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Test Code P53CA Hematologic Neoplasms, TP53 Somatic Mutation, DNA Sequencing Exons 4-9, Varies

Useful For

Evaluating chronic lymphocytic leukemia patients at diagnosis or during disease course for the presence of TP53 gene variants indicating high risk of disease progression and adverse outcomes

 

This test is not intended for the evaluation of patients suspected of having an inherited or germline TP53 cancer syndrome (eg, Li Fraumeni syndrome)

Testing Algorithm

Flow cytometry will be performed on peripheral blood samples to verify diagnosis of chronic lymphocytic leukemia (CLL) and to selectively enrich for B cells in samples with a clonal population.

 

For more information see TP53 Sequencing Testing Algorithm.

Reporting Name

TP53 gene somatic mutation analysis

Specimen Type

Varies


Ordering Guidance


For the evaluation of patients suspected of having an inherited or germline TP53 cancer syndrome (eg, Li Fraumeni syndrome), order one of the following tests containing TP53:

-XCP/ Hereditary Expanded Cancer Panel, Varies

-COMCP / Hereditary Common Cancer Panel, Varies

-BRGYP / Hereditary Breast/Gynecologic Cancer Panel, Varies

-CRCGP / Hereditary Gastrointestinal Cancer Panel, Varies

-PANCP / Hereditary Pancreatic Cancer Panel, Varies

-ENDCP / Hereditary Endocrine Cancer Panel, Varies

-THYRP / Hereditary Thyroid Cancer Panel, Varies

-WILMP / Hereditary Wilms Tumor Panel, Varies

-RENCP / Hereditary Renal Cancer Panel, Varies

-PRS8P / Hereditary Prostate Cancer Panel, Varies



Shipping Instructions


Blood and bone marrow specimens must arrive within 10 days of collection.



Necessary Information


The following information is required:

1. Pertinent clinical history

2. Clinical or morphologic suspicion

3. Date of collection

4. Specimen source



Specimen Required


Submit only 1 of the following specimens:

 

Specimen Type: Blood (preferred)

Container/Tube: Lavender top (EDTA) or yellow top (ACD solution B)

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send whole blood specimen in original tube. Do not aliquot.

3. Label specimen as blood.

Specimen Stability Information: Ambient/Refrigerate <10 days

 

Specimen Type: Bone marrow

Container/Tube: Lavender top (EDTA), yellow top (ACD solution B), or green top (heparin)

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix bone marrow.

2. Send bone marrow specimen in original tube. Do not aliquot.

3. Label specimen as bone marrow.

Specimen Stability Information: Ambient/Refrigerate <10 days

 

Specimen Type: Tissue

Container/Tube: Plastic container

Specimen Volume: 100 mg

Collection Instructions: Stabilize fresh tissue in tissue culture medium or freeze immediately after collection.

Specimen Stability Information: Refrigerate 24 hours/ Frozen


Specimen Minimum Volume

Blood, bone marrow: 1 mL

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Varies 10 days

Reject Due To

Gross hemolysis Reject
Extracted DNA Reject
Moderately to severely clotted
Formalin-fixed paraffin-embedded tissue		 Reject

Clinical Information

Patients with chronic lymphocytic leukemia (CLL) have variable disease course influenced by a series of tumor biologic factors. The presence of chromosomal 17p- or a TP53 gene variant confers a very poor prognosis to a subset of CLL patients, both at time of initial diagnosis, as well as at disease progression, or in the setting of therapeutic resistance. TP53 gene variant status in CLL has emerged as the single most predictive tumor genetic abnormality associated with adverse outcome and poor response to standard immunochemotherapy; however, patients can be managed with alternative therapeutic options.

 

Although the prognostic relevance of an acquired TP53 gene variant is best studied for CLL, similar findings are also reported for other hematologic malignancies including low-grade B-cell lymphoma, diffuse large B-cell lymphoma, and some types of myelodysplastic syndromes and acute myeloid leukemia. Therefore, while this test has been developed to be primarily focused on high-risk CLL patients, TP53 gene sequencing analysis can also be performed in additional neoplasms, as clinically indicated.

Reference Values

Genetic variants present or absent as compared to a reference sequence of the normal TP53 gene

Interpretation

Results are reported in standard nomenclature according to the most recent Human Genome Variation Society recommendations and an interpretive comment regarding the nature of the sequence variant (eg, known deleterious, suspected deleterious, synonymous change) will be included to complete the clinical report.

Cautions

This test will not detect all possible acquired variants in the TP53 gene because it is restricted to analyzing exons 4 to 9. However, this region encompasses more than 90% of described disease-causing variants and covers the coding exons of the critical DNA binding regions.

 

The analytical sensitivity of the assay can be affected by the absolute B-cell number in the peripheral blood or tissue sample, as well as the often subclonal nature of this tumor genetic abnormality. The assay attempts to compensate in part for this by performing an initial screening flow cytometry to assess B-cell quantity and by performing the cell enrichment step (for the peripheral blood specimens only) to isolate relatively pure CD19+ B cells for analysis. Nevertheless, the nature of the Sanger sequencing method is such that typical reproducible analytic sensitivity will be in the order of 25% variant allele burden.

 

Because optimal cell enrichment is dependent on the absolute B-cell quantity, samples with a very low white blood cell (WBC) or initial percentage of B cells (determined from flow cytometry or WBC automated cell count) will likely result in poor assay performance and inability to detect possible TP53 gene variants in the tumor population.

Clinical Reference

1. Zenz T, Krober A, Scherer K, et al: Monoallelic TP53 inactivation is associated with poor prognosis in chronic lymphocytic leukemia: results from a detailed genetic characterization with long-term follow-up. Blood. 2008;112:3322-3329

2. Lehmann S, Oqawa S, Raynaud SD, et al: Molecular allelokaryotyping of early-stage, untreated chronic lymphocytic leukemia. Cancer. 2008;112:1296-1305

3. Rossi D, Cerri M, Deambrogi C, et al: The prognostic value of TP53 mutations in chronic lymphocytic leukemia is independent of Del17p13: implications for overall survival and chemorefractoriness. Clin Cancer Res. 2009;15(3):995-1004

4. Zent CS, Call TG, Hogan WJ, et al: Update on risk-stratified management for chronic lymphocytic leukemia. Leuk Lymphoma. 2006;47(9):1738-1746

5. Trbusek M, Smardova J, Malcikova J, et al: Missense mutations located in structural p53 DNA-binding motifs are associated with extremely poor survival in chronic lymphocytic leukemia. J Clin Oncol. 2011;29:2703-2708

6. Halldorsdottir AM, Lundin A, Murray F, et al: Impact of TP53 mutation and 17p deletion in mantle cell lymphoma. Leukemia. 2011;25:1904-1908

7. Young KH, Leroy K, Moller MB, et al: Structural profiles of TP53 gene mutations predict clinical outcome in diffuse large B-cell lymphoma: an international collaborative study. Blood. 2008;112:3088-3098

8. Malcikova J, Tausch E, Rossi D, et al: ERIC recommendations for TP53 mutation analysis in chronic lymphocytic leukemia - update on methodological approaches and results interpretation. Leukemia. 2018;32:1070-1080

Method Description

Peripheral blood specimens from chronic lymphocytic leukemia (CLL) patients only will be analyzed by a screening flow cytometry method to determine B-cell content and confirm the presence of a clonal B-cell population. Blood (but not bone marrow) samples from patients with CLL are enriched for B lymphocytes by cell sorting, and DNA is extracted from the B-cell fraction. For other sample types (bone marrow, fresh or frozen tissues) DNA is extracted directly without prior enrichment. Polymerase chain reaction and Sanger sequencing of TP53 exons 4 to 9 is performed. Sequence analysis is performed using Mutation Surveyor and Alamut software. The presence of a detected variant is then assessed using curated public databases of known TP53 gene mutations.(National Cancer Institute: The TP53 Database. National Institutes of Health; 2022. Accessed October 5, 2022. Available at https://tp53.isb-cgc.org/; den Dunnen JT, Antonarakis SE: Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum Mutat. 2000;15:7-12)

Day(s) Performed

Monday through Friday

Report Available

8 to 14 days

Specimen Retention Time

Blood/Bone marrow: 2 weeks; Extracted DNA 3 months

Performing Laboratory

Mayo Clinic Laboratories in Rochester

Test Classification

This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. It has not been cleared or approved by the US Food and Drug Administration.

CPT Code Information

81352-TP53 (tumor protein 53) (eg, tumor samples), full gene sequence or targeted sequence analysis of >5 exons

LOINC Code Information

Test ID Test Order Name Order LOINC Value
P53CA TP53 gene somatic mutation analysis 21739-8

 

Result ID Test Result Name Result LOINC Value
MP018 Specimen Type: 31208-2
607075 Signing Pathologist 19139-5
35759 Final Diagnosis: 34574-4

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
CSP53 TP53 Pre-Analysis Cell Sorting, V No No

Method Name

Polymerase Chain Reaction (PCR) and Sanger Sequencing

Secondary ID

62402

Highlights

This test is complementary to fluorescence in situ hybridization analysis for the 17p- abnormality but more appropriately identifies the presence of variant alteration and gene inactivation in tumor cells.