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Prostate CancerNCT04873427

In Situ Clonal Heterogeneity in Prostatic Diagnostic Biopsies

An observational study of Prostate Cancer and Genetic Predisposition, run by Clinica Luganese Moncucco at 1 site in Switzerland.

Terminated

Stopped early. The study ended before it was planned to and will not resume.

Official record
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Trial summary

This is a retrospective, proof of concept study, which aims at reconstructing the cellular heterogeneity of the tumor in multi-needle diagnostic prostate biopsy as well as any biopsy containing potentially pre-malignant tissue, to study its implications in the clinical history of the disease. Read more about this study

Who is it for?
Any age, men only
Conditions the study is for
Prostate Cancer, Genetic Predisposition
What is being tested?
clonal heterogeneity evaluation
How many people
40 participants
Where
1 siteSwitzerland
Study dates
15 Apr 2021to 15 Jan 2023
Phase
Observational
Are there results?
None posted in the registry

Key requirements

Who can take part, as listed by the sponsor. Only the study team can confirm whether you are eligible, so take this list to your doctor.

  • Ages Any age
  • Men only
  • No healthy volunteers
  • Child, Adult, Older adult

Study population: patients with prostate cancer

Who may be able to join

None listed.

Who cannot join

  • insufficient material on the tissue biopsy to be left in archives for further evaluations/analyses;
  • insufficient amount of tumor cells at baseline;

Trial locations and contacts

1 site in 1 country.

Switzerland1 site
  • Alessandra Franzetti Pellanda

    Lugano, Canton Ticino, 6900

Other trials in Switzerland

About this study

Official title: In Situ Clonal Heterogeneity in Prostatic Diagnostic Biopsies: Impact on Prostate Cancer Evolution and Clinical Outcome. A Retrospective, Proof of Concept Study

This is a retrospective, proof of concept study, which aims at reconstructing the cellular heterogeneity of the tumor in multi-needle diagnostic prostate biopsy as well as any biopsy containing potentially pre-malignant tissue, to study its implications in the clinical history of the disease. For each patient, 2 or more samples will be prepared starting from the FFPE diagnostic material. The biopsy used for assigning the Gleason score will be sequenced, together with two or more of the local peri-proximal biopsies with a higher level of differentiation. Samples will undergo Whole Exome Sequencing with an average coverage of 300x at the Wellcome Sanger Institute (WSI, Hinxton, UK). Sequencing data will be analysed for single nucleotide variants, copy number variants and structural variants by using state-of-the-art data analysis pipeline at WSI.

  1. Reconstruction of local PCa heterogeneity in multi-needle diagnostic biopsy with different Gleason scores (6-10) using high-coverage whole exome sequencing (WES) and DP-based clonal analysis;
  2. Characterization of the relationships between pathological differentiation (Gleason score) and genomics-measured heterogeneity and malignancy features;
  3. Assessment of clinical implications of clonal heterogeneity.

The study will include an average of 150 prostatic diagnostic biopsies from a cohort of 20 early metastatic PC patients and 20 non-relapsing/non-metastatic patients with indolent malignant disease.

Read the detailed description

Prostate cancer (PCa) is the leading malignancy of the male population. In current clinical practice, diagnostic confirmation of PCa is based on image-guided multi-needle biopsy, in order to capture the intrinsic biological heterogeneity of tumors and to provide a more accurate prediction of clinical outcomes. However, current morphology-based approaches (Gleason score) may not completely describe the complexity of a malignant gland. Not enough is currently known on the impact of genomic heterogeneity in a poorly-differentiated prostate, especially with regards to the development of an indolent versus metastatic prostate malignancy

This is a retrospective, proof of concept study, which aims at reconstructing the cellular heterogeneity of the tumor in multi-needle diagnostic prostate biopsy as well as any biopsy containing potentially pre-malignant tissue, to study its implications in the clinical history of the disease. For each patient, 2 or more samples will be prepared starting from the FFPE diagnostic material. The biopsy used for assigning the Gleason score will be sequenced, together with two or more of the local peri-proximal biopsies with a higher level of differentiation. Samples will undergo Whole Exome Sequencing with an average coverage of 300x at the Wellcome Sanger Institute (WSI, Hinxton, UK). Sequencing data will be analysed for single nucleotide variants, copy number variants and structural variants by using state-of-the-art data analysis pipeline at WSI.

