Global diversity, population stratification, and selection of human copy-number variation

  title={Global diversity, population stratification, and selection of human copy-number variation},
  author={Peter H. Sudmant and Swapan Mallick and Bradley J. Nelson and Fereydoun Hormozdiari and Niklas Krumm and John Huddleston and Bradley P. Coe and Carl A. Baker and Susanne Nordenfelt and Michael J. Bamshad and Lynn B. Jorde and Olga L. Posukh and Hovhannes Sahakyan and W. Scott Watkins and Levon Yepiskoposyan and Muhd Syafiq Abdullah and Claudio Marcelo Bravi and Cristian Capelli and Tor Audun Hervig and Joseph T. S. Wee and Chris Tyler-Smith and George van Driem and Irene Gallego Romero and Aashish R. Jha and Sena Karachanak-Yankova and Draga Toncheva and David Comas and Brenna M. Henn and Toomas Kivisild and Andr{\'e}s Ruiz-Linares and Antti Sajantila and Ene Metspalu and Jüri Parik and Richard Villems and Elena B. Starikovskaya and George Ayodo and Cynthia M. Beall and Anna Di Rienzo and Michael F. Hammer and Rita I. Khusainova and Elza K. Khusnutdinova and William Klitz and Cheryl A. Winkler and Damian Labuda and Mait Metspalu and Sarah A. Tishkoff and Stanislav V. Dryomov and Rem I. Sukernik and Nick J. Patterson and David Reich and Evan E. Eichler},
Duplications and deletions in the human genome Duplications and deletions can lead to variation in copy number for genes and genomic loci among humans. Such variants can reveal evolutionary patterns and have implications for human health. Sudmant et al. examined copy-number variation across 236 individual genomes from 125 human populations. Deletions were under more selection, whereas duplications showed more population-specific structure. Interestingly, Oceanic populations retain large… 

Gene Copy‐Number Changes in Evolution

A comprehensive understanding of how CNVs contribute to the evolution of genomes will require a combination of high-throughput genomics with analysis of the functional and fitness consequences of CNVs in experimental and natural populations.

Population-based approaches to characterize copy number variation from whole-genome sequencing in healthy individuals and disease cohorts

A different approach that uses a large set of reference samples to correct for technical variation and was found to be more sensitive than other methods for CNV detection and to investigate copy number variation in low-mappability regions.

Genome-wide analysis reveals differential selection involved with copy number variation in diverse Chinese Cattle

This study performed a genome-wide CNV analysis using high density SNP array in Chinese native cattle to investigate the diversity and population-genetic properties of CNVs and their diverse selection patterns, and identified many lineage-differentiated CNV genes across four groups.

Intronic CNVs cause gene expression variation in human populations

It is found that intronic losses are the most frequent copy number variants in protein-coding genes in human, with more than 12,986 intronic deletions, affecting 4,147 genes (including 1,154 essential genes and 1,638 disease-related genes).

CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data

CONGA, tailored for genotyping CNVs at low coverage, paves the way for systematic CNV analyses in ancient genomes, despite the technical challenges posed by low and variable genome coverage.

Intronic CNVs and gene expression variation in human populations

It is found that intronic losses are the most frequent copy number variants (CNVs) in protein-coding genes in human, with 12,986 intronic deletions, affecting 4,147 genes (including 1,154 essential genes and 1,638 disease-related genes).

Population-Specific Genetic and Expression Differentiation in Europeans

Results reveal that a branch-based estimator of population-specific differentiation in four populations can aid in uncovering genes involved in population- specific genetic and expression differentiation, and that such genes often play important roles in a diversity of adaptive and disease-related phenotypes in humans.



Diversity of Human Copy Number Variation and Multicopy Genes

This work identified 4.1 million “singly unique nucleotide” positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families, revealing extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species.

Global variation in copy number in the human genome

A first-generation CNV map of the human genome is constructed through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia, underscoring the importance of CNV in genetic diversity and evolution and the utility of this resource for genetic disease studies.

Genotype, haplotype and copy-number variation in worldwide human populations

The analysis of high-quality genotypes at 525,910 single-nucleotide polymorphisms (SNPs) and 396 copy-number-variable loci in a worldwide sample of 29 populations produces new inferences about inter-population variation, support the utility of CNVs in human population-genetic research, and serve as a genomic resource for human- genetic studies in diverse worldwide populations.

Population analysis of large copy number variants and hotspots of human genetic disease.

Origins and functional impact of copy number variation in the human genome

It is concluded that the heritability void left by genome-wide association studies will not be accounted for by common CNVs, and 30 loci with CNVs that are candidates for influencing disease susceptibility are identified.

Population-genetic properties of differentiated human copy-number polymorphisms.

Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome.

A combination of BAC-based and high-density customized oligonucleotide arrays were used to resolve the molecular basis of structural rearrangements and underscore the need for complete maps of genetic variation in duplication-rich regions of the genome.

Mapping copy number variation by population scale genome sequencing

A map of unbalanced SVs is constructed based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations, and serves as a resource for sequencing-based association studies.

Integrated detection and population-genetic analysis of SNPs and copy number variation

A map of human CNV (at 2-kb breakpoint resolution) informed by integer genotypes for 1,320 copy number polymorphisms (CNPs) that segregate at an allele frequency >1% is developed, indicating that large (>100 kb) CNVs affect much less of the genome than initially reported.

Large-Scale Copy Number Polymorphism in the Human Genome

It is shown that large-scale copy number polymorphisms (CNPs) (about 100 kilobases and greater) contribute substantially to genomic variation between normal humans.