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  • 1.
    Ameur, Adam
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Natl Genom Infrastruct, Sci Life Lab, Stockholm, Sweden..
    Dahlberg, Johan
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine. Natl Genom Infrastruct, Sci Life Lab, Stockholm, Sweden.
    Olason, Pall
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Natl Bioinformat Infrastruct, Sci Life Lab, Stockholm, Sweden..
    Vezzi, Francesco
    Natl Genom Infrastruct, Sci Life Lab, Stockholm, Sweden.;Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden..
    Karlsson, Robert
    Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden..
    Martin, Marcel
    Natl Bioinformat Infrastruct, Sci Life Lab, Stockholm, Sweden.;Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden..
    Viklund, Johan
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics. Natl Bioinformat Infrastruct, Sci Life Lab, Stockholm, Sweden..
    Kähäri, Andreas
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics. Natl Bioinformat Infrastruct, Sci Life Lab, Stockholm, Sweden..
    Lundin, Par
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden..
    Che, Huiwen
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Thutkawkorapin, Jessada
    Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden..
    Eisfeldt, Jesper
    Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden..
    Lampa, Samuel
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Natl Bioinformat Infrastruct, Sci Life Lab, Stockholm, Sweden.
    Dahlberg, Mats
    Natl Bioinformat Infrastruct, Sci Life Lab, Stockholm, Sweden.;Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden..
    Hagberg, Jonas
    Natl Bioinformat Infrastruct, Sci Life Lab, Stockholm, Sweden.;Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden..
    Jareborg, Niclas
    Natl Bioinformat Infrastruct, Sci Life Lab, Stockholm, Sweden.;Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden..
    Liljedahl, Ulrika
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine. Natl Genom Infrastruct, Sci Life Lab, Stockholm, Sweden.
    Jonasson, Inger
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Natl Genom Infrastruct, Sci Life Lab, Stockholm, Sweden..
    Johansson, Åsa
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik.
    Feuk, Lars
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik.
    Lundeberg, Joakim
    Natl Genom Infrastruct, Sci Life Lab, Stockholm, Sweden.;Royal Inst Technol, Div Gene Technol, Sch Biotechnol, Sci Life Lab, Stockholm, Sweden..
    Syvänen, Ann-Christine
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine. Natl Genom Infrastruct, Sci Life Lab, Stockholm, Sweden.
    Lundin, Sverker
    Royal Inst Technol, Div Gene Technol, Sch Biotechnol, Sci Life Lab, Stockholm, Sweden..
    Nilsson, Daniel
    Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden..
    Nystedt, Björn
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Natl Bioinformat Infrastruct, Sci Life Lab, Stockholm, Sweden..
    Magnusson, Patrik K. E.
    Natl Genom Infrastruct, Sci Life Lab, Stockholm, Sweden.;Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden..
    Gyllensten, Ulf B.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik.
    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.

  • 2. Aulchenko, Yurii S
    et al.
    Ripatti, Samuli
    Lindqvist, Ida
    Boomsma, Dorret
    Heid, Iris M
    Pramstaller, Peter P
    Penninx, Brenda W J H
    Janssens, A Cecile J W
    Wilson, James F
    Spector, Tim
    Martin, Nicholas G
    Pedersen, Nancy L
    Kyvik, Kirsten Ohm
    Kaprio, Jaakko
    Hofman, Albert
    Freimer, Nelson B
    Jarvelin, Marjo-Riitta
    Gyllensten, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Campbell, Harry
    Rudan, Igor
    Johansson, Åsa
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Marroni, Fabio
    Hayward, Caroline
    Vitart, Veronique
    Jonasson, Inger
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Pattaro, Cristian
    Wright, Alan
    Hastie, Nick
    Pichler, Irene
    Hicks, Andrew A
    Falchi, Mario
    Willemsen, Gonneke
    Hottenga, Jouke-Jan
    de Geus, Eco J C
    Montgomery, Grant W
    Whitfield, John
    Magnusson, Patrik
    Saharinen, Juha
    Perola, Markus
    Silander, Kaisa
    Isaacs, Aaron
    Sijbrands, Eric J G
    Uitterlinden, Andre G
    Witteman, Jacqueline C M
    Oostra, Ben A
    Elliott, Paul
    Ruokonen, Aimo
    Sabatti, Chiara
    Gieger, Christian
    Meitinger, Thomas
    Kronenberg, Florian
    Döring, Angela
    Wichmann, H-Erich
    Smit, Johannes H
    McCarthy, Mark I
    van Duijn, Cornelia M
    Peltonen, Leena
    Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts2009In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 41, no 1, p. 47-55Article in journal (Refereed)
    Abstract [en]

