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  • 1.
    Ahmadian, Afshin
    et al.
    KTH, Superseded Departments, Biotechnology.
    Russom, Aman
    KTH, Superseded Departments, Biotechnology.
    Andersson, Helene
    KTH, Superseded Departments, Biotechnology.
    Uhlén, Mathias
    KTH, Superseded Departments, Biotechnology.
    Stemme, Göran
    KTH, Superseded Departments, Biotechnology.
    Nilsson, Peter
    KTH, Superseded Departments, Biotechnology.
    SNP analysis by allele-specific extension in a micromachined filter chamber2002In: BioTechniques, ISSN 0736-6205, E-ISSN 1940-9818, Vol. 32, no 4, p. 748-754Article in journal (Refereed)
  • 2. Ameur, Adam
    et al.
    Dahlberg, Johan
    Olason, Pall
    Vezzi, Francesco
    Karlsson, Robert
    Martin, Marcel
    Viklund, Johan
    Kahari, Andreas Kusalananda
    Lundin, Par
    Che, Huiwen
    Thutkawkorapin, Jessada
    Eisfeldt, Jesper
    Lampa, Samuel
    Dahlberg, Mats
    Hagberg, Jonas
    Jareborg, Niclas
    Liljedahl, Ulrika
    Jonasson, Inger
    Johansson, Asa
    Feuk, Lars
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Syvanen, Ann-Christine
    Lundin, Sverker
    Nilsson, Daniel
    Nystedt, Bjorn
    Magnusson, Patrik K. E.
    Gyllensten, Ulf
    SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population2017In: European Journal of Human Genetics, ISSN 1018-4813, E-ISSN 1476-5438, Vol. 25, no 11, p. 1253-1260Article in journal (Refereed)
    Abstract [en]

    Here we describe the SweGen data set, a comprehensive map of genetic variation in the Swedish population. These data represent a basic resource for clinical genetics laboratories as well as for sequencing-based association studies by providing information on genetic variant frequencies in a cohort that is well matched to national patient cohorts. To select samples for this study, we first examined the genetic structure of the Swedish population using high-density SNP-array data from a nation-wide cohort of over 10 000 Swedish-born individuals included in the Swedish Twin Registry. A total of 1000 individuals, reflecting a cross-section of the population and capturing the main genetic structure, were selected for whole-genome sequencing. Analysis pipelines were developed for automated alignment, variant calling and quality control of the sequencing data. This resulted in a genome-wide collection of aggregated variant frequencies in the Swedish population that we have made available to the scientific community through the website https://swefreq.nbis.se. A total of 29.2 million single-nucleotide variants and 3.8 million indels were detected in the 1000 samples, with 9.9 million of these variants not present in current databases. Each sample contributed with an average of 7199 individual-specific variants. In addition, an average of 8645 larger structural variants (SVs) were detected per individual, and we demonstrate that the population frequencies of these SVs can be used for efficient filtering analyses. Finally, our results show that the genetic diversity within Sweden is substantial compared with the diversity among continental European populations, underscoring the relevance of establishing a local reference data set.

  • 3.
    Dawed, A. Y.
    et al.
    Univ Dundee, Mol & Clin Med, Dundee, Scotland..
    Mari, A.
    CNR, Inst Neurosci, Padua, Italy..
    McDonald, T. J.
    Royal Devon & Exeter Hosp, NIHR Exeter Clin Res Facil, Exeter, Devon, England..
    Hong, Mun-Gwan
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO).
    Sharma, S.
    Helmholtz Zentrum Muenchen, Inst Epidemiol 2, Res Unit Mol Epidemiol, Munich, Germany..
    Robertson, N. R.
    Univ Oxford, Wellcome Trust Ctr Human Genet, Oxford, England..
    Mahajan, A.
    Univ Oxford, Wellcome Trust Ctr Human Genet, Oxford, England..
    Walker, M.
    Newcastle Univ, Inst Cellular Med, Newcastle Upon Tyne, Tyne & Wear, England..
    Gough, S.
    NIHR Oxford Biomed Res Ctr, Oxford Ctr Diabet Endocrinol & Metab, Oxford, England..
    Zhou, K.
    Univ Dundee, Mol & Clin Med, Dundee, Scotland..
    Forgie, I
    Univ Dundee, Mol & Clin Med, Dundee, Scotland..
    Ruetten, H.
    Sanofi Aventis Deutschland GmbH, TMED, Frankfurt, Germany..
    Jones, A. G.
    Royal Devon & Exeter Hosp, NIHR Exeter Clin Res Facil, Exeter, Devon, England..
    Pearson, E. R.
    Univ Dundee, Mol & Clin Med, Dundee, Scotland..
    GLP-1 RECEPTOR VARIANTS MARKEDLY DIFFERENTIATE GLYCAEMIC RESPONSE TO GLP-1 RECEPTOR AGONISTS: A DIRECT STUDY2018In: Basic & Clinical Pharmacology & Toxicology, ISSN 1742-7835, E-ISSN 1742-7843, Vol. 123, p. 13-14Article in journal (Other academic)
  • 4. 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.

