ArticleBMC genetics2008
Improved detection of global copy number variation using high density, non-polymorphic oligonucleotide probes.
Article in BMC genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Progress in Methods for Copy Number Variation Profiling.International journal of molecular sciences · 2022Review
- Cri-Du-Chat Syndrome: Clinical Profile and Chromosomal Microarray Analysis in Six Patients.BioMed research international · 2016Article
- Human genetics and genomics a decade after the release of the draft sequence of the human genome.Human genomics · 2011Review
- High-resolution human genome structure by single-molecule analysis.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Detecting copy number variations from array CGH data based on a conditional random field model.Journal of bioinformatics and computational biology · 2010Article
- Population-genetic nature of copy number variations in the human genome.Human molecular genetics · 2010Article
- Pathway-Targeted Pharmacogenomics of CYP1A2 in Human Liver.Frontiers in pharmacology · 2010Article
- Article
- Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances.Nucleic acids research · 2009Article
- An optimization framework for unsupervised identification of rare copy number variation from SNP array data.Genome biology · 2009Article
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDNA sequence diversity within the human genome may be more greatly affected by copy number variations (CNVs) than single nucleotide polymorphisms (SNPs). Although the importance of CNVs in genome wide association studies (GWAS) is becoming widely accepted, the optimal methods for identifying these variants are still under evaluation. We have previously reported a comprehensive view of CNVs in the HapMap DNA collection using high density 500 K EA (Early Access) SNP genotyping arrays which revealed greater than 1,000 CNVs ranging in size from 1 kb to over 3 Mb. Although the arrays used most commonly for GWAS predominantly interrogate SNPs, CNV identification and detection does not necessarily require the use of DNA probes centered on polymorphic nucleotides and may even be hindered by the dependence on a successful SNP genotyping assay.
resultsIn this study, we have designed and evaluated a high density array predicated on the use of non-polymorphic oligonucleotide probes for CNV detection. This approach effectively uncouples copy number detection from SNP genotyping and thus has the potential to significantly improve probe coverage for genome-wide CNV identification. This array, in conjunction with PCR-based, complexity-reduced DNA target, queries over 1.3 M independent NspI restriction enzyme fragments in the 200 bp to 1100 bp size range, which is a several fold increase in marker density as compared to the 500 K EA array. In addition, a novel algorithm was developed and validated to extract CNV regions and boundaries.
conclusionUsing a well-characterized pair of DNA samples, close to 200 CNVs were identified, of which nearly 50% appear novel yet were independently validated using quantitative PCR. The results indicate that non-polymorphic probes provide a robust approach for CNV identification, and the increasing precision of CNV boundary delineation should allow a more complete analysis of their genomic organization.
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