    Recent genome-wide association (GWA) studies of lipids have been conducted in samples ascertained for other phenotypes, particularly diabetes. Here we report the first GWA analysis of loci affecting total cholesterol (TC), low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol and triglycerides sampled randomly from 16 population-based cohorts and genotyped using mainly the Illumina HumanHap300-Duo platform. Our study included a total of 17,797-22,562 persons, aged 18-104 years and from geographic regions spanning from the Nordic countries to Southern Europe. We established 22 loci associated with serum lipid levels at a genome-wide significance level (P < 5 x 10(-8)), including 16 loci that were identified by previous GWA studies. The six newly identified loci in our cohort samples are ABCG5 (TC, P = 1.5 x 10(-11); LDL, P = 2.6 x 10(-10)), TMEM57 (TC, P = 5.4 x 10(-10)), CTCF-PRMT8 region (HDL, P = 8.3 x 10(-16)), DNAH11 (LDL, P = 6.1 x 10(-9)), FADS3-FADS2 (TC, P = 1.5 x 10(-10); LDL, P = 4.4 x 10(-13)) and MADD-FOLH1 region (HDL, P = 6 x 10(-11)). For three loci, effect sizes differed significantly by sex. Genetic risk scores based on lipid loci explain up to 4.8% of variation in lipids and were also associated with increased intima media thickness (P = 0.001) and coronary heart disease incidence (P = 0.04). The genetic risk score improves the screening of high-risk groups of dyslipidemia over classical risk factors.

  • 3. Demirkan, Ayse
    et al.
    van Duijn, Cornelia M.
    Ugocsai, Peter
    Isaacs, Aaron
    Pramstaller, Peter P.
    Liebisch, Gerhard
    Wilson, James F.
    Johansson, Åsa
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Genomics.
    Rudan, Igor
    Aulchenko, Yurii S.
    Kirichenko, Anatoly V.
    Janssens, A. Cecile J. W.
    Jansen, Ritsert C.
    Gnewuch, Carsten
    Domingues, Francisco S.
    Pattaro, Cristian
    Wild, Sarah H.
    Jonasson, Inger
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Polasek, Ozren
    Zorkoltseva, Irina V.
    Hofman, Albert
    Karssen, Lennart C.
    Struchalin, Maksim
    Floyd, James
    Igl, Wilmar
    Biloglav, Zrinka
    Broer, Linda
    Pfeufer, Arne
    Pichler, Irene
    Campbell, Susan
    Zaboli, Ghazal
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Kolcic, Ivana
    Rivadeneira, Fernando
    Huffman, Jennifer
    Hastie, Nicholas D.
    Uitterlinden, Andre
    Franke, Lude
    Franklin, Christopher S.
    Vitart, Veronique
    Nelson, Christopher P.
    Preuss, Michael
    Bis, Joshua C.
    O'Donnell, Christopher J.
    Franceschini, Nora
    Witteman, Jacqueline C. M.
    Axenovich, Tatiana
    Oostra, Ben A.
    Meitinger, Thomas
    Hicks, Andrew A.
    Hayward, Caroline
    Wright, Alan F.
    Gyllensten, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Genomics.
    Campbell, Harry
    Schmitz, Gerd
    Genome-Wide Association Study Identifies Novel Loci Associated with Circulating Phospho- and Sphingolipid Concentrations2012In: PLoS Genetics, ISSN 1553-7390, Vol. 8, no 2, p. e1002490-Article in journal (Refereed)
    Abstract [en]