  1. Reconstruction of local PCa heterogeneity in multi-needle diagnostic biopsy with different Gleason scores (6-10) using high-coverage whole exome sequencing (WES) and DP-based clonal analysis;
  2. Characterization of the relationships between pathological differentiation (Gleason score) and genomics-measured heterogeneity and malignancy features;
  3. Assessment of clinical implications of clonal heterogeneity.

The study will include an average of 150 prostatic diagnostic biopsies from a cohort of 20 early metastatic PC patients and 20 non-relapsing/non-metastatic patients with indolent malignant disease.

Descriptive statistics will be carried out and a Mann-Whitney test will be applied on a synthetic parameter for each patient biopsy heterogeneity result, grouped by indolent vs aggressive disease cohort.

The null hypotheses (no difference between the two cohort in heterogeneity) will be rejected if p < 0.05.

The proposed project will evaluate the impact of diagnostic intra-prostatic cell heterogeneity on the clinical course of PCa. The potential prognostic value of local disease clonality could indeed impact the clinical practice: patient with Gleason <7 and lower level of clonal heterogeneity may be moved from an active disease treatment to an active surveillance (AS) approach, avoiding overtreatment for the subjects. Conversely, patients with a similar Gleason score but a more heterogenous malignant population may be required to undergo more aggressive procedures.

Being tested
clonal heterogeneity evaluation
Keywords
Prostate Cancer, genetic heterogeneity, personalized medicine
Medical subject headings
Prostatic Neoplasms, Genetic Predisposition to Disease

What participants receive

What participants receive. In a randomised study each person is assigned to one group by chance.

  • clonal heterogeneity evaluationGenetic

    Reconstruction of local PCa heterogeneity in multi-needle diagnostic biopsy with different Gleason scores (6-10) using high-coverage whole exome sequencing (WES) and DP-based clonal analysis

Study groups in NCT04873427
Study groupRoleWhat they receive
early metastatic prostate cancer patientsReconstruction of local PCa heterogeneity in multi-needle diagnostic biopsy with different Gleason scores (6-10) using high-coverage whole exome sequencing (WES) and DP-based clonal analysis
Receives: Genetic: clonal heterogeneity evaluation
non-relapsing/non-metastatic patients with indolent malignant diseaseReconstruction of local PCa heterogeneity in multi-needle diagnostic biopsy with different Gleason scores (6-10) using high-coverage whole exome sequencing (WES) and DP-based clonal analysis
Receives: Genetic: clonal heterogeneity evaluation

What is being measured

The primary outcome is the main question the study is designed to answer.

  1. reconstruction of local PCa heterogeneity

    Primary endpoint is the reconstruction of local PCa heterogeneity in multi-needle diagnostic biopsy with different Gleason scores (6-10) using high-coverage whole exome sequencing (WES) and DP-based clonal analysis

    Measured: through study completion, an average of 2 years

Secondary outcomes (1)
  1. relationships between pathological differentiation (Gleason score) and genomics-measured heterogeneity

    Secondary endpoints are characterization of the relationships between pathological differentiation (Gleason score) and genomics-measured heterogeneity and malignancy features; and assessment of clinical implications of clonal heterogeneity.

    Measured: through study completion, an average of 2 years

Timeline

From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.

  1. First posted5 May 2021
  2. Study start15 Apr 2021
  3. Primary completion15 Jan 2023
  4. Study completion15 Jan 2023

Why it stopped: The results of the genomic analyses were compromised due to the low DNA concentration.