  • 5.
    Fasterius, Erik
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Al-Khalili Szigyarto, Cristina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Analysis of public RNA-sequencing data reveals biological consequences of genetic heterogeneity in cell line populations2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 11226Article in journal (Refereed)
    Abstract [en]

    Meta-analysis of datasets available in public repositories are used to gather and summarise experiments performed across laboratories, as well as to explore consistency of scientific findings. As data quality and biological equivalency across samples may obscure such analyses and consequently their conclusions, we investigated the comparability of 85 public RNA-seq cell line datasets. Thousands of pairwise comparisons of single nucleotide variants in 139 samples revealed variable genetic heterogeneity of the eight cell line populations analysed as well as variable data quality. The H9 and HCT116 cell lines were found to be remarkably stable across laboratories (with median concordances of 99.2% and 98.5%, respectively), in contrast to the highly variable HeLa cells (89.3%). We show that the genetic heterogeneity encountered greatly affects gene expression between same-cell comparisons, highlighting the importance of interrogating the biological equivalency of samples when comparing experimental datasets. Both the number of differentially expressed genes and the expression levels negatively correlate with the genetic heterogeneity. Finally, we demonstrate how comparing genetically heterogeneous datasets affect gene expression analyses and that high dissimilarity between same-cell datasets alters the expression of more than 300 cancer-related genes, which are often the focus of studies using cell lines.

  • 6.
    Fasterius, Erik
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Al-Khalili Szigyarto, Cristina
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Single-cell RNA-seq variant analysis for exploration of genetic heterogeneity in cancer2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 9524Article in journal (Refereed)
    Abstract [en]

    Inter-and intra-tumour heterogeneity is caused by genetic and non-genetic factors, leading to severe clinical implications. High-throughput sequencing technologies provide unprecedented tools to analyse DNA and RNA in single cells and explore both genetic heterogeneity and phenotypic variation between cells in tissues and tumours. Simultaneous analysis of both DNA and RNA in the same cell is, however, still in its infancy. We have thus developed a method to extract and analyse information regarding genetic heterogeneity that affects cellular biology from single-cell RNA-seq data. The method enables both comparisons and clustering of cells based on genetic variation in single nucleotide variants, revealing cellular subpopulations corroborated by gene expression-based methods. Furthermore, the results show that lymph node metastases have lower levels of genetic heterogeneity compared to their original tumours with respect to variants affecting protein function. The analysis also revealed three previously unknown variants common across cancer cells in glioblastoma patients. These results demonstrate the power and versatility of scRNA-seq variant analysis and highlight it as a useful complement to already existing methods, enabling simultaneous investigations of both gene expression and genetic variation.

  • 7. Huang, Cheng-cai
    et al.
    Yan, Shi-hai
    Chen, Dan
    Chen, Bi-cheng
    Zhao, Ning-wei
    KTH, School of Biotechnology (BIO).
    Application of On-Line nanoLC-IT-TOF in the Identification of Serum beta-Catenin Complex in Mice Scald Model2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 10, p. e46530-Article in journal (Refereed)
    Abstract [en]

    Severe burn shock remains an unresolved clinical problem with an urgent need to explore novel therapeutic treatments. Intracellular beta-catenin, through interaction with other proteins, has been reported to be able to regulate the size of cutaneous wounds. Higher expression of beta-catenin is associated with larger sized wounds. However, the identification of serum beta-catenin complex is difficult and has been rarely reported. The exploitation of more binding partners can contribute to uncovering the exact mechanisms behind serum beta-catenin mediated biological effects. Here, we describe a method that consists of immunoprecipitation, SDS-PAGE, in-gel digestion, and nanoLC coupled to LCMS-IT-TOF for the investigation of serum beta-catenin complex in mice scald model. Among selected gel bands obtained from the protein gels, a total of 31 peptides were identified and sequenced with high statistical significance (p<0.01). Three proteins (alpha-2-marcoglobulin, serine protease inhibitor A3K, and serine protease inhibitor A1A) were identified and validated with high reliability and high reproducibility. It was inferred that these proteins might interact with serum beta-catenin, which could affect the wound healing resulting from burn shock. Our study demonstrated that the on-line coupling of nano-LC with a LCMS-IT-TOF mass spectrometer was capable of sensitive and automated characterization of the serum beta-catenin complex in mice scald model.

