We've just opened a position in the Division of Genetic Medicine at the Lausanne University Hospital (CHUV). This role will likely play a crucial part in our adoption of long-read sequencing (probably PacBio) in a clinical diagnostic setting:

https://recrutement.chuv.ch/vacancy/bio-informaticienne-chargee-de-recherche-311168.html

Big plus if you are a Bioconductor contributor with experience developing code/packages using GenomicRanges! (also French is not required but it would be helpful)

Job offer: Bioinformatician - Development of NGS pipelines (human genome)

### Location

Genetic Medicine Department, Lausanne University Hospital, Lausanne, Switzerland The CHUV Genetic Medicine Department comprises a clinical unit, as well as molecular and cytogenetics laboratories. The clinical unit comprises three senior physicians, three senior registrars, three assistants, four genetic counselors, and one psychologist. More than 5,000 patients are seen in consultations each year (neurogenetics, oncogenetics, cardiogenetics, nephrogenetics, etc.). The molecular and chromosomal diagnostics laboratories comprise four FAMH biologists, six scientific experts, one bioinformatician, and ten laboratory technicians. More than 2,500 analyses are performed each year using a variety of methods (karyotyping, FISH, array CGH, Sanger, MLPA, NGS, etc.). For complex cases, advanced sequencing technologies such as exome and trio analysis are often used. You will join a newly established and rapidly growing research team. The projects focus on patients followed in the Genetic Medicine department who remain without a molecular diagnosis despite extensive analyses. We aim to identify novel genes responsible for rare monogenic diseases and understand the pathophysiological mechanisms underlying these disorders using various functional validation approaches (including organoids and in vivo models). Our work is particularly focused on genes implicated in neurodevelopmental disorders and monogenic ataxias.

### Main tasks

Participate in research and development projects (80%)

• Design, develop, and maintain automated pipelines for the analysis of human genome sequencing data (short-read and long-read) as part of our research activities (80%) and for diagnostic purposes (20%), in close collaboration with the bioinformatician working in the department.
• Integrate and evaluate open-source and proprietary tools (alignment, variant detection, annotation, QC). Develop new computational tools (e.g., statistical methods, software) and apply these tools to data generated through various projects.
• Participate in the interpretation of genomic data in close collaboration with the bioinformatician working in the department, the postdoctoral fellow, and other collaborators.

Contribute to the management, organization, and standardization of genomic data (10%)

• Ensure the structuring, secure storage, and harmonization of data to guarantee its traceability and reusability.
• Participate in the implementation of strategies for the management and standardization of genomic data to promote its integration, interoperability, and scientific exploitation.

Participate in the drafting of bioinformatics quality procedures (5%)

• Develop, document, and update standardized procedures to ensure compliance with quality and regulatory standards and alignment with best practices in bioinformatics.

Contribute to training (5%)

• Contribute to bioinformatics teaching within the Faculty of Biology and Medicine at the University of Lausanne (masters and doctoral students; participation in undergraduate/graduate teaching in biomedical data science).
• Communicate and interact with internal and external collaborators.

### Required profile

Education:

• Desirable: PhD in biostatistics/bioinformatics (or similar)
• Required: Master's degree in bioinformatics applied to the field of human genomics with a minimum of 2 years of post-masters experience

Technical skills:

• Proficiency in R
• Experience with workflows (e.g. Nextflow).
• Solid foundation in NGS analysis: BWA, GATK, SAMtools, bcftools, VEP/ANNOVAR.
• Knowledge of Linux environments, big data management, HPC/Cloud.
• Good practices in quality control and version management (Git).