Laboratory Test Guide

Known Mutation Testing

General Information

Lab Name

Known Mutation Testing

Lab Code

KMU

Epic Name

Known Mutation Testing

Description

This test detects the presence or absence of a specific familial variant that was previously detected using the BROCA, ColoSeq™, or Megalencephaly panels. The specific mutation should be written on the requisition. See BROCA Cancer Risk Panel BROCA Cancer Risk Panel [BROCA], ColoSeq - Lynch and Polyposis Panel ColoSeq - Lynch and Polyposis Panel [COSEQ], and Megalencephaly Panel Megalencephaly Panel [MEGPX] for the full list of genes. Testing for familial variants detected through testing of retired panels, Immunoplex, EpiPlex™ or MarrowSeq™, is available; please contact the laboratory prior to sending a sample.

NOTE: If requesting testing for a known mutation based on testing from an outside laboratory, an order for a Single Gene Analysis Single Gene Analysis [SGN] is required.

References

  • Walsh T, et al. Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc Natl Acad Sci U S A 2010, 107:12629-33. 20616022
  • Nord AS, Lee M, King MC, and Walsh T. Accurate and exact CNV identification from targeted high-throughput sequence data. BMC Genomics 2011, 12:184. 21486468
  • Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11:31-46. 19997069

Synonyms

Adenomatous polyposis, APC, BRCA1, BRCA2, CDH1, Colon cancer, EPCAM, familial mutation, FAP, Hereditary nonpolyposis colorectal cancer, HNPCC, known mutation, Lynch Syndrome, MLH1, MSH2, MSH6, MUTYH, Next-generation sequencing, PMS2, PTEN, single mutation, site specific analysis (SSA), STK11, TP53

Components

Code Name
KMUGS Known Mutation Gene Analyzed
KMURE Known Mutation Result
KMUIN Known Mutation Interpretation
KMUCH Known Mutation Clin History
KMUMT Known Mutation Methods

Interpretation

Method

Targeted DNA Sequencing or Next Generation Sequencing

For DNA sequencing the region of the specific mutation in the family is amplified by PCR and sequenced bidirectionally by Sanger sequencing. Large deletions and duplications and some smaller variants are tested using Next Generation Sequencing. See methods descriptions for BROCA, ColoSeq™, EpiPlex™, MarrowSeq™, Megalencephaly or Immunoplex™ panels.

Reference Range

See individual components

Ref. Range Notes

No mutations detected

Guidelines

Ordering & Collection

Specimen Type

Accepted: peripheral blood, saliva, purified DNA from peripheral blood and saliva. Conditionally accepted: Cultured fibroblasts, amniocytes, chorionic villi – contact the laboratory prior to sending (genelab@uw.edu).

Collection

BLOOD:

  • 10 mL whole blood in LAVENDER TOP EDTA tube.
  • Also acceptable: YELLOW TOP ACD tube, purified DNA from peripheral blood or cultured cells.

SALIVA:

  • Contact laboratory for validated saliva collection kit (cgateam@uw.edu).

Blood and Saliva are the only acceptable sample types. All other samples, contact the laboratory (genelab@uw.edu) for other testing options.

Forms & Requisitions

Requisition Form and Ordering Instructions:

  1. Fill out a Genetics Requisition form.
  2. Under “Check Test Requested,” check: "Known Mutation".
  3. Enter the gene and specific mutation to be identified in the line provided.
  4. Provide a copy of the family member's test results. If the family member's report is not available, please provide their name and date of birth, in addition to their specific mutation.

Genetics Preauthorization Form (preauthorization is only done for providers who are external to the UW system).

Handling Instructions

Ship specimen at room temperature for overnight delivery.

Blood specimens can be held for up to 7 days before shipping if refrigerated.

Ship specimens to:

UW MEDICAL CENTER

LABORATORY MEDICINE - GENETICS LAB

1959 NE PACIFIC ST, ROOM NW220

SEATTLE, WA 98195-7110

Quantity

requested: entire sample
minimum: 5 mL whole blood

Processing

Blood: Refrigerate whole blood

Unacceptable Conditions: Frozen or clotted specimens

Stability (collection to initiation of testing): Ambient: 5 days; Refrigerated: 7 days; Frozen: Unacceptable

Purified DNA: Refrigerate DNA specimens. Frozen is acceptable.

Saliva:
Contact laboratory for validated collection kit.

Performance

LIS Dept Code

Genetics (GEN)

Performing Location(s)

UW-MT Genetics

Attention: Genetics Lab
Clinical lab, Room NW220
University of Washington Medical Center
1959 NE Pacific Street
Seattle, WA 98195

Tel: 206-598–6429 M–F (7:30 AM–4:00 PM)
Fax: 206-616-4584
Lab email: cgateam@uw.edu

Tel (EXOME only): 206-543-0459

Faculty
Jillian Buchan, PhD, FACMG
Runjun Kumar, MD, PhD
Regina Kwon, MD, MPH
Christina Lockwood, PhD, DABCC, DABMGG
Abbye McEwen, MD, PhD
Colin Pritchard, MD, PhD
Vera Paulson, MD, PhD
Eric Konnick, MD, MS
He Fang, PhD

Frequency

Results within 4 weeks, once sample arrives in the laboratory

Available STAT?

No

Billing & Coding

CPT codes

Billing Comments

For additional test/billing information, see following page: Known Mutation CPT codes.

For pricing information, contact Client Support Services 206-520-4600 or 800-713-5198.

Billing and Insurance Pre-Authorization

We offer insurance pre-authorization services (preauthorization is only done for providers who are external to the UW system).

Email: gpab@uw.edu or call 1-855-320-4869 for more information.

Genetics Preauthorization Form

LOINC

35474-6

Interfaced Order Code

UOW2832