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Translational Genomics Platform

 

Ultrasensitive Nucleic Acids Analysis

This platform is a research initiative to bring innovations within nucleic acid analysis into healthcare. Ultrasensitive sequencing techniques can accurately detect individual disease-associated molecules in liquid biopsies sampled from different body fluids. In cancer, analysis of tumor-derived molecules in blood provides detailed diagnostic and prognostic information. This precision medicine approach opens up the possibility for early diagnostics, monitoring of treatment efficacy and detection of relapses. The Translational Genomics Platform is a partner in several ongoing national and international studies, especially at Sahlgrenska University Hospital, exploring the clinical utility of ultrasensitive nucleic acid analysis.

Our specific aims include:

  • To develop ultrasensitive molecular techniques that enable the analysis of individual nucleic acid molecules with nucleotide resolution and their modifications.
  • To demonstrate the clinical utility of analyzing circulating tumor-derived nucleic acids in liquid biopsies.
  • To develop and validate liquid biopsy workflows, from sampling to data analysis.
  • To facilitate and support clinical studies at all stages using liquid biopsy analysis.
     

Current technologies lack sensitivity to reliably detect rare variant alleles or are limited to interrogate few pre-defined variants. To overcome these challenges we developed Simple, multiplexed, PCR-based barcoding of DNA for sensitive allele variant detection using sequencing” (SiMSen-Seq). This technique has a straightforward workflow that allows flexible targeting of multiple sequences and may be applied on minute quantities of DNA (< 5 ng DNA). SiMSen-Seq enables the detection and quantification of individual DNA molecules with single nucleotide resolution, covering several kilobases of DNA. It can be applied to essential all clinical sample types, including body fluids such as blood, urine, saliva, cerebrospinal fluid and pleural fluid. Data analysis is standardized and can be performed with freely available open source softwares. The Translational Genomics Platform uses SiMSen-Seq and related technologies to meet the clinical need to diagnose and monitor patients with high sensitivity and specificity. Detection of extremely rare variant alleles within a complex mixture of DNA molecules is also becoming increasingly relevant in many other areas, such as prenatal testing, forensics, immunology, pathogen detection, neurological and metabolic diseases. These applications are developed in collaborations with experts in respective fields.

Responsible Principal Investigator

Anders Ståhlberg

Associate Professor in Molecular Medicine
anders.stahlberg@gu.se

Group Members

Tobias Österlund, PhD, Researcher
Helena Kristiansson, PhD, Researcher
Soheila Dolatabadi, PhD, Researcher
Emma Jonasson, PhD, Researcher
Peter Micallef, PhD, Researcher
Daniel Andersson, PhD, Researcher
Parmida Ranji, PhD, Researcher
Amin Forootan, MSc, PhD student
Stefan Filges, MSc, PhD student
Lisa Andersson, MSc, PhD student
Manuel Luna Santa-María, MSc, PhD student
Gustav Johansson, MSc, PhD student
Florian Puls, MD, PhD student
Mahnaz Irani Shemirani, MSc, PhD student
Jennifer Pettersson, MSc, associated PhD student
Emma Persson, MSc, associated PhD student
Christoffer Vannas, MD, associated PhD student
Cristiana Rimniceanu, MSc, associated PhD student
Malin Nilsson, MSc, associated PhD student
Anna Gustafsson, MSc, associated PhD student
Karoline Berger, MSc, associated PhD student
Malin Lindén, MSc, associated PhD student
Hana Komic, MSc, associated PhD student
Elisabeth Mellström, MD, associated PhD student
Marta Berndsen, MD, associated PhD student
Ida Rahmqvist, MSc, associated PhD student

Publications

https://www.ncbi.nlm.nih.gov/pubmed/?term=St%C3%A5hlberg+A

 

Page Manager: Mattias Lindgren|Last update: 3/6/2020
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