  • 8. Hudson, Thomas J.
    et al.
    Anderson, Warwick
    Aretz, Axel
    Barker, Anna D.
    Bell, Cindy
    Bernabe, Rosa R.
    Bhan, M. K.
    Calvo, Fabien
    Eerola, Iiro
    Gerhard, Daniela S.
    Guttmacher, Alan
    Guyer, Mark
    Hemsley, Fiona M.
    Jennings, Jennifer L.
    Kerr, David
    Klatt, Peter
    Kolar, Patrik
    Kusuda, Jun
    Lane, David P.
    Laplace, Frank
    Lu, Youyong
    Nettekoven, Gerd
    Ozenberger, Brad
    Peterson, Jane
    Rao, T. S.
    Remacle, Jacques
    Schafer, Alan J.
    Shibata, Tatsuhiro
    Stratton, Michael R.
    Vockley, Joseph G.
    Watanabe, Koichi
    Yang, Huanming
    Yuen, Matthew M. F.
    Knoppers, M.
    Bobrow, Martin
    Cambon-Thomsen, Anne
    Dressler, Lynn G.
    Dyke, Stephanie O. M.
    Joly, Yann
    Kato, Kazuto
    Kennedy, Karen L.
    Nicolas, Pilar
    Parker, Michael J.
    Rial-Sebbag, Emmanuelle
    Romeo-Casabona, Carlos M.
    Shaw, Kenna M.
    Wallace, Susan
    Wiesner, Georgia L.
    Zeps, Nikolajs
    Lichter, Peter
    Biankin, Andrew V.
    Chabannon, Christian
    Chin, Lynda
    Clement, Bruno
    de Alava, Enrique
    Degos, Francoise
    Ferguson, Martin L.
    Geary, Peter
    Hayes, D. Neil
    Johns, Amber L.
    Nakagawa, Hidewaki
    Penny, Robert
    Piris, Miguel A.
    Sarin, Rajiv
    Scarpa, Aldo
    van de Vijver, Marc
    Futreal, P. Andrew
    Aburatani, Hiroyuki
    Bayes, Monica
    Bowtell, David D. L.
    Campbell, Peter J.
    Estivill, Xavier
    Grimmond, Sean M.
    Gut, Ivo
    Hirst, Martin
    Lopez-Otin, Carlos
    Majumder, Partha
    Marra, Marco
    Ning, Zemin
    Puente, Xose S.
    Ruan, Yijun
    Stunnenberg, Hendrik G.
    Swerdlow, Harold
    Velculescu, Victor E.
    Wilson, Richard K.
    Xue, Hong H.
    Yang, Liu
    Spellman, Paul T.
    Bader, Gary D.
    Boutros, Paul C.
    Flicek, Paul
    Getz, Gad
    Guigo, Roderic
    Guo, Guangwu
    Haussler, David
    Heath, Simon
    Hubbard, Tim J.
    Jiang, Tao
    Jones, Steven M.
    Li, Qibin
    Lopez-Bigas, Nuria
    Luo, Ruibang
    Pearson, John V.
    Quesada, Victor
    Raphael, Benjamin J.
    Sander, Chris
    Speed, Terence P.
    Stuart, Joshua M.
    Teague, Jon W.
    Totoki, Yasushi
    Tsunoda, Tatsuhiko
    Valencia, Alfonso
    Wheeler, David A.
    Wu, Honglong
    Zhao, Shancen
    Zhou, Guangyu
    Stein, Lincoln D.
    Lathrop, Mark
    Ouellette, B. F. Francis
    Thomas, Gilles
    Yoshida, Teruhiko
    Axton, Myles
    Gunter, Chris
    McPherson, John D.
    Miller, Linda J.
    Kasprzyk, Arek
    Zhang, Junjun
    Haider, Syed A.
    Wang, Jianxin
    Yung, Christina K.
    Cros, Anthony
    Liang, Yong
    Gnaneshan, Saravanamuttu
    Guberman, Jonathan
    Hsu, Jack
    Chalmers, Don R. C.
