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Copy Number Studies in Noisy Samples
System noise was analyzed in 77 Affymetrix 6.0 samples from a previous clinical study of copy number variation (CNV). Twenty-three samples were classified as eligible for CNV detection, 29 samples as ineligible and 25 were classified as being of intermediate quality. New software (“noise-free-cnv”)...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003442/ https://www.ncbi.nlm.nih.gov/pubmed/27605193 http://dx.doi.org/10.3390/microarrays2040284 |
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author | Ginsbach, Philip Chen, Bowang Jiang, Yanxiang Engelter, Stefan T. Grond-Ginsbach, Caspar |
author_facet | Ginsbach, Philip Chen, Bowang Jiang, Yanxiang Engelter, Stefan T. Grond-Ginsbach, Caspar |
author_sort | Ginsbach, Philip |
collection | PubMed |
description | System noise was analyzed in 77 Affymetrix 6.0 samples from a previous clinical study of copy number variation (CNV). Twenty-three samples were classified as eligible for CNV detection, 29 samples as ineligible and 25 were classified as being of intermediate quality. New software (“noise-free-cnv”) was developed to visualize the data and reduce system noise. Fresh DNA preparations were more likely to yield eligible samples (p < 0.001). Eligible samples had higher rates of successfully genotyped SNPs (p < 0.001) and lower variance of signal intensities (p < 0.001), yielded fewer CNV findings after Birdview analysis (p < 0.001), and showed a tendency to yield fewer PennCNV calls (p = 0.053). The noise-free-cnv software visualized trend patterns of noise in the signal intensities across the ordered SNPs, including a wave pattern of noise, being co-linear with the banding pattern of metaphase chromosomes, as well as system deviations of individual probe sets (per-SNP noise). Wave noise and per-SNP noise occurred independently and could be separately removed from the samples. We recommend a two-step procedure of CNV validation, including noise reduction and visual inspection of all CNV calls, prior to molecular validation of a selected number of putative CNVs. |
format | Online Article Text |
id | pubmed-5003442 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-50034422016-09-06 Copy Number Studies in Noisy Samples Ginsbach, Philip Chen, Bowang Jiang, Yanxiang Engelter, Stefan T. Grond-Ginsbach, Caspar Microarrays (Basel) Article System noise was analyzed in 77 Affymetrix 6.0 samples from a previous clinical study of copy number variation (CNV). Twenty-three samples were classified as eligible for CNV detection, 29 samples as ineligible and 25 were classified as being of intermediate quality. New software (“noise-free-cnv”) was developed to visualize the data and reduce system noise. Fresh DNA preparations were more likely to yield eligible samples (p < 0.001). Eligible samples had higher rates of successfully genotyped SNPs (p < 0.001) and lower variance of signal intensities (p < 0.001), yielded fewer CNV findings after Birdview analysis (p < 0.001), and showed a tendency to yield fewer PennCNV calls (p = 0.053). The noise-free-cnv software visualized trend patterns of noise in the signal intensities across the ordered SNPs, including a wave pattern of noise, being co-linear with the banding pattern of metaphase chromosomes, as well as system deviations of individual probe sets (per-SNP noise). Wave noise and per-SNP noise occurred independently and could be separately removed from the samples. We recommend a two-step procedure of CNV validation, including noise reduction and visual inspection of all CNV calls, prior to molecular validation of a selected number of putative CNVs. MDPI 2013-11-06 /pmc/articles/PMC5003442/ /pubmed/27605193 http://dx.doi.org/10.3390/microarrays2040284 Text en © 2013 by the authors; licensee MDPI, Basel, Switzerland. http://creativecommons.org/licenses/by/3.0/ This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/). |
spellingShingle | Article Ginsbach, Philip Chen, Bowang Jiang, Yanxiang Engelter, Stefan T. Grond-Ginsbach, Caspar Copy Number Studies in Noisy Samples |
title | Copy Number Studies in Noisy Samples |
title_full | Copy Number Studies in Noisy Samples |
title_fullStr | Copy Number Studies in Noisy Samples |
title_full_unstemmed | Copy Number Studies in Noisy Samples |
title_short | Copy Number Studies in Noisy Samples |
title_sort | copy number studies in noisy samples |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003442/ https://www.ncbi.nlm.nih.gov/pubmed/27605193 http://dx.doi.org/10.3390/microarrays2040284 |
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