CNV-seq, a new method to detect copy number variation using high-throughput sequencing
Open accessAbstract
BACKGROUND: DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations. RESULTS: Here, we describe a method to detect copy number variation using shotgun sequencing, CNV-seq. The method is based on a robust statistical model that describes the complete analysis procedure and allows the computation of essential confidence values for detection of CNV. Our results show that the number of reads, not the length of the reads is the key factor determining the resolution of detection. This favors the next-generation sequencing methods that rapidly produce large amount of short reads. CONCLUSION: Simulation of various sequencing methods with coverage between 0.1x to 8x show overall specificity between 91.7 - 99.9%, and sensitivity between 72.2 - 96.5%. We also show the results for assessment of CNV between two individual human genomes.
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Clinical diagnostic methods currently include FISH, CGH, SNP arrays, deep sequencing and real-time quantitative PCR (qPCR).
“Clinical diagnostic methods currently include fluorescence in situ hybridization (FISH), comparative genome hybridisation (CGH), single nucleotide polymorphism (SNP) arrays, deep sequencing and real-time quantitative PCR (qPCR) (8–10).”
From Comparison of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation (2012) · cites this paper as [9]
The Background (page unavailable) says array comparative genomic hybridization is commonly used to detect copy-number variation, and describes sequencing-based methods. It does not establish that these are clinical diagnostic methods or identify FISH, SNP arrays, and real-time qPCR as methods in the claimed list. (LLM, conf=0.85)
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- Authors
- Xie, C., & Tammi, M. T.
- Affiliations
- National University of Singapore (SG)
- Corresponding author
- Tammi, Martti T
- Venue
- BMC Bioinformatics
- Published
- 2009-03-06
- Volume
- 10
- Issue
- 1
- Pages
- 80-80
- ISSN
- 1471-2105 (ISSN-L)
- PMC
- PMC2667514
- OpenAlex
- W2035593347
- Cited by
- 582
- References
- 35
- Citations by year
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- FWCI
- 18.52
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- BMC Bioinformatics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- National University of Singapore (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- National University of Singapore
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- copy number variation, CNV-seq, shotgun sequencing, CNV detection, statistical models, confidence scores, sequencing depth, read length, sensitivity and specificity
- MeSH terms
- Algorithms, DNA, Humans, Genetic Variation, Genome, Human, Sequence Analysis, DNA, Gene Dosage, Genomics
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