    Hasel, Karl W.
    Kaan, Terry S. H.
    Knoppers, Bartha M.
    Lowrance, William W.
    Masui, Tohru
    Rodriguez, Laura Lyman
    Vergely, Catherine
    Cloonan, Nicole
    Defazio, Anna
    Eshleman, James R.
    Etemadmoghadam, Dariush
    Gardiner, Brooke B.
    Kench, James G.
    Sutherland, Robert L.
    Tempero, Margaret A.
    Waddell, Nicola J.
    Wilson, Peter J.
    Gallinger, Steve
    Tsao, Ming-Sound
    Shaw, Patricia A.
    Petersen, Gloria M.
    Mukhopadhyay, Debabrata
    DePinho, Ronald A.
    Thayer, Sarah
    Muthuswamy, Lakshmi
    Shazand, Kamran
    Beck, Timothy
    Sam, Michelle
    Timms, Lee
    Ballin, Vanessa
    Ji, Jiafu
    Zhang, Xiuqing
    Chen, Feng
    Hu, Xueda
    Yang, Qi
    Tian, Geng
    Zhang, Lianhai
    Xing, Xiaofang
    Li, Xianghong
    Zhu, Zhenggang
    Yu, Yingyan
    Yu, Jun
    Tost, Joerg
    Brennan, Paul
    Holcatova, Ivana
    Zaridze, David
    Brazma, Alvis
    Egevad, Lars
    Prokhortchouk, Egor
    Banks, Rosamonde Elizabeth
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Viksna, Juris
    Pontén, Fredrik
    Skryabin, Konstantin
    Birney, Ewan
    Borg, Ake
    Borresen-Dale, Anne-Lise
    Caldas, Carlos
    Foekens, John A.
    Martin, Sancha
    Reis-Filho, Jorge S.
    Richardson, Andrea L.
    Sotiriou, Christos
    van't Veer, Laura
    Birnbaum, Daniel
    Blanche, Helene
    Boucher, Pascal
    Boyault, Sandrine
    Masson-Jacquemier, Jocelyne D.
    Pauporte, Iris
    Pivot, Xavier
    Vincent-Salomon, Anne
    Tabone, Eric
    Theillet, Charles
    Treilleux, Isabelle
    Bioulac-Sage, Paulette
    Decaens, Thomas
    Franco, Dominique
    Gut, Marta
    Samuel, Didier
    Zucman-Rossi, Jessica
    Eils, Roland
    Brors, Benedikt
    Korbel, Jan O.
    Korshunov, Andrey
    Landgraf, Pablo
    Lehrach, Hans
    Pfister, Stefan
    Radlwimmer, Bernhard
    Reifenberger, Guido
    Taylor, Michael D.
    von Kalle, Christof
    Majumder, Partha P.
    Pederzoli, Paolo
    Lawlor, Rita T.
    Delledonne, Massimo
    Bardelli, Alberto
    Gress, Thomas
    Klimstra, David
    Zamboni, Giuseppe
    Nakamura, Yusuke
    Miyano, Satoru
    Fujimoto, Akihiro
    Campo, Elias
    de Sanjose, Silvia
    Montserrat, Emili
    Gonzalez-Diaz, Marcos
    Jares, Pedro
    Himmelbauer, Heinz
    Bea, Silvia
    Aparicio, Samuel
    Easton, Douglas F.
    Collins, Francis S.
    Compton, Carolyn C.
    Lander, Eric S.
    Burke, Wylie
    Green, Anthony R.
    Hamilton, Stanley R.
    Kallioniemi, Olli P.
    Ley, Timothy J.
    Liu, Edison T.
    Wainwright, Brandon J.
    International network of cancer genome projects2010In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 464, no 7291, p. 993-998Article in journal (Refereed)
    Abstract [en]

