Sample Testing

Somatic and germline mutations are relevant for prostate cancer patients1,2

Important to note, tissue testing includes both somatic and/or germline alterations and cannot distinguish between them. If the analysis is done on tissue sample, confirmatory testing for germline alterations is needed. If the analysis is done on blood sample, whole blood is used for germline testing, and blood plasma enriched with ctDNA fraction provides more information on acquired tumor specific genetic alterations. 8,9


  1. Abida, W. et al. (2017) 'Prospective Genomic Profiling of Prostate Cancer Across Disease States Reveals Germline and Somatic Alterations That May Affect Clinical Decision Making', JCO Precision Oncology.
  2. MedlinePlus (2025) 'Gene Mutation'. Available at: https://medlineplus.gov/genetics/understanding/mutationsanddisorders/genemutation/ (Accessed: 12 February 2025).
  3. National Cancer Institute (2025) 'Germline Mutation'. Available at: https://www.cancer.gov/publications/dictionaries/cancer-terms/def/germline-mutation (Accessed: 12 February 2025).
  4. National Cancer Institute (2025) 'BRCA Fact Sheet'. Available at: https://www.cancer.gov/about-cancer/causes-prevention/genetics/brca-fact-sheet#q1 (Accessed: 12 February 2025).
  5. National Cancer Institute (2025) 'Somatic Mutation'. Available at: https://www.cancer.gov/publications/dictionaries/cancer-terms/def/somatic-mutation (Accessed: 12 February 2025).
  6. Dentro, S. et al. (2017) 'Principles of Reconstructing the Subclonal Architecture of Cancers', Cold Spring Harbor Perspectives in Medicine.
  7. Cimadamore, A. et al. (2021) 'Circulating Tumor DNA Testing for Homology Recombination Repair Genes in Prostate Cancer: From the Lab to the Clinic', International Journal of Molecular Sciences.
  8. Foundation Medicine (2025) 'FoundationOne CDx'. Available at: https://www.foundationmedicine.com/test/foundationone-cdx (Accessed: 12 February 2025).
  9. Foundation Medicine (2025) 'FoundationOne Liquid CDx'. Available at: https://www.foundationmedicine.com/test/foundationone-liquid-cdx (Accessed: 12 February 2025).

There are different ways to obtain sample for somatic biomarker testing1

There are several different methods available to biopsy a tumor, and it is usually the location of the tumor that directs the type of biopsy. Each have their advantages and disadvantages in the complexity of the procedure, invasiveness for the patient and the amount of material recovered to support testing.

  1. American Cancer Society (2025) 'How Is a Biopsy Done? | Types of Biopsies for Cancer'. Available at: https://www.cancer.org/cancer/cancer-basics/biopsy.html (Accessed: 12 February 2025).

Tumour tissue is the gold standard for biomarker testing

The PROfound Phase III Study Experience (mCRPC) – US-based Study¹

Real-world data showing tissue biopsy practices for HRR testing in prostate cancer:
• Both archived and fresh tissue can be used for the test
• Little difference in testing success rate was observed when comparing newly obtained vs archived tissue
• Little difference in testing success rate was observed when comparing sample collected from primary tissue vs metastatic tissue

1. Hussain, M. et al. (2022) 'Tumor Genomic Testing for >4,000 Men with Metastatic Castration-resistant Prostate Cancer in the Phase III Trial PROfound (Olaparib)', Clinical Cancer Research.

Liquid biopsy brings additional value for maximizing patient identification, complementing the standard of tissue testing1-4

Advantages

  • Less invasive for the patient and minimal pain / risk
  • Allows tumor molecular profiling, even when a tissue biopsy cannot be obtained
  • Sequential testing: Enables monitoring tumors, therapy response and acquired resistance
  • Relatively quick
  • Capturing intra- and inter-tumor heterogeneity
  1. Cimadamore, A. et al. (2021) 'Circulating Tumor DNA Testing for Homology Recombination Repair Genes in Prostate Cancer: From the Lab to the Clinic', International Journal of Molecular Sciences.
  2. Healio (2025) 'What is a Liquid Biopsy?'. Available at: https://www.healio.com/hematology-oncology/learn-genomics/introduction-to-liquid-biopsies/what-is-a-liquid-biopsy (Accessed: 12 February 2025).
  3. Roche (2025) 'Liquid Biopsy'. Available at: https://www.roche.com/research_and_development/what_we_are_working_on/oncology/liquid-biopsy.htm (Accessed: 12 February 2025).
  4. Armstrong, A.J. et al. (2024) 'Germline and somatic testing for homologous repair deficiency in patients with prostate cancer (part 1 of 2)', Prostate Cancer and Prostatic Diseases.

