02 · Testing & Interpretation
MTAP status can be assessed at the protein level by immunohistochemistry, at the gene level by FISH, or as part of comprehensive genomic profiling. Each method has strengths and trade-offs. The right choice depends on your laboratory workflow and the clinical question being asked.
Immunohistochemistry
TAT · 24–48h
Loss of cytoplasmic MTAP staining in tumor cells, with retained internal control in stroma and lymphocytes, suggests homozygous deletion.
Fluorescence in situ hybridization
TAT · 3–5d
A two-probe assay for 9p21 (MTAP/CDKN2A) versus a control locus directly visualizes homozygous deletion in tumor nuclei.
Next-generation sequencing
TAT · 10–14d
Comprehensive genomic profiling panels report MTAP copy number alongside CDKN2A and other actionable alterations.
Confirming MTAP loss
When more than one of these align on the same case, confidence in a true homozygous MTAP deletion is high — even when any single assay is equivocal.
MTAP
Deletion present by NGS
or loss of cytoplasmic staining by IHC (with retained internal control)
CDKN2A
Co-deletion present by NGS
9p21.3 passenger pattern — supports a true homozygous event
p16
Negative by IHC
protein product of CDKN2A — corroborates the locus-level deletion
Didn't test at diagnosis?
MTAP status is a stable genomic feature. If a patient's original biopsy was banked, the pathology department can usually pull the block and run IHC, FISH, or NGS retrospectively. For patients who have progressed on standard therapy and may now be trial candidates, this is often the fastest path to an answer.
Common testing challenges
The science is settled. The friction is operational. These are the four most common reasons MTAP status doesn't make it onto the chart — each with a practical workaround.
Challenge
Insufficient tissue
Solution
Run MTAP IHC first — a single unstained slide is usually enough. Reserve remaining tissue for NGS or FISH only if IHC is equivocal.
Challenge
MTAP not on your NGS panel
Solution
Most large panels (Tempus xT, Caris MI, FoundationOne CDx, MSK-IMPACT) report MTAP copy number. If yours doesn't, ask your lab to enable it or reflex CDKN2A-deleted cases to IHC.
Challenge
Result buried in the report
Solution
Standardize an interpretive comment that calls MTAP status out by name and flags therapeutic relevance — not a line item in a copy-number table.
Challenge
IHC and NGS disagree
Solution
Trust IHC loss with retained internal control over a borderline NGS call — purity-driven false negatives are common below 30%. Reflex to FISH when both are ambiguous.
Interpretation pitfalls
Heterogeneous IHC loss
Patchy staining can reflect tumor heterogeneity or fixation artifact. Confirm equivocal IHC with FISH or NGS before reporting deletion.
Low tumor purity on NGS
Copy-number deletions require adequate neoplastic cellularity. Below 20–30% purity, homozygous loss can be missed or miscalled.
Single-copy CDKN2A loss
CDKN2A and MTAP are usually co-deleted, but not always. Reporting MTAP status explicitly — not inferring it from CDKN2A — matters.
Epigenetic silencing
A minority of MTAP-deficient tumors retain the gene but silence it by promoter methylation. These cases may behave biologically similar but are not detected by FISH or copy-number NGS.
Recommended reporting language
// Sample report excerpt
MTAP (9p21.3): homozygous deletion detected by FISH (0 signals in >80% of tumor nuclei, internal control retained).
CDKN2A: co-deleted.
// Interpretive comment
Homozygous MTAP deletion may render tumor cells selectively sensitive to PRMT5-targeted therapies under clinical investigation. Consider referral to molecular tumor board.
Clinical trials
Investigational PRMT5 inhibitors are being studied in patients whose tumors carry homozygous MTAP loss. Refer eligible patients early — site activation, screening, and consent take time.
Search the trial directory