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Genotyping console gtc 4

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The Genotyping Console (GTC) 4.0 software is a tool used for analyzing and managing genotyping data. It provides functionality for data processing, visualization, and reporting.

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Lab products found in correlation

Affymetrix 6.0 snp array, by Thermo Fisher Scientific (3 mentions)

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Genotyping Console (57 citations) Genotyping Console 4.0 (13 citations)

3 protocols using genotyping console gtc 4

1

Affymetrix 6.0 SNP Array Genotyping

Cited 1 time
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DNA labelling, hybridization, and array scanning were performed with Affymetrix 6.0 SNP arrays (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol and processed using Affymetrix Genotyping Console (GTC) 4.0 software. Data were processed as previously described [6 (link)]. When SNP 6.0 data was not available, copy number data were calculated based on the CGI relative coverage smoothed in 100-kb windows, corrected for the GC content, and normalized using composite baseline coverage from multiple healthy samples. Segments defined by a minimum of 8 probes with segment log2 mean <-0.5 or >+0.5 were considered lost and gained, respectively, unless otherwise indicated.
Gadd S., Huff V., Walz A.L., Ooms A.H., Armstrong A.E., Gerhard D.S., Smith M.A., Guidry Auvil J.M., Meerzaman D., Chen Q.R., Hsu C.H., Yan C., Nguyen C., Hu Y., Hermida L.C., Davidsen T., Gesuwan P., Ma Y., Zong Z., Mungall A.J., Moore R.A., Marra M.A., Dome J.S., Mullighan C.G., Ma J., Wheeler D.A., Hampton O.A., Ross N., Gastier-Foster J.M., Arold S.T, & Perlman E.J. (2017). A Children's Oncology Group and TARGET Initiative Exploring the Genetic Landscape of Wilms Tumor. Nature genetics, 49(10), 1487-1494.
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2

Affymetrix 6.0 SNP Array Genotyping

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
DNA labelling, hybridization, and array scanning were performed with Affymetrix 6.0 SNP arrays (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol and processed using Affymetrix Genotyping Console (GTC) 4.0 software. Data were processed as previously described [6 (link)]. When SNP 6.0 data was not available, copy number data were calculated based on the CGI relative coverage smoothed in 100-kb windows, corrected for the GC content, and normalized using composite baseline coverage from multiple healthy samples. Segments defined by a minimum of 8 probes with segment log2 mean <-0.5 or >+0.5 were considered lost and gained, respectively, unless otherwise indicated.
Gadd S., Huff V., Walz A.L., Ooms A.H., Armstrong A.E., Gerhard D.S., Smith M.A., Guidry Auvil J.M., Meerzaman D., Chen Q.R., Hsu C.H., Yan C., Nguyen C., Hu Y., Hermida L.C., Davidsen T., Gesuwan P., Ma Y., Zong Z., Mungall A.J., Moore R.A., Marra M.A., Dome J.S., Mullighan C.G., Ma J., Wheeler D.A., Hampton O.A., Ross N., Gastier-Foster J.M., Arold S.T, & Perlman E.J. (2017). A Children's Oncology Group and TARGET Initiative Exploring the Genetic Landscape of Wilms Tumor. Nature genetics, 49(10), 1487-1494.
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3

Affymetrix 6.0 SNP Array Analysis

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Nucleic acid labeling, hybridization, and array scanning were performed on 11 CCSKs according to the manufacturer's protocol for the Affymetrix 6.0 SNP array (Affymetrix, Santa Clara, CA, USA) and processed with the Affymetrix Genotyping Console (GTC) 4.0 software. Reference normalization was performed as described by Pounds et al [49 (link)]. Circular binary segmentation (CBS) was performed using DNAcopy from BioConductor (http://www.bioconductor.org). Segmented regions of autosomal chromosomes containing at least 8 markers in which the log2 value was > +0.5 or < −0.5 were considered regions of gain or loss, respectively. For the other 2 CCSK samples, copy number was assessed by using relative coverage generated by whole genome sequencing.
Gooskens S.L., Gadd S., Guidry Auvil J.M., Gerhard D.S., Khan J., Patidar R., Meerzaman D., Chen Q.R., Hsu C.H., Yan C., Nguyen C., Hu Y., Mullighan C.G., Ma J., Jennings L.J., de Krijger R.R., van den Heuvel-Eibrink M.M., Smith M.A., Ross N., Gastier-Foster J.M, & Perlman E.J. (2015). TCF21 hypermethylation in genetically quiescent clear cell sarcoma of the kidney. Oncotarget, 6(18), 15828-15841.
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