Key publications

Borgström E, Redin D, Lundin S, Berglund E, Andersson AF, Ahmadian A.
Phasing of single DNA molecules by massively parallel barcoding.
Nature Communications. 2015 Jun 9;6.
DOI: 10.1038/ncomms8173

Redin D, Borgström E, He M, Aghelpasand H, Käller M, Ahmadian A.
Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules.
Nucleic Acids Research. 2017 Jul 1;45(13).
doi: 10.1093/nar/gkx436

Redin D, Frick T, Aghelpasand H, Käller M, Borgström E, Olsen RA, et al.
High throughput barcoding method for genome-scale phasing.
Scientific Reports. 2019 Dec 1;9(1).
doi: 10.1038/s41598-019-54446-x

Stiller C, Aghelpasand H, Frick T, Westerlund K, Ahmadian A, Karlström AE.
Fast and Efficient Fc-Specific Photoaffinity Labeling to Produce Antibody-DNA Conjugates.
Bioconjugate Chemistry. 2019 Nov 20;30(11):2790–8.
DOI: 10.1021/acs.bioconjchem.9b00548

Banijamali M, Höjer P, Nagy A, Hååg P, Paz Gomero E, Stiller C, Kaminskyy V, Ekman S, Lewensohn R, Eriksson Karlström A, Viktorsson K, Ahmadian A.
Characterizing single extracellular vesicles by droplet barcode sequencing for protein analysis.
Journal of Extracellular Vesicles 2022 Nov 11:12277
doi: 10.1002/jev2.12277

We are developing novel technologies for high throughput analysis of genomes, transcriptomes and proteins. The most recent method developed by the group is called Droplet Barcode Sequencing (DBS). In two pioneering studies, we demonstrated use of DBS for DNA barcoding (Borgström et al. 2015 and Redin et al., 2017). We then further developed DBS allowing for haplotyping of the entire human genome (Redin et al., 2019). The DBS technology is now being applied to haplotype-resolve cancer genomes to link somatic mutations to each other and also to structural variants in a haplotype context. This will ultimately result in better understanding of the cumulative effects of interactions between genetic variations across long distances that may lead to carcinogenesis. In addition to the molecular method, we are developing bioinformatics pipelines capable to handle DBS linked-read data.

The DBS technology is also applied for analysis of proteins (Stiller et al., 2019). This method, denoted DBS for protein analysis (DBS-Pro) was recently further developed for characterizing surface proteins on individual exosomes (Banijamali et al. 2022). In this proof-of-concept study we demonstrated that DBS-Pro allows for analysis of single exosomes. A total of over 120,000 individual exosomes obtained from a NSCLC cell line and from three malignant pleural effusion fluid of NSCLC patients were analyzed based on their surface proteins. We also showed that the method enables single vesicle surface protein profiling and by extension characterization of exosome-subtypes, which is essential to identify the cellular origin of vesicles in cancer samples. In addition, for high resolution exosome characterization, we are today trying to utilize DBS for simultaneous analysis of transcripts and proteins of single vesicles.


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Last updated: 2023-03-23

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