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Prospective Study to Assess Medical Performance of Optical Mapping and Long Read Sequencing in Detecting Numerical and Structural Chromosome Abnormalities. CHROmosome MAPping and Sequencing (CHROMAPS)

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ClinicalTrials.gov Identifier: NCT05290051
Recruitment Status : Unknown
Verified March 2022 by Institut National de la Santé Et de la Recherche Médicale, France.
Recruitment status was:  Not yet recruiting
First Posted : March 22, 2022
Last Update Posted : March 22, 2022
Sponsor:
Information provided by (Responsible Party):
Institut National de la Santé Et de la Recherche Médicale, France

Brief Summary:

Chromosomal aberrations are major causes of developmental disorders (Intellectual disability (ID), multiple congenital anomalies (MCA), autism spectrum disorders (ASD)) as well as reproductive disorders (RD) in particular gametogenesis defects and recurrent miscarriages. Current first tier genetic investigations for chromosome analysis in clinical settings include karyotyping in case of RD (5 ~ 10% diagnosis rate) and chromosomal microarrays (CMA) in case of ID/MM (10 ~ 20% diagnosis rate). However, both assays show significant drawbacks, e.g. low resolution for karyotyping and inability to detect balanced structural rearrangement for CMA.

Optical genome mapping and long read genome sequencing are emerging technologies that offer new opportunities to overcome these limitations and allow for a higher resolution chromosome analysis.

This project aims at assessing the performance of optical mapping and long read whole genome sequencing compared to current gold standard cytogenetics methods in a prospective study. The investigator will evaluate their ability to become the all-in-one methodology for genomic analysis that could replace both karyotype and CMA and their added-value compared to these latter by uncovering new diagnoses.


Condition or disease Intervention/treatment Phase
Infertility Intellectual Disability Malformation Genetic: Optical Genome Mapping (Bionano®) Genetic: Longread sequencing (Nanopore®) Not Applicable

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Study Type : Interventional  (Clinical Trial)
Estimated Enrollment : 300 participants
Allocation: N/A
Intervention Model: Single Group Assignment
Intervention Model Description: Comparison of new diagnostic procedures with gold standard used in clinical setting
Masking: None (Open Label)
Masking Description: Gold standard analyses run as usual with results issued to patients Evaluated analyses run and analyzed blind to care provider and investigator Comparison of results between gold standard and tested analyses at the end of the study
Primary Purpose: Diagnostic
Official Title: Etude Prospective Comparative Des Performances de Détection Des Variations de Nombre et de Structure Des Chromosomes Par Les Techniques de Cartographie Moléculaire et de Séquençage de Grands Fragments
Estimated Study Start Date : April 2022
Estimated Primary Completion Date : September 2023
Estimated Study Completion Date : April 2024

Arm Intervention/treatment
Experimental: Patients referred for cytogenetic analysis
Analysis of patient DNA with Optical Genome Mapping (Bionano®) and long read Sequencing (Nanopore®) in search for chromosome abnormalities (aneuploidies and SV)
Genetic: Optical Genome Mapping (Bionano®)
Search for chromosome abnormalities through alteration of the optical map of the genome compared to reference genome using the Bionano® 's pipeline.

Genetic: Longread sequencing (Nanopore®)
Search for chromosome abnormalities from the sequencing data obtain from high molecular weight DNA molecules using dedicated analysis pipeline.




Primary Outcome Measures :
  1. Percentage of verified clinically significant chromosomal aberrations detected by Bionano® and Nanopore® compared to the percentage of those detected by karyotyping or CMA according to reason for referral. [ Time Frame: Through study completion, an average of 1 year ]
    The significance of an aberration is assessed according to international guidelines, clinical history, as well as publications and public databases.


Secondary Outcome Measures :
  1. Incidence and distribution of different kinds of chromosomal aberrations per category of referral. [ Time Frame: Through study completion, an average of 1 year ]
    Two main referral indication: infertility or Intellectual deficiency/Malformation

  2. Type of chromosome abnormalities that are overlooked by Bionano® and/or Nanopore® while detected by standard-of-care techniques [ Time Frame: Through study completion, an average of 1 year ]
    Abnormalities detected with either karyotype or CMA and not by OGM (Optical Genome Mapping) or longread sequencing

  3. Percentage of patients for which the detection of a chromosomal aberration by Bionano® or Nanopore® and not by karyotyping or CMA resulted in a change in the disease management [ Time Frame: Through study completion, an average of 1 year ]
    Abnormalities detected by either OGM or lrNGS but not by gold standard techniques leading to a change in patient care (including genetic counselling).

  4. Overall cost and benefit of each technique including delay to diagnosis and changes in the disease management [ Time Frame: Through study completion, an average of 1 year ]
    Medico-economic evaluation of the new technologies compared to gold standard diagnostic tools.



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Ages Eligible for Study:   Child, Adult, Older Adult
Sexes Eligible for Study:   All
Accepts Healthy Volunteers:   No
Criteria

Inclusion Criteria: patient requiring chromosome analysis either in case of infertility or in case of Intellectual deficiency/malformation

-

Exclusion Criteria: no exclusion criteria but we defined Non-inclusion criteria

  • ID in a context of perinatal suffering (e.g. hypoxia during labor)
  • Children born to non-native French-speaking parents in case of speech/language retardation
  • Obstructive azoospermia
  • Children under 5kg or whenever blood sampling cannot meet the required volume.
  • Missing or wrong blood collection tube
  • Insufficient blood volume
  • Missing or incomplete consent to research (e.g. only one parental consent for a child)
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Responsible Party: Institut National de la Santé Et de la Recherche Médicale, France
ClinicalTrials.gov Identifier: NCT05290051    
Other Study ID Numbers: C21-35
First Posted: March 22, 2022    Key Record Dates
Last Update Posted: March 22, 2022
Last Verified: March 2022

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Studies a U.S. FDA-regulated Drug Product: No
Studies a U.S. FDA-regulated Device Product: No
Additional relevant MeSH terms:
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Intellectual Disability
Infertility
Genital Diseases
Urogenital Diseases
Neurobehavioral Manifestations
Neurologic Manifestations
Nervous System Diseases
Neurodevelopmental Disorders
Mental Disorders