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  • 1.
    Asp, Michaela
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Borgström, Erik
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Stuckey, Alexander
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Gruselius, Joel
    Carlberg, Konstantin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Andrusivova, Zaneta
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Salmén, Fredrik
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Käller, Max
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ståhl, Patrik
    Lundeberg, Joakim
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Spatial Isoform Profiling within Individual Tissue SectionsManuscript (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.

  • 2. Eisfeldt, J.
    et al.
    Pettersson, M.
    Vezzi, F.
    Wincent, J.
    Käller, Max
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gruselius, J.
    Nilsson, D.
    Syk Lundberg, E.
    Carvalho, C. M. B.
    Lindstrand, A.
    Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements2019In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 15, no 2Article in journal (Refereed)
    Abstract [en]

    Complex chromosomal rearrangements (CCRs) are rearrangements involving more than two chromosomes or more than two breakpoints. Whole genome sequencing (WGS) allows for outstanding high resolution characterization on the nucleotide level in unique sequences of such rearrangements, but problems remain for mapping breakpoints in repetitive regions of the genome, which are known to be prone to rearrangements. Hence, multiple complementary WGS experiments are sometimes needed to solve the structures of CCRs. We have studied three individuals with CCRs: Case 1 and Case 2 presented with de novo karyotypically balanced, complex interchromosomal rearrangements (46,XX,t(2;8;15)(q35;q24.1;q22) and 46,XY,t(1;10;5)(q32;p12;q31)), and Case 3 presented with a de novo, extremely complex intrachromosomal rearrangement on chromosome 1. Molecular cytogenetic investigation revealed cryptic deletions in the breakpoints of chromosome 2 and 8 in Case 1, and on chromosome 10 in Case 2, explaining their clinical symptoms. In Case 3, 26 breakpoints were identified using WGS, disrupting five known disease genes. All rearrangements were subsequently analyzed using optical maps, linked-read WGS, and short-read WGS. In conclusion, we present a case series of three unique de novo CCRs where we by combining the results from the different technologies fully solved the structure of each rearrangement. The power in combining short-read WGS with long-molecule sequencing or optical mapping in these unique de novo CCRs in a clinical setting is demonstrated.

  • 3. Eisfeldt, Jesper
    et al.
    Nazaryan-Petersen, Lusine
    Lundin, Johanna Lundin
    Pettersson, Maria
    Nilsson, Daniel
    Wincent, Josephine
    Lieden, Agne
    Vezzi, Francesco
    Wirta, Valteri
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Käller, Max
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Duelund, Tina
    Houssari, Rayan
    Pignata, Laura
    Bak, Mads
    Tommerup, Niels
    Lundberg, Elisabeth Syk
    Tumer, Zeynep
    Lindstrand, Anna
    Whole genome characterization of array defined clustered CNVs reveals two distinct complex rearrangement subclasses generated through either non homologous repair or template switching2017In: Molecular Cytogenetics, ISSN 1755-8166, E-ISSN 1755-8166, Vol. 10Article in journal (Other academic)
  • 4. Engstrom, Karin
    et al.
    Wojdacz, Tomasz K.
    Marabita, Francesco
    Ewels, Philip
    Käller, Max
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Vezzi, Francesco
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Prezza, Nicola
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gruselius, Joel
    Vahter, Marie
    Broberg, Karin
    Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women2017In: Archives of Toxicology, ISSN 0340-5761, E-ISSN 1432-0738, Vol. 91, no 5, p. 2067-2078Article in journal (Refereed)
    Abstract [en]