    The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.

  • 9. Larsson, Anna H.
    et al.
    Lehn, Sophie
    Wangefjord, Sakarias
    Karnevi, Emelie
    Kuteeva, Eugenia
    Sundström, Magnus
    Nodin, Björn
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Eberhard, Jakob
    Birgisson, Helgi
    Jirström, Karin
    Significant association and synergistic adverse prognostic effect of podocalyxin-like protein and epidermal growth factor receptor expression in colorectal cancer2016In: Journal of Translational Medicine, ISSN 1479-5876, E-ISSN 1479-5876, Vol. 14, article id 128Article in journal (Refereed)
    Abstract [en]

    Background: Podocalyxin-like 1 (PODXL) is an anti-adhesive transmembrane protein that has been demonstrated to be an independent factor of poor prognosis in colorectal cancer (CRC). The gene encoding PODXL is located to chromosome 7, which also harbours the gene for the epidermal growth factor receptor (EGFR). The aim of this study was to examine the associations between PODXL and EGFR expression in CRC in vitro and in vivo. Methods: EGFR expression was analysed in tumours from three independent patient cohorts; cohort 1 (n = 533), cohort 2 (n = 259) and cohort 3 (n = 310), previously analysed for immunohistochemical PODXL expression and KRAS and BRAF mutations (cohort 1 and 3). Levels of EGFR and PODXL were determined by western blot in six different CRC cell lines. Results: High expression of PODXL was significantly associated with high EGFR expression (p < 0.001) in all three cohorts, and with BRAF mutation (p < 0.001) in cohort 1 and 3. High EGFR expression correlated with BRAF mutation (p < 0.001) in cohort 1. High EGFR expression was associated with adverse clinicopathological factors and independently predicted a reduced 5-year overall survival (OS) in cohort 1 (HR 1.77; 95 % CI 1.27-2.46), cohort 2 (HR 1.58; 95 % CI 1.05-2.38) and cohort 3 (HR 1.83; 95 % CI 1.19-2.81). The highest risk of death within 5 years was observed in patients with tumours displaying high expression of both EGFR and PODXL in cohort 1 and 3 (HR 1.97; 95 % CI 1.18-3.28 and HR 3.56; 95 % CI 1.75-7.22, respectively). Western blot analysis showed a uniform expression of PODXL and EGFR in all six examined CRC cell lines. Conclusions: The results from this study demonstrate that high expression of EGFR is an independent factor of poor prognosis in CRC. Moreover, strong links have been uncovered between expression of the recently proposed biomarker candidate PODXL with EGFR expression in CRC in vivo and in vitro, and with BRAF mutation in vivo. High expression of both PODXL and EGFR may also have a synergistic adverse effect on survival. These findings suggest a potential functional link in CRC between PODXL, EGFR and BRAF, all originating from chromosome 7, which may be highly relevant in the clinical setting and therefore merit future in-depth study.

  • 10. Leandro-Garcia, Luis J.
    et al.
    Inglada-Perez, Lucia
    Pita, Guillermo
    Hjerpe, Elisabet
    Leskelae, Susanna
    Jara, Carlos
    Mielgo, Xabier
    Gonzalez-Neira, Anna
    Robledo, Mercedes
    Avall-Lundqvist, Elisabeth
    Gréen, Henrik
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Rodriguez-Antona, Cristina
    Genome-wide association study identifies ephrin type A receptors implicated in paclitaxel induced peripheral sensory neuropathy2013In: Journal of Medical Genetics, ISSN 0022-2593, E-ISSN 1468-6244, Vol. 50, no 9, p. 599-605Article in journal (Refereed)
    Abstract [en]

    Background Peripheral neuropathy is the dose limiting toxicity of paclitaxel, a chemotherapeutic drug widely used to treat solid tumours. This toxicity exhibits great inter-individual variability of unknown origin. The present study aimed to identify genetic variants associated with paclitaxel induced neuropathy via a whole genome approach. Methods A genome-wide association study (GWAS) was performed in 144 white European patients uniformly treated with paclitaxel/carboplatin and for whom detailed data on neuropathy was available. Per allele single nucleotide polymorphism (SNP) associations were assessed by Cox regression, modelling the cumulative dose of paclitaxel up to the development of grade 2 sensory neuropathy. Results The strongest evidence of association was observed for the ephrin type A receptor 4 (EPHA4) locus (rs17348202, p=1.0x10(-6)), and EPHA6 and EPHA5 were among the top 25 and 50 hits (rs301927, p=3.4x10(-5) and rs1159057, p=6.8x10(-5)), respectively. A meta-analysis of EPHA5-rs7349683, the top marker for paclitaxel induced neuropathy in a previous GWAS (r(2)=0.79 with rs1159057), gave a hazard ratio (HR) estimate of 1.68 (p=1.4x10(-9)). Meta-analysis of the second hit of this GWAS, XKR4-rs4737264, gave a HR of 1.71 (p=3.1x10(-8)). Imputed SNPs at LIMK2 locus were also strongly associated with this toxicity (HR=2.78, p=2.0x10(-7)). Conclusions This study provides independent support of EPHA5-rs7349683 and XKR4-rs4737264 as the first markers of risk of paclitaxel induced neuropathy. In addition, it suggests that other EPHA genes also involved in axonal guidance and repair following neural injury, as well as LIMK2 locus, may play an important role in the development of this toxicity. The identified SNPs could form the basis for individualised paclitaxel chemotherapy.

