Comparing CNV detection methods for SNP arrays.

Data from whole genome association studies can now be used for dual purposes, genotyping and copy number detection. In this review we discuss some of the methods for using SNP data to detect copy number events. We examine a number of algorithms designed to detect copy number changes through the use of signal-intensity data and consider methods to evaluate the changes found. We describe the use of several statistical models in copy number detection in germline samples. We also present a comparison of data using these methods to assess accuracy of prediction and detection of changes in copy number.

[1]  Joshua M. Korn,et al.  Mapping and sequencing of structural variation from eight human genomes , 2008, Nature.

[2]  N. Carter.  Methods and strategies for analyzing copy number variation using DNA microarrays , 2007, Nature Genetics.

[3]  C. Yau,et al.  QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data , 2007, Nucleic acids research.

[4]  Tomi D. Berney,et al.  High-density SNP association study and copy number variation analysis of the AUTS1 and AUTS5 loci implicate the IMMP2L–DOCK4 gene region in autism susceptibility , 2009, Molecular Psychiatry.

[5]  R. Ophoff,et al.  Detection, imputation, and association analysis of small deletions and null alleles on oligonucleotide arrays. , 2008, American journal of human genetics.

[6]  Joshua M. Korn,et al.  Integrated detection and population-genetic analysis of SNPs and copy number variation , 2008, Nature Genetics.

[7]  Pardis C Sabeti,et al.  Common deletion polymorphisms in the human genome , 2006, Nature Genetics.

[8]  Joshua M. Korn,et al.  Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs , 2008, Nature Genetics.

[9]  L. Cardon,et al.  Association study designs for complex diseases , 2001, Nature Reviews Genetics.

[10]  E. Birney,et al.  Challenges and standards in integrating surveys of structural variation , 2007, Nature Genetics.

[11]  Joseph T. Glessner,et al.  PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. , 2007, Genome research.

[12]  Emmanuel Barillot,et al.  ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays , 2008, Bioinform..

[13]  Tomas W. Fitzgerald,et al.  A robust statistical method for case-control association testing with copy number variation , 2008, Nature Genetics.

[14]  D. Conrad,et al.  Global variation in copy number in the human genome , 2006, Nature.

[15]  Yan Guo,et al.  Genome-wide copy-number-variation study identified a susceptibility gene, UGT2B17, for osteoporosis. , 2008, American journal of human genetics.

[16]  E. Eichler,et al.  Fine-scale structural variation of the human genome , 2005, Nature Genetics.

[17]  S. P. Fodor,et al.  Large-scale genotyping of complex DNA , 2003, Nature Biotechnology.

[18]  Philip M. Kim,et al.  Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome , 2007, Science.

[19]  Iuliana Ionita-Laza,et al.  On the analysis of copy‐number variations in genome‐wide association studies: a translation of the family‐based association test , 2008, Genetic epidemiology.

[20]  Peter J. Park,et al.  Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data , 2005, Bioinform..

[21]  M. Wigler,et al.  Circular binary segmentation for the analysis of array-based DNA copy number data. , 2004, Biostatistics.

[22]  E. Eichler,et al.  Systematic assessment of copy number variant detection via genome-wide SNP genotyping , 2008, Nature Genetics.

[23]  L. Feuk,et al.  Detection of large-scale variation in the human genome , 2004, Nature Genetics.

[24]  P. Visscher,et al.  Rare chromosomal deletions and duplications increase risk of schizophrenia , 2008, Nature.

[25]  Mahlet G. Tadesse,et al.  Modeling genetic inheritance of copy number variations , 2008, Nucleic acids research.

[26]  Antonio Ortega,et al.  Sparse representation and Bayesian detection of genome copy number alterations from microarray data , 2008, Bioinform..

[27]  Philippe Froguel,et al.  Array CGH analysis of copy number variation identifies 1284 new genes variant in healthy white males: implications for association studies of complex diseases. , 2007, Human molecular genetics.

[28]  Kenny Q. Ye,et al.  Large-Scale Copy Number Polymorphism in the Human Genome , 2004, Science.

[29]  Cheng Li,et al.  Major copy proportion analysis of tumor samples using SNP arrays , 2008, BMC Bioinformatics.

[30]  S. Mccarroll,et al.  Copy-number variation and association studies of human disease , 2007, Nature Genetics.

[31]  William Stafford Noble,et al.  Unsupervised segmentation of continuous genomic data , 2007, Bioinform..

[32]  K. Gunderson,et al.  High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. , 2006, Genome research.