SUPR
Evaluation of long-read sequencing for clinical applications
Dnr:

sens2022566

Type:

SNIC SENS

Principal Investigator:

Claes Ladenvall

Affiliation:

Uppsala universitet

Start Date:

2022-09-26

End Date:

2024-10-01

Primary Classification:

30107: Medical Genetics

Webpage:

Allocation

  • Castor /proj at UPPMAX: 14000 GiB
  • Cygnus /proj at UPPMAX: 14000 GiB
  • Cygnus /proj/nobackup at UPPMAX: 5000 GiB
  • Castor /proj/nobackup at UPPMAX: 5000 GiB
  • Bianca at UPPMAX: 2 x 1000 core-h/month

Abstract

Sequencing facilities in Uppsala have been established as pioneers in evaluating and making long-read sequencing technologies available to the research community. In general, long read sequencing technologies have matured significantly, error rates have been lowered and costs have come down. There is now an increased interest also from the clinical genomics community to evaluate how long-read sequencing could be used in the clinical setting. For this purpose the SciLifeLab facilities NGI Uppsala and Clinical Genomics Uppsala (CGU) have initiated a collaboration where sequence data on research consented patients will be sequenced at NGI and bioinformatics solutions will be tested/developed jointly. The projects that are being planned include: - Whole genome ONT sequencing of hematological T/N patients - Targeted sequencing of patients with repeat expansions (CAS9 enrichment / Adaptive sequencing) - Targeted sequencing to detect fusion transcripts The project involves staff from NGI Uppsala, from CGU and clinical researchers from the Clinical Genetics Department at the Uppsala University Hospital. The project has already generated the first sequencing data and we have come to realize that we need a common platform for storing and analyzing the data so that all parties can access and work with the data.