ES analysis was performed at BG as previously described32 (link). Samples were also concurrently analyzed by SNP arrays (Illumina HumanExome-12 or CoreExome-24 array) for quality control of the ES data, as well as for detecting large copy-number variants (CNVs) and regions of absence of heterozygosity (AOH)33 (link),34 (link). Homozygous/hemizygous deletions were also analyzed using an in-house developed pipeline based on exome read-depth analysis as previously described35 (link). The ES-targeted regions cover >23,000 genes for capture design (VCRome by NimbleGen®), including both coding and untranslated region exons. The mean coverage of target bases was >100×, and >95% of target bases were covered at >20×32 (link). PCR amplification and Sanger sequencing was performed to verify all candidate variants in the probands according to standard procedures. Of note, reanalysis of ES data for individuals who had their first ES analysis prior to January 2020 was performed as described recently36 (link) to evaluate for the presence of other potentially causative variants. No other potential molecular diagnoses contributed by other loci were identified by the reanalyses.
Copy number variants DeletionsExomeExonsGenes Hemizygous Heterozygosity Homozygous Molecular diagnoses Untranslated region
Corresponding Organization :
Other organizations :
Baylor College of Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Peking Union Medical College Hospital, University of Rochester, University of Arkansas for Medical Sciences, Children's Hospital of Pittsburgh, University of Toronto, Children's National, Nationwide Children's Hospital, The Ohio State University, Mount Sinai Hospital, University Health Network, University of Colorado Denver, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Rush University Medical Center, Stanford University, Texas Children's Hospital
Concurrent analysis of samples by SNP arrays (Illumina HumanExome-12 or CoreExome-24 array)
In-house developed pipeline based on exome read-depth analysis for detecting homozygous/hemizygous deletions
dependent variables
Quality control of the ES data
Detection of large copy-number variants (CNVs)
Detection of regions of absence of heterozygosity (AOH)
control variables
ES-targeted regions covering >23,000 genes for capture design (VCRome by NimbleGen®)
Mean coverage of target bases >100×
>95% of target bases covered at >20×
controls
Positive control: PCR amplification and Sanger sequencing performed to verify all candidate variants in the probands according to standard procedures
Negative control: Not explicitly mentioned
Annotations
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