Resources

More details

For doctors and researchers: how the study is designed, who runs it, and its registry IDs.

Study design
Study type
Observational
Observational model
Case only
Time perspective
Retrospective
Enrolment
40 participants (actual)
IDs, dates and publications
ClinicalTrials.gov ID
NCT04873427
Sponsor's protocol ID
CLM_RAD_001
Status last verified
Feb 2023
First submitted
28 Apr 2021
Last updated
15 Feb 2023
Results posted
No
Data monitoring committee
No
FDA-regulated drug
No
FDA-regulated device
No
Individual data sharing
No

Publications

  • Altmann A, Weber P, Bader D, Preuss M, Binder EB, Muller-Myhsok B. A beginners guide to SNP calling from high-throughput DNA-sequencing data. Hum Genet. 2012 Oct;131(10):1541-54. doi: 10.1007/s00439-012-1213-z. Epub 2012 Aug 11.

    PubMed 22886560
  • Beltran H, Prandi D, Mosquera JM, Benelli M, Puca L, Cyrta J, Marotz C, Giannopoulou E, Chakravarthi BV, Varambally S, Tomlins SA, Nanus DM, Tagawa ST, Van Allen EM, Elemento O, Sboner A, Garraway LA, Rubin MA, Demichelis F. Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. Nat Med. 2016 Mar;22(3):298-305. doi: 10.1038/nm.4045. Epub 2016 Feb 8.

    PubMed 26855148
  • Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014 Aug 1;30(15):2114-20. doi: 10.1093/bioinformatics/btu170. Epub 2014 Apr 1.

    PubMed 24695404
  • Bolli N, Avet-Loiseau H, Wedge DC, Van Loo P, Alexandrov LB, Martincorena I, Dawson KJ, Iorio F, Nik-Zainal S, Bignell GR, Hinton JW, Li Y, Tubio JM, McLaren S, O' Meara S, Butler AP, Teague JW, Mudie L, Anderson E, Rashid N, Tai YT, Shammas MA, Sperling AS, Fulciniti M, Richardson PG, Parmigiani G, Magrangeas F, Minvielle S, Moreau P, Attal M, Facon T, Futreal PA, Anderson KC, Campbell PJ, Munshi NC. Heterogeneity of genomic evolution and mutational profiles in multiple myeloma. Nat Commun. 2014;5:2997. doi: 10.1038/ncomms3997.

    PubMed 24429703
  • Chen X, Schulz-Trieglaff O, Shaw R, Barnes B, Schlesinger F, Kallberg M, Cox AJ, Kruglyak S, Saunders CT. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics. 2016 Apr 15;32(8):1220-2. doi: 10.1093/bioinformatics/btv710. Epub 2015 Dec 8.

    PubMed 26647377
  • Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013 Mar;31(3):213-9. doi: 10.1038/nbt.2514. Epub 2013 Feb 10.

    PubMed 23396013
  • Epstein JI, Allsbrook WC Jr, Amin MB, Egevad LL; ISUP Grading Committee. The 2005 International Society of Urological Pathology (ISUP) Consensus Conference on Gleason Grading of Prostatic Carcinoma. Am J Surg Pathol. 2005 Sep;29(9):1228-42. doi: 10.1097/01.pas.0000173646.99337.b1. No abstract available.

    PubMed 16096414
  • Epstein JI, Zelefsky MJ, Sjoberg DD, Nelson JB, Egevad L, Magi-Galluzzi C, Vickers AJ, Parwani AV, Reuter VE, Fine SW, Eastham JA, Wiklund P, Han M, Reddy CA, Ciezki JP, Nyberg T, Klein EA. A Contemporary Prostate Cancer Grading System: A Validated Alternative to the Gleason Score. Eur Urol. 2016 Mar;69(3):428-35. doi: 10.1016/j.eururo.2015.06.046. Epub 2015 Jul 10.

