Microarray-Based Copy Number Variation Analysis

In Family 1, Affymetrix 6.0 chips and Agilent 1 M microarrays were hybridized as previously described (10 (link)) (Santa Clara, CA). Agilent 244 k arrays were performed on individual CDH12. Birdsuite (broadinstitute.org) and Agilent Feature Extraction (10.7.3.1), respectively, were used to generate CNV calls. Clinical microarrays were obtained on 2-II-1 [ClariSure CGH, Quest Diagnostics (Madison, NJ)], 2-II-2 and 2-II-3 [GenomeDx v5, GeneDx (Gaithersburg, MD)].

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Longoni M., Russell M.K., High F.A., Darvishi K., Maalouf F.I., Kashani A., Tracy A.A., Coletti C.M., Loscertales M., Lage K., Ackerman K.G., Woods S.A., Ward-Melver C., Andrews D., Lee C., Pober B.R, & Donahoe P.K. (2014). Prevalence and penetrance of ZFPM2 mutations and deletions causing congenital diaphragmatic hernia. Clinical genetics, 87(4), 362-367.

Publication 2014

Feature Extraction (10.7.3.1),

Chips Diagnostics Microarrays

Corresponding Organization : Massachusetts General Hospital

Other organizations : Harvard University, Boston Children's Hospital, Brigham and Women's Hospital, Broad Institute, University of Rochester, Akron Children's Hospital, Northeast Ohio Medical University, Jackson Laboratory

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Variable analysis

independent variables

Affymetrix 6.0 chips
Agilent 1 M microarrays
Agilent 244 k arrays

dependent variables

CNV calls

control variables

Clinical microarrays obtained on 2-II-1 [ClariSure CGH, Quest Diagnostics (Madison, NJ)], 2-II-2 and 2-II-3 [GenomeDx v5, GeneDx (Gaithersburg, MD)]

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