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GTR Home > Tests > Rubinstein-Taybi Syndrome via the EP300 Gene

Methodology

Methodology

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Molecular Genetics
DDeletion/duplication analysis
Next-Generation (NGS)/Massively parallel sequencing (MPS)
  • Other
CSequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
  • Other
TTargeted variant analysis
Bi-directional Sanger Sequence Analysis
  • Applied Biosystems 3730 capillary sequencing instrument

Test development

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Test developed by laboratory (no manufacturer test name)

Test procedure

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We use a combination of Next Generation Sequencing (NGS) and Sanger sequencing technologies to cover the full coding regions of the listed genes plus ~10 bases of non-coding DNA flanking each exon. As required, genomic DNA is extracted from the patient specimen. For NGS, patient DNA corresponding to these regions is captured using an optimized set of DNA hybridization probes. Captured DNA is sequenced using Illumina’s Reversible Dye Terminator (RDT) platform (Illumina, San Diego, CA, USA). Regions with insufficient coverage by NGS are covered by Sanger sequencing. Copy number variants (CNVs) such as deletions and duplications are detected from next generation sequencing data. We utilize a CNV calling algorithm that compares mean read depth and distribution for each target in the test sample against multiple matched controls. Neighboring target read depth and distribution, and zygosity of any variants within each target region are used to reinforce CNV calls. All CNVs are confirmed using another technology such as PCR, aCGH or MLPA before they are reported. This test is also offered via our exome backbone with CNV detection. The exome-based test may be higher priced than this test depending on the amount of Sanger backfill requested. However, the exome-based test permits reflex to the entire exome or to any other set of clinically relevant genes.

Citations

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