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Programme de Recherche Translationnelle en Santé (PRTS)
Edition 2013


ANI


Molecular characterization of apparently balanced chromosomal rearrangements by next-generation sequencing in 55 patients with intellectual disability and/or multiple congenital anomalies

Next-generation sequencing for chromosomal anomalies in mental retardation
Next-generation sequencing is a new technology for the rapid characterization of apparently balanced chromosomal rearrangements (ABCR), improving genetic counseling of patients with ABCR and intellectual disability and / or malformations.

Apparently balanced chromosomal rearrangements with abnormal phenotype
Apparently balanced chromosomal rearrangements (ABCR) associated with intellectual disability and / or malformations are rare events but are challenging for genetic counseling. The phenotype may be secondary to gene disruption by the breakpoint. However, breakpoints characterization by conventional methods is time consuming and expensive and is not routinely performed. NGS is a rapid and efficient method to characterize the breakpoints of ABCR. The main objective is to study 55 patients with ABCR by NGS to identify genes responsible for developmental abnormalities, accounting for clinical features. This study will improve the management and genetic counseling of patients. It will also allow to better understand the mechanisms and functional consequences of ABCR and to identify new genes responsible for intellectual disability.

Next-generation sequencing to characterize balanced chromosomal rearrangements
Next-generation sequencing (NGS) is able to determine the sequence of millions of DNA molecules in parallel. Bioinformatics analysis compares each sequence obtained on the reference genome and thus determines the exact position and explores possible variations. Structural variations, such as chromosomal breakpoints, can be characterized by studying the distance and orientation of the sequences.
The breakpoints of patients will be determined by NGS. These results will be verified by conventional Sanger sequencing. A bioinformatics analysis will determine the characteristics of each breakpoint (sequence, repeated elements, genes, regulatory sequences). For each breakpoint, expression study will be performed for the disrupted gene and two adjacent genes in order to examine the functional consequences.

Results

The study of the 6 first patients showed that ABCR are often more complex as they appear. We identified a case of constitutional chromothripsis, a rare type of complex rearrangement, whose mechanisms are still unclear. Among 7 disrupted genes, 2 allowed to explain the phenotype of 2 patients. In 2 patients, breakpoints localization was not possible because they lie in heterochromatine. An alternative analysis should be developed for these cases.

Outlook

In 2 patients, ABCR disrupted known pathogenic genes, allowing a diagnosis in these cases. It shows the relevance of this strategy in diagnostic. Gene disruption has been reported only once for each gene, to our knowledge. A case of constitutional chromothripsis was identified. It offers the opportunity to better understand the mechanisms of these rare complex rearrangements.

Scientific outputs and patents

A preliminary study on this project has already been published (Schluth-Bolard et al, J Med Genet, 2013. 50:144-150). The results of the present study will be published and presented to the scientific community, clinicians and patients.

Partners

AP-HP - Hôpital Necker AP-HP - Hôpital Necker - Enfants malades- Service de Cytogénétique

AP-HP - GH Pitié-Salpêtrière AP-HP - GH Pitié-Salpêtrière - Département de Génétique

AP-HP - Hôpital Armand Trousseau AP-HP - Hôpital Armand Trousseau- Service de Génétique et Embryologie Médicales

AP-HP - Hôpital Robert Debré AP-HP - Hôpital Robert Debré - Laboratoire de Cytogénétique

AP-HP -Hôpital Jean Verdier - AP-HP AP-HP -Hôpital Jean Verdier - AP-HP- Laboratoire de Cytogénétique, Service d'Histologie Embryologie Cytogénétique BDR CECOS

AP-HP Hôpitaux Universitaires Paris Centre - Hôpital Cochin AP-HP Hôpitaux Universitaires Paris Centre - Hôpital Cochin - Laboratoire de Cytogénétique Constitutionnelle Pré et Postnatale

CH Chambéry CH Chambéry-Laboratoire de Génétique Chromosomique

CH Mulhouse CH Mulhouse Laboratoire de Génétique

CH Valence CH Valence - Service de Cytogénétique

CHRU Lille CHRU Lille - Institut de Génétique Médicale

CHU Dijon CHU Dijon-Laboratoire de Cytogénétique

CHU Estaing - Clermont-Ferrand CHU Estaing - Clermont-Ferrand - Service de Cytogénétique Médicale

