Glioblastoma Molecular Profiling Tests Compared
When a glioblastoma diagnosis arrives, the pathology report may not answer every question your oncologist needs to build a treatment plan. Molecular profiling - a closer look at the tumor's DNA and sometimes RNA - fills those gaps. It can confirm the WHO 2021 classification, predict how the tumor may respond to temozolomide, and flag mutations that might open a clinical trial door.
Three platforms show up most often in second-opinion talks and tumor board discussions: Foundation Medicine's FoundationOne CDx, Tempus's xT panel, and Guardant Health's Guardant360 CDx. Each takes a different approach. Choosing between them is not simple. This article explains what each test looks for, where each falls short, and what to discuss with your neuro-oncology team before ordering.
What is glioblastoma molecular profiling?
Molecular profiling tests tumor DNA - and sometimes RNA - for gene mutations, deletions, and other changes. For glioblastoma, the key markers are IDH status, MGMT promoter methylation, TERT promoter mutation, EGFR amplification, and 1p/19q codeletion. These results guide prognosis, confirm diagnosis under the WHO 2021 classification, and help determine eligibility for certain clinical trials. No single commercial panel detects all of them.
A 2023 review of molecular diagnostic assays for gliomas notes that next-generation sequencing (NGS) is now considered essential for diagnostic purposes in diffuse gliomas, though its therapeutic value remains limited to specific mutations such as IDH and BRAF alterations in defined clinical contexts. That distinction matters when deciding which test to prioritize and which result to act on.
The markers that actually matter in glioblastoma
Before comparing platforms, it helps to understand the six markers that most directly affect GBM decisions.
IDH mutation (IDH1 or IDH2). IDH-mutant and IDH-wildtype are different diseases. IDH-wildtype GBM carries a harder prognosis; IDH-mutant tumors are now classified as Grade 4 astrocytoma under the 2021 WHO scheme and tend to behave somewhat differently. All three major platforms detect IDH mutations reliably from tumor tissue.
MGMT promoter methylation. This is the marker most caregivers ask about first. Tumors with a methylated MGMT promoter are more likely to respond to temozolomide. Here is the critical point: none of the three commercial multicancer panels discussed here detect MGMT promoter methylation. It requires a separate dedicated assay - typically pyrosequencing or methylation-specific PCR - run by the pathology laboratory on the same tumor tissue block. Your oncologist must order it separately; do not assume it is included in any NGS report.
TERT promoter mutation. TERT mutations appear in roughly two-thirds of IDH-wildtype GBMs and help confirm the diagnosis when histology is ambiguous. All three tissue-based platforms detect TERT mutations.
EGFR amplification and EGFRvIII deletion. EGFR amplification is present in roughly 30% of GBMs and is both a diagnostic marker and a potential trial-eligibility marker. Reliable detection of EGFR copy number changes requires tumor tissue, not a blood test.
1p/19q codeletion. This marker distinguishes oligodendroglioma from astrocytoma. If the initial diagnosis is uncertain, 1p/19q status is critical. A published validation study showed that FoundationOne CDx detected whole-arm 1p/19q codeletion with 96.7% concordance compared to FISH testing, the long-standing standard method.
CDKN2A/B homozygous deletion. This alteration was added as a grading criterion in the WHO 2021 classification. Its presence can upgrade a lower-grade IDH-mutant astrocytoma to Grade 4. Comprehensive tissue panels detect it; blood-based tests are less reliable for copy number changes in brain tumors.
For a fuller explanation of how these markers appear in a written neuropathology report, see What Your Glioblastoma Pathology Report Really Means.
How do FoundationOne CDx, Tempus xT, and Guardant360 compare for glioblastoma?
| Feature | FoundationOne CDx (tissue) | Tempus xT (tissue + RNA) | Guardant360 CDx (blood) |
|---|---|---|---|
| Sample type | FFPE tumor tissue from surgery or biopsy | FFPE tumor tissue plus matched RNA | Blood draw - no tumor tissue required |
| Genes analyzed | ~324 cancer-associated genes | ~648 genes (DNA and RNA sequencing) | ~360 genes (cell-free DNA in plasma) |
| MGMT methylation | Not included - must be ordered separately | Not included - must be ordered separately | Not included - must be ordered separately |
| 1p/19q codeletion | Yes - ~96.7% concordance with FISH in published validation | Yes - via copy number variation analysis | Unreliable - blood-based CNV detection is limited for brain tumors |
| RNA fusion detection | Not included (DNA sequencing only) | Yes - RNA sequencing detects fusions and splice variants | Not included |
| Blood-brain barrier impact | Not applicable (tissue-based test) | Not applicable (tissue-based test) | High - GBM sheds low circulating tumor DNA into blood |
Sources: FoundationOne CDx 1p/19q validation, PMC; Glioma molecular diagnostics review, PMC; Tempus xT, NIH Genetic Testing Registry
The main finding is straightforward. For glioblastoma, tissue-based testing is the default because blood-based detection of GBM-derived DNA is unreliable. Between the two tissue platforms, Tempus xT adds RNA sequencing - which may catch gene fusions that a DNA-only panel misses. FoundationOne CDx has the largest published validation dataset for glioma-specific markers, including the 1p/19q concordance study cited above. Guardant360 CDx has a role when tumor tissue is truly unavailable, but expect lower sensitivity in brain tumors specifically.
Why liquid biopsy is limited for glioblastoma right now
Guardant360 CDx is FDA-approved across solid tumors and works well in lung, colorectal, and breast cancers. The appeal for families is real: a blood draw, no surgery, no waiting for a tissue block to be released. But the blood-brain barrier prevents most tumor-derived DNA from reaching the bloodstream. Research on liquid biopsy in GBM consistently shows that circulating tumor DNA is detectable in blood in only a subset of patients, and sensitivity varies by tumor size, location, and grade.
