data has become a common practice for research and clinical purpose and, consequently, the demand for more and more efficient and accurate methods has incr...
متن کاملCLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data
MOTIVATION Several algorithms exist for detecting copy number variants (CNVs) from human exome sequencing read depth, but previous tools have not been well suited for large population studies on the order of tens or hundreds of thousands of exomes. Their limitations include being difficult to integrate into automated variant-calling pipelines and being ill-suited for detecting common variants. ...
متن کاملCEQer: A Graphical Tool for Copy Number and Allelic Imbalance Detection from Whole-Exome Sequencing Data
Copy number alterations (CNA) are common events occurring in leukaemias and solid tumors. Comparative Genome Hybridization (CGH) is actually the gold standard technique to analyze CNAs; however, CGH analysis requires dedicated instruments and is able to perform only low resolution Loss of Heterozygosity (LOH) analyses. Here we present CEQer (Comparative Exome Quantification analyzer), a new gra...
متن کاملEstimation of Copy Number Alterations from Exome Sequencing Data
Exome sequencing constitutes an important technology for the study of human hereditary diseases and cancer. However, the ability of this approach to identify copy number alterations in primary tumor samples has not been fully addressed. Here we show that somatic copy number alterations can be reliably estimated using exome sequencing data through a strategy that we have termed exome2cnv. Using ...
متن کاملCANOES: detecting rare copy number variants from whole exome sequencing data
We present CANOES, an algorithm for the detection of rare copy number variants from exome sequencing data. CANOES models read counts using a negative binomial distribution and estimates variance of the read counts using a regression-based approach based on selected reference samples in a given dataset. We test CANOES on a family-based exome sequencing dataset, and show that its sensitivity and ...
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ژورنال
عنوان ژورنال: Genome Research
سال: 2019
ISSN: 1088-9051,1549-5469
DOI: 10.1101/gr.245928.118