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Borgström, Erik
Alternative names
Publications (4 of 4) Show all publications
Hard, J., Al Hakim, E., Kindblom, M., Bjorklund, A. K., Sennblad, B., Demirci, I., . . . Frisen, J. (2019). Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing. Genome Biology, 20, Article ID 68.
Open this publication in new window or tab >>Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing
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2019 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 20, article id 68Article in journal (Refereed) Published
Abstract [en]

Accurate variant calling and genotyping represent major limiting factors for downstream applications of single-cell genomics. Here, we report Conbase for the identification of somatic mutations in single-cell DNA sequencing data. Conbase leverages phased read data from multiple samples in a dataset to achieve increased confidence in somatic variant calls and genotype predictions. Comparing the performance of Conbase to three other methods, we find that Conbase performs best in terms of false discovery rate and specificity and provides superior robustness on simulated data, in vitro expanded fibroblasts and clonal lymphocyte populations isolated directly from a healthy human donor.

Place, publisher, year, edition, pages
BMC, 2019
Keywords
Single-cell DNA sequencing, Single-cell variant calling, Somatic variation
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-249805 (URN)10.1186/s13059-019-1673-8 (DOI)000463101600001 ()30935387 (PubMedID)2-s2.0-85063796386 (Scopus ID)
Note

QC 20190424

Available from: 2019-04-24 Created: 2019-04-24 Last updated: 2019-04-24Bibliographically approved
Redin, D., Frick, T., Aghelpasand, H., Käller, M., Borgström, E., Olsen, R.-A. & Ahmadian, A. (2019). High throughput barcoding method for genome-scale phasing. Scientific Reports, 9, Article ID 18116.
Open this publication in new window or tab >>High throughput barcoding method for genome-scale phasing
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2019 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 18116Article in journal (Refereed) Published
Abstract [en]

The future of human genomics is one that seeks to resolve the entirety of genetic variation through sequencing. The prospect of utilizing genomics for medical purposes require cost-efficient and accurate base calling, long-range haplotyping capability, and reliable calling of structural variants. Short-read sequencing has lead the development towards such a future but has struggled to meet the latter two of these needs. To address this limitation, we developed a technology that preserves the molecular origin of short sequencing reads, with an insignificant increase to sequencing costs. We demonstrate a novel library preparation method for high throughput barcoding of short reads where millions of random barcodes can be used to reconstruct megabase-scale phase blocks.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2019
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-265973 (URN)10.1038/s41598-019-54446-x (DOI)000500558400001 ()31792271 (PubMedID)2-s2.0-85075912541 (Scopus ID)
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20191220

Available from: 2019-12-20 Created: 2019-12-20 Last updated: 2020-01-13Bibliographically approved
Borgström, E., Redin, D., Lundin, S., Berglund, E., Andersson, A. F. & Ahmadian, A. (2015). Phasing of single DNA molecules by massively parallel barcoding. Nature Communications, 6, Article ID 7173.
Open this publication in new window or tab >>Phasing of single DNA molecules by massively parallel barcoding
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2015 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 7173Article in journal (Refereed) Published
Abstract [en]

High-throughput sequencing platforms mainly produce short-read data, resulting in a loss of phasing information for many of the genetic variants analysed. For certain applications, it is vital to know which variant alleles are connected to each individual DNA molecule. Here we demonstrate a method for massively parallel barcoding and phasing of single DNA molecules. First, a primer library with millions of uniquely barcoded beads is generated. When compartmentalized with single DNA molecules, the beads can be used to amplify and tag any target sequences of interest, enabling coupling of the biological information from multiple loci. We apply the assay to bacterial 16S sequencing and up to 94% of the hypothesized phasing events are shown to originate from single molecules. The method enables use of widely available short-read-sequencing platforms to study long single molecules within a complex sample, without losing phase information.

National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-171312 (URN)10.1038/ncomms8173 (DOI)000357166400001 ()26055759 (PubMedID)2-s2.0-84931275307 (Scopus ID)
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20150727

Available from: 2015-07-27 Created: 2015-07-27 Last updated: 2018-10-02Bibliographically approved
Asp, M., Borgström, E., Stuckey, A., Gruselius, J., Carlberg, K., Andrusivova, Z., . . . Lundeberg, J.Spatial Isoform Profiling within Individual Tissue Sections.
Open this publication in new window or tab >>Spatial Isoform Profiling within Individual Tissue Sections
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Spatial Transcriptomics has been shown to be a persuasive RNA sequencing

technology for analyzing cellular heterogeneity within tissue sections. The

technology efficiently captures and barcodes 3’ tags of all polyadenylated

transcripts from a tissue section, and thus provides a powerful platform when

performing quantitative spatial gene expression studies. However, the current

protocol does not recover the full-length information of transcripts, and

consequently lack information regarding alternative splice variants. Here, we

introduce a novel protocol for spatial isoform profiling, using Spatial

Transcriptomics barcoded arrays.

National Category
Biological Sciences
Research subject
Biotechnology
Identifiers
urn:nbn:se:kth:diva-235650 (URN)
Note

QC 20181002

Available from: 2018-10-01 Created: 2018-10-01 Last updated: 2019-12-20Bibliographically approved
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