    Arsenic, a carcinogen with immunotoxic effects, is a common contaminant of drinking water and certain food worldwide. We hypothesized that chronic arsenic exposure alters gene expression, potentially by altering DNA methylation of genes encoding central components of the immune system. We therefore analyzed the transcriptomes (by RNA sequencing) and methylomes (by target-enrichment next-generation sequencing) of primary CD4-positive T cells from matched groups of four women each in the Argentinean Andes, with fivefold differences in urinary arsenic concentrations (median concentrations of urinary arsenic in the lower- and high-arsenic groups: 65 and 276 mu g/l, respectively). Arsenic exposure was associated with genome-wide alterations of gene expression; principal component analysis indicated that the exposure explained 53% of the variance in gene expression among the top variable genes and 19% of 28,351 genes were differentially expressed (false discovery rate < 0.05) between the exposure groups. Key genes regulating the immune system, such as tumor necrosis factor alpha and interferon gamma, as well as genes related to the NF-kappa-beta complex, were significantly downregulated in the high-arsenic group. Arsenic exposure was associated with genome-wide DNA methylation; the high-arsenic group had 3% points higher genome-wide full methylation (> 80% methylation) than the lower-arsenic group. Differentially methylated regions that were hyper-methylated in the high-arsenic group showed enrichment for immune-related gene ontologies that constitute the basic functions of CD4-positive T cells, such as isotype switching and lymphocyte activation and differentiation. In conclusion, chronic arsenic exposure from drinking water was related to changes in the transcriptome and methylome of CD4-positive T cells, both genome wide and in specific genes, supporting the hypothesis that arsenic causes immunotoxicity by interfering with gene expression and regulation.

  • 5.
    Garcia, M.
    et al.
    Karolinska Inst, BarnTumorBanken, Dept Oncol Pathol, Sci Life Lab, Solna, Sweden..
    Juhos, S.
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Solna, Sweden..
    Larsson, M.
    Linkoping Univ, Dept Phys Chem & Biol, Sci Life Lab, Linkoping, Sweden..
    de Stahl, T. Diaz
    Karolinska Inst, Dept Oncol Pathol, BarnTumorBanken, Solna, Sweden..
    Eisfeldt, J.
    Karolinska Inst, Dept Mol Med & Surg, Clin Genet, Solna, Sweden..
    DiLorenzo, S.
    Uppsala Univ, Dept Med Sci, Sci Life Lab, Natl Bioinformat Infrastruct Sweden, Uppsala, Sweden..
    Olason, P.
    Uppsala Univ, Dept Cell & Mol Biol, Sci Life Lab, Uppsala, Sweden..
    Nystedt, B.
    Uppsala Univ, Dept Cell & Mol Biol, Sci Life Lab, Uppsala, Sweden..
    Nister, M.
    Karolinska Inst, Dept Oncol Pathol, BarnTumorBanken, Solna, Sweden..
    Käller, Max
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    CAW - Cancer Analysis Workflow to process normal/tumor WGS data2018In: European Journal of Human Genetics, ISSN 1018-4813, E-ISSN 1476-5438, Vol. 26, p. 702-702Article in journal (Other academic)
  • 6.
    Hu, Yue O. O.
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ndegwa, Nelson
    Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden..
    Alneberg, Johannes
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Johansson, Sebastian
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden..
    Logue, Jurg Brendan
    Huss, Mikael
    Käller, Max
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lundeberg, Joakim
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Fagerberg, Jens
    Stockholm Vatten Och Avfall AB, Stockholm, Sweden..
    Andersson, Anders F.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 11907Article in journal (Refereed)
    Abstract [en]

    Urban sewer systems consist of wastewater and stormwater sewers, of which only wastewater is processed before being discharged. Occasionally, misconnections or damages in the network occur, resulting in untreated wastewater entering natural water bodies via the stormwater system. Cultivation of faecal indicator bacteria (e.g. Escherichia coli; E. coli) is the current standard for tracing wastewater contamination. This method is cheap but has limited specificity and mobility. Here, we compared the E. coli culturing approach with two sequencing-based methodologies (Illumina MiSeq 16S rRNA gene amplicon sequencing and Oxford Nanopore MinION shotgun metagenomic sequencing), analysing 73 stormwater samples collected in Stockholm. High correlations were obtained between E. coli culturing counts and frequencies of human gut microbiome amplicon sequences, indicating E. coli is indeed a good indicator of faecal contamination. However, the amplicon data further holds information on contamination source or alternatively how much time has elapsed since the faecal matter has entered the system. Shotgun metagenomic sequencing on a subset of the samples using a portable real-time sequencer, MinION, correlated well with the amplicon sequencing data. This study demonstrates the use of DNA sequencing to detect human faecal contamination in stormwater systems and the potential of tracing faecal contamination directly in the field.

