Diagnosis; Mutation Confirmation; Pre-symptomatic; Risk Assessment; Screening

PreventionGenetics’ Exome-Wide CNV Analysis utilizes exome sequencing data to identify chromosomal imbalances similar to those detected by chromosomal microarray (CMA). Our algorithm has been extensively validated to ensure appropriate identification of aneuploidy, triploidy, unbalanced rearrangements (e.g., unbalanced translocations), and known microdeletion and microduplication syndromes. This method will also identify unique … PreventionGenetics’ Exome-Wide CNV Analysis utilizes exome sequencing data to identify chromosomal imbalances similar to those detected by chromosomal microarray (CMA). Our algorithm has been extensively validated to ensure appropriate identification of aneuploidy, triploidy, unbalanced rearrangements (e.g., unbalanced translocations), and known microdeletion and microduplication syndromes. This method will also identify unique CNV events. This add on option allows for cost-effective identification and reporting of potentially important, large CNVs across the full exome in conjunction with any sequencing variants and/or smaller CNVs identified within the panel ordered. Exome-Wide CNV results will be included in the panel test report. View more

Copy Number Variants (CNVs) are 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 … Copy Number Variants (CNVs) are 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 reported CNVs are confirmed using another technology such as aCGH, MLPA, or PCR. For Exome-Wide CNV Analysis, we will generally only report deletions ≥ 250 kb in size and duplications ≥ 500 kb in size. View more

Tests performed
Entire test performed in-house

As of March 2016, 6.36 Mb of sequence (83 genes, 1557 exons) generated in our lab was compared between Sanger and NextGen methodologies. We detected no differences between the two methods. The comparison involved 6400 total sequence variants (differences from the reference sequences). Of these, 6144 were nucleotide substitutions and … As of March 2016, 6.36 Mb of sequence (83 genes, 1557 exons) generated in our lab was compared between Sanger and NextGen methodologies. We detected no differences between the two methods. The comparison involved 6400 total sequence variants (differences from the reference sequences). Of these, 6144 were nucleotide substitutions and 256 were insertions or deletions. About 65% of the variants were heterozygous and 35% homozygous. The insertions and deletions ranged in length from 1 to over 100 nucleotides. In silico validation of insertions and deletions in 20 replicates of 5 genes was also performed. The validation included insertions and deletions of lengths between 1 and 100 nucleotides. Insertions tested in silico: 2200 between 1 and 5 nucleotides, 625 between 6 and 10 nucleotides, 29 between 11 and 20 nucleotides, 25 between 21 and 49 nucleotides, and 23 at or greater than 50 nucleotides, with the largest at 98 nucleotides. All insertions were detected. Deletions tested in silico: 1813 between 1 and 5 nucleotides, 97 between 6 and 10 nucleotides, 32 between 11 and 20 nucleotides, 20 between 21 and 49 nucleotides, and 39 at or greater than 50 nucleotides, with the largest at 96 nucleotides. All deletions less than 50 nucleotides in length were detected, 13 greater than 50 nucleotides in length were missed. Our standard NextGen sequence variant calling algorithms are generally not capable of detecting insertions (duplications) or heterozygous deletions greater than 100 nucleotides. Large homozygous deletions appear to be detectable. The PGxome test detects most larger deletions and duplications including intragenic CNVs and large cytogenetic events; however aberrations in a small percentage of regions may not be accurately detected due to sequence paralogy (e.g., pseudogenes, segmental duplications), sequence properties, deletion/duplication size (e.g., 1-3 exons vs. 4 or more exons), and inadequate coverage. In general, sensitivity for single, double, or triple exon CNVs is ~70% and for CNVs of four exon size or larger is >95%, but may vary from gene-to-gene based on exon size, depth of coverage, and characteristics of the region. View more

Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Intra-Laboratory

Software used to interpret novel variations Help
GeneSplicer, Human Splicing Finder, MaxEntScan, Mutation Taster, NNSPLICE, PolyPhen 2, SIFT and Splice Site Finder.

Laboratory's policy on reporting novel variations Help
Sequence variants found in our patients are contributed to ClinVar. Anonymous patient sequence data will also be shared with researchers for preparation of peer-reviewed publications.