Background:
A fraction of all cancers are associated mutations in susceptibility genes that have been genetically transmitted, often through several generations. Understanding the molecular etiology of such cancer incidence can help guide treatment and proper surveillance. Our next-generation sequencing test is designed to detect mutations in the coding region of 53 genes associated with cancer, or increasing the risk for cancer onset. Our microarray test is designed to identify single exon deletions and duplications in the same 53 cancer-associated genes. Combining deletion/duplication data analyzed by microarray with next generation sequencing data will allow KDL to improve diagnostic yield and deliver more comprehensive results. This set of genes includes genes associated with: breast/ovarian/endometrial cancers; GI cancers, such as Lynch syndrome; renal and pancreatic cancers; melanoma; endocrine tumors, including multiple endrocrine neoplasia; and syndromes associated with single gene defects, such as Birt-Hogg-Dube, Bloom, Gorlin, Li-Fraumeni and Von-Hippel-Lindau, among others. It is recommended that this testing be accompanied by a complete family history and genetic counseling.
Reasons for Referral:
- Confirmation of a clinical diagnosis of an inherited cancer.
- Testing for individuals with a positive family history for inherited cancer (targeted testing is available if familial mutation is known)
Methodology:
Next generation sequencing will analyze the exons or coding regions of 53 inherited cancer-associated genes using Illumina NextSeq 500 technology and preparing samples using hybridization probes to enrich exonic regions.This assay does not assess regions of insufficient coverage, introns and promoter regions; pseudogenes; where the reference genome is inaccurate or contains gaps and insertions; and regions of high GC or polynucleotide repeats, but may contain variants that impact gene function.
Exon-level deletion/duplication analysis is performed by running the NGS data through the Genome Analysis Toolkit (GATK) Germline Copy Number Variation best practices pipeline from GATK, version 4.1.4.1. A Bayesian model was validated clinically in our lab. The model can detect copy changes at a resolution of three (3) or more probe targets (exons) for deletions and duplications in genes that do not have pseudogenes, and is not designed to detect low-level mosaicism or balanced alterations.
The 53 inherited cancer-associated genes are listed below:
APC, ATM, BAP1, BARD1, BLM, BMPR1A, BRCA1, BRCA2, BRIP1, CDC73, CDH1, CDK4, CDKN1B, CDKN2A, CHEK2, EPCAM, FH, FLCN, HOXB13, MAX, MEN1, MET, MITF, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, NF1, PALB2, PMS2, PRKAR1A, PTCH1, PTEN, RAD50, RAD51C, RAD51D, RB1, RET, SDHA, SDHAF2, SDHB, SDHC, SDHD, SMAD4, STK11, TMEM127, TP53, TSC1, TSC2, VHL, XRCC2
Specimen Requirements:
Blood: EDTA or ACD (Solution A or B):
- Adult: 5 mL
- Child: 5 mL
- Infant: 2-3 mL
Saliva: 2 ORAgene™ Saliva Collection Kit(s) (OGR-500) used according to manufacturer instructions.Please contact KDL Client Services for a Saliva Collection Kit for patients that cannot provide a blood sample.
Assisted Saliva: 4 ORAgene™ Assisted Saliva Collection Kits (OGR-575) used according to manufacturer instructions. Please contact KDL Client Services for an Assisted Saliva Collection Kit for patients that cannot provide a blood sample.
Skin Fibroblast: Punch Biopsy (Cell cultures will be prepared at KDL and used for testing), or 2 T-25 confluent flasks.
DNA: 10µg at a minimum of 60-100ng/µL (DNA must be extracted in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the CAP and/or CMS).
For routine testing of blood, saliva and buccal swabs, KDL does NOT accept samples from patients within two (2) weeks of a packed cell/platelet transfusion or within four (4) weeks of a whole blood transfusion. For extraordinary circumstances, where testing must be performed outside of the above windows, please contact our lab.
A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES. Please include detailed clinical information, including ethnicity, clinical history, and family history.
Test Performed (Days):
Weekly
Turn Around Time:
3 weeks
Shipment Sensitivity Requirements:
- Package and ship specimen to remain cold, but not frozen.
- Ship via overnight express, using the FedEx priority overnight label provided.
- Contact Client Services for shipping kits and instructions at (855) 535-1522.
References:
Additional Info: