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A novel scatterplot...
A novel scatterplot-based method to detect copy number variation (CNV)
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- Qiao, Jia Lu (författare)
- University Hospital Heidelberg
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- Levinson, Rebecca T. (författare)
- University Hospital Heidelberg
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Chen, Bowang (författare)
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visa fler...
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- Engelter, Stefan T. (författare)
- University of Basel
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- Erhart, Philipp (författare)
- University Hospital Heidelberg
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- Gaynor, Brady J. (författare)
- University of Maryland School of Medicine
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- McArdle, Patrick F. (författare)
- University of Maryland School of Medicine
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- Schlicht, Kristina (författare)
- University Medical Center Schleswig-Holstein
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- Krawczak, Michael (författare)
- University Medical Center Schleswig-Holstein
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- Stenman, Martin (författare)
- Lund University,Lunds universitet,Klinisk strokeforskning,Forskargrupper vid Lunds universitet,Clinical Stroke Research Group,Lund University Research Groups,Skåne University Hospital
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- Lindgren, Arne G. (författare)
- Lund University,Lunds universitet,Klinisk strokeforskning,Forskargrupper vid Lunds universitet,Clinical Stroke Research Group,Lund University Research Groups,Skåne University Hospital
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- Cole, John W. (författare)
- University of Maryland School of Medicine
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- Grond-Ginsbach, Caspar (författare)
- University Hospital Heidelberg
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(creator_code:org_t)
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- 2023
- 2023
- Engelska.
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Ingår i: Frontiers in Genetics. - 1664-8021. ; 14
- Relaterad länk:
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http://dx.doi.org/10... (free)
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https://lup.lub.lu.s...
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https://doi.org/10.3...
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Abstract
Ämnesord
Stäng
- Objective: Most methods to detect copy number variation (CNV) have high false positive rates, especially for small CNVs and in real-life samples from clinical studies. In this study, we explored a novel scatterplot-based method to detect CNVs in microarray samples. Methods: Illumina SNP microarray data from 13,254 individuals were analyzed with scatterplots and by PennCNV. The data were analyzed without the prior exclusion of low-quality samples. For CNV scatterplot visualization, the median signal intensity of all SNPs located within a CNV region was plotted against the median signal intensity of the flanking genomic region. Since CNV causes loss or gain of signal intensities, carriers of different CNV alleles pop up in clusters. Moreover, SNPs within a deletion are not heterozygous, whereas heterozygous SNPs within a duplication show typical 1:2 signal distribution between the alleles. Scatterplot-based CNV calls were compared with standard results of PennCNV analysis. All discordant calls as well as a random selection of 100 concordant calls were individually analyzed by visual inspection after noise-reduction. Results: An algorithm for the automated scatterplot visualization of CNVs was developed and used to analyze six known CNV regions. Use of scatterplots and PennCNV yielded 1019 concordant and 108 discordant CNV calls. All concordant calls were evaluated as true CNV-findings. Among the 108 discordant calls, 7 were false positive findings by the scatterplot method, 80 were PennCNV false positives, and 21 were true CNVs detected by the scatterplot method, but missed by PennCNV (i.e., false negative findings). Conclusion: CNV visualization by scatterplots allows for a reliable and rapid detection of CNVs in large studies. This novel method may thus be used both to confirm the results of genome-wide CNV detection software and to identify known CNVs in hitherto untyped samples.
Ämnesord
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
Nyckelord
- copy number variation (CNV)
- filtering
- pennCNV
- quality control
- scatterplot
Publikations- och innehållstyp
- art (ämneskategori)
- ref (ämneskategori)
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Qiao, Jia Lu
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Levinson, Rebecc ...
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Chen, Bowang
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Engelter, Stefan ...
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Erhart, Philipp
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Gaynor, Brady J.
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visa fler...
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McArdle, Patrick ...
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Schlicht, Kristi ...
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Krawczak, Michae ...
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Stenman, Martin
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Lindgren, Arne G ...
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Cole, John W.
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Grond-Ginsbach, ...
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visa färre...
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- NATURVETENSKAP
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NATURVETENSKAP
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och Biologi
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och Genetik
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- MEDICIN OCH HÄLSOVETENSKAP
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MEDICIN OCH HÄLS ...
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Frontiers in Gen ...
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