Cerebrospinal fluid (CSF) liquid biopsy - where doctors extract tumor DNA from a lumbar puncture sample - shows more promise for brain tumors than blood-based testing. CSF sits closer to the tumor and captures more tumor-derived material. However, CSF liquid biopsy is not yet part of standard clinical practice and is mostly available through research protocols. If a patient's team is considering liquid biopsy and tumor tissue from surgery is available, discuss whether tissue-based profiling would give a more complete and reliable result first.
The MGMT gap every family needs to know about
MGMT promoter methylation is often the most clinically useful molecular marker in GBM treatment decisions. Patients whose tumors have a methylated MGMT promoter tend to respond better to temozolomide, the standard chemotherapy drug in the Stupp protocol.
None of the three major commercial platforms - FoundationOne CDx, Tempus xT, or Guardant360 CDx - test for MGMT methylation. This is not a flaw in any one company; it reflects a technical limitation of standard next-generation sequencing. MGMT methylation is an epigenetic change (a change to how the gene is controlled, not to the DNA sequence itself), and detecting it reliably requires bisulfite-based sequencing or pyrosequencing - methods that are run separately from NGS panels.
A patient can receive a detailed NGS report from any of these platforms and still not know their MGMT status. If the neuropathology report does not include MGMT methylation results, ask the treating oncologist or neuropathologist to order it as a standalone assay from the same tissue block. Pyrosequencing is the most commonly used method and has been validated in multicenter studies as clinically reliable for GBM patients.
How molecular profiling connects to clinical trials
One of the clearest practical uses of comprehensive genomic profiling in GBM is trial matching. Many Phase I and Phase II trials require a specific molecular alteration as an eligibility criterion - for example, EGFR amplification, an FGFR alteration, or IDH mutation. A detailed NGS report from FoundationOne CDx or Tempus xT can be submitted directly to trial coordinators or cross-referenced against the National Cancer Institute's clinical trials search.
A 2025 real-world study in npj Precision Oncology found that NGS results in glioma patients revealed actionable alterations in a meaningful proportion of cases, though the fraction of GBM patients with a fully matched therapy option currently remains modest. The value of profiling is not a guaranteed treatment match. It is a clearer picture that enables a sharper conversation at tumor board and a better-informed decision about whether to pursue a specific trial.
For a practical guide to using molecular results when evaluating trial eligibility, see Glioblastoma Immunotherapy Trials and Your Molecular Profile.
Which test should your oncologist order for GBM?
In most newly-diagnosed GBM cases, the pathology laboratory will already run IDH testing and EGFR analysis as part of standard neuropathology. Beyond that, a practical framework for the broader panel:
- Adequate tumor tissue available from surgery: FoundationOne CDx or Tempus xT. Both give a comprehensive molecular picture. Tempus xT adds RNA sequencing, which may catch fusions a DNA-only panel misses - potentially useful in younger patients or atypical presentations.
- Tissue is scarce or re-biopsy is not feasible: Guardant360 CDx is an option to discuss with the oncologist, but understand that sensitivity is lower in GBM than in other solid tumors because of the blood-brain barrier.
- Regardless of which platform is used: Request MGMT methylation testing separately. It is not included in any of the three platforms and must be ordered as a standalone assay from the same tissue block.
- Uncertain diagnosis or unusual tumor location: A panel that includes RNA fusion detection - such as Tempus xT - may add useful information, particularly if diffuse midline glioma, pediatric GBM, or gliosarcoma is being considered in the differential diagnosis.
It is also worth knowing that most major academic neuro-oncology centers run their own in-house molecular panels alongside or instead of commercial options. MSK-IMPACT, Mayo Clinic's institutional panel, and similar assays may be ordered in parallel. If the patient is being treated at a community hospital, requesting a referral to an academic neuro-oncology tumor board - or arranging an external pathology review - can be the difference between a generic treatment plan and a molecularly-informed one. If you are weighing options after receiving a molecular report and want it interpreted alongside imaging by a specialist team, you can arrange a remote second opinion through Art of Healing Cancer. For a step-by-step guide to gathering and sharing records before an external review, see How to Prepare for a Glioblastoma Second Opinion.
Practical steps before your next oncology appointment
- Ask your neuropathologist or oncologist whether they ran comprehensive NGS on your tumor tissue, and if so, which platform they used.
- Ask whether they tested MGMT methylation separately. If not, ask whether enough tissue remains in the paraffin block to run it now.
- Request a copy of the full molecular report, not just the clinical summary. The complete alterations list may contain trial-relevant findings the summary omits.
- Ask whether the results were reviewed at a multidisciplinary tumor board that included a neuro-oncologist.
- If the patient was diagnosed more than 12 months ago and has since progressed, discuss whether re-biopsy for updated molecular profiling is clinically appropriate. GBM tumors evolve, and the recurrent tumor's profile may differ from the original.
When to talk to your doctor
Raise the topic of comprehensive molecular profiling at your next appointment if the pathology report covers only IDH status without a broader NGS panel, if a clinical trial is under consideration, or if a second-opinion team has recommended additional molecular testing. Your oncologist or neuropathologist can advise on which test fits the clinical question and the tissue that is available.
To submit your molecular report and imaging for a remote review, visit the Glioblastoma Center patient-journey page.
This article is for general information and is not a substitute for medical advice. Always consult your oncologist or care team about your specific situation.