NextStepDx PLUS

Performance Characteristics

• Specimen preparation performed at an outside lab
• Report generated in-house
• Wet lab work performed at an outside lab
• Interpretation performed at an outside lab
• Our CAP approved and CLIA certified laboratory partner performs the analytical components of testing as well as the primary interpretation. Lineagen clinical team, including licensed/certified genetic counselors and boarded molecular geneticists, review results and provides additional clinical information as we generate the provider-facing report.

This assay has been validated per standard guidelines including CAP and CLIA. All the variants with quality score less than 500 (roughly 40X of coverage for a heterozygous variant) will be confirmed by Sanger sequencing. Only variants classified as pathogenic, likely-pathogenic, or unknown significance which are thought to be related to the patient’s phenotype or test indication are reported. When a single pathogenic or likely pathogenic variant is identified in a gene with autosomal-recessive inheritance, the laboratory ensures that 100% of coding sequences of that gene are covered either through NGS or Sanger sequencing technologies.

All laboratory tests have limitations. These results assume that the specimen received in the laboratory belongs to the named individual and that no mixup or co-mingling of specimens has occurred. Positive results do not imply that there are no other pathogenic alterations in the patient’s genome, and negative results do not rule out a genetic cause for the indication for testing. This assay assumes that any stated familial relationships are accurate. This assay is not designed or validated for the detection of somatic mosaicism or somatic mutations. This assay will not detect certain types of genomic aberrations which may cause disease such as, but not limited to, translocations or inversions. Result interpretation assumes that the human reference sequences are correct at the queried loci. Official gene names change over time and we use the most up to date gene names based on HUGO Gene Nomenclature Committee (https://www.genenames.org) recommendations. Result interpretation is based on the collected information available at the time of reporting; additional information may exist in the future which will not be represented. DNA alterations in regulatory regions or deep intronic regions (greater than 20bp from an exon) will not be detected by this test. All sequencing technologies have limitations. There are technical limitations on the ability of DNA sequencing to detect small insertions and deletions. Our laboratory uses a sensitive detection algorithm, however these types of alterations are not detected as reliably as single nucleotide variants. Rarely, due to systematic chemical or computational issues, or human error, DNA variants may be missed. Repeat expansions (eg. trinucleotides or hexanucleotides) are not reliably detected by NGS, and pathogenic expansions will not be detected in disease-related genes, even if those genes are sequenced. Although next generation sequencing technologies and our bioinformatics analysis significantly reduce the contribution of pseudogene sequences or other highly-homologous sequences, sometimes, these may still interfere with the technical ability of the assay to identify pathogenic variant alleles in both sequencing and deletion/duplication analyses. Del/dup analysis can identify deletions or duplications of genomic regions which are two or more contiguous exons in size; single exon deletions or duplications will not be routinely detected by this test. When duplications of DNA are identified, if they have not been well-characterized, it is not possible to discern the genomic location or orientation of the duplicated segment, and therefore it is not possible to determine the effect of the duplication. Where deletions are detected, it is not always possible to determine whether the predicted product will remain in-frame or not.

Is proficiency testing performed for this test? HelpWhether the test undergoes periodic internal or external evaluation of the accuracy of test results. Lab-provided.

Yes

Method used for proficiency testingHelpMethod used for external or internal evaluation of the accuracy of test results. Lab-provided.

Inter-Laboratory

FDA Category Designation

Not Applicable