High concordance between tissue and ctDNA testing reported in the literature

ctDNA - Circulating Tumor DNA; HRR - Homologous Recombination Repair; m - Mutated; mCRPC - Metastatic Castration-Resistant Prostate Cancer

  1. Azad, A. et al. (2023) 'Use of circulating tumor DNA (ctDNA) to complement tumor tissue homologous recombination repair (HRR) gene alteration testing in TALAPRO-2, a phase 3 study of talazoparib (TALA) + enzalutamide (ENZA) versus placebo (PBO) + ENZA as first-line (1L) treatment in patients (pts) with metastatic castration-resistant prostate cancer (mCRPC)', Abstract 5056 presented at ASCO.
  2. Armstrong, A.J. et al. (2022) 'Detection of mutations in homologous recombination repair (HRR) genes in tumour tissue (TT) and circulating tumour DNA (ctDNA) from patients (pts) with metastatic castrate-resistant prostate cancer (mCRPC) in the phase III PROpel trial', Poster 1370P presented at ESMO.
  3. Chi, K.N. et al. (2023) 'Detection of BRCA1, BRCA2, and ATM Alterations in Matched Tumor Tissue and Circulating Tumor DNA in Patients with Prostate Cancer Screened in PROfound', Clinical Cancer Research.
  4. Tukachinsky, H. et al. (2021) 'Genomic Analysis of Circulating Tumor DNA in 3,334 Patients with Advanced Prostate Cancer Identifies Targetable BRCA Alterations and AR Resistance Mechanisms', Clinical Cancer Research.

Sample Challenges

Data from the PROfound study revealed that significant portion of tissue samples does not meet criteria for HRR biomarker testing1

HRR = Homologous Recombination Repair, mCRPC = Metastatic Castration Resistant Prostate Cancer, QC = Quality Control, CDx = Companion Diagnostic

1. Hussain, M. et al. (2022) 'Tumor Genomic Testing for >4,000 Men with Metastatic Castration-resistant Prostate Cancer in the Phase III Trial PROfound (Olaparib)', Clinical Cancer Research.

Understanding testing challenges and standardizing practices for sample collection and processing can increase tissue availability and improve access to HRR testing¹


Testing Challenges with Archival Tissue Biopsy

  • Not always available or sometimes with insufficient tumor content
  • Old tumor tissue can lead to poor quality DNA
  • May underestimate the heterogeneous character of the tumor / metastases
  • Does not allow for monitoring tumor in real time


Recommendations

  • Latest available sample should be utilized for biomarker testing
  • If only old archival material is available, resection specimens, ideally with high tumor cellularity, are preferred over core biopsies.
  • Optimal fixation of tumor tissue is necessary to minimize DNA degradation
  • Selection of FFPE block with sufficient tumor content is critical for biomarker testing
  • Macrodissection can be used to increase tumour content and DNA yield
 

Protocols for processing bone metastasis need to be optimized¹


Testing Challenges with Metastatic Tissue Biopsy

  • Invasive
  • The most common metastatic site for prostate cancer is bone (≥80% of patients with metastatic prostate cancer).. Bone metastases in prostate cancer are most often sclerotic, rather than lytic, making bone biopsies technically challenging as often the sample is inadequate for diagnosis and molecular analysis
  • Processes for isolating DNA from bone involves acid washes which can also degrade DNA leading to issues for molecular analysis


Recommendations

  • Utilize soft-tissue metastases (e.g. lymph nodes) over bone metastases where feasible
  • If new tissue is procured for NGS testing, ideally multiple core biopsies per lesion should be obtained
  • It is recommended to avoid harsh acid-based decalcification methods for bone metastases and rather use ethylenediaminetetraacetic acid-based calcium extraction
 

If the result from liquid biopsy testing is negative, testing should be repeated with tissue sample to exclude false negative result¹'²


Testing Challenges with Liquid Biopsy

  • Some tumors barely shed ctDNA, can generate false negative results
  • Clonal hematopoiesis of indeterminate potential (CHIP) can generate false positive results
  • Release of ctDNA varies between disease stages
  • Accurate determination of CNVs has been shown to be difficult, especially in low tumor fraction settings. Detection of structural variants like homozygous deletions and large rearrangements can also be challenging.
  • Low variant allele frequency (VAF)
  • Highly fragmented (+/-170bp)


Recommendations

  • If results of ctDNA analysis are negative, test should be repeated with tissue to exclude false negative results. It is critical to include test limitations in the report, for correct interpretation of the results.
  • Test standardization for ctDNA testing is needed
  • More sensitive methods are necessary to decrease the incidence of false negative results
 

1. Armstrong, A.J. et al. (2024) 'Germline and somatic testing for homologous repair deficiency in patients with prostate cancer (part 1 of 2)', Prostate Cancer and Prostatic Diseases.
2. Van de Haar, J. et al. (2024) 'ESMO Recommendations on clinical reporting of genomic test results for solid cancers', Annals of Oncology. Available at: https://www.annalsofoncology.org/article/S0923-7534(24)01011-1/fulltext (Accessed: 12 February 2025).

Up Next

The Testing Process

International guidelines recommend testing for HRR mutations in prostate cancer. Testing approach can be focused on single genes or HRR panel testing.

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