SUPR
Implementing whole-genome sequencing of acute leukemias in a diagnostic setting
Dnr:

sens2019012

Type:

SNIC SENS

Principal Investigator:

Richard Rosenquist Brandell

Affiliation:

Karolinska Institutet

Start Date:

2019-04-17

End Date:

2024-07-01

Primary Classification:

30107: Medical Genetics

Webpage:

Allocation

  • Castor /proj at UPPMAX: 80000 GiB
  • Cygnus /proj at UPPMAX: 80000 GiB
  • Castor /proj/nobackup at UPPMAX: 45000 GiB
  • Cygnus /proj/nobackup at UPPMAX: 45000 GiB
  • Bianca at UPPMAX: 100 x 1000 core-h/month

Abstract

As a key project within Genomics Medicine Sweden initiative, we aim to develop a robust approach to detect all types of genetic aberration in acute leukemia samples based on whole-genome sequencing (WGS). Retrospectively collected acute leukemia tumor-normal sample pairs are sequenced at 90x/30x depth to assess the capacity of detecting clinically relevant genetic events required in the diagnostic setting and to identify novel types of coding/non-coding aberrations.To this purpose, we have included different cohorts of patient samples: 1) Acute myeloid leukemia (AML) samples extensively characterized by whole-exome sequencing (WES) and RNA-sequencing (RNA-seq), 2), two AML and acute lymphoblastic leukemia (ALL) cohorts analyzed by traditional karyotyping, FISH and molecular methods and 3) Samples submitted to sequencing using the 10X Chromium technology. We also aim to build a national resource based on WGS data in acute leukemias that can be used to identify novel types of genetic lesion of potential clinical and therapeutic impact. All samples include human genetic information, considered as sensitive personal data.