Clinical trial NCT04698551: NIPD on cffDNA for Triplet Repeat Diseases
Official title: Comparison of Two NGS Phasing Techniques of Parental Haplotypes for NIPD of Triplet Expansion Diseases
Study type: OBSERVATIONAL
Overall status: UNKNOWN
Conditions: Myotonic Dystrophy 1
Huntington Disease
Fragile X Syndrome
Keywords: Non Invasive Prenatal Diagnosis (NIPD)
Circulating Fetal DNA (CFTC)
triplet expansion diseases
Lead sponsor: University Hospital, Montpellier
Sponsor class: OTHER
Collaborators: name: Agence de La Biomédecine
First posted: 2021-01-07
Enrollment: 36
Sex: ALL
Minimum age (years): 18
Standard ages: CHILD
ADULT
OLDER_ADULT
Accepts healthy volunteers: no
Observational model: COHORT
Time perspective: RETROSPECTIVE
Sampling method: NON_PROBABILITY_SAMPLE
Study population: Retrospective study of 16 couples at risk of transmitting a disease with triplet expansions (Myotonic dystrophy of Steinert, Huntington's disease, FRAXA) Couples undergoing prenatal diagnosis for a monogenic disease caused by dynamic mutation

Brief summary: The purprose of this study is to develop and validate an analytical NIPD test for triplet repeat disesases by NGS analysis from maternal blood, searching for the familial mutation in families at risk of having one of the following triplet repeat diseases: Huntington's disease, Myotonic dystrophy, Fragile X syndrome.. A comparison of two 3rd generation long fragment DNA sequencing techniques will be performed. These methods are based of the phasing techniques of parental haplotypes without the proband.

Detailed description: Context:

The ability to sequence fetal cfDNA has led to exciting new developments for the non-invasive genetic diagnosis of monogenic diseases (DPNI_MGR). Various tests are proposed for diseases with predominantly de novo dominant, dominant paternal and some recessive paternal mutations. However, technical difficulties related to the determination of the maternal allelic balance remain, in particular during the phasing of parental haplotypes according to a trio strategy which requires the availability of parental genomic DNAs and at least one healthy or affected child. Moreover 2nd generation sequencers do not allow the haplotyping of alleles carrying dynamic mutations.

Objectives:

This project proposes the validation of a semi-universal DPNI_MGR test applicable to the majority of the genes and mutations involved in DPN requests from phasing of parental haplotypes by 3rd generation long-fragment DNA sequencing techniques coupled with targeted sequencing of free circulating DNA from maternal plasma. This test will be validated using triplet expansion diseases, which are the second indication of DPN at the national level.

Methodology :

Retrospective study of 16 couples at risk of transmitting a disease with triplet expansions (Myotonic dystrophy of Steinert, Huntington's disease, FRAXA, SCA1, 2, 3)

Phase 1 :

* Determination for 8 pairs of parental haplotypes according to the technique "Nanopore Cas9 Targeted-Sequencing" (nCATS) and validation of the analytical parameters and quality of this method (coverage rate of the regions of interest, error rate, identification of the morbid allele carrying the expansion ...),
* Comparison of the parental haplotypes obtained in "Nanopore" technique versus those obtained by the "Linked Reads 10xGenomics" technique in these same 8 pairs (the sequencing and phasing data by this 2nd approach are available from a previous study),
* Evaluation of the concordance of the fetal genotype results obtained during the standard examination (DPN by amniocentesis or choriocentesis) and those obtained with these new approaches of phasing in PNID.

Phase 2:

- Validation of the best performing workflow (efficiency / cost) of phase 1 over 8 additional pairs for a clinical transfer of the approach.

Expected results and prospects:

This study should make it possible to define the best performing test for the DPNI of triplet expansion diseases in accordance with the knowledge of the art and to validate the transfer conditions in clinical practice of the approach (equipment, reagents, cost analysis, analytical validation criteria ....).

The validated workflow should be as universal as possible to secondarily provide national level access to a wide range of rare diseases NIDP by future adjustments of the gene content of the free circulating DNA sequencing panels.

Eligibility criteria: Inclusion criteria:

* Couple at risk (based on family history or echographic findings) for one of the following diseases: Huntington's disease, Steinert's myotonic dystrophy, fragile X
* Written informed consent was obtained for DIACCIMEX study and mentionned "authorization for use for further studies on familial pathology. Indeed, the DNA can be used anonymized for the development of new analyzes of non-invasive prenatal diagnosis".
* Prenatal diagnosis has been done for the pregnancy during which maternal blood has been collected
* Couple molecular diagnosis results for one of the following diseases (Huntington's disease, Steinert's myotonic dystrophy, fragile X and spinocerebellar ataxias 1, 2 or 3 ) MUST BE AVAILABLE.

Exclusion criteria:

* Couple Genomic DNA are unavailable
* Subjects at risk of transmitting the family disease, but not wishing to know their molecular status
* Individuals under guardianship by court order

Primary outcomes:
measure: Concordance rate between cell free foetal DNA based genetic
timeFrame: 36 months
Secondary outcomes:
measure: Qualitative process to define the differents steps to analysis of the cell free foetal DNA
timeFrame: 36 months
Other outcomes:
Locations:
city: Montpellier
country: France
facility: CHU Montpellier
Study officials:
affiliation: University Hospital, Montpellier
name: Marie Claire VINCENT, PhD-PharmaD
role: PRINCIPAL_INVESTIGATOR
References:
citation: Liautard-Haag C, Durif G, VanGoethem C, Baux D, Louis A, Cayrefourcq L, Lamairia M, Willems M, Zordan C, Dorian V, Rooryck C, Goizet C, Chaussenot A, Monteil L, Calvas P, Miry C, Favre R, Le Boette E, Fradin M, Roux AF, Cossee M, Koenig M, Alix-Panabiere C, Guissart C, Vincent MC. Noninvasive prenatal diagnosis of genetic diseases induced by triplet repeat expansion by linked read haplotyping and Bayesian approach. Sci Rep. 2022 Jul 6;12(1):11423. doi: 10.1038/s41598-022-15307-2.