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Test Code LAB10177 Genome Analysis

Aliases

Germline testing

Special Collection Notes

Collect specimen according to standard operating procedure

Specimen Type

Whole Blood/Purple Top Tube (K2 EDTA) or Buccal Swab.  

Specimen Volume

  • Optimal Volume: 4.0 ml
  • Minimum Volume: 0.5 ml

Additional Notes

The diagnostic rate of whole genome sequencing (WGS) tests is estimated at 34% (95% Confidence Interval, 95% CI, 30-38%) across all age and ancestry groups. The diagnostic rate is influenced by patient age at testing, sequencing family structure (e.g., singleton, trio), clinical indication for testing, sequencing manner (rapid/nonrapid), and rate of consanguinity. When subset by age, the diagnostic rate is higher in pediatric patients (40%, 95% CI 37-43%) compared to adult patients (18%, 95% CI 16-19%). Trio testing yields a higher diagnostic rare compared with singleton testing, largely due to the ability to identify de novo variants. Neurological indications are reported to have the highest diagnostic rate across all age and ancestry groups (43%, 95% CI 38-49%). Rapid testing (turn-around time of 2-4 weeks) has a significantly higher diagnostic rate (44%, 95% CI 38-50%) than non-rapid testing (0.37, 95% CI 35-39%). This is likely a reflection of clinical indication severity and critical patient status that typically necessitates rapid testing.

TAT

4 weeks

Method

Next Generation Sequencing

CPT

Proband Only – 81425
Duo Analysis – 81425
Trio Analysis – 81425

Performing Section

PRECISION DIAGNOSTICS

Purpose/Principle

The CHCO PDL whole genome sequencing test and panel reflex to genome sequencing test utilizes next-generation sequencing technology to detect genetic variants in genes that are included in this test. The assay interrogates the coding regions and flanking intronic bases of the cited genes, with the capacity to detect sequence variants, copy number variants (CNVs), and mitochondrial variants. Uniform genomic coverage is achieved through standardized specimen processing and short-read sequencing. Sequencing data are monitored by quality control metrics to ensure high confidence in the accuracy and specificity of the variant calls. The CNV resolution threshold is approximately 1 Mb, although smaller events may be detected depending on regional complexity and data quality.