title: Global patterns of large copy number variations in the human genome reveal complexity in chromosome organization.
abstract: Global patterns of copy number variations (CNVs) in chromosomes are required to understand the dynamics of genome organization and complexity. For this study, analysis was performed using the Affymetrix Genome-Wide Human SNP Array 6.0 chip and CytoScan High-Density arrays. We identified a total of 44 109 CNVs from 1715 genomes with a mean of 25 CNVs in an individual, which established the first drafts of population-specific CNV maps providing a rationale for prioritizing chromosomal regions. About 19 905 ancient CNVs were identified across all chromosomes and populations at varying frequencies. CNV count, and sometimes CNV size, contributed to the bulk CNV size of the chromosome. Population specific lengthening and shortening of chromosomal length was observed. Sex bias for CNV presence was largely dependent on ethnicity. Lower CNV inheritance rate was observed for India, compared to YRI and CEU. A total of 33 candidate CNV hotspots from 5382 copy number (CN) variable region (CNVR) clusters were identified. Population specific CNV distribution patterns in p and q arms disturbed the assumption that CNV counts in the p arm are less common compared to long arms, and the CNV occurrence and distribution in chromosomes is length independent. This study unraveled the force of independent evolutionary dynamics on genome organization and complexity across chromosomes and populations.
authors.affiliation: Genetics and Genomics Lab,Department of Studies in Genetics & Genomics,University of Mysore,Manasagangotri,Mysore-06,Karnataka,India.
authors.forename: Avinash M
authors.initials: AM
authors.lastname: Veerappa
authors.affiliation: Genetics and Genomics Lab,Department of Studies in Genetics & Genomics,University of Mysore,Manasagangotri,Mysore-06,Karnataka,India.
authors.forename: Raviraj V
authors.initials: RV
authors.lastname: Suresh
authors.affiliation: Genetics and Genomics Lab,Department of Studies in Genetics & Genomics,University of Mysore,Manasagangotri,Mysore-06,Karnataka,India.
authors.forename: Sangeetha
authors.initials: S
authors.lastname: Vishweswaraiah
authors.affiliation: Genetics and Genomics Lab,Department of Studies in Genetics & Genomics,University of Mysore,Manasagangotri,Mysore-06,Karnataka,India.
authors.forename: Kusuma
authors.initials: K
authors.lastname: Lingaiah
authors.affiliation: Genetics and Genomics Lab,Department of Studies in Genetics & Genomics,University of Mysore,Manasagangotri,Mysore-06,Karnataka,India.
authors.forename: Megha
authors.initials: M
authors.lastname: Murthy
authors.affiliation: Nitte University Centre for Science Education & Research,K. S. Hegde Medical Academy,Nitte,University,Deralakatte,Mangalore-18,Karnataka,India.
authors.forename: Dinesh S
authors.initials: DS
authors.lastname: Manjegowda
authors.affiliation: Department of Studies in Psychology,University of Mysore,Manasagangotri,Mysore-06,Karnataka,India.
authors.forename: Prakash
authors.initials: P
authors.lastname: Padakannaya
authors.affiliation: Genetics and Genomics Lab,Department of Studies in Genetics & Genomics,University of Mysore,Manasagangotri,Mysore-06,Karnataka,India.
authors.forename: Nallur B
authors.initials: NB
authors.lastname: Ramachandra
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods; D019295:Computational Biology / Q000379:methods; D056915:DNA Copy Number Variations; D005260:Female; D005787:Gene Frequency; D005828:Genetics, Population / Q000379:methods; D015894:Genome, Human / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000379:methods*; D060005:Genotyping Techniques / Q000379:methods; D014943:Global Health; D006801:Humans; D040582:Inheritance Patterns; D008297:Male; D008875:Middle Aged; D009154:Mutation; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D055815:Young Adult