  • 11.
    Orlova, A.
    et al.
    Uppsala Univ, Uppsala, Sweden..
    Rosestedt, M.
    Uppsala Univ, Uppsala, Sweden..
    Rinne, S. S.
    Uppsala Univ, Uppsala, Sweden..
    Mitran, B.
    Uppsala Univ, Uppsala, Sweden..
    Vorobyeva, A.
    Uppsala Univ, Uppsala, Sweden..
    Andersson, Ken G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Protein Engineering.
    Löfblom, John
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Protein Engineering.
    Tolmachev, V.
    Uppsala Univ, Uppsala, Sweden..
    Imaging contrast of HER3 expression using monomeric affibody-based imaging probe can be improved by co-injection of affibody trimer2018In: European Journal of Nuclear Medicine and Molecular Imaging, ISSN 1619-7070, E-ISSN 1619-7089, Vol. 45, p. S673-S673Article in journal (Other academic)
  • 12.
    Oroujeni, M.
    et al.
    Uppsala Univ, Uppsala, Sweden..
    Garousi, J.
    Uppsala Univ, Uppsala, Sweden..
    Andersson, Ken G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Protein Engineering.
    Löfblom, John
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Protein Engineering.
    Mitran, B.
    Uppsala Univ, Uppsala, Sweden..
    Orlova, A.
    Uppsala Univ, Uppsala, Sweden..
    Tolmachev, V.
    Uppsala Univ, Uppsala, Sweden..
    Comparative evaluation of anti-EFGR affibody molecules labelled with gallium-68 and zirconium-89 using desferrioxamine B as a chelator2018In: European Journal of Nuclear Medicine and Molecular Imaging, ISSN 1619-7070, E-ISSN 1619-7089, Vol. 45, p. S674-S675Article in journal (Other academic)
  • 13. Rubin, C.
    et al.
    Nathanaelsson, C.
    KTH.
    Lundeberg, Joakim
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Nilsson, O.
    Ljunggren, O.
    Kindmark, A.
    MicroRNA repertoire of primary human bone derived cells and MG63-cells - Polymorphic binding sites in putative target genes2007In: Calcified Tissue International, ISSN 0171-967X, E-ISSN 1432-0827, Vol. 80, p. S34-S35Article in journal (Other academic)
  • 14.
    Russom, Aman
    KTH, School of Electrical Engineering (EES).
    Microfluidic bead-based methods for DNA analysis2005Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    With the completion of the human genome sequencing project, attention is currently shifting toward understanding how genetic variation, such as single nucleotide polymorphism (SNP), leads to disease. To identify, understand, and control biological mechanisms of living organisms, the enormous amounts of accumulated sequence information must be coupled to faster, cheaper, and more powerful technologies for DNA, RNA, and protein analysis. One approach is the miniaturization of analytical methods through the application of microfluidics, which involves the manipulation of fluids in micrometer-sized channels. Advances in microfluidic chip technology are expected to play a major role in the development of cost-effective and rapid DNA analysis methods.

    This thesis presents microfluidic approaches for different DNA genotyping assays. The overall goal is to combine the potential of the microfluidic lab-on-a-chip concept with biochemistry to develop and improve current methods for SNP genotyping. Three genotyping assays using miniaturized microfluidic approaches are addressed.

    The first two assays are based on primer extension by DNA polymerase. A microfluidic device consisting of a flow-through filter chamber for handling beads with nanoliter liquid volumes was used in these studies. The first assay involved an allelespecific extension strategy. The microfluidic approach took advantage of the different reaction kinetics of matched and mismatched configurations at the 3’-ends of a primer/template complex. The second assay consisted of adapting pyrosequencing technology, a bioluminometric DNA sequencing assay based on sequencing-bysynthesis, to a microfluidic flow-through platform. Base-by-base sequencing was performed in a microfluidic device to obtain accurate SNP scoring data on nanoliter volumes. This thesis also presents the applications of monolayer of beads immobilized by microcontact printing for chip-based DNA analysis. Single-base incorporation could be detected with pyrosequencing chemistry on these monolayers.

    The third assay developed is based on a hybridization technology termed Dynamic Allele-Specific Hybridization (DASH). In this approach, monolayered beads containing DNA duplexes were randomly immobilized on the surface of a microheater chip. DNA melting-curve analysis was performed by dynamically heating the chip while

    simultaneously monitoring the DNA denaturation profile to determine the genotype. Multiplexing based on single-bead analysis was achieved at heating rates more than 20 times faster than conventional DASH provides.

  • 15.
    Russom, Aman
    et al.
    KTH, Superseded Departments, Signals, Sensors and Systems.
    Ahmadian, Afshin
    KTH, Superseded Departments, Biotechnology.
    Andersson, Helene
    KTH, Superseded Departments, Signals, Sensors and Systems.
    Nilsson, Peter
    KTH, Superseded Departments, Biotechnology.
    Stemme, Göran
    KTH, Superseded Departments, Signals, Sensors and Systems.
    Single-nucleotide polymorphism analysis by allele-specific extension of fluorescently labeled nucleotides in a microfluidic flow-through device2003In: Electrophoresis, ISSN 0173-0835, E-ISSN 1522-2683, Vol. 24, no 1-2, p. 158-161Article in journal (Refereed)
    Abstract [en]

    We describe a microfluidic approach for allele-specific extension of fluorescently labeled nucleotides for scoring of single-nucleotide polymorphism (SNP). The method takes advantage of the fact that the reaction kinetics differs between matched and mismatched configurations of allele-specific primers hybridized to DNA template. A microfluidic flow-through device for biochemical reactions on beads was used to take advantage of the reaction kinetics to increase the sequence specificity of the DNA polymerase, discriminating mismatched configurations from matched. The volume of the reaction chamber was 12.5 nL. All three possible variants of an SNP site at codon 72 of the p53 gene were scored using our approach. This work demonstrates the possibility of scoring SNP by allele-specific extension of fluorescently labeled nucleotides in a microfluidic flow-through device, The sensitive detection system and easy microfabrication of the microfluidic device enable further miniaturization and production of an array format of microfluidic devices for high-throughput SNP analysis.

