Modeling read counts for CNV detection in exome sequencing data

DOI10.2202/1544-6115.1732MaRDI QIDQ458185zbMATH OpenOpenAlexWikidataFDO

Authors Alena Myšičková, Ruping Sun, Vera Kalscheuer, Stefan A. Haas, Michael I. Love, Martin Vingron

Publication date 7 October 2014

Published in Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)

Full work available at URL http://europepmc.org/articles/pmc3517018

zbMATH Keywords

HMMhidden Markov modelCNVcopy number variantexome sequencingtargeted sequencing

Mathematics Subject Classification ID

General biostatistics (92B15) Genetics and epigenetics (92D10)

Recommendations

• Modeling the next generation sequencing read count data for DNA copy number variant study
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• MGP-HMM: detecting genome-wide CNVs using an HMM for modeling mate pair insertion sizes and read counts
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• The screening and ranking algorithm to detect DNA copy number variations

Cites work

• Hidden Markov models approach to the analysis of array CGH data

Cited in

(5)

• Assignment of endogenous retrovirus integration sites using a mixture model
• Modeling the next generation sequencing read count data for DNA copy number variant study
• The number of candidate variants in exome sequencing for Mendelian disease under no genetic heterogeneity
• MGP-HMM: detecting genome-wide CNVs using an HMM for modeling mate pair insertion sizes and read counts
• Allele-specific copy number estimation by whole exome sequencing

Describes a project that uses

Uses Software

• R
• Bioconductor
• edgeR
• DEseq
• BioHMM
• CNV-seq
• ExomeCNV

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