;">
About Stanford Clinical LaboratoryContact UsPublications



Home
Test Directory
Specimen Collection
Critical Values
Esoteric Program
Pathology


What's New

DEPARTMENT:     MOLECULAR GENETIC PATHOLOGY

DIRECTOR:   Iris Schrijver, M.D.
DIRECTOR:   James Zehnder, M.D.

NEW TEST

BCR-ABL KINASE DOMAIN MUTATION ANALYSIS

Test Description and Clinical Indications: Translocation of the ABL gene on chromosome 9 to the BCR gene on chromosome 22 creates a chimeric BCR-ABL gene, also known as the Philadelphia Chromosome or t(9:22).  Mutations in the ABL Kinase Domian (KD) of BCR-ABL can occur, both de novo and in treated patients.  Expansion of such a KD mutant clone may be associated with resistance to treatment and with progression to advanced phase disease.  Depending on the specific mutation, such resistance may be overcome by dose escalation of Imatinib or treatment with second-generation tyrosine-kinase inhibitors.  This sequencing assay detects mutations in the ABL Kinase Domain.

BCR-ABL Kinase Domain Mutation Analysis

Order Code:  BCRKDM
   

Synonyms:

ABL Mutation; BCRABL Kinase Domain

Specimen Type:

Whole Blood

Container Type:

Lavender-top tube (EDTA), Light-blue-top tube (sodium citrate), Yellow-top tube Acid Citrate Dextrose Solution A (ACD)

Required Volume:

4 mL

Minimum Volume (Pediatric):

3 mL

Special Handling:

Refrigerate. Ship on wet ice/cold packs.  To be received within 48 hours of collection

Methodology:

RT-PCR followed by sequencing analysis

TAT:

7-14 days

CPT Codes:

83891, 83894, 83898, 83902, 83904 x 4, 83912

Report:

Negative or Positive, with an interpretation and description of the modification.
Causes For Rejection: Heparin

 

NEW TEST

Familial Gastric Cancer

Test Description and Clinical Indications: Familial diffuse gastric and lobular breast cancer predisposition, diagnostic test. The CDH1 gene encodes the cell adhesion protein e-cadherin. E-cadherin germline mutations are associated with both hereditary diffuse gastric cancer and lobular breast cancer. The inheritance pattern is autosomal dominant with incomplete penetrance (~80% for diffuse gastric cancer and ~40% for lobular breast cancer). Mutations are widely distributed throughout the gene, and associated with loss of function of the mutated e-cadherin allele. By the time gastric cancer becomes symptomatic, it is rarely curable. However, a high cure rate (>90% 5 year survival) is possible if the stomach is removed prior to tumor invasion through the gastric wall. Identification of individuals at high risk of developing diffuse gastric cancer, then, affords the opportunity for elective prophylactic gastrectomy. The e-cadherin gene locus (CDH1) is tested for the presence of sequence variants by polymerase chain reaction followed by direct DNA sequencing of the 16 exons as well as surrounding non-coding regions. Because mutations are distributed across all coding exons of the CDH1 gene, an analysis of all exons is recommended. For families with a known mutation, sequencing of a single exon may be appropriate. This is offered separately in our laboratory.

Familial Gastric Cancer

Order Code:  CDH1

   

Synonyms:

CDH1 by Sequencing

Specimen Type:

Whole Blood

Container Type:

Lavender-top tube (EDTA)

Required Volume:

2 mL

Special Handling:

Mix by gentle inversion several times. DO NOT CENTRIFUGE. Transport original tube promptly, at room temperature.

Methodology:

Polymerase Chain Reaction (PCR)

TAT:

14-21 days

CPT Codes:

83891, 83894, 83898 x 9, 83904 x 9, 83912; Site specific testing for a known familial mutation is 83891, 83898, 83894, 83904 x2, 83912.

Report:

Negative or Positive, with an interpretation and description of the modification.

