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GTR Home > Tests > Comprehensive Epilepsy and Seizure Panel

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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For PGxome® we use Next Generation Sequencing (NGS) technologies to cover the coding regions of targeted genes plus 10 bases of flanking non-coding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. As required, genomic DNA is extracted from patient specimens. Patient DNA corresponding to these regions is captured using Agilent Clinical Research Exome hybridization probes. Captured DNA is sequenced on the NovaSeq 6000 using 2x150 bp paired-end reads (Illumina, San Diego, CA, USA). The following quality control metrics are generally achieved: >97% of target bases are covered at >20x, and mean coverage of target bases >120x. Data analysis and interpretation is performed by the internally developed Infinity pipeline. Variant calls are made by the GATK haplotype caller (through Sentieon) and annotated using in house software and Jannovar. For Sanger sequencing, polymerase chain reaction (PCR) is used to amplify targeted regions. After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit. PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer. In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions. Copy number variants (CNVs) are also detected from NGS 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 aCGH, MLPA, or PCR before they are reported. We are happy to accommodate requests for testing single genes in this panel or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered via our PGxome Custom Panel tool.

Citations

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Genes

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