Single Gene Analysis

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General Information

Lab Name
Single Gene Analysis
Lab Code
SGN
Epic Ordering
SINGLE GENE ANALYSIS
Description

This test is for a single gene selected from the BROCA, ColoSeq™, and Megalencephaly panels, which must be clearly indicated in the space provided on the requisition. Additional single gene testing can be ordered via UW OncoPlex Single Gene [OPG].

For the complete list of genes, see the following pages:

This test uses next-generation sequencing to detect most mutations in the gene tested. Mutations in these genes are associated with hereditary cancer risk and megalencephaly syndromes. The assay completely sequences all exons, non-repetitive introns, and flanking regions of these genes AND detects large deletions and duplications.

References
  • Pritchard CC, et al. ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing. J Mol Diagn 2012, 14:357-66. 22658618
  • 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
Forms & Requisitions

Requisition Form and Ordering Instructions

1. Fill out a Genetics Requisition Form

Providers with access to the UW implementation of Epic (i.e., FHCC, HMC, SCCA, UWMC, UWNW) may order this test using the order "UW Genetics and Solid Tumor Test Request."

2. Check "Single Gene Analysis"

3. Indicate specific gene/genes desired in the space provided

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

Synonyms
ABCC9, Adenomatous polyposis, AKT1, AKT2, AKT3, APC, ATM, ATR, AXIN2, BAP1, BARD1, BMPR1A, BRCA1, BRCA2, breast cancer, BRIP1, BRWD3, CCND2, CDH1, CDK4, CDKN1C, CDKN2A, CHD8, CHEK2, Colon cancer, Cowden, CTNNA1, CTNNB1, DEPDC5, DICER1, DNMT3A, EED, EPCAM, EZH2, familial adenomatous polyposis, FANCM, FAP, FH, FLCN, GALNT12, GEN1, GLI3, GNAQ, GNAS, GPC3, GREM1, HDGC, hereditary diffuse gastric cancer, Hereditary nonpolyposis colorectal cancer, Hereditary paraganglioma, Hereditary pheochromocytoma, hereditary prostate, HNPCC, HOXB13, KCNJ8, Li-Fraumeni, Lynch Syndrome, MED12, megalencephaly, MEN1, MET, MITF, MLH1, MLH3, MSH2, MSH3, MSH6, MTOR, MUTYH, NBN, Next-generation sequencing, NF1, NF2, NPRL2, NPRL3, NSD1, NTHL1, PALB2, Peutz-Jeghers, PHOX2B, PIK3CA, PMS2, POLD1, POLE, POT1, PRKAR1A, PTCH1, PTEN, RAD51B, RAD51C, RAD51D, RB1, RECQL, RET, RNF135, RNF43, RPS20, SDHA, SDHB, SDHC, SDHD, SETD2, SMAD4, SMARCA4, STK11, Succinate dehydrogenase, TP53, TSC1, TSC2, VHL, Von Hippel Lindau
Components

Interpretation

Method

Next-generation sequencing.

Sequences are aligned to the human genome reference (hg19). Test performed by targeted capture for listed genes followed by next-generation sequencing with Illumina technology. This test was developed and its performance characteristics determined by the University of Washington Department of Laboratory Medicine. It has not been cleared or approved by the US Food and Drug Administration. This laboratory is certified under the Clinical Laboratory Improvement Amendments (CLIA) as qualified to perform high complexity clinical laboratory testing. This test is used for clinical purposes. It should not be regarded as investigational or for research.

Reference Range
See individual components
Ref. Range Notes

No mutations detected.

References
  • Pritchard CC, et al. ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing. J Mol Diagn 2012, 14:357-66. 22658618
  • 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
Guidelines

Ordering & Collection

Specimen Type
Peripheral Blood, saliva, or purified DNA from peripheral blood or saliva ONLY. For other sample types, including cultured cells such as fibroblasts or amniocytes, please order Oncoplex Single gene testing (OPG).
Collection

BLOOD:

Preferred: 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 collection kit.

Forms & Requisitions

Requisition Form and Ordering Instructions

1. Fill out a Genetics Requisition Form

Providers with access to the UW implementation of Epic (i.e., FHCC, HMC, SCCA, UWMC, UWNW) may order this test using the order "UW Genetics and Solid Tumor Test Request."

2. Check "Single Gene Analysis"

3. Indicate specific gene/genes desired in the space provided

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

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
Brian Shirts, MD, PhD
Abbye McEwen, MD, PhD
Colin Pritchard, MD, PhD
Vera Paulson, MD, PhD
Eric Konnick, MD, MS
He Fang, PhD
Frequency
Typical Turnaround: 3 weeks *Turn around times may vary based on factors such as tissue acquisition and insurance preauthorization.
Available STAT?
No

Billing & Coding

CPT codes
Billing Comments

For additional test/billing information, see following page: Single Gene 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
UOW2819