CHU Grenoble CHU Grenoble - Laboratoire de Génétique Chromosomique

CHU Marseille CHU Marseille - Laboratoire de Cytogénétique

CHU Nantes CHU Nantes - Laboratoire de Cytogénétique

CHU Pontchaillou - Rennes CHU Pontchaillou - Rennes - Laboratoire de Cytogénétique et Biologie Cellulaire

CHU Saint-Etienne CHU Saint-Etienne - Service de Génétique Clinique, Chromosomique et Moléculaire

CHU Strasbourg CHU Strasbourg - Laboratoire de Cytogénétique

CRNL - CNRS TIGER team

Hospices Civils de Lyon Hospices Civils de Lyon - Centre de Biotechnologie Cellulaire

Hospices Civils de Lyon Hospices Civils de Lyon -Laboratoire de Cytogénétique Constitutionnelle

ANR grant: 79 612 euros
Beginning and duration: février 2014 - 36 mois

Submission abstract

Apparently balanced chromosomal rearrangement (ABCR) associated with an abnormal phenotype is a rare but problematic event. It occurs in 6% of de novo reciprocal translocations and 9% of de novo inversions. Abnormal phenotype, including intellectual disability and / or multiple congenital anomalies (ID/MCA) may be explained either by associated cryptic genomic imbalances detectable by array-CGH or by gene disruption at the breakpoint. However, breakpoint cloning using conventional methods (i.e., fluorescent in situ hybridization (FISH), Southern blot) is often laborious and time consuming and cannot be performed routinely. Without complete investigation of these rearrangements, genetic counseling is a real challenge. Recently, we and others showed that Next-Generation Sequencing (NGS) is a powerful and rapid technique to characterize ABCR breakpoints at the molecular level.
The ANI project (ABCR NGS ID) aims at characterizing at the molecular level ABCR in 55 patients presenting with intellectual disability and/or multiple congenital anomalies (ID/MCA) using NGS. We make the hypothesis that ABCR account for the patient phenotype, either by gene disruption or position effect, since genomic imbalance would have been previously excluded by array-CGH.
The ANI project is a 3-year-long study that will be conducted by a consortium of 21 partners, including 19 french hospital cytogenetics laboratories, a research team (TIGER), and a cellular biotechnology center. Patients will be recruited by each Cytogenetics laboratory. ABCR breakpoints will be molecularly characterized by NGS and a first bio-informatics analysis. The results will be verified by amplification of junction fragments by PCR followed by Sanger sequencing, allowing the localization of breakpoints at the base-pair level. In some complex cases, FISH experiment will be necessary to clarify the results. A second bio-informatics analysis will then determine breakpoints’ characteristics (sequence, repeated elements, gene and regulatory elements). Finally, for each breakpoint, gene expression studies will be performed including the gene disrupted by the breakpoint and two neighboring genes. All these data, together with those already available in the literature and databases will be integrated to determine if the gene could account for the patient’s phenotype, allowing an appropriate genetic counseling.
This project will identify new candidate genes involved in ID and developmental anomalies. It will also contribute to the development and evaluation of NGS as a diagnostic tool for ABCR and ID/MCA. It will also allow unraveling mechanisms and functional consequences of ABCR, in particular in term of position effect.
In conclusion, the ANI project will contribute to the improvement of diagnostic management and genetic counseling of patients with ID/MCA and ABCR. It will also contribute to the understanding of ABCR patho-physiology and to the unraveling of pathway involved in development and brain function, thus improving genetic counseling for ID/MCA patients in general.

 

ANR Programme: Programme de Recherche Translationnelle en Santé (PRTS) 2013

Project ID: ANR-13-PRTS-0005

Project coordinator:
Madame Caroline SCHLUTH-BOLARD (Hospices Civils de Lyon -Laboratoire de Cytogénétique Constitutionnelle)

 

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The project coordinator is the author of this abstract and is therefore responsible for the content of the summary. The ANR disclaims all responsibility in connection with its content.