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Whole genome sequencing of consanguineous families reveals novel pathogenic variants in intellectual disability
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.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik. Uppsala University, Science for Life Laboratory, SciLifeLab.
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. (Lars Feuk)ORCID iD: 0000-0001-8367-8391
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.
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2019 (English)In: Clinical Genetics, ISSN 0009-9163, E-ISSN 1399-0004, Vol. 95, no 3, p. 436-439Article in journal, Letter (Refereed) Published
Place, publisher, year, edition, pages
2019. Vol. 95, no 3, p. 436-439
National Category
Medical Genetics
Identifiers
URN: urn:nbn:se:uu:diva-326281DOI: 10.1111/cge.13470ISI: 000458956100013PubMedID: 30525197OAI: oai:DiVA.org:uu-326281DiVA, id: diva2:1119769
Funder
EU, European Research Council, 282330Available from: 2017-07-04 Created: 2017-07-04 Last updated: 2019-03-14Bibliographically approved
In thesis
1. Sequence based identification of genetic variation associated with intellectual disability
Open this publication in new window or tab >>Sequence based identification of genetic variation associated with intellectual disability
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Intellectual disability (ID) is a common neurodevelopmental condition, often caused by genetic defects. De novo variation (DNV) is an important cause of ID, especially in severe or syndromic forms of the disorder. Next generation sequencing has been a successful application for finding pathogenic variation in ID patients. The main focus of this thesis is to use whole exome sequencing (WES) and whole genome sequencing (WGS) to identify pathogenic variants in undiagnosed ID patients. In Paper I, WES was used in family trios to identify pathogenic DNVs in patients diagnosed with ID in combination with epilepsy. This work led to the identification of several DNVs in both new and known disease genes, including the first report of variation in the HECW2 gene in association with neurodevelopmental disorder and epilepsy. Paper II is the first independent validation of PIGG as a disease-causing gene in patients with developmental disorder. We used WES to identify the homozygous variation in PIGG, and transcriptome analysis as well as flow-cytometry studies were used to validate the pathogenicity of the PIGG variation. We discovered that PIGG variation give different effects in different cell types, contributing new insights into the disease mechanism. Paper III is also an application of WES in trio families with patients diagnosed with ID in order to identify causal variants, a strategy similar to that of Paper I. Several pathogenic variants were identified in this study; in particular, the gene NAA15 is highlighted as a new disease gene, and was recently confirmed in independent studies. This study also adds evidence to support that variation in the PUF60 gene is causing the symptoms in patients with Verheij syndrome. In Paper IV, WGS was used to analyze families with consanguineous marriages. All families in this study had been previously analyzed with WES without finding a disease cause. A number of new disease-causing variants were identified in the study, including a first validation of FRMD4A as a disease-associated gene. This study also shows that WGS performs better than WES in finding variants, even for variants in coding parts of the genome.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2017. p. 35
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 1343
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-326283 (URN)978-91-513-0007-8 (ISBN)
Public defence
2017-09-13, B7 111:a, BMC, Husargatan 3, Uppsala, 09:00 (English)
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Supervisors
Available from: 2017-08-21 Created: 2017-07-04 Last updated: 2017-09-08

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Thuresson, Ann-CharlotteZander, CeciliaZhao, Jin JamesHalvardson, JonatanMaqbool, KhurramFeuk, Lars

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