Molecular Diagnostics in Colorectal Cancer – Standard of Care (Stage-Specific)

Note: This blog is in progress, and I’m verifying the information and sources.

The Modern Role of Molecular Diagnostics in Colorectal Cancer

Molecular diagnostics has become an essential component of how we detect, monitor, and treat colorectal cancer (CRC). From early screening to tumor profiling, minimal residual disease (MRD) detection, and long-term surveillance, the diagnostic toolkit for patients has expanded dramatically in the past decade. These assays not only guide treatment decisions but also influence frequency of testing, cost considerations, and insurance coverage.

In this article, I outline the current state of molecular diagnostics for colon cancer patients — focusing on their use cases, clinical utility, and practical realities in today’s healthcare system. For those not in the biotech/medical field, I’ve added a glossary of terms at the end to help you get through the jargon.

Disclaimer:
I am a biotech scientist, not a medical doctor. Much of this content is from a collaboration with AI and evaluation of the current literature. This article is for educational and informational purposes only. It should not be interpreted as medical advice. Patients should always consult their physician or qualified healthcare provider for guidance on diagnosis and treatment.

Overview

Stage / Setting Assay / Biomarker Technology Output / Actionability Frequency Insurance Coverage Clinical Notes
Screening (average risk, age ≥45) Stool DNA (mt-sDNA, e.g., Cologuard) DNA methylation + mutation panel Positive → colonoscopy every 3 yrs if negative Medicare & most commercial Higher sensitivity than FIT; lower specificity; better adherence.
Screening (emerging) Blood-based CRC screening (Shield™) cfDNA methylation Positive → colonoscopy every 3 yrs (Medicare) Medicare covers FDA-approved May increase uptake in reluctant patients.
All stages (at diagnosis) MMR IHC ± MSI PCR/NGS IHC, PCR, NGS Lynch screening; predicts ICI benefit Once at diagnosis Standard of care Reflex MLH1 methylation if MLH1 loss.

Stage II (localized, resected)

Assay / Biomarker Technology Output / Actionability Frequency Coverage Notes
Tumor MMR/MSI IHC, PCR, NGS MSI-H → no adjuvant 5-FU (stage II) Once Covered MSI-H/dMMR stage II → avoid chemo.
MRD (ctDNA) Personalized or fixed-panel cfDNA NGS Detects residual disease → guides adjuvant chemo Baseline post-op, then every 3–6mo for 2 yrs Medicare MolDX (Signatera, Guardant Reveal) Strong prognostic value; driving clinical trials.
Germline testing (if indicated) Germline NGS Detects Lynch, FAP, MAP Once Covered with criteria Triggered by young age/family history/MSI-high tumor.

Stage III (node-positive)

Assay / Biomarker Technology Output / Actionability Frequency Coverage Notes
Tumor MMR/MSI IHC, PCR, NGS Lynch screen; ICI prediction if recurrent Once Covered MSI-H less common in stage III; still important.
MRD (ctDNA) cfDNA NGS Detects clearance vs persistence after surgery → risk stratification Baseline post-op, then every 3–6mo Medicare MolDX May guide chemo escalation/de-escalation (ongoing trials).
Germline testing Germline NGS Lynch, FAP, MAP Once if criteria met Covered Cascade testing key.

Stage IV (metastatic/advanced)

Assay / Biomarker Technology Output / Actionability Frequency Coverage Notes
Somatic profiling (KRAS/NRAS, BRAF, HER2, NTRK, KRAS G12C, TMB) NGS (tissue or plasma) Guides targeted therapy & clinical trial selection At diagnosis, may repeat on progression Medicare NCD 90.2; commercial RAS WT & left-sided → EGFR therapy; BRAF V600E → poor prognosis; HER2+ → trastuzumab; KRAS G12C → adagrasib/sotorasib.
Immunotherapy biomarkers NGS, IHC MSI-H/dMMR → pembrolizumab/nivolumab At diagnosis Covered Actionable even after multiple lines.
Resistance monitoring Plasma ctDNA NGS Detects acquired KRAS/NRAS mutations on anti-EGFR At progression Expanding May enable anti-EGFR rechallenge when resistant clone wanes.
Germline testing (if young or family history) Germline NGS Identifies inherited syndromes Once if criteria met Covered with criteria Even in metastatic setting, informs family risk.

Surveillance (all stages post-treatment)

Assay / Biomarker Technology Output / Actionability Frequency Coverage Notes
MRD (ctDNA) cfDNA NGS Detects recurrence earlier than imaging every 3–6mo for 2–3 yrs Medicare MolDX May replace/augment CEA in future SOC.
CEA ELISA Non-specific recurrence marker every 3–6mo x 2 yrs, then every 6mo x 3 yrs Covered Low sensitivity/specificity but still standard.

Closing Thoughts: The Future and Hurdles of Early Cancer Screening

When I look across the landscape of molecular diagnostics in colon cancer, the piece that excites me the most — and that I believe could have the greatest impact — is true early screening. Right now, most of our molecular tools are applied at diagnosis or afterward: we test tumors for biomarkers to guide therapy, and we use ctDNA to track recurrence risk once the cancer has already declared itself.

The problem is that by the time minimal residual disease (MRD) monitoring lights up, the biology has often outrun us. Detecting that a tumor is likely to recur doesn’t always give patients and doctors enough time or options to meaningfully change the outcome. MRD is a powerful prognostic tool, but it’s still fundamentally reactive.

Early detection, on the other hand, has the potential to change the story entirely. If we could reliably pick up cancers—or even high-risk precancerous lesions—before they progress, the benefits would be enormous. This is why blood-based assays for colorectal cancer screening, and eventually multi-cancer early detection (MCED) tests, are so important. However, we’re not there yet, and a significant hurdle stands in the way.

