Cgh analytics v3

Manufactured by Agilent Technologies

CGH Analytics v3.4.40 is a software application for the analysis of comparative genomic hybridization (CGH) data. It provides tools for data processing, normalization, and visualization of CGH arrays.

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Lab products found in correlation

Whole genome 1 m oligonucleotide array, by Agilent Technologies (2 mentions) Cytogenomics v2, by Agilent Technologies (2 mentions) Feature extraction v9, by Agilent Technologies (2 mentions)

Close spelling variants of this product

Agilent CGH Analytics software (v3.4) CGH analytics software v3.4

2 protocols using cgh analytics v3

Genome-wide Array CGH Analysis

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All experiments were done with genomic DNA extracted from blood samples. Array CGH for family 1, 3, and 4 was carried out using a whole genome 1 M oligonucleotide array (Agilent, Santa Clara, CA). 1 M arrays were analyzed by Feature Extraction v9.5.3.1 and CGH Analytics v3.4.40 software or Cytogenomics v2.5.8.11, respectively (Agilent, Santa Clara, CA). Family 2 was tested on Roche NimbleGen platform with use of 1.4 M oligo arrays according to standard protocols provided by the manufacturer. Analysis settings: aberration algorithm: ADM-2; threshold: 6.0; window size: 0.2 Mb; filter: 5probes, log2ratio = 0.29. The genomic profile was visualized by the SignalMap software (SignalMap v1.9.0.03, NimbleGen Systems Inc.). Data were submitted to the DECIPHER database (http://decipher.sanger.ac.uk); accession numbers: BER284939, BER284938, BER284937, and BER285016.

Tayebi N., Jamsheer A., Flöttmann R., Sowinska-Seidler A., Doelken S.C., Oehl-Jaschkowitz B., Hülsemann W., Habenicht R., Klopocki E., Mundlos S, & Spielmann M. (2014). Deletions of exons with regulatory activity at the DYNC1I1 locus are associated with split-hand/split-foot malformation: array CGH screening of 134 unrelated families. Orphanet Journal of Rare Diseases, 9, 108.

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Comparative Genomic Hybridization via Array

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Microarray-based comparative genomic hybridization (array CGH) for family 2 was carried out using a whole-genome 1-M oligonucleotide array (Agilent); 1 M arrays were analyzed by feature extraction v9.5.3.1 and CGH analytics v3.4.40 software or cytogenomics v2.5.8.11, respectively (Agilent). Analysis settings were as follows: aberration algorithm, ADM-2; threshold, 6.0; window size, 0.2 Mb; filter, 5probes; log2ratio = 0.29. The genomic profile was visualized by the SignalMap software (SignalMap v1.9.0.03, NimbleGen Systems).

Spielmann M., Kakar N., Tayebi N., Leettola C., Nürnberg G., Sowada N., Lupiáñez D.G., Harabula I., Flöttmann R., Horn D., Chan W.L., Wittler L., Yilmaz R., Altmüller J., Thiele H., van Bokhoven H., Schwartz C.E., Nürnberg P., Bowie J.U., Ahmad J., Kubisch C., Mundlos S, & Borck G. (2016). Exome sequencing and CRISPR/Cas genome editing identify mutations of ZAK as a cause of limb defects in humans and mice. Genome Research, 26(2), 183-191.

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