Identification of Copy Number Variants from SNP Arrays Using PennCNV

Li Fang; Kai Wang

doi:10.1007/978-1-4939-8666-8_1

Identification of Copy Number Variants from SNP Arrays Using PennCNV

Methods Mol Biol. 2018:1833:1-28. doi: 10.1007/978-1-4939-8666-8_1.

Authors

Li Fang¹, Kai Wang²

Affiliations

¹ Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
² Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA. [email protected].

PMID: 30039360
DOI: 10.1007/978-1-4939-8666-8_1

Abstract

High-resolution single-nucleotide polymorphism (SNP) genotyping arrays offer a sensitive and affordable method for genome-wide detection of copy number variants (CNVs). PennCNV is a hidden Markov model (HMM)-based CNV caller for SNP arrays, first released 10 years ago. A typical CNV calling procedure using PennCNV includes preparation of input files, CNV calling, filtering CNV calls, CNV annotation, and CNV visualization. Here we describe several protocols for CNV calling using PennCNV, together with descriptions on several recent improvements to the software tool.

Keywords: Copy number variants; Hidden Markov model; PennCNV; SNP array.

MeSH terms

Animals
Gene Dosage*
Humans
Markov Chains
Oligonucleotide Array Sequence Analysis / methods*
Polymorphism, Single Nucleotide*
Sequence Analysis, DNA / methods*