Hematological Malignancies TP53 Somatic Mutation Testing

The TP53 gene encodes a tumor suppressor protein, which regulates expression of genes involved in cell cycle arrest, apoptosis, senescence, DNA repair, and changes in metabolism.  In cancer, loss of TP53 function is most commonly due to mutations or deletions leading to increased cell survival, DNA damage, and cell proliferation.

Somatic TP53 mutations are detected in at least 50% of all adult tumors including a variety of solid tumors and hematopoietic malignancies and are generally associated with a poor prognosis. Germline mutations in TP53 are the cause of Li-Fraumeni Syndrome. This assay sequences the entire coding region of TP53 (exons 2 through 11) with a sensitivity of ~2% mutant allele for single nucleotide substitutions and ~5 % mutant allele for short insertions/deletions, with strict next generation sequencing quality control parameters.

This test is performed by PCR-based Next Generation Sequencing of DNA extracted from formalin fixed, paraffin embedded (FFPE) tissue or fresh tissue including peripheral blood and bone marrow.  The entire coding region of TP53 (exons 2 through 11) is sequenced using massively parallel sequencing (next-generation sequencing) with a combination of multiplexed PCR (customized QIAseq Targeted DNA panel) and sequencing on an Illumina platform. An in-house bioinformatics analysis pipeline has been used that employs multiple established variant calling tools (FreeBayes, MuTect2 and Scalpel) and variant annotation tool (Oncotator). The genomic variants have been interpreted in accordance with the 2017 guideline recommendations by AMP/ASCO/CAP (PMID: 27993330). The assay is validated in accordance with the AMP guidelines (PMID: 28341590).

• 5-10 mL of blood or bone marrow — yellow (ACD) or purple (EDTA) tube; or
  Formalin-fixed paraffin-embedded (FFPE) tissue blocks.
• 10 unstained slides (4-5 microns)
• Fresh Tissue:
  • Stabilize in Allprotect Tissue Reagent (Qiagen) and ship at room temperature – OR
  • Suspend in sterile culture media (RPMI or DMEM) or non-bacteriostatic normal saline in a sterile container and shipped at room temperature – OR
  • Snap Frozen and shipped on dry ice
• If sending DNA: please send 200ng at a minimum of 10ng/µL (DNA must be extracted in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the CAP and/or CMS)
• Pathology report MUST accompany sample for interpretation of results.

A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES.  Please include detailed clinical information.

Twice per week

10-14 days

• Package and ship specimen to remain cold, but not frozen (except for snap-frozen fresh tissue). 
• Ship via overnight express, using the FedEx priority overnight label provided. 
• Contact Client Services for shipping kits and instructions at (855) 535-1522.

 

1. Robels AI, Jen J, Harris CC. Clinical Outcomes of TP53 Mutations in Cancers. Cold Spring Harb Perspect Med. 2016 Sep 1;6(9):a026294. PMID: 27449973
2. Olivier M, Hollstein M, Hainaut P. TP53 mutations in human cancers: origins, consequences, and clinical use. Cold Spring Harb Perspect Biol. 2010 Jan; 2(1): a001008. PMID: 20182602