Skip to main content

TGL Test Descriptions

Test Name 

CPT Code 

Test Description 

BTD
Sequencing

81404

Mutations in BTD have been identified in autosomal recessive biotinidase deficiency. Sanger sequencing detects approximately 99% of patients with biotinidase deficiency.  Mutation analysis is useful to differentiate between profound and partial biotinidase deficiency, to detect carriers, and for family studies.  The BTD gene is analyzed by bidirectional Sanger DNA sequencing from whole blood-EDTA or DNA samples, using Sequencher sequencing analysis software. Sequences are compared to NCBI reference sequences for the BTD gene (NM_000060.3 and NP_000051.1).

Confirmation of
a Research Finding

81479

Prior to being reported to physicians and entered into the patients’ medical record, sequencing variants identified under research protocols require confirmation by Sanger sequencing in a CLIA certified laboratory, such as TGL. Confirmation testing under CLIA allows patients and their physicians to receive the results and to use them in clinical management decisions. An appropriate exon of the gene of interest is analyzed by bidirectional Sanger DNA sequencing from whole blood or bone marrow sample using Sequencer sequencing analysis software. Sequences are compared to the appropriate NCBI reference sequences for the gene of interest.

NOTE: TGL must receive an original blood sample from an approved phlebotomy location.  Samples extracted by research laboratories will not be accepted for Confirmation of a Research Finding.

CYP2C19 Genotyping

81225

Clopidogrel (Plavix) response is due in part to variation in the Cytochrome P450 2C19 gene (CYP2C19). Six variants (*2,*3, *4, *6, *8, and *17) in the CYP2C19 gene are analyzed by Taqman genotyping for rs121913499, This assay does not detect other CYP2C19 variants

CYP2C19 Sequencing

81479

Clopidogrel (Plavix) response is due in part to mutations in the Cytochrome P450 2C19 gene (CYP2C19). The CYP2C19 gene's 5’ untranslated region (UTR) and exons 4 and 5 (which include the common *2,*3, and *17 variants) are analyzed by bidirectional Sanger DNA sequencing from DNA or whole blood samples, using Sequencer sequencing analysis software. Sequences are compared to NCBI reference sequences for the CYP2C19 gene (NM_000769.1 and NP_000760.1).

Cytogenomic Microarray

81229

Genomic imbalance is a major cause of congenital or developmental abnormalities. Genome-wide DNA copy number analysis is performed using the Affymetrix Cytoscan High Density (HD) ™ protocol along with the Command Console and Chromosome Analysis Suite software (CHAS). This array includes >1.8 million Copy Number Variant probes and >750,000 SNP probes, providing genotyping information that enables detection of copy number neutral loss of heterozygosity (CN-LOH) and detection of some Uniparental Disomy (UPD) cases.

Extract and Hold

NA

DNA can be extracted in our CLIA/CAP laboratory to allow for an initial work-up to be completed prior to determining if additional testing is necessary. The intent is for DNA to be used for future clinical testing and is not intended for long term storage or banking of samples. DNA will be extracted by either the EZ1 DNA Blood or the EZ1 DNA Tissue kit and stored for up to twelve months from receipt of the sample.

FLT3 ITD and TKD Analysis

81245 and 81246

FLT3 is a receptor tyrosine kinase with important roles in hematopoietic stem/progenitor cell survival and proliferation. This assay is used in testing for common FLT3 variants in patients with acute myeloid leukemia (AML). The FLT3 internal tandem duplication (FLT3-ITD) variant is present in about 30% of newly diagnosed AML patients and results in a poor prognosis and decreased disease-free survival.1-5 The FLT3 tyrosine kinase domain (FLT3-TKD) variant occurs in residue D835 or I836 of the kinase domain and confers resistance to FLT3 inhibitors.

Fragment size analysis using capillary electrophoresis and the GeneMapper software package of two different regions of the FLT3 gene.

  • Amplification of a 328 base pair (bp) region within the FLT3 gene is achieved using site-specific fluorescently labeled primers. The presence of the FLT3-ITD
  • variant is detected by observing the amplification of this targeted region. A fragment size identical to the negative control is indicative of a negative result and a fragment size larger than the negative control is indicative of a positive result.
  • The detection of variants within the FLT3-TKD is accomplished by amplifying a region of the DNA coding for this region of the FLT3 protein using fluorescently labeled primers. This product is then digested with a restriction enzyme, EcoRV. Bases coding for the D835 and the I836 codons are included in the restriction site for EcoRV, and variants in these codons will result in loss of the EcoRV site. In the negative control sample two fragments will be observed as a result of cleavage by the enzyme and if the site is mutated only one larger fragment will be observed.

IDH1 R132_IDH2 R140 and R172 Sequencing

81403 x 2

IDH1 (isocitrate dehydrogenase 1 (NADP+), soluble) and IDH2 (isocitrate dehydrogenase 1 (NADP+), mitochondrial) are mutated in approximately 15-23% of de novo Acute Myeloid Leukemia (AML) cases. Variants have also been identified in 5% of myelodysplastic syndromes (MDS) and 10% of myeloproliferative neoplasms (MPN). IDH1 codon 132, IDH2 codons 140 and 172 and the surrounding sequences within exon 4 are analyzed by bidirectional Sanger DNA sequencing for whole blood or bone marrow samples, using Sequencher sequencing analysis software. Sequences are compared to NCBI reference sequences for IDH1 (NM_005896.3 and NP_005887.2) and IDH2 (NM_002168.3 and NP_002159.2) genes.

Once a specific variant has been identified within a family, site-specific testing by Sanger sequencing can be performed for other family members, rather than full gene sequencing.  An appropriate exon or fragment of the gene of interest is analyzed by bidirectional Sanger DNA sequencing from whole blood or bone marrow sample using Sequencer sequencing analysis software. Sequences are compared to the appropriate NCBI reference sequences for the gene of interest.

Site-Specific Familial Variant Analysis

81479

NOTE: TGL must receive an original blood sample from an approved phlebotomy location.  Samples extracted by research laboratories will not be accepted for Site-specific Familial Variant Analysis. In addition, TGL must have either a copy of the family member’s clinical report or have previously tested a family member.

 

 Back to Translational Genomics Laboratory >>