Single Gene Analysis

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General Information

Lab Name
Single Gene Analysis
Lab Code
SGN
ORCA Name
Single Gene Analysis
Description

This test is for a single gene selected from the BROCA, ColoSeq™, EpiPlex™, MarrowSeq™, or Immunoplex™ panels, which must be clearly indicated in the space provided on the requisition.

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, bone marrow failure, immunodeficiency, epilepsy and megalencephaly. 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
  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
ABCB7, ADA, AK2, AKT1, AKT3, ALDH7A1, ANKRD26, AP3B1, APC, ARX, ATM, ATR, ATRX, AXIN2, Abraxas, Adenomatous polyposis, BAP1, BARD1, BLM, BLNK, BMPR1A, BRCA1, BRCA2, BRIP1, BTK, C15ORF41, CARD11, CBL, CD247, CD27, CD3D, CD3E, CD3G, CD79A, CD79B, CD8A, CDAN1, CDH1, CDK4, CDKL5, CDKN2A, CEBPA, CHD2, CHD7, CHEK1, CHEK2, CIITA, CORO1A, CSF3R, CTC1, CTLA4, CTNNA1, CXCR4, Colon cancer, Cowden, DCLRE1C, DKC1, DOCK8, EBF1, ELA2, ELANE, EPCAM, ERCC4, ETV6, FAM175A, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FAP, FH, FLCN, FOXG1, FOXN1, FOXP3, G6PC3, GABRA1, GABRG2, GALNT12, GATA1, GATA2, GEN1, GFI1, GREM1, HAX1, HDGC, HNPCC, HOXB13, Hereditary nonpolyposis colorectal cancer, IGLL1, IKBKB, IKZF1, IL2RA, IL2RG, IL7R, ITK, JAGN1, JAK2, JAK3, KCNQ2, KCNQ3, KCNT1, KIF23, KLF1, LCK, LIG4, LRRC8A, LYST, Li-Fraumeni, Lynch Syndrome, MAGT1, MALT1, MECP2, MEF2C, MEN1, MEN2, MET, MITF, MLH1, MPL, MRE11A, MSH2, MSH6, MUTYH, NBN, NF1, NFKBIA, NHEJ1, NHP2, NOP10, NTHL1, Next-generation sequencing, ORAI1, PALB2, PALLD, PAX5, PCDH19, PDGFRA, PIK3CA, PIK3R1, PIK3R2, PMS2, PNKP, PNP, PNPO, POLD1, POLE, POT1, PRF1, PRKAR1A, PRKDC, PRSS1, PTCH1, PTEN, PTPRC, Peutz-Jeghers, RAB27A, RAD50, RAD51B, RAD51C, RAD51D, RAG1, RAG2, RB1, RBM8A, RECQL, RET, RFX5, RFXANK, RFXAP, RINT1, RMRP, RNF168, RPL10, RPL11, RPL26, RPL35A, RPL5, RPS10, RPS14, RPS17, RPS19, RPS20, RPS24, RPS26, RPS7, RTEL1, RUNX1, SBDS, SCID, SCN1A, SCN2A, SCN8A, SDHB, SDHC, SDHD, SEC23B, SH2D1A, SLC2A1, SLC9A6, SLX4, SMAD4, SMARCA4, SP110, SRP72, STAT1, STAT5B, STIM1, STK11, STK4, STX11, STXBP1, STXBP2, SYNGAP1, TAP1, TAP2, TAPBP, TAZ, TBX1, TCF4, TCIRG1, TERC, TERT, TINF2, TP53, TTC7A, UBE3A, UNC13D, USB1, VHL, VPS45, Von Hippel Lindau, WAS, WRAP53, XIAP, XRCC2, ZAP70, breast cancer, epilepsy, hereditary prostate, immunodeficiency, megalencephaly
Components

Interpretation

Method

Next-generation sequencing.

This assay sequences all exons and flanking intronic sequences of one user-selected gene from the BROCA, ColoSeq™, EpiPlex™, Immunoplex™, MarrowSeq™ of Megancephaly panels. DNA is sequenced at an average coverage of 320 to >1,000 sequencing reads per bp. Genomic regions are captured using biotinylated RNA oliognucleotides (SureSelect), prepared in paired-end libraries with ~200 bp insert size, and sequenced on an Illumina HiSeq2000 instrument with 100 bp read lengths, in a modification of a procedure described by Pritchard et al. 2012. Large deletions and duplications are detected using methods described by Nord et al. 2011.

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

Ordering & Collection

Specimen Type
Peripheral Blood, cultured cells from skin biopsy, purified DNA from peripheral blood or cultured cells
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.

SKIN BIOPSY:

  • Collection and transport: Obtain 2-4 mm punch biopsy of skin sample under sterile conditions and place in transport media (e.g. Alpha-MEM media, RPMI). Transport media can be supplied by the lab; call 206-598-4488 to request. If transport media is not available, the following media are acceptable alternatives if shipping time will not exceed 24 hours: lactated Ringer's solution, viral transport medium, or sterile saline. DO NOT USE formaldehyde, formalin, alcohol, or 5% dextrose, or tissue culture medium buffered with bicarbonate.

CULTURED CELLS:

  • (2) T23 or (1) T75 flask (minimum 1-T25 flask)*.

*Prenatal testing requires concomitant testing for maternal cell contamination (see Online Test Guide [[MCC]] for ordering and specimen requirements)

Forms & Requisitions

Requisition Form and Ordering Instructions:

  1. Fill out a Genetics Requisition Form
  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.

Performance

LIS Dept Code
Genetics (GEN)
Performing Location(s)
UWMC 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: 206-598–0304
Lab email: genelab@uw.edu

Supervisor

Robert Livingston, PhD bobl@uw.edu

Genetic Counselors

Angela Jacobson, MS, LGC agibson@uw.edu
Ginger Tsai, MS, LGC, gjtsai@uw.edu

Faculty

Colin C. Pritchard, MD, PhD
Brian H. Shirts, MD, PhD
Christina Lockwood, PhD, DABCC
Stephen Salipante, MD, PhD
Eric Konnick, MD, MS
Karen Stephens, PhD, FACMG
Jonathan F. Tait, MD, PhD
Vera Paulson, MD, PhD

Frequency
Results within 4 weeks, once sample arrives in laboratory
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: ngsbill@uw.edu or call 1-855-320-4869 for more information.

Genetics Preauthorization Form

LOINC
35474-6