Cargando…

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”)...

Descripción completa

Detalles Bibliográficos
Autores principales: Ginsbach, Philip, Chen, Bowang, Jiang, Yanxiang, Engelter, Stefan T., Grond-Ginsbach, Caspar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2013
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
_version_ 1782450647414603776
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
work_keys_str_mv AT ginsbachphilip copynumberstudiesinnoisysamples
AT chenbowang copynumberstudiesinnoisysamples
AT jiangyanxiang copynumberstudiesinnoisysamples
AT engelterstefant copynumberstudiesinnoisysamples
AT grondginsbachcaspar copynumberstudiesinnoisysamples