    Phospho- and sphingolipids are crucial cellular and intracellular compounds. These lipids are required for active transport, a number of enzymatic processes, membrane formation, and cell signalling. Disruption of their metabolism leads to several diseases, with diverse neurological, psychiatric, and metabolic consequences. A large number of phospholipid and sphingolipid species can be detected and measured in human plasma. We conducted a meta-analysis of five European family-based genome-wide association studies (N = 4034) on plasma levels of 24 sphingomyelins (SPM), 9 ceramides (CER), 57 phosphatidylcholines (PC), 20 lysophosphatidylcholines (LPC), 27 phosphatidylethanolamines (PE), and 16 PE-based plasmalogens (PLPE), as well as their proportions in each major class. This effort yielded 25 genome-wide significant loci for phospholipids (smallest P-value = 9.88 x 10(-204)) and 10 loci for sphingolipids (smallest P-value = 3.10 x 10(-57)). After a correction for multiple comparisons (P-value, 2.2 x 10(-9)), we observed four novel loci significantly associated with phospholipids (PAQR9, AGPAT1, PKD2L1, PDXDC1) and two with sphingolipids (PLD2 and APOE) explaining up to 3.1% of the variance. Further analysis of the top findings with respect to within class molar proportions uncovered three additional loci for phospholipids (PNLIPRP2, PCDH20, and ABDH3) suggesting their involvement in either fatty acid elongation/saturation processes or fatty acid specific turnover mechanisms. Among those, 14 loci (KCNH7, AGPAT1, PNLIPRP2, SYT9, FADS1-2-3, DLG2, APOA1, ELOVL2, CDK17, LIPC, PDXDC1, PLD2, LASS4, and APOE) mapped into the glycerophospholipid and 12 loci (ILKAP, ITGA9, AGPAT1, FADS1-2-3, APOA1, PCDH20, LIPC, PDXDC1, SGPP1, APOE, LASS4, and PLD2) to the sphingolipid pathways. In large meta-analyses, associations between FADS1-2-3 and carotid intima media thickness, AGPAT1 and type 2 diabetes, and APOA1 and coronary artery disease were observed. In conclusion, our study identified nine novel phospho- and sphingolipid loci, substantially increasing our knowledge of the genetic basis for these traits.

  • 4.
    Gyllensten, Ulf
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Genomics.
    Johansson, Åsa
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Genomics.
    Enroth, Stefan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Genomics.
    Jonasson, Inger
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Assessing The Effects Of Climate Change On Health And Lifestyle In Sub-Arctic Areas In Sweden - The Northern Sweden Population Health Study2013In: International Journal of Circumpolar Health, ISSN 1239-9736, E-ISSN 2242-3982, Vol. 72, no Suppl. 1, p. 516-517Article in journal (Other academic)
  • 5.
    Johansson, Åsa
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Marroni, Fabio
    Hayward, Caroline
    Franklin, Christopher S.
    Kirichenko, Anatoly V.
    Jonasson, Inger
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Hicks, Andrew A.
    Vitart, Veronique
    Isaacs, Aaron
    Axenovich, Tatiana
    Campbell, Susan
    Dunlop, Malcolm G.
    Floyd, Jamie
    Hastie, Nick
    Hofman, Albert
    Knott, Sara
    Kolcic, Ivana
    Pichler, Irene
    Polasek, Ozren
    Rivadeneira, Fernando
    Tenesa, Albert
    Uitterlinden, André G.
    Wild, Sarah H.
    Zorkoltseva, Irina V.
    Meitinger, Thomas
    Wilson, James F.
    Rudan, Igor
    Campbell, Harry
    Pattaro, Cristian
    Pramstaller, Peter
    Oostra, Ben A.
    Wright, Alan F.
    Duijn, Cornelia M. van
    Aulchenko, Yurii S.
    Gyllensten, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Common variants in the JAZF1 gene associated with height identified by linkage and genome-wide association analysis2009In: Human Molecular Genetics, ISSN 0964-6906, E-ISSN 1460-2083, Vol. 18, no 2, p. 373-380Article in journal (Refereed)
    Abstract [en]

    Genes for height has gained interest for decades, but only recently have candidate genes started to be identified. We have performed linkage analysis and genome-wide association for height in approximately 4,000 individuals from five European populations. A total of 5 chromosomal regions showed suggestive linkage and in one of these regions, two SNPs (rs849140 and rs1635852) were associated with height (nominal p=7.0 x 10(-8) and p=9.6 x 10(-7) respectively). In total, five SNPs across the genome showed an association with height that reached the threshold of genome-wide significance (nominal p<1.6 x 10(-7)). The association with height was replicated for two SNPs (rs1635852 and rs849140) using three independent studies (N=31,077, N=1,268 and N=5,746) with overall meta p-values of 9.4x10(-10) and 5.3x10(-8). These SNPs are located in the JAZF1 gene, which has recently been associated with type II diabetes, prostate and endometrial cancer. JAZF1 is a transcriptional repressor of NR2C2, which results in low IGF1 serum concentrations, perinatal and early postnatal hypoglycaemia and growth retardation when knocked-out in mice. Both the linkage and association analyses independently identified the JAZF1 region affecting human height. We have demonstrated, through replication in additional independent populations, the consistency of the effect of the JAZF1 SNPs on height. Since this gene also has a key function in the metabolism of growth, JAZF1 represents one of the strongest candidates influencing human height so far identified.

