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Test Code MCBPP MayoComplete Bladder and Prostate Cancer Panel, Next-Generation Sequencing, Tumor


Ordering Guidance


Multiple oncology (cancer) gene panels are available. For more information see Hematology, Oncology, and Hereditary Test Selection Guide.



Necessary Information


A pathology report (final or preliminary), at minimum containing the following information, must accompany specimen for testing to be performed:

1. Patient name
2. Block number-must be on all blocks, slides, and paperwork (can be handwritten on the paperwork)
3. Tissue collection date
4. Source of the tissue



Specimen Required


This assay requires at least 20% tumor nuclei.

-Preferred amount of tumor area with sufficient percent tumor nuclei: tissue 216 mm(2)
-Minimum amount of tumor area: tissue 36 mm(2)
-These amounts are cumulative over up to 10 unstained slides and must have adequate percent tumor nuclei.
-Tissue fixation: 10% neutral buffered formalin, not decalcified
-For specimen preparation guidance, see Tissue Requirement for Solid Tumor Next-Generation Sequencing. In this document, the sizes are given as 4 mm x 4 mm x 10 slides as preferred: approximate/equivalent to 144 mm(2) and the minimum as 3 mm x 1 mm x 10 slides: approximate/equivalent to 36 mm(2).

 

Preferred:
Specimen Type: Tissue block
Collection Instructions: Submit a formalin-fixed, paraffin-embedded tissue block with acceptable amount of tumor tissue.

 

Acceptable:
Specimen Type: Tissue slide
Slides: 1 Stained and 10 unstained
Collection Instructions: Submit 1 slide stained with hematoxylin and eosin and 10 unstained, nonbaked slides with 5-micron thick sections of the tumor tissue.
Note: The total amount of required tumor nuclei can be obtained by scraping up to 10 slides from the same block.
Additional Information: Unused unstained slides will not be returned.

Specimen Type: Cytology slide (direct smears or ThinPrep)
Slides: 1 to 3 Slides
Collection Instructions: Submit 1 to 3 slides stained and coverslipped with a preferred total of 5000 nucleated cells, or a minimum of at least 3000 nucleated cells.
Note: Glass coverslips are preferred; plastic coverslips are acceptable but will result in longer turnaround times.
Additional Information: Cytology slides will not be returned.


Secondary ID

619604

Useful For

Primarily for determining if patients will respond to targeted therapy

 

Assessment of microsatellite instability for immunotherapy decisions

Genetics Test Information

This test uses targeted next-generation sequencing to determine microsatellite instability (MSI) status and evaluate for somatic mutations within the APC, AR, ARID1A, ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CDK12, CDKN2A, CHD1, CHEK1, CHEK2, CTNNB1, EGFR, ERBB2, ERCC2, FANCA, FANCC, FANCL, FGFR1, FGFR2, FGFR3, FOXA1, MLH1, MSH2, MSH6, PALB2, PMS2, PTEN, RAD51B, RAD51C, RAD51D, RAD54L, RB1, SPOP, TERT, and TP53 genes. See Targeted Genes and Methodology Details for MayoComplete Bladder and Prostate Cancer Panel for details regarding the targeted gene regions evaluated by this test.

 

This test is performed to evaluate for somatic mutations within solid tumor samples. This test does not assess for germline alterations within the genes listed.

Highlights

This panel, performed on formalin-fixed, paraffin-embedded tumor or cytology slides, includes a curated list of 39 genes important for the clinical management of patients with prostate or bladder cancer.

 

It identifies alterations in the FGFR genes that may predict response to targeted therapies and DNA damage response genes associated with therapeutic eligibility to poly(adenosine diphosphate-ribose) polymerase inhibitors.

 

This test evaluates mismatch repair genes and microsatellite instability (MSI) status (MSS, MSI-H) as this is often clinically actionable for determining the efficacy of immunotherapy in solid tumors.

Additional Tests

Test ID Reporting Name Available Separately Always Performed
SLIRV Slide Review in MG No, (Bill Only) Yes

Testing Algorithm

When this test is ordered, slide review will always be performed at an additional charge.

Method Name

Sequence Capture Next-Generation Sequencing (NGS)

Reporting Name

MayoComplete Bladder/Prostate Panel

Specimen Type

Varies

Specimen Minimum Volume

See Specimen Required

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Ambient (preferred)
  Refrigerated 

Reject Due To

Specimens that have been decalcified (all methods)
Specimens that have not been formalin-fixed, paraffin-embedded, except for cytology slides
Extracted nucleic acid (DNA/RNA)		 Reject

Clinical Information

Molecular genetic profiling is often needed to identify targets amenable to targeted therapies and to minimize treatment costs and therapy-associated risks. Microsatellite instability (MSI) status is an increasingly important biomarker for determining effective immunotherapeutic treatment options for patients with solid tumors.

 

This test uses formalin-fixed paraffin-embedded tissue or cytology slides to assess for somatic mutations involving the following genes known to be associated with bladder/prostate cancer: APC, AR, ARID1A, ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CDK12, CDKN2A, CHD1, CHEK1, CHEK2, CTNNB1, EGFR, ERBB2, ERCC2, FANCA, FANCC, FANCL, FGFR1, FGFR2, FGFR3, FOXA1, MLH1, MSH2, MSH6, PALB2, PMS2, PTEN, RAD51B, RAD51C, RAD51D, RAD54L, RB1, SPOP, TERT, and TP53. The results of this test can be useful for assessing prognosis and guiding treatment of individuals with bladder/prostate tumors. The data can also be used to help determine clinical trial eligibility for patients with alterations in genes not amenable to current US Food and Drug Administration-approved targeted therapies.

Reference Values

An interpretive report will be provided.

Interpretation

The interpretation of molecular biomarker analysis includes an overview of the results and the associated diagnostic, prognostic, and therapeutic implications.

Cautions

This test cannot differentiate between somatic and germline alterations. Additional testing may be necessary to clarify the significance of results if there is a potential hereditary risk.

 

DNA variants of uncertain significance may be identified.

 

A negative result does not rule out the presence of a variant that may be present below the limits of detection of this assay. In a specimen with 20% or more tumor content, the analytical sensitivity of this assay for sequence reportable alterations is 5% mutant allele frequency with a minimum coverage of 500X.

 

Point mutations and small deletion-insertion mutations will be detected in the APC, AR, ARID1A, ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CDK12, CDKN2A, CHD1, CHEK1, CHEK2, CTNNB1, EGFR, ERBB2, ERCC2, FANCA, FANCC, FANCL, FGFR1, FGFR2, FGFR3, FOXA1, MLH1, MSH2, MSH6, PALB2, PMS2, PTEN, RAD51B, RAD51C, RAD51D, RAD54L, RB1, SPOP, TERT (5'UTR), and TP53 genes only. This test may detect single exon deletions but does not detect multi-exon deletions, duplications, or genomic copy number variants.

 

Variant allele frequency (VAF) is the percentage of sequencing reads supporting a specific variant divided by the total sequencing reads at that position. In somatic testing, VAF should be interpreted in the context of several factors including, but not limited to: tumor purity/heterogeneity/copy number status (ploidy, gains/losses, loss of heterozygosity) and sequencing artifact/misalignment.(1,2)

 

Rare alterations (ie, polymorphisms) may be present that could lead to false-negative or false-positive results.

 

The presence or absence of a variant may not be predictive of response to therapy in all patients.

 

Test results should be interpreted in the context of clinical, tumor sampling, histopathological, and other laboratory data. If results obtained do not match other clinical or laboratory findings, contact the laboratory for discussion. Misinterpretation of results may occur if the information provided is inaccurate or incomplete.

 

Reliable results are dependent on adequate specimen collection and processing. This test has been validated on cytology slides and formalin-fixed, paraffin-embedded tissues; other types of fixatives are discouraged. Improper treatment of tissues, such as decalcification, may cause polymerase chain reaction failure.

Supportive Data

Performance Characteristics:

The limit of detection for calling a somatic variant (single nucleotide variants [SNV] and deletions/insertions [delins, formerly indel]) is 5% variant allele frequency (VAF) and having at least 500x deduplicated coverage.

 

Verification studies demonstrated concordance between this test and the reference method for detection of SNV and delins is 98.5% (673/683) and 98.4% (122/124) of variants, respectively. Concordance for the detection of delins was 99.0% (100/101) in variants 1 to 10 base pairs (bp) in size, 93.3% (14/15) in variants 11 to 50 bp in size, and 100% (8/8) in variants over 50 bp in size.

 

Microsatellite instability (MSI) evaluation is accurate at a tumor purity of at least 10% for colorectal tumors and 20% for other tumor types. During verification studies, 98% (200/204) concordance for MSI status was observed between this test and the reference method.

 

To ensure accuracy, this test will be performed on cases that are estimated by a pathologist to have at least 20% tumor cells.

Clinical Reference

1. Strom SP. Current practices and guidelines for clinical next-generation sequencing oncology testing. Cancer Biol Med. 2016;13(1):3-11. doi:10.28092/j.issn.2095-3941.2016.0004

2. Spurr L, Li M, Alomran N, et al. Systematic pan-cancer analysis of somatic allele frequency. Sci Rep. 2018;8(1):7735. Published 2018 May 16. doi:10.1038/s41598-018-25462-0

3. Abida W, Armenia J, Gopalan A, et al: Prospective genomic profiling of prostate cancer across disease states reveals germline and somatic alterations that may affect clinical decision making. JCO Precis Oncol. 2017;2017:PO.17.00029

4. Robertson AG, Kim J, Al-Ahmadie H, et al: Comprehensive molecular characterization of muscle-invasive bladder cancer. Cell. 2017;171(3):540-556.e25

5. Siefker-Radtke AO, Necchi A, Park SH, et al: Efficacy and safety of erdafitinib in patients with locally advanced or metastatic urothelial carcinoma: long-term follow-up of a phase 2 study. Lancet Oncol. 2022;23(2):248-258

6. Marcus L, Lemery SJ, Keegan P, Pazdur R: FDA Approval Summary: Pembrolizumab for the treatment of microsatellite instability-high solid tumors. Clin Cancer Res. 2019;25(13):3753-3758

Method Description

Next-generation sequencing is performed to determine microsatellite instability (MSI) status and evaluate the presence of a mutation in most coding regions of the APC, AR, ARID1A, ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CDK12, CDKN2A, CHD1, CHEK1, CHEK2, CTNNB1, EGFR, ERBB2, ERCC2, FANCA, FANCC, FANCL, FGFR1, FGFR2, FGFR3, FOXA1, MLH1, MSH2, MSH6, PALB2, PMS2, PTEN, RAD51B, RAD51C, RAD51D, RAD54L, RB1, SPOP, TERT, and TP53 genes. See Targeted Genes and Methodology Details for MayoComplete Bladder and Prostate Cancer Panel for details regarding the targeted gene regions identified by this test.(Unpublished Mayo method)

 

A pathology review and macro dissection to enrich for tumor cells is performed prior to slide scraping.

Day(s) Performed

Monday through Friday

Report Available

12 to 20 days

Specimen Retention Time

FFPE tissue block: Unused portions of blocks will be returned 10 to 14 days after testing is complete; FFPE tissue/cytology slides: Unused slides are stored indefinitely; Digital images are obtained and stored for all slides used in testing.

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

88381-Microdissection, manual
81457

LOINC Code Information

Test ID Test Order Name Order LOINC Value
MCBPP MayoComplete Bladder/Prostate Panel 105589-6

 

Result ID Test Result Name Result LOINC Value
619605 Result 82939-0
619606 Interpretation 69047-9
619607 Additional Information 48767-8
619608 Specimen 31208-2
619609 Tissue ID 80398-1
619610 Method 85069-3
619611 Disclaimer 62364-5
619612 Released By 18771-6

Forms

If not ordering electronically, complete, print, and send an Oncology Test Request (T729) with the specimen.