Sema4 Sigal Hereditary Cancer Breast Guidelines Panel

Related Gene(s): ATM, BRCA1, BRCA2, CDH1, CHEK2, NBN, NF1, PALB2, PTEN, STK11, TP53

The Breast Guidelines Panel is a comprehensive 11-gene panel that includes genes associated with increased risk for breast cancer that have published medical management guidelines.

Test description/technology:

The Breast Guidelines Panel analyzes 11 genes (listed above) by next generation sequencing (NGS). This test detects variants within the exons and the intron-exon boundaries of the target regions. Variants outside these regions are not reported unless they are clinically significant. Most regions not meeting a minimum of >20X read depth across the exon are further analyzed by Sanger sequencing. Copy Number Variant (CNV) analysis is performed by relative depth analysis of NGS data. In addition, CNVs in BRCA1 and BRCA2 are analyzed by Multiplex Ligation-Dependent Probe Amplification (MLPA). Variants are classified using the ACMG/AMP framework and variants classified as uncertain significance, likely pathogenic, pathogenic are confirmed using an alternate technology (SNVs and indels: Sanger sequencing, CNVs: qPCR, MLPA or ddPCR). This test has an analytic sensitivity of >99 % (SNVs and small indels) and 89 % (CNVs). This test has not been validated to reliably detect certain variant types including mosaic variants, variants located within repeat expansions or structural genomic variation.

Single gene testing is available.  In addition, known familial variant testing can be ordered (please include a copy of the family member’s test report with the requisition form).


Turnaround Time

  • 14-21 days from receipt of specimen
  • 10-14 days from receipt of specimen if ordered as STAT for surgical decision making

Specimen Requirements

  • Whole blood samples: 2 lavender-top (EDTA) tubes, 5-10 mL of blood from the patient are required.
  • Extracted DNA samples: We request 20 µL DNA (50-250 ng/µL) or at minimum require 10 µL DNA (50-250 ng/µL). Causes for rejection include impurities in the test or reference DNA samples, including NaCl or KCl (>40 mM) and other salts, phenol, ethanol, heparin, EDTA (>1.5 mM), and Fe, contaminated DNA, and low concentration of DNA (<20 ng/µL).
  • Saliva samples: Saliva samples should be collected in Oragene DNA (OG-500) kits by DNA Genotek.
  • Cheek swab: 1 Isohelix(SK-1) cheek swab specimen from the patient is required.

Tubes of blood should be kept and shipped refrigerated or at room temperature (PLEASE DO NOT FREEZE).


Related Tests


Resources

Hereditary Cancer Requisition
Hereditary Cancer Re-Requisition
Hereditary Cancer Genetic Testing Consent
Hereditary Cancer Provider Brochure