  • 7.
    Käller, Max
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ewels, P.
    Krueger, F.
    Andrews, S.
    Cluster Flow: A user-friendly bioinformatics workflow tool2016In: F1000 Research, E-ISSN 2046-1402, Vol. 5, article id 2824Article in journal (Refereed)
    Abstract [en]

    Pipeline tools are becoming increasingly important within the field of bioinformatics. Using a pipeline manager to manage and run workflows comprised of multiple tools reduces workload and makes analysis results more reproducible. Existing tools require significant work to install and get running, typically needing pipeline scripts to be written from scratch before running any analysis. We present Cluster Flow, a simple and flexible bioinformatics pipeline tool designed to be quick and easy to install. Cluster Flow comes with 40 modules for common NGS processing steps, ready to work out of the box. Pipelines are assembled using these modules with a simple syntax that can be easily modified as required. Core helper functions automate many common NGS procedures, making running pipelines simple. Cluster Flow is available with an GNU GPLv3 license on GitHub. Documentation, examples and an online demo are available at http://clusterflow.io.

  • 8.
    Nazaryan-Petersen, L.
    et al.
    Univ Copenhagen, Inst Cellular & Mol Med, Wilhelm Johannsen Ctr Funct Genome Res, Copenhagen, Denmark..
    Eisfeldt, J.
    Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden.;Karolinska Inst Sci Pk, Sci Life Lab, Solna, Sweden..
    Lundin, J.
    Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden.;Karolinska Univ Hosp, Dept Clin Genet, Stockholm, Sweden..
    Pettersson, M.
    Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden..
    Nilsson, D.
    Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden.;Karolinska Inst Sci Pk, Sci Life Lab, Solna, Sweden.;Karolinska Univ Hosp, Dept Clin Genet, Stockholm, Sweden..
    Wincent, J.
    Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden..
    Lieden, A.
    Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden.;Karolinska Univ Hosp, Dept Clin Genet, Stockholm, Sweden..
    Vezzi, F.
    Stockholm Univ, Dept Biochem & Biophys, SciLifeLab, Stockholm, Sweden..
    Wirta, Valtteri
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Käller, Max
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Duelund, T.
    Rigshosp, Copenhagen Univ Hosp, Dept Clin Genet, Kennedy Ctr, Copenhagen, Denmark..
    Houssari, R.
    Rigshosp, Copenhagen Univ Hosp, Dept Clin Genet, Kennedy Ctr, Copenhagen, Denmark..
    Pignata, L.
    Rigshosp, Copenhagen Univ Hosp, Dept Clin Genet, Kennedy Ctr, Copenhagen, Denmark..
    Bak, M.
    Univ Copenhagen, Inst Cellular & Mol Med, Wilhelm Johannsen Ctr Funct Genome Res, Copenhagen, Denmark..
    Tommerup, N.
    Univ Copenhagen, Inst Cellular & Mol Med, Wilhelm Johannsen Ctr Funct Genome Res, Copenhagen, Denmark..
    Lundberg, E. S.
    Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden.;Karolinska Univ Hosp, Dept Clin Genet, Stockholm, Sweden..
    Tumer, Z.
    Rigshosp, Copenhagen Univ Hosp, Dept Clin Genet, Kennedy Ctr, Copenhagen, Denmark..
    Lindstrand, A.
    Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden.;Karolinska Univ Hosp, Dept Clin Genet, Stockholm, Sweden..
    Whole genome characterization of array defined clustered CNVs reveals two distinct complex rearrangement subclasses generated through either non-homologous repair or template switching2018In: European Journal of Human Genetics, ISSN 1018-4813, E-ISSN 1476-5438, Vol. 26, p. 60-60Article in journal (Other academic)
  • 9.
    Nazaryan-Petersen, Lusine
    et al.
    Univ Copenhagen, Wilhelm Johannsen Ctr Funct Genome Res, Inst Cellular & Mol Med, Copenhagen, Denmark..
    Eisfeldt, Jesper
    Karolinska Inst, Dept Mol Med & Surg, Ctr Mol Med, Stockholm, Sweden.;Karolinska Inst Sci Pk, Sci Life Lab, Solna, Sweden..
    Pettersson, Maria
    Karolinska Inst, Dept Mol Med & Surg, Ctr Mol Med, Stockholm, Sweden..
    Lundin, Johanna
    Karolinska Inst, Dept Mol Med & Surg, Ctr Mol Med, Stockholm, Sweden.;Karolinska Univ Hosp, Dept Clin Genet, Stockholm, Sweden..
    Nilsson, Daniel
    Karolinska Inst, Dept Mol Med & Surg, Ctr Mol Med, Stockholm, Sweden.;Karolinska Inst Sci Pk, Sci Life Lab, Solna, Sweden.;Karolinska Univ Hosp, Dept Clin Genet, Stockholm, Sweden..
    Wincent, Josephine
    Karolinska Inst, Dept Mol Med & Surg, Ctr Mol Med, Stockholm, Sweden.;Karolinska Univ Hosp, Dept Clin Genet, Stockholm, Sweden..
    Lieden, Agne
    Karolinska Inst, Dept Mol Med & Surg, Ctr Mol Med, Stockholm, Sweden.;Karolinska Univ Hosp, Dept Clin Genet, Stockholm, Sweden..
    Lovmar, Lovisa
    Sahlgrens Univ Hosp, Dept Clin Genet, Gothenburg, Sweden..
    Ottosson, Jesper
    Sahlgrens Univ Hosp, Dept Clin Genet, Gothenburg, Sweden..
    Gacic, Jelena
    Linkoping Univ Hosp, Dept Clin Genet, Linkoping, Sweden..
    Makitie, Outi
    Karolinska Inst, Dept Mol Med & Surg, Ctr Mol Med, Stockholm, Sweden.;Karolinska Univ Hosp, Dept Clin Genet, Stockholm, Sweden.;Univ Helsinki, Childrens Hosp, Helsinki, Finland.;Helsinki Univ Hosp, Helsinki, Finland.;Folkhalsan Inst Genet, Helsinki, Finland..
    Nordgren, Ann
    Karolinska Inst, Dept Mol Med & Surg, Ctr Mol Med, Stockholm, Sweden.;Karolinska Univ Hosp, Dept Clin Genet, Stockholm, Sweden..
    Vezzi, Francesco
    Stockholm Univ, SciLifeLab, Dept Biochem & Biophys, Stockholm, Sweden.;Devyser AB, Instrumentvagen 19, Hagersten, Sweden..
    Wirta, Valtteri
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Käller, Max
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hjortshoj, Tina Duelund
    Rigshosp, Kennedy Ctr, Dept Clin Genet, Copenhagen Univ Hosp, Glostrup, Denmark..
    Jespersgaard, Cathrine
    Rigshosp, Kennedy Ctr, Dept Clin Genet, Copenhagen Univ Hosp, Glostrup, Denmark..
    Houssari, Rayan
    Rigshosp, Kennedy Ctr, Dept Clin Genet, Copenhagen Univ Hosp, Glostrup, Denmark..
    Pignata, Laura
    Rigshosp, Kennedy Ctr, Dept Clin Genet, Copenhagen Univ Hosp, Glostrup, Denmark..
    Bak, Mads
    Univ Copenhagen, Wilhelm Johannsen Ctr Funct Genome Res, Inst Cellular & Mol Med, Copenhagen, Denmark..
    Tommerup, Niels
    Univ Copenhagen, Wilhelm Johannsen Ctr Funct Genome Res, Inst Cellular & Mol Med, Copenhagen, Denmark..
    Lundberg, Elisabeth Syk
    Karolinska Inst, Dept Mol Med & Surg, Ctr Mol Med, Stockholm, Sweden.;Karolinska Univ Hosp, Dept Clin Genet, Stockholm, Sweden..
    Tumer, Zeynep
    Rigshosp, Kennedy Ctr, Dept Clin Genet, Copenhagen Univ Hosp, Glostrup, Denmark.;Univ Copenhagen, Fac Hlth & Med Sci, Dept Clin Med, Copenhagen, Denmark..
    Lindstrand, Anna
    Karolinska Inst, Dept Mol Med & Surg, Ctr Mol Med, Stockholm, Sweden.;Karolinska Univ Hosp, Dept Clin Genet, Stockholm, Sweden..
    Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization2018In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 14, no 11, article id e1007780Article in journal (Refereed)
    Abstract [en]

