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Summary of Post
Delivering on strategic commitments to invest in advanced research infrastructure and services, RCSI has developed a Genomics Laboratory. This facility provides researchers with genomics data generation capacity from Next Generation Sequencing (NGS) and other relevant platforms. It is an integrated clinical and research laboratory, fully accredited, providing a service to RCSI/Beaumont as well as national clinicians and researchers. The core facility integrates NGS with biobanking, digital pathology, clinical trials and data science in an end-to-end platform. Our vision is to optimise the potential of individual patient testing to ensure the greatest potential for diagnostics, innovation and discovery.
The successful candidate will be responsible for analysis of clinical and research NGS genomic datasets for integrated research and clinical applications. The role will span rare disease and cancer genetics – involving analysis of germline and somatic variation. Responsibilities include conducting analysis of genomic datasets involving SNVs, structural abnormalities and copy number abnormalities. They will ensure data received and generated by the Laboratory is handled in an efficient, standardised, secure and accurate manner using cutting edge technologies and adhering to data governance ethical standards. This includes facilitating the analysis of sequencing data derived from tissue, blood and single-cell technologies, including NGS data from Illumina MiSeq and NextSeq platforms and 10x Genomics data analysis. Additionally, the role will involve enabling the enrichment of RCSI-associated biobanks, with consented genomic datasets generated through diagnostic laboratories. The successful candidate will form part of the team at the RCSI Genomics Laboratory, providing support to the RCSI research community.
Specifically, the duties of the post are:
1. Conduct analysis of whole genome and whole exome sequencing data including genome comparison for cancer and somatic genomes, for diagnostic and research purposes.
2. Conduct data analysis for diagnostic and research purposes; involving SNVs, copy number abnormalities, structural abnormalities, mutations and graphical representation of this data for scientific presentation and publication.
3. Develop and manage databases for the storage of genomic data (WGS/exome/expression etc) and other relevant biological information.
4. Facilitate transfer of consented NGS/genomic data generated through overseas service laboratories for Beaumont diagnostics.
5. Develop and maintain analytical pipelines (including GATK) for alignment, variant calling, annotation and variant shortlisting for candidate gene/exome/whole genome diagnostic testing.
6. Facilitate genomic diagnostics for rare disease, via the application of ACMG/AMP, ClinGen and AGCS guidelines.
7. Analyse molecular datasets, such as genomic sequence data, microarray data or proteomics data for clinical or basic research purposes.
8. Develop analytical pipelines to facilitate projects utilizing RNA, DNA and single cell sequencing technologies and the development of laboratory standard operating procedures for data analysis for the purpose of accreditation.
9. Provide advice on experimental design and data interpretation in collaboration with research and clinical scientists.
10. Interrogate/manipulate publicly accessible, commercial or proprietary genomic or post-genomic databases, genomic analysis tools (e.g. GSEA) and collaborate with laboratory scientists for the clinical application of this data.
11. Keep abreast of new technologies, instrumentation or software by reading scientific literature and attending professional conferences. This includes independent presentation of data at conferences in digital, poster and oral forms.
12. Communicate research results through conference presentations, scientific publications or project reports.
Qualifications – (Essential):
* PhD in Genomics Data Science or Bioinformatics or other directly relevant field, or equivalent research experience (i.e. 3+ years working experience directly in analysis of genomic data).
Knowledge & Experience – (Essential):
* Minimum of three years’ experience in a genomics data science position, post qualification with undergraduate degree.
* Independent competence in the analysis of cancer and somatic genomes including large scale comparative analysis and management of large data, datasets including WGS, WES, RNAseq, single cell sequencing (e.g 10X) and RNA seq.
* Experience working with genomic scientists for the generation, analysis and storage of NGS data.
* Working knowledge of medical terminology and medical experience.
* Strong independent coding skills (R, Python).
* Familiarity with Linux / Unix.
* Experience working in a GDPR compliant environment.
Knowledge & Experience – (Desirable):
* Experience and proficiency with applications of American College of Medical Genetics (ACMG) variant annotation guidelines.
* Experience in genomic database development, management, annotation, storage, sharing and public deposition for publication.
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