  • 16.
    Russom, Aman
    et al.
    KTH, School of Electrical Engineering (EES), Microsystem Technology (Changed name 20121201).
    Haasl, Sjoerd
    KTH, School of Electrical Engineering (EES), Microsystem Technology (Changed name 20121201).
    Brookes, Anthony J.
    Andersson, Helene
    KTH, School of Electrical Engineering (EES), Microsystem Technology (Changed name 20121201).
    Stemme, Göran
    KTH, School of Electrical Engineering (EES), Microsystem Technology (Changed name 20121201).
    Rapid melting curve analysis on monolayered beads for high-throughput genotyping of single-nucleotide polymorphisms2006In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 78, no 7, p. 2220-2225Article in journal (Refereed)
    Abstract [en]

    This report describes a rapid solid-phase melting curve analysis method for single-nucleotide polymorphism (SNP) genotyping. The melting curve analysis is based on dynamic allele-specific hybridization (DASH). The DNA duplexes are conjugated on beads that are immobilized on the surface of a microheater chip with integrated heaters and temperature sensors. SNP on PCR products were scored, illustrating the sensitivity and robustness of the system. The method is based on random bead immobilization by microcontact printing. Single-bead detection and multiplexing were performed with a heating rate more than 20 times faster than conventional DASH. Analyses that took more than 15 min could be performed in less that 1 min, enabling ultrarapid SNP analysis. In addition, an array version of the chip was implemented enabling the preparation of an array of bead arrays for high-throughput and rapid SNP genotyping.

  • 17.
    Russom, Aman
    et al.
    KTH, Superseded Departments, Signals, Sensors and Systems.
    Haasl, Sjoerd
    KTH, Superseded Departments, Signals, Sensors and Systems.
    Ohlander, Anna
    KTH, Superseded Departments, Signals, Sensors and Systems.
    Andersson, Helene
    KTH, Superseded Departments, Signals, Sensors and Systems.
    Stemme, Göran
    KTH, Superseded Departments, Signals, Sensors and Systems.
    Genotyping by dynamic heating of monolayered beads on a microheated surface2004In: Electrophoresis, ISSN 0173-0835, E-ISSN 1522-2683, Vol. 25, no 21-22, p. 3712-3719Article in journal (Refereed)
    Abstract [en]

     A miniaturized bead-based dynamic allele-specific hybridization (DASH) approach for sing le-nucleotide polymorphism analysis is presented. Chips with integrated heater and temperature sensors for open-surface DNA analysis were microfabricated. Microcontact printing using a poly(dimethylsiloxane) (PDMS) stamp was employed to create monolayers of immobilized beads on the surface of the chip. This chip allows fast, well-controllable temperature ramping. The temperature distribution was homogeneous over the entire heater area. All three possible variants of an SNP site of a synthesized oligonucleotide were accurately scored using the bead-based DASH approach. Our assay has a nonoptimized temperature ramping rate of 4degreesC-6degreesC/min compared to earlier reported values of 2degreesC-3degreesC/min, thereby reducing the total analysis time by a factor of 2. Reliable DASH measurement data from areas as small as 12 x 13 mum was achieved. Our bead-based DASH approach has enabled a dramatic volume reduction and is a step towards developing a cost-effective high-throughput DASH method on arrays of single beads.

  • 18.
    Russom, Aman
    et al.
    KTH, School of Electrical Engineering (EES), Microsystem Technology (Changed name 20121201).
    Tooke, N.
    Andersson, Helene
    KTH, School of Electrical Engineering (EES), Microsystem Technology (Changed name 20121201).
    Stemme, Göran
    KTH, School of Electrical Engineering (EES), Microsystem Technology (Changed name 20121201).
    Pyrosequencing in a microfluidic flow-through device2005In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 77, no 23, p. 7505-7511Article in journal (Refereed)
    Abstract [en]

    To explore genome variation meaningfully, there is a critical need for a high-throughput and inexpensive platform for DNA analysis. Pyrosequencing is a nonelectrophoretic bioluminometric DNA sequencing method that uses a four-enzyme mixture reaction to monitor nucleotide incorporation in real time. Currently, the commercialized pyrosequencing technique is limited to a 96-microtiter plate format. However, high throughput and inexpensive pyrosequencing is required to meet the need of screening large numbers of samples. We present here DNA pyrosequencing on a nanoliter-volume microfluidic platform. The microfluidic approach involves the trapping of the DNA on microbeads in an on-chip filter chamber and flow-through of the pyrosequencing reagents to monitor the reaction in real time. Two single-nucleotide polymorphisms were successfully scored to evaluate the microfluidic platform. In addition to significantly reducing reagent costs, microfluidic systems promise to improve the read length by eliminating intermediate product accumulation by constant removal of unincorporated nucleotides and elimination of dilution effects at each reaction cycle in the current plate format. Although only one filter chamber was used in this study, the platform should be readily adaptable to parallel analyses of nanoliter samples using filter chamber arrays to obtain high-throughput DNA analysis.