  • 6.
    Lopes, Fatima
    et al.
    Univ Minho, Life & Hlth Sci Res Inst ICVS, Sch Hlth Sci, P-4710057 Braga, Portugal.;ICVS 3Bs PT Govt Associate Lab, Braga, Portugal..
    Barbosa, Mafalda
    Icahn Sch Med Mt Sinai, Dept Genet & Genom Sci, Mindich Child Hlth & Dev Inst, Seaver Autism Ctr Res & Treatment, New York, NY 10029 USA.;Inst Gulbenkian Ciencias, Oeiras, Portugal..
    Ameur, Adam
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Soares, Gabriela
    Ctr Hosp Porto, Ctr Med Genet Dr Jacinto Magalhaes, Oporto, Portugal..
    de Sa, Joaquim
    Ctr Hosp & Univ Coimbra, Hosp Pediat, Serv Genet Med, Coimbra, Portugal..
    Dias, Ana Isabel
    Ctr Hosp Lisboa Cent, Hosp D Estefania, Serv Neurol Pediat, Lisbon, Portugal..
    Oliveira, Guiomar
    Ctr Hosp & Univ Coimbra, Hosp Pediat, Unidade Neurodesenvolvimento & Autismo, Ctr Desenvolvimento Crianca, Coimbra, Portugal.;Ctr Hosp & Univ Coimbra, Hosp Pediat, Ctr Invest & Formacao Clin, Coimbra, Portugal.;Univ Coimbra, Univ Clin Pediat, Fac Med, Coimbra, Portugal.;Univ Coimbra, Inst Biomed Imaging & Life Sci, Coimbra, Portugal..
    Cabral, Pedro
    Egas Moniz Hosp, Dept Neurol, Lisbon, Portugal..
    Temudo, Teresa
    Ctr Hosp Porto, Dept Neuropediat, Oporto, Portugal..
    Calado, Eulalia
    Ctr Hosp Lisboa Cent, Hosp D Estefania, Serv Neurol Pediat, Lisbon, Portugal..
    Cruz, Isabel Fineza
    Ctr Hosp Univ Coimbra, Ctr Desenvolvimento Luis Borges, Hosp Pediat, Coimbra, Portugal..
    Vieira, Jose Pedro
    Ctr Hosp Lisboa Cent, Hosp D Estefania, Serv Neurol Pediat, Lisbon, Portugal..
    Oliveira, Renata
    Ctr Hosp & Univ Coimbra, Hosp Pediat, Serv Genet Med, Coimbra, Portugal..
    Esteves, Sofia
    Univ Minho, Life & Hlth Sci Res Inst ICVS, Sch Hlth Sci, P-4710057 Braga, Portugal.;ICVS 3Bs PT Govt Associate Lab, Braga, Portugal..
    Sauer, Sascha
    Max Planck Inst Mol Genet, Otto Warburg Lab, Ihnestr 73, D-14195 Berlin, Germany.;Univ Wurzburg, CU Syst Med, D-97070 Wurzburg, Germany..
    Jonasson, Inger
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Syvänen, Ann-Christine
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine. Uppsala Univ, Mol Med & Sci Life Lab, Dept Med Sci, Uppsala, Sweden..
    Gyllensten, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik.
    Pinto, Dalila
    Icahn Sch Med Mt Sinai, Dept Genet & Genom Sci, Mindich Child Hlth & Dev Inst, Seaver Autism Ctr Res & Treatment, New York, NY 10029 USA..
    Maciel, Patricia
    Univ Minho, Life & Hlth Sci Res Inst ICVS, Sch Hlth Sci, P-4710057 Braga, Portugal.;ICVS 3Bs PT Govt Associate Lab, Braga, Portugal..
    Identification of novel genetic causes of Rett syndrome-like phenotypes2016In: Journal of Medical Genetics, ISSN 0022-2593, E-ISSN 1468-6244, Vol. 53, no 3, p. 190-199Article in journal (Refereed)
    Abstract [en]

