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Translational Genomics Platform

Ultra-sensitive Allele Variant Analysis

In addition to recruitment of excellent researchers, the Wallenberg Centre for Molecular and Translational Medicine together with Västra Götalandsregionen has initiated a research platform within ultrasensitive mutation detection – the Translational Genomics Platform.

The platform is a research initiative with the attempt to bring innovation into healthcare. This new, ultrasensitive technique allows individual molecules related to diseases like cancer to be detected. Tumor DNA enters the blood in cancer patients and by analyzing the amount of these disease-specific DNA sequences the tumor burden is assessed. Thereby the method not only opens up the possibility for early diagnostics, but also to customize the treatment for patients before tumors are seen through traditional imaging methods. The initiative has already attracted attention at Sahlgrenska University Hospital and several surgeons and oncologist are using the platform.

Detection of extremely rare variant alleles within a complex mixture of DNA molecules is becoming increasingly relevant in many areas of clinical and basic research. The limitations of most technologies are that they are not sensitive enough to reliable detect rare allele variants or that they only interrogate a few pre-defined variants. Simple, multiplexed, PCR-based barcoding of DNA for sensitive allele variant detection using sequencing (SiMSen-seq) was developed to meet these needs. SiMSen-Seq has an easy workflow that allows flexible multiplexing options and the method can be applied on minimal DNA input (< 5 ng DNA). SiMSen-seq enables detection and quantification of individual DNA molecules with single-bp resolution covering several kilobases of DNA. Data analysis is standardized and can be performed with freely available software. Suitable sample types include cytological aspirates, fixed tissues and liquid biopsies like blood, urine, saliva, cerebrospinal fluid, and pleural fluid. Applications include cancer diagnostics, prenatal testing, and detection of organ rejection, forensics, and pathogen detection among others.

Responsible Principal Investigator

Anders Ståhlberg

Docent in Molecular Medicine
anders.stahlberg@gu.se

Group Members

Gustav Johansson
PhD student

Bioinformatician
Amir Feizi, PhD

Molecular biologist
Helena Kristiansson, PhD

Key publications

Ståhlberg A, Krzyzanowski PM, Egyud M, Filges S, Stein L, Godfrey TE
Simple multiplexed PCR-based barcoding of DNA for ultrasensitive mutation detection by next-generation sequencing.
Nat Protoc. 2017 Apr;12(4):664-682. https://www.ncbi.nlm.nih.gov/pubmed/28253235


Ståhlberg A, Krzyzanowski PM, Jackson JB, Egyud M, Stein L, Godfrey TE
Simple, multiplexed, PCR-based barcoding of DNA enables sensitive mutation detection in liquid biopsies using sequencing.
Nucleic Acids Res. 2016 Jun 20;44(11) https://www.ncbi.nlm.nih.gov/pubmed/27060140
 

Flexible new method for early cancer diagnosis

Read the press release about the Translational Genomics Platform (May 18, 2017)

Contact Information

Anders Ståhlberg

anders.stahlberg@gu.se

Avd för patologi och genetik
SU Sahlgrenska
41345 Göteborg

Visiting Address:
Gula Stråket 2 B
SU/Sahlgrenska
41345 Göteborg

Page Manager: Pontus Sundén|Last update: 8/10/2017
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Denna text är utskriven från följande webbsida:
http://wcmtm.gu.se/research-groups/genomics-platform/
Utskriftsdatum: 2017-11-21