 

DISCONTINUED TEST

FLT3 Gene Analysis Blood, Bone Marrow, Fluid

FLT3 Gene Analysis FLT3, BMFLT3 & FFLT3 tests have been discontinued and replaced with:

NEW TESTS

  • AML Prognosis Assay, Blood, Test Code AMLP   and
  • AML Prognosis Assay, Bone Marrow BMAML

Test Description and Clinical Indications: The FLT3 gene encodes a receptor tyrosine kinase that regulates proliferation and differentiation of hematopoietic stem cells. An internal tandem duplication of the FLT3 gene (FLT3-ITD) has been reported in nearly 25% of patients with AML. A further 7% of AML patients have a mutation of aspartic acid residue 835 (D835) in the activation loop of the second kinase domain, which leads to constitutive activation. Both FLT3 mutations are associated with a poor prognosis. The NPM1 gene encodes nucleophosmin, a nucleolar phoshoprotein that constantly shuttles between the nucleolus and cytoplasm. Insertion mutations in exon 12 of NPM1 occur in approximately one-third of de novo AMLs and confer a favorable prognosis. This assay is based on fluorescent-PCR combined with restriction enzyme digestion, capillary electrophoresis and GeneScan analysis to detect and identify the FLT3-ITD and FLT3-D835 mutations, as well as exon 12 NPM1 insertion mutations, in a single reaction.

AML Prognosis Assay, Blood

Order Code:  AMLP

   

Synonyms:

FLT3-NPM1; FLT3-ITD; FLT3-D835; Tyrosine Kinase; Nucleophosmin

Specimen Type:

Whole Blood

Container Type:

Lavender-top tube (EDTA), Yellow-top tube Acid Citrate Dextrose Solution A (ACD), or Light-blue-top tube (sodium citrate) whole blood

Required Volume:

2 mL whole blood

Minimum Volume (Pediatric):

500 µL whole blood

Special Handling:

Room Temperature

Methodology:

PCR amplification, restriction enzyme digestion, capillary electrophoresis

Components:

FLT3-NPM1; FLT3-ITD; FLT3-D835

TAT:

7-14 days

CPT Codes:

83891, 83892, 83900, 83901, 83909 x 2, 83912

Report:

Negative or Positive, with an interpretation and description of the modification.

Causes For Rejection: Contact with heparin

 

AML Prognosis Assay, Bone Marrow

Order Code:  BMAML

   

Synonyms:

FLT3-NPM1; FLT3-ITD; FLT3-D835; Tyrosine Kinase; Nucleophosmin

Specimen Type:

Bone Marrow Aspirate

Container Type:

Lavender-top tube (EDTA), Yellow-top tube Acid Citrate Dextrose Solution A (ACD), or Light-blue-top tube (sodium citrate)

Required Volume:

1 mL bone marrow aspirate

Minimum Volume (Pediatric):

500 µL bone marrow aspirate

Special Handling:

Room Temperature

Methodology:

PCR amplification, restriction enzyme digestion, capillary electrophoresis

Components:

FLT3-NPM1; FLT3-ITD; FLT3-D835

TAT:

7-14 days

CPT Codes:

83891, 83892, 83900, 83901, 83909 x 2, 83912

Report: Negative or Positive, with an interpretation and description of the modification.
Causes For Rejection: Contact with heparin

 

NEW SPECIMEN TYPE

BCR-ABL, Quantitative, Fluid

Order Code:  FBCRQT

Specimen Type:

Body Fluid

Container Type:

Sterile container

Required Volume:

8 mL

Minimum Volume (Pediatric):

8 mL

Special Handling:

Transport Refrigerated, ship on wet ice/cold packs to be received within 48 hours of collection.

Methodology:

Quantitative RT-PCR

TAT:

7-14 days
CPT Codes: 83891, 83896 x 2, 83898 x 2, 83902, 83912

Report:

The results are expressed as a ratio of the BCR-ABL transcripts versus ABL transcripts


ORDER CODE CHANGE:  From TMSI to TMS see red text.

Microsatellite Instability

Order Code:  TMS

Specimen Type:

Frozen Tissue Frozen, Paraffin Tissue (must include a normal tissue or whole blood sample)

Container Type:

Frozen Tissue in sterile container Paraffin block plus normal tissue or Whole blood in Lavender-top tube (EDTA)

Required Volume:

Tissue, amount varies; Whole blood, 2 mL

Minimum Volume (Pediatric):

Varies

Special Handling:

Transport at Room Temperature

Methodology:

PCR / Fragment Analysis

TAT:

7-14 days

CPT Codes: 83891 x 2, 83900 x 2, 83901 x 6, 83909 x 2, 83912

Report:

Negative or Positive, with an interpretation and description of the assay.