    Background The aim of this work was to identify new genetic causes of Rett-like phenotypes using array comparative genomic hybridisation and a whole exome sequencing approach. Methods and results We studied a cohort of 19 Portuguese patients (16 girls, 3 boys) with a clinical presentation significantly overlapping Rett syndrome (RTT). Genetic analysis included filtering of the single nucleotide variants and indels with preference for de novo, homozygous/compound heterozygous, or maternally inherited X linked variants. Examination by MRI and muscle biopsies was also performed. Pathogenic genomic imbalances were found in two patients (10.5%): an 18q21.2 deletion encompassing four exons of the TCF4 gene and a mosaic UPD of chromosome 3. Variants in genes previously implicated in neurodevelopmental disorders (NDD) were identified in six patients (32%): de novo variants in EEF1A2, STXBP1 and ZNF238 were found in three patients, maternally inherited X linked variants in SLC35A2, ZFX and SHROOM4 were detected in two male patients and one homozygous variant in EIF2B2 was detected in one patient. Variants were also detected in five novel NDD candidate genes (26%): we identified de novo variants in the RHOBTB2, SMARCA1 and GABBR2 genes; a homozygous variant in EIF4G1; compound heterozygous variant in HTT. Conclusions Network analysis reveals that these genes interact by means of protein interactions with each other and with the known RTT genes. These findings expand the phenotypical spectrum of previously known NDD genes to encompass RTT-like clinical presentations and identify new candidate genes for RTT-like phenotypes.

  • 7.
    Lopes, Fatima
    et al.
    Univ Minho, Sch Hlth Sci, Life & Hlth Sci Res Inst ICVS, Braga, Portugal.;ICVS 3Bs PT Govt Associate Lab, Braga, Portugal..
    Barbosa, Mafalda
    Mt Sinai Sch Med, Mindich Child Hlth & Dev Inst, Seaver Autism Ctr, Dept Psychiat, New York, NY USA.;Mt Sinai Sch Med, Mindich Child Hlth & Dev Inst, Seaver Autism Ctr, Dept Genet & Genom Sci, New York, NY USA..
    Temudo, Teresa
    Hosp Geral St Antonio, Oporto, Portugal..
    de Sa, Joaquim
    Hosp Pediat Coimbra, Serv Genet Med, Coimbra, Portugal..
    Dias, Ana Isabel
    Hosp Dona Estefania, Lisbon, Portugal..
    Oliveira, Guiomar
    Hosp Pediat Coimbra, Ctr Desenvolvimento Crianca, Coimbra, Portugal..
    Cabra, Pedro
    Hosp S Francisco Xavier, Lisbon, Portugal..
    Calado, Eulalia
    Hosp Dona Estefania, Lisbon, Portugal..
    Cruz, Isabel Fineza
    Hosp Pediat Coimbra, Ctr Desenvolvimento Crianca, Coimbra, Portugal..
    Soares, Gabriela
    Mt Sinai Sch Med, Mindich Child Hlth & Dev Inst, Seaver Autism Ctr, Dept Psychiat, New York, NY USA.;Mt Sinai Sch Med, Mindich Child Hlth & Dev Inst, Seaver Autism Ctr, Dept Genet & Genom Sci, New York, NY USA..
    Vieira, Jose Pedro
    Hosp Dona Estefania, Lisbon, Portugal..
    Venancio, Maria Margarida
    Hosp Pediat Coimbra, Serv Genet Med, Coimbra, Portugal..
    Oliveira, Renata
    Hosp Pediat Coimbra, Serv Genet Med, Coimbra, Portugal..
    Jonasson, Inger
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ameur, Adam
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Pinto, Dalila
    Mt Sinai Sch Med, Mindich Child Hlth & Dev Inst, Seaver Autism Ctr, Dept Psychiat, New York, NY USA.;Mt Sinai Sch Med, Mindich Child Hlth & Dev Inst, Seaver Autism Ctr, Dept Genet & Genom Sci, New York, NY USA..
    Gyllensten, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Maciel, Patricia
    Univ Minho, Sch Hlth Sci, Life & Hlth Sci Res Inst ICVS, Braga, Portugal.;ICVS 3Bs PT Govt Associate Lab, Braga, Portugal..
    Identification of novel genetic causes of Rett syndrome-like phenotypes by whole exome sequencing2015In: International Journal of Developmental Neuroscience, ISSN 0736-5748, E-ISSN 1873-474X, Vol. 47, p. 99-99Article in journal (Other academic)
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