The ASD families were genotyped on the Illumina Infinium® 1Mv1 (338 families), Infinium® 1Mv3 Duo (1,191 families) or the HumanOmni2.5-8 (996 families) microarrays (Illumina Inc, USA). All three microarray types had over 180 probes within the BP1-BP2 region. CNV prediction was performed by PennCNV (PN) [Wang et al. 2007 (link)], QuantiSNP (QT) [Colella et al. 2007 (link)], and Gnosis [Sanders et al. 2011 (link)], using CNVision [Sanders et al. 2011 (link)]. Detailed CNV detection protocol was described in [Sanders et al. 2011 (link)]. Sample identity within the family, including correct assignment of paternity and maternity, was confirmed using genetically-inferred identity by descent for all study participants including the de novo deletion of BP1-BP2 in a proband.
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CNV Detection in Autism Spectrum Disorder Families
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Corresponding Organization : University of Washington
Other organizations : University of California, San Francisco, Yale University, Birla Institute of Technology and Science - Hyderabad Campus, Baylor College of Medicine, University of Michigan–Ann Arbor, Center for Autism and Related Disorders, University of California, Los Angeles, Boston Children's Hospital, Harvard University, Oregon Health & Science University, Icahn School of Medicine at Mount Sinai, Autism & Developmental Medicine Institute, Geisinger Health System, Cornell University, Brown University, Providence College, Howard Hughes Medical Institute, Vanderbilt University, University of Illinois Chicago
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Variable analysis
independent variables
- Microarray type (Illumina Infinium® 1Mv1, Infinium® 1Mv3 Duo, or HumanOmni2.5-8)
- CNV prediction methods (PennCNV, QuantiSNP, and Gnosis)
- CNV detection within the BP1-BP2 region
- Number of probes within the BP1-BP2 region (over 180 probes for all three microarray types)
- Sample identity confirmation (using genetically-inferred identity by descent)
- Positive control: Confirmation of sample identity, including correct assignment of paternity and maternity, for all study participants
- Negative control: Not explicitly mentioned
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