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Kendy K. Wong

Bio: Kendy K. Wong is an academic researcher. The author has contributed to research in topics: Copy-number variation & Comparative genomic hybridization. The author has an hindex of 1, co-authored 3 publications receiving 513 citations.

Papers
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Journal ArticleDOI
TL;DR: An in-depth survey of CNVs across the human genome provides a valuable baseline for studies involving human genetics and raises the possibility of the contribution of microRNAs to phenotypic diversity in humans.
Abstract: Segmental copy-number variations (CNVs) in the human genome are associated with developmental disorders and susceptibility to diseases. More importantly, CNVs may represent a major genetic component of our phenotypic diversity. In this study, using a whole-genome array comparative genomic hybridization assay, we identified 3,654 autosomal segmental CNVs, 800 of which appeared at a frequency of at least 3%. Of these frequent CNVs, 77% are novel. In the 95 individuals analyzed, the two most diverse genomes differed by at least 9 Mb in size or varied by at least 266 loci in content. Approximately 68% of the 800 polymorphic regions overlap with genes, which may reflect human diversity in senses (smell, hearing, taste, and sight), rhesus phenotype, metabolism, and disease susceptibility. Intriguingly, 14 polymorphic regions harbor 21 of the known human microRNAs, raising the possibility of the contribution of microRNAs to phenotypic diversity in humans. This in-depth survey of CNVs across the human genome provides a valuable baseline for studies involving human genetics.

517 citations

Journal ArticleDOI
TL;DR: In this paper, the authors described the application of more robust statistical modeling for the determination of false negative and false positive rates in their copy-number variation (CNV) study and concluded that the inclusion of dependence in the model increases the false negative rate while leaving the false positive rate unaltered.
Abstract: To the Editor: The letter by Lynch et al.1(in this issue) described the application of more-robust statistical modeling for the determination of false-negative and false-positive rates in our copy-number variation (CNV) study. Their conclusion is that the inclusion of dependence in the model increases the false-negative rate while leaving the false-positive rate unaltered.
Journal ArticleDOI
TL;DR: The importance of interpreting CNV data with caution, with respect to correlations with genes or phenotypes, is emphasized, as well as the need to be aware of potential correlations with OMIM diseases.
Abstract: To the Editor: Dr. Hegele called attention to the disparities between the observed frequencies of copy-number variations (CNVs) and the reported frequencies of some OMIM diseases.1(in this issue) We share Dr. Hegele’s concern and emphasize the importance of interpreting CNV data with caution, with respect to correlations with genes or phenotypes.

Cited by
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Journal ArticleDOI
TL;DR: PennCNV, a hidden Markov model (HMM) based approach, is presented for kilobase-resolution detection of CNVs from Illumina high-density SNP genotyping data, demonstrating the feasibility of whole-genome fine-mapping ofCNVs via high- density SNP genotypesing.
Abstract: Comprehensive identification and cataloging of copy number variations (CNVs) is required to provide a complete view of human genetic variation. The resolution of CNV detection in previous experimental designs has been limited to tens or hundreds of kilobases. Here we present PennCNV, a hidden Markov model (HMM) based approach, for kilobase-resolution detection of CNVs from Illumina high-density SNP genotyping data. This algorithm incorporates multiple sources of information, including total signal intensity and allelic intensity ratio at each SNP marker, the distance between neighboring SNPs, the allele frequency of SNPs, and the pedigree information where available. We applied PennCNV to genotyping data generated for 112 HapMap individuals; on average, we detected approximately 27 CNVs for each individual with a median size of approximately 12 kb. Excluding common rearrangements in lymphoblastoid cell lines, the fraction of CNVs in offspring not detected in parents (CNV-NDPs) was 3.3%. Our results demonstrate the feasibility of whole-genome fine-mapping of CNVs via high-density SNP genotyping.

1,752 citations

Journal ArticleDOI
01 May 2008-Nature
TL;DR: This work employs a clone-based method to interrogate intermediate structural variation in eight individuals of diverse geographic ancestry and provides the first high-resolution sequence map of human structural variation—a standard for genotyping platforms and a prelude to future individual genome sequencing projects.
Abstract: Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale--particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number between individuals. Complete sequencing of 261 structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence map of human structural variation--a standard for genotyping platforms and a prelude to future individual genome sequencing projects.

1,183 citations

Journal ArticleDOI
TL;DR: Current models of the mechanisms that cause copy number variation focus on perturbation of DNA replication and replication of non-contiguous DNA segments and cellular stress might induce repair of broken replication forks to switch from high-fidelity homologous recombination to non-homologous repair, thus promoting copy number change.
Abstract: Deletions and duplications of chromosomal segments (copy number variants, CNVs) are a major source of variation between individual humans and are an underlying factor in human evolution and in many diseases, including mental illness, developmental disorders and cancer CNVs form at a faster rate than other types of mutation, and seem to do so by similar mechanisms in bacteria, yeast and humans Here we review current models of the mechanisms that cause copy number variation Non-homologous end-joining mechanisms are well known, but recent models focus on perturbation of DNA replication and replication of non-contiguous DNA segments For example, cellular stress might induce repair of broken replication forks to switch from high-fidelity homologous recombination to non-homologous repair, thus promoting copy number change

1,169 citations

Journal ArticleDOI
21 Feb 2008-Nature
TL;DR: 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.
Abstract: Genome-wide patterns of variation across individuals provide a powerful source of data for uncovering the history of migration, range expansion, and adaptation of the human species. However, high-resolution surveys of variation in genotype, haplotype and copy number have generally focused on a small number of population groups. Here we report 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. Analysis of SNP genotypes yields strongly supported fine-scale inferences about population structure. Increasing linkage disequilibrium is observed with increasing geographic distance from Africa, as expected under a serial founder effect for the out-of-Africa spread of human populations. New approaches for haplotype analysis produce inferences about population structure that complement results based on unphased SNPs. Despite a difference from SNPs in the frequency spectrum of the copy-number variants (CNVs) detected--including a comparatively large number of CNVs in previously unexamined populations from Oceania and the Americas--the global distribution of CNVs largely accords with population structure analyses for SNP data sets of similar size. Our results produce 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.

872 citations

Journal ArticleDOI
TL;DR: It is proposed that breakage of replication forks in stressed cells that are deficient in homologous recombination induces an aberrant repair process with features of break-induced replication (BIR) that will anneal with microhomology on any single-stranded DNA nearby, priming low-processivity polymerization with multiple template switches generating complex rearrangements, and eventual re-establishment of processive replication.
Abstract: Chromosome structural changes with nonrecurrent endpoints associated with genomic disorders offer windows into the mechanism of origin of copy number variation (CNV). A recent report of nonrecurrent duplications associated with Pelizaeus-Merzbacher disease identified three distinctive characteristics. First, the majority of events can be seen to be complex, showing discontinuous duplications mixed with deletions, inverted duplications, and triplications. Second, junctions at endpoints show microhomology of 2–5 base pairs (bp). Third, endpoints occur near pre-existing low copy repeats (LCRs). Using these observations and evidence from DNA repair in other organisms, we derive a model of microhomology-mediated break-induced replication (MMBIR) for the origin of CNV and, ultimately, of LCRs. We propose that breakage of replication forks in stressed cells that are deficient in homologous recombination induces an aberrant repair process with features of break-induced replication (BIR). Under these circumstances, single-strand 3′ tails from broken replication forks will anneal with microhomology on any single-stranded DNA nearby, priming low-processivity polymerization with multiple template switches generating complex rearrangements, and eventual re-establishment of processive replication.

763 citations