Contribution of Optical Genome Mapping (OGM) in the Diagnosis of Multiple Congenital Malformations With or Without Intellectual Disability Without Genetic Abnormality

Study Workflow

Pre-analytical Phase

Participation in the study will be offered to all patients meeting the inclusion and non-inclusion criteria by an investigator from the Department of Genetics, during a medical consultation in which the non-contributive whole-genome sequencing (WGS) result will have been communicated (Figure 1). Information regarding the study procedures and objectives will be provided at that time. The information sheet and consent form will be given to the patient (if an adult) or to the holders of parental authority (if the patient is a minor). After obtaining consent for both the genetic investigations and participation in the research project, the patient may be enrolled in the study. Blood samples required for the study will be collected, transferred to the laboratory, and secured for analysis according to the following protocol:

Patient > 20 kg:

2 × 5 mL EDTA blood tubes

• × 5 mL heparinized blood tube

Patient 12-20 kg:

• × 5 mL EDTA blood tubes

Patient 5-12 kg:

1 × 5 mL EDTA blood tube

Samples will be sent to the Cytogenetics Department, where they will be pseudonymized and secured. At least three aliquots of 1.5 mL EDTA blood and the remaining volume will be frozen at -80 °C for DNA extraction and long-fragment DNA extraction. A cell culture (peripheral blood lymphocytes) will also be performed to obtain a fixed chromosomal pellet from the heparinized tube, when available. If the heparinized sample is not available and the results of optical genome mapping require confirmation of a chromosomal abnormality by karyotype or FISH (i.e., contributive result), a second blood draw will be proposed during the clinical results-return consultation.

Analysis Frozen samples from the Cytogenetics Department of Clermont-Ferrand University Hospital (one per patient) will be transferred via TSE to the Department of Genetics at Reims University Hospital, designated to perform optical genome mapping while awaiting installation of the Saphyr scanner at Clermont-Ferrand University Hospital (DAN 2025 application).

Extraction, labeling, and imaging of long DNA molecules will be performed using the manufacturer's kits, following the provided instructions.

Results and Interpretation

Raw data will be analyzed and validated by cytogeneticists at Reims University Hospital using Bionano Access and Solve® software. Data will also be securely shared with the project lead, responsible for:

Performing a second independent analysis (with Bionano Access and Solve, available in the Cytogenetics Department), leveraging expertise acquired through participation in previous projects.

Providing final interpretation of results and disseminating clinically relevant findings for patient management.

Each sample will therefore benefit from dual review and dual expertise, ensuring the reliability of the results.

Parental segregation studies may be proposed to facilitate biological interpretation. If needed, collection of parental samples and consent procedures will be coordinated by the Department of Medical Genetics at Clermont-Ferrand University Hospital. Conclusive results will be communicated to the clinician who prescribed the WGS for patient management and genetic counselling.

Inclusion criteria

• Patients presenting with at least two congenital anomalies, with or without intellectual disability, and weighing more than 5 kg.
• Whole-genome sequencing performed by the AURAGEN laboratory deemed non-contributive (absence of class 4 or 5 variants, or identification of a VUS, or identification of only one variant in the context of a recessive disorder).
• Patient covered by a social security scheme.
• Patient able to understand and to oppose participation in the study.
• Written informed consent for genetic analyses, signed either by the patient or by their legal representatives (for minors), after clear and fair information about the study has been provided.

Non-Inclusion Criteria

• Patients for whom a non-genetic cause (infectious, environmental, or toxic) has been previously identified.
• Inability to obtain a compliant sample.
• Patient or holder of parental authority under guardianship or legal protection, deprived of liberty, or placed under court-ordered protection.