CPT CODE UPDATE:  Changes see red text

Maternal Cell Contamination, tissue

Order Code:  TMCC

   

Specimen Type:

Chorionic villi Tissue & Maternal Blood

Container Type:

Tissue in sterile container; Maternal Blood, Lavender-top tube (EDTA)

Required Volume:

Tissue, amount varies; Maternal Blood, 4 mL

Minimum Volume (Pediatric):

Varies

Special Handling:

Transport at Room Temperature

Methodology:

PCR / Fragment Analysis

TAT:

7-14 days

CPT Codes: 83891, 83900, 83901, 83909, 83912

Report:

Negative or Positive, with an interpretation and description of the assay.


Maternal Cell Contamination

Order Code:  MCC

   

Specimen Type:

Amniotic Fluid plus maternal whole blood sample

Container Type:

Amniotic Fluid in sterile container; Maternal Blood in Lavender-top tube (EDTA)

Required Volume:

Amniotic Fluid 1-5 mL; Maternal whole blood, 4 mL

Special Handling:

Transport at Room Temperature

Methodology:

PCR / Fragment Analysis

TAT:

7-14 days

CPT Codes: 83891, 83900, 83901, 83909, 83912

Report:

Negative or Positive, with an interpretation and description of the assay.

 

Alpha Thalassemia, Amniotic Fluid

Order Code:  FATHAL

   

Specimen Type:

Amniotic Fluid

Container Type:

Sterile container

Required Volume:

8 mL

Minimum Volume (Pediatric):

8 mL

Special Handling:

Transport at Room Temperature

Methodology:

Polymerase Chain Reaction (PCR)

TAT:

7-14 days

CPT Codes: 83891, 83894, 83900, 83901 x 5, 831912, 83896x 2, 83898

Report:

Negative or Positive, with an interpretation and description of the assay.


Alpha Thalassemia, Blood

Order Code:  ATHAL

   

Specimen Type:

Whole Blood

Container Type:

Lavender-top tube (EDTA)

Required Volume:

4 mL

Minimum Volume (Pediatric):

2 mL

Special Handling:

Transport at Room Temperature

Methodology:

Polymerase Chain Reaction (PCR)

TAT:

7-14 days

CPT Codes: 83891, 83894, 83900, 83901 x 5, 83912, 83896 x 2, 83898

Report:

Negative or Positive, with an interpretation and description of the assay.

 

Alpha Thalassemia, Tissue

Order Code:  TATHAL

   

Specimen Type:

Fresh or Frozen Tissue

Container Type:

Fresh Tissue in a sterile saline or RPMI.  Frozen Tissue in Sterile container

Required Volume:

Amount varies

Minimum Volume (Pediatric):

Varies

Special Handling:

Transport Fresh Tissue at Room Temperature, Transport Frozen Tissue Frozen

Methodology:

Polymerase Chain Reaction (PCR)

TAT:

7-14 days

CPT Codes: 83891, 83894, 83900, 83901 x 5, 83912, 83896 x 2, 83898

Report:

Negative or Positive, with an interpretation and description of the assay.

 

TEST VOLUME UPDATE: Change see red text

T(15;17) PML-RAR, Fluid, PCR

Order Code:  FT1517

   

Specimen Type:

Body Fluid

Container Type:

Sterile container

Required Volume:

8 mL

Minimum Volume (Pediatric):

8 mL

Special Handling:

Transport Refrigerated, ship on wet ice/cold packs to be received within 48 hours of collection.

Methodology:

Quantitative RT-PCR

TAT:

7-14 days

CPT Codes:

83891, 83896 x 4, 83898, 83900, 83901, 83902, 83912

Report:

Negative or Positive, with an interpretation and description of the assay.

 

DISCONTINUED TESTS

Solid Tumor Testing: The following 3 tests have been discontinued

  • Alvelor Rhabdomyosarcoma, Tissue       Order Code TARS
  • Ewing’s Sarcoma, Tissue                       Order Code TEWS
  • Synovial Sarcoma, Tissue                      Order Code TSYS

Back to Top
 
 


 
Home | About Stanford Clinical Labs | Contact Us | Legal Notices & Disclaimer