The Challenge: The Positive Predictive Value (PPV) Problem

The single biggest challenge for broad, population-level screening is positive predictive value (PPV). PPV answers a critical question: “If a patient tests positive, what is the actual probability that they have cancer?”

For MCED tests, the current PPV can be low. This means a significant number of positive results are false positives. This isn’t just a statistical issue; it has profound real-world consequences:

  • Patient Anxiety: A positive result can cause immense stress and fear, even if it turns out to be a false alarm.
  • Costly, Invasive Workups: A positive test without a clear “tissue of origin” signal can trigger a cascade of expensive and invasive diagnostic procedures, like full-body PET-CT scans and biopsies, as doctors search for a cancer that may not exist.
  • System Burden: Widespread false positives could overwhelm our healthcare system with unnecessary follow-up appointments and procedures.

Essentially, a test that cries wolf too often erodes trust and can potentially cause more harm than good through over-investigation.

The Path Forward: How Screening Will Improve

The future of early detection hinges on solving the PPV problem. Fortunately, the path to improvement is clear and involves advancing on multiple fronts:

  1. More Sophisticated Technology: The first generation of tests primarily looks at DNA methylation. Future iterations will be multi-omic, integrating signals from multiple biological sources. Tests that analyze not just ctDNA methylation, but also proteomics (cancer-related proteins), fragmentomics (patterns of DNA breakage), and other biomarkers simultaneously can provide more information to improve PPV. Layering these signals with powerful AI and machine learning algorithms will allow us to more accurately distinguish a true cancer signal from biological noise (like inflammation or benign conditions).

  2. Smarter Screening Strategies: Instead of screening the entire population, the initial rollout will likely focus on high-risk groups (e.g., individuals over 50, those with a family history, or smokers). Because cancer is more prevalent in these groups, the PPV of the test automatically increases. A positive result in a high-risk person is statistically more likely to be a true positive.

  3. Refined Clinical Pathways: The process won’t be a simple “positive test → full body scan.” We will likely see two-step confirmation processes. An initial positive screen might trigger a second, more specific blood test or a highly targeted imaging scan based on the test’s prediction for the tumor’s tissue of origin. This avoids the “diagnostic odyssey” and focuses the search.

If these technologies deliver on their promise—by becoming more accurate, targeted, and intelligently deployed—they could still mark the biggest shift in cancer diagnostics we’ve seen in decades. The goal remains the same: moving us from a world of catching cancer late to one where we intercept it early.

Glossary

MRD (Minimal Residual Disease) Refers to the tiny amounts of cancer that may remain in the body after treatment, often below the level detectable by imaging. MRD tests (commonly using ctDNA) help predict whether a cancer is likely to come back.

MCED (Multi-Cancer Early Detection) A new class of blood-based tests designed to screen for multiple types of cancer at once, often before symptoms appear. These tests analyze cfDNA patterns such as methylation or fragmentation.

PPV (Positive Predictive Value) A measure of how likely it is that a positive test result actually means a person has cancer. Higher PPV means fewer false alarms.

ctDNA (Circulating Tumor DNA) Fragments of DNA shed by cancer cells into the bloodstream. ctDNA can be analyzed to detect mutations, monitor treatment response, and track recurrence.

cfDNA (Cell-Free DNA) General term for DNA fragments circulating in the blood, which come from both normal and cancerous cells. ctDNA is a subset of cfDNA.

NGS (Next-Generation Sequencing) A powerful technology that allows rapid, large-scale DNA sequencing. In cancer, NGS panels can test dozens to hundreds of genes at once to guide treatment decisions.

IHC (Immunohistochemistry) A lab test that uses antibodies to detect specific proteins in tumor tissue. Often used to check for MMR status and other biomarkers.

MSI-H (Microsatellite Instability–High) A genetic signature caused by defective DNA repair. MSI-H cancers are more likely to respond to immunotherapy.

MMR (Mismatch Repair) A system cells use to fix errors in DNA. When MMR genes are defective, tumors can become MSI-H. Testing MMR status is standard for colon cancer diagnosis.

mt-sDNA (Multitarget Stool DNA Test, e.g., Cologuard®) A non-invasive stool-based screening test that looks for DNA mutations, methylation changes, and blood associated with colon cancer or polyps.

CEA (Carcinoembryonic Antigen) A blood protein often used as a traditional tumor marker in colon cancer. Elevated levels can indicate cancer but are less precise than modern ctDNA tests.

RAS / BRAF Mutations Common genetic mutations tested in colon cancer. Their presence can determine which therapies (like anti-EGFR antibodies) will or won’t work.

HER2 (Human Epidermal Growth Factor Receptor 2) A gene that can be amplified in a small subset of colon cancers. When present, it may be targeted by specific therapies.

Key Sources

  • NCCN Colon Cancer Guidelines (2025)
  • USPSTF CRC screening recommendations (2021)
  • Medicare NCD 90.2 – NGS in advanced cancer
  • CMS MolDX LCDs – MRD coverage (Signatera, Guardant Reveal)
  • FDA approval of Guardant Shield™ blood CRC test
  • NCI PDQ + NCCN for universal MMR/MSI testing

References

PMC article digest

PMC open access review

AGA CRC toolkit

```mermaid

flowchart TB A[Screening — FIT, stool DNA, ctDNA blood tests] –> B[Diagnosis — Colonoscopy, biopsy, histopathology] B –> C[Molecular Profiling — NGS panel, MSI, RAS/BRAF, HER2] C –> D[MRD Monitoring — ctDNA assays for recurrence risk] D –> E[Surveillance — ctDNA, CEA, imaging]

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class A,B stage;
class C,D,E action;