When to Conduct Pathological Specimen DNA Identity Testing
- Determining specimen identity in the case of suspected mislabeling
- Confirming possible tissue contaminants (“floaters”) identified on histologic block or slide
BSI's Human Tissue Specimen Authentication
Bio-Synthesis offers the most comprehensive STR DNA testing available by examining of a panel of 15 highly polymorphic genetic markers plus one gender marker (amelogenin), to generate an STR DNA profile that uniquely identifies a patient sample. The results are reported as the number of identical or nonidentical alleles between the known and unknown samples. If the suspected source tissue is provided, an interpretation as to the identity of the unknown specimens also is given. If the suspected contaminant and patient’s known sample derived from unrelated individuals, there is a > 99.9999%
likelihood that one or more loci will be different.
BSI uses STR (Short Tandem Repeat) Analysis for Clinical Specimen Authentication
DNA fingerprinting analysis by PCR is a highly accurate technique for determining the patient identity of a tissue
sample. This assay uses PCR amplification of short tandem repeats (STRs) with number of highly polymorphic unlinked loci.
Each STR locus has two alleles, and each allele has a specific length that is stably inherited. PCR amplification of 15 highly polymorphic STR loci [D3S1358, THO1, D21S11, PentaE, D5S818, D13S317, D7S820, D16S539, CSF1PO, PentaD, vWA, D8S1179, TPOX, D18S51, FGA] and a sex chromosome specific locus (amelogenin) is performed. The loci used for patient sample identification are utilized for human sample identity, and are not designed to detect non-human DNA.
DNA STR analysis can be performed on formalin-fixed, paraffin-embedded tissue, blood in EDTA, or fresh/frozen tissue. The submitting pathologist must designate the suspected contaminant/mix-up as well as the patient’s known sample with which to compare. It is optional to include the suspected source tissue.
Testing on whole Blood and Bone Marrow
- Samples collected in purple-topped tubes (sodium EDTA anticoagulant) should be shipped on wet ice by FedEx overnight.
- 2 ml of blood or bone marrow is needed (Do not freeze whole blood or bone marrow). However, the scientist could extract and isolate DNA and send us genomic DNA. The gDNA should have the concentration 20 ng/ul and the volume 100 ul. The gDNA must be in distilled water and send with regular FedEx.
Testing on Solid Tumor/Frozen Tissue Specimens
- Lymph node, skin or other tissue biopsies may be utilized as a source of DNA for molecular assay. Each should be obtained in a sterile manner and transported frozen to preserve DNA integrity.
- 10-20 mg of tissue generally is sufficient for DNA STR testing. Again, the scientist could extract and isolate DNA and send us 20 ng/ul and the volume of 100 ul.
Testing on Paraffin-Embedded Tumor Tissues
For DNA testing, we can utilize paraffin-embedded tissue or sections prepared on glass slides. If paraffin material is used for testing, specific requirement will be required.
Slide sample requirement:
- Thickness: 6 micron
- No cover glass
- No dye/stained
- No fat tissue
- 4-5 slides