    PubMed 26166626
  • Ferguson, T. S., 1973. A Bayesian analysis of some nonparametric problems.. Annals of Statistics, Volume 1, pp. 209-230.

  • Gandellini P, Casiraghi N, Rancati T, Benelli M, Doldi V, Romanel A, Colecchia M, Marenghi C, Valdagni R, Demichelis F, Zaffaroni N. Core Biopsies from Prostate Cancer Patients in Active Surveillance Protocols Harbor PTEN and MYC Alterations. Eur Urol Oncol. 2019 May;2(3):277-285. doi: 10.1016/j.euo.2018.08.010. Epub 2018 Sep 10.

    PubMed 31200842
  • Hamid AA, Gray KP, Shaw G, MacConaill LE, Evan C, Bernard B, Loda M, Corcoran NM, Van Allen EM, Choudhury AD, Sweeney CJ. Compound Genomic Alterations of TP53, PTEN, and RB1 Tumor Suppressors in Localized and Metastatic Prostate Cancer. Eur Urol. 2019 Jul;76(1):89-97. doi: 10.1016/j.eururo.2018.11.045. Epub 2018 Dec 12.

    PubMed 30553611
  • Helpap B, Egevad L. Modified Gleason grading. An updated review. Histol Histopathol. 2009 May;24(5):661-6. doi: 10.14670/HH-24.661.

    PubMed 19283673
  • Hofman MS, Emmett L. Tumour Heterogeneity and Resistance to Therapy in Prostate Cancer: A Fundamental Limitation of Prostate-specific Membrane Antigen Theranostics or a Key Strength? Eur Urol. 2019 Oct;76(4):479-481. doi: 10.1016/j.eururo.2019.07.030. Epub 2019 Jul 25. No abstract available.

    PubMed 31351666
  • Hugosson J, Carlsson S. Overdetection in screening for prostate cancer. Curr Opin Urol. 2014 May;24(3):256-63. doi: 10.1097/MOU.0000000000000054.

    PubMed 24670870
  • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18.

    PubMed 19451168

Questions about this trial

What is this clinical trial studying?

An observational study of Prostate Cancer and Genetic Predisposition, run by Clinica Luganese Moncucco at 1 site in Switzerland.

The full registered description is in the About this study section and the official record.

Who may be eligible to take part?

The sponsor lists 0 inclusion and 2 exclusion criteria. Eligibility is decided by the study team after screening, so read the full criteria and contact a listed site.

Is this clinical trial currently recruiting?

The record says: stopped early, as of the sponsor's last update on 15 Feb 2023. Status can change between updates, so confirm with the study contact before making plans.

Where is the study taking place?

The record lists 1 site in Switzerland. Whether a site is taking part right now should be confirmed with that site. See every site.

What are the possible benefits and risks?

They depend on the study and the treatment, and no study can promise a benefit. The study team explains the known risks during informed consent, before anyone joins; the record itself does not list them.

Are results available for this study?

The study was stopped early (reason given: The results of the genomic analyses were compromised due to the low DNA concentration.). Results are not available in the source record.

How can a doctor refer a patient or contact the research team?

The record lists no contact. The official record names the sponsor, who can be asked directly. AzTrials does not enrol participants or take referrals.

What does the primary outcome measure?

reconstruction of local PCa heterogeneity (time frame: through study completion, an average of 2 years). It is what the study was designed to measure, not a finding.

Where can I read the original study information?

On the ClinicalTrials.gov record for NCT04873427, which also lists 23 linked publications.

Does a listing mean the treatment is approved or proven to work?

No. A listing means the study is registered. It does not show that the treatment is safe, works, or is approved by a regulator.

How often is this information updated?

AzTrials copies changed records from ClinicalTrials.gov every night and reloads the whole registry every week. The sponsor last updated this record on 15 Feb 2023.

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