    Clustered copy number variants (CNVs) as detected by chromosomal microarray analysis (CMA) are often reported as germline chromothripsis. However, such cases might need further investigations by massive parallel whole genome sequencing (WGS) in order to accurately define the underlying complex rearrangement, predict the occurrence mechanisms and identify additional complexities. Here, we utilized WGS to delineate the rearrangement structure of 21 clustered CNV carriers first investigated by CMA and identified a total of 83 breakpoint junctions (BPJs). The rearrangements were further sub-classified depending on the patterns observed: I) Cases with only deletions (n = 8) often had additional structural rearrangements, such as insertions and inversions typical to chromothripsis; II) cases with only duplications (n = 7) or III) combinations of deletions and duplications (n = 6) demonstrated mostly interspersed duplications and BPJs enriched with microhomology. In two cases the rearrangement mutational signatures indicated both a breakage-fusion-bridge cycle process and haltered formation of a ring chromosome. Finally, we observed two cases with Alu- and LINE-mediated rearrangements as well as two unrelated individuals with seemingly identical clustered CNVs on 2p25.3, possibly a rare European founder rearrangement. In conclusion, through detailed characterization of the derivative chromosomes we show that multiple mechanisms are likely involved in the formation of clustered CNVs and add further evidence for chromoanagenesis mechanisms in both "simple" and highly complex chromosomal rearrangements. Finally, WGS characterization adds positional information, important for a correct clinical interpretation and deciphering mechanisms involved in the formation of these rearrangements.

  • 10. Nilsson, D.
    et al.
    Pettersson, M.
    Gustavsson, P.
    Förster, A.
    Hofmeister, W.
    Wincent, J.
    Zachariadis, V.
    Anderlid, B. -M
    Nordgren, A.
    Mäkitie, O.
    Wirta, Valtteri
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Käller, Max
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Vezzi, F.
    Lupski, J. R.
    Nordenskjöld, M.
    Syk Lundberg, E.
    Carvalho, C. M. B.
    Lindstrand, A.
    Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation2017In: Human Mutation, ISSN 1059-7794, E-ISSN 1098-1004, Vol. 38, no 2, p. 180-192Article in journal (Refereed)
    Abstract [en]

    Most balanced translocations are thought to result mechanistically from nonhomologous end joining or, in rare cases of recurrent events, by nonallelic homologous recombination. Here, we use low-coverage mate pair whole-genome sequencing to fine map rearrangement breakpoint junctions in both phenotypically normal and affected translocation carriers. In total, 46 junctions from 22 carriers of balanced translocations were characterized. Genes were disrupted in 48% of the breakpoints; recessive genes in four normal carriers and known dominant intellectual disability genes in three affected carriers. Finally, seven candidate disease genes were disrupted in five carriers with neurocognitive disabilities (SVOPL, SUSD1, TOX, NCALD, SLC4A10) and one XX-male carrier with Tourette syndrome (LYPD6, GPC5). Breakpoint junction analyses revealed microhomology and small templated insertions in a substantive fraction of the analyzed translocations (17.4%; n = 4); an observation that was substantiated by reanalysis of 37 previously published translocation junctions. Microhomology associated with templated insertions is a characteristic seen in the breakpoint junctions of rearrangements mediated by error-prone replication-based repair mechanisms. Our data implicate that a mechanism involving template switching might contribute to the formation of at least 15% of the interchromosomal translocation events.