  • 19.
    Russom, Aman
    et al.
    KTH, Superseded Departments, Signals, Sensors and Systems.
    Tooke, Nigel
    Andersson, Helene
    KTH, Superseded Departments, Signals, Sensors and Systems.
    Stemme, Göran
    KTH, Superseded Departments, Signals, Sensors and Systems.
    Single nucleotide polymorphism analysis by allele-specific primer extension with real-time bioluminescence detection in a microfluidic device2003In: Journal of Chromatography A, ISSN 0021-9673, E-ISSN 1873-3778, Vol. 1014, no 1-2, p. 37-45Article in journal (Refereed)
    Abstract [en]

    A microfluidic approach for rapid bioluminescent real-time detection of single nucleotide polymorphism (SNP) is presented. The method is based on single-step primer extension using pyrosequencing chemistry to monitor nucleotide incorporations in real-time. The method takes advantage of the fact that the reaction kinetics differ between matched and mismatched primer-template configurations. We show here that monitoring the initial reaction in real time accurately scores SNPs by comparing the initial reaction kinetics between matched and mismatched configurations. Thus, no additional treatment is required to improve the sequence specificity of the extension, which has been the case for many allele-specific extension assays. The microfluidic approach was evaluated using four SNPs. Three of the SNPs included primer-template configurations that have been previously reported to be difficult to resolve by allele-specific primer extension. All SNPs investigated were successfully scored. Using the microfluidic device, the volume for the bioluminescent assay was reduced dramatically, thus offering a cost-effective and fast SNP analysis method.

  • 20.
    Wiklundh, E.
    et al.
    Karolinska Inst, Dept Med, Stockholm, Sweden..
    Hellström, Cecilia
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Van Moorsel, C. H.
    St Antonius Hosp Pulmonol, Nieuwegein, Netherlands..
    Grutters, J. C.
    St Antonius Hosp, Dept Pulmonol, NL-3435 CM Nieuwegein, Netherlands..
    Nilsson, Peter
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Crestani, B.
    Hop Bichat Claude Bernard, Serv Pneumol, Paris, France..
    The Autoimmune Repertoire in Idiopathic Pulmonary Fibrosis2018In: American Journal of Respiratory and Critical Care Medicine, ISSN 1073-449X, E-ISSN 1535-4970, Vol. 197Article in journal (Other academic)
  • 21.
    Zhao, Ning-Wei
    KTH, School of Biotechnology (BIO).
    Interleukin (IL)-35 is raising our expectations2010In: Revista médica de Chile (Impresa), ISSN 0034-9887, E-ISSN 0717-6163, Vol. 138, no 6, p. 758-766Article, review/survey (Refereed)
    Abstract [en]

    Purpose: To elucidate and discuss the role of IL-35 in immunity to parasitic and bacterial infections as well as in autoimmunity in terms of its anti-inflammatory properties, we highlight significant findings on this novel member of the IL-12 family. Methods: Studies using genetically deficient mice have greatly enhanced our understanding of the biology of IL-35. On the basis of data derived from the analysis of these genetically deficient mice published by NIH, we focus on the key features of this heterodimeric cytokine, especially its relation to the other IL-12 family members, and discuss its potential relevance to the clinical usage. Principal findings: IL-35 is required for the CD4(+)CD25(+) Treg cells-mediated immune regulation, the alleviation of some inflammatory responses, as well as the expansion of CD4(+)CD25(-) Teff cells simultaneously. Moreover, administration or augmentation of IL-35 suppresses some diseases of autoimmune or allergic origin like collagen-induced arthritis or Helicobacter- induced colitis in animal models, demonstrating its potential in therapy of diseases mediated by inflammatory cytokines. However, some questions involving it are still unclear, including the composition of IL-35 receptor, IL-35-related cell signaling pathway, the different expression patterns of IL-35 between human and murine T cells, etc. Conclusion: As our understanding of the IL-35 is rapidly growing and changing, it will bring us more therapeutic strategies towards some intractable immune diseases such as Lupus Erythematosus.

1 - 21 of 21
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