  • 11.
    Redin, David
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Frick, Tobias
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Aghelpasand, Hooman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Käller, Max
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Borgström, Erik
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Olsen, Remi-Andre
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Box 1031, S-17121 Solna, Sweden..
    Ahmadian, Afshin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    High throughput barcoding method for genome-scale phasing2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 18116Article in journal (Refereed)
    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.

  • 12.
    Tiukova, Ievgeniia A.
    et al.
    Chalmers Univ Technol, Dept Biol & Biol Engn, Syst & Synthet Biol, Gothenburg, Sweden.;Swedish Univ Agr Sci, Dept Mol Sci, Uppsala, Sweden..
    Pettersson, Mats E.
    Uppsala Univ, Dept Med Biochem & Microbiol, Uppsala, Sweden..
    Hoeppner, Marc P.
    Uppsala Univ, Dept Med Biochem & Microbiol, Uppsala, Sweden.;NBIS, Uppsala, Sweden.;Christian Albrechts Univ Kiel, Inst Clin Mol Biol, Kiel, Germany.;Royal Inst Technol KTH, Sci Life Lab, Div Gene Technol, Sch Biotechnol, Solna, Sweden..
    Olsen, Remi-Andre
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Käller, Max
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. Stockholm Univ, Dept Biochem & Biophys, SciLifeLab, Stockholm, Sweden..
    Nielsen, Jens
    Chalmers Univ Technol, Dept Biol & Biol Engn, Syst & Synthet Biol, Gothenburg, Sweden..
    Dainat, Jacques
    Uppsala Univ, Dept Med Biochem & Microbiol, Uppsala, Sweden.;NBIS, Uppsala, Sweden..
    Lantz, Henrik
    Uppsala Univ, Dept Med Biochem & Microbiol, Uppsala, Sweden.;NBIS, Uppsala, Sweden..
    Soderberg, Jonas
    Uppsala Univ, Dept Cell & Mol Biol, Mol Evolut, Uppsala, Sweden..
    Passoth, Volkmar
    Swedish Univ Agr Sci, Dept Mol Sci, Uppsala, Sweden..
    Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis2019In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 14, no 5, article id e0215077Article in journal (Refereed)
    Abstract [en]

    Here, we present the genome of the industrial ethanol production strain Brettanomyces bruxellensis CBS 11270. The nuclear genome was found to be diploid, containing four chromosomes with sizes of ranging from 2.2 to 4.0 Mbp. A 75 Kbp mitochondrial genome was also identified. Comparing the homologous chromosomes, we detected that 0.32% of nucleotides were polymorphic, i.e. formed single nucleotide polymorphisms (SNPs), 40.6% of them were found in coding regions (i.e. 0.13% of all nucleotides formed SNPs and were in coding regions). In addition, 8,538 indels were found. The total number of protein coding genes was 4897, of them, 4,284 were annotated on chromosomes; and the mitochondrial genome contained 18 protein coding genes. Additionally, 595 genes, which were annotated, were on contigs not associated with chromosomes. A number of genes was duplicated, most of them as tandem repeats, including a six-gene cluster located on chromosome 3. There were also examples of interchromosomal gene duplications, including a duplication of a six-gene cluster, which was found on both chromosomes 1 and 4. Gene copy number analysis suggested loss of heterozygosity for 372 genes. This may reflect adaptation to relatively harsh but constant conditions of continuous fermentation. Analysis of gene topology showed that most of these losses occurred in clusters of more than one gene, the largest cluster comprising 33 genes. Comparative analysis against the wine isolate CBS 2499 revealed 88,534 SNPs and 8,133 indels. Moreover, when the scaffolds of the CBS 2499 genome assembly were aligned against the chromosomes of CBS 11270, many of them aligned completely, some have chunks aligned to different chromosomes, and some were in fact rearranged. Our findings indicate a highly dynamic genome within the species B. bruxellensis and a tendency towards reduction of gene number in long-term continuous cultivation.

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