title: Loss of function of PGAP1 as a cause of severe encephalopathy identified by Whole Exome Sequencing: Lessons of the bioinformatics pipeline.
abstract: We evaluated a multiple consanguineous Turkish family with two children, a boy and a girl, affected by severe encephalopathy, hypotonia, microcephaly and retinal dystrophy by a combination of linkage analysis and Whole Exome Sequencing (WES). We analyzed the sequence data by two different bioinformatics pipelines which did not differ in overall processing strategy but involved differences in software used, minor allele frequency (MAF) thresholds and reference data sets, the usage of in-house control exomes and filter settings to prioritize called variants. Assuming autosomal recessive mode of inheritance, only homozygous variants present in both children were considered. The resulting variant lists differed partially (nine variants identified by both pipelines, ten variants by only one pipeline). Major reasons for this discrepancy were different filters for MAF and different variant prioritizations. Combining the variant lists with the results of linkage analysis and further prioritization by expression data and prediction tools, an intronic homozygous splice variant (c.1090-2A>G; IVS9-2A>G; p.?) in PGAP1 (Post-GPI Attachment To Proteins 1) was identified and validated by cDNA analysis. PGAP1 ensures the first step of maturation of GPI (glycosylphosphatidylinositol)-anchor proteins. Recently, a homozygous loss-of-function mutation in PGAP1 has been reported in one family with two children affected by a similar phenotype. The present report not only illustrates the possible influence of specific filtering settings on the results of WES but also confirms PGAP1 as a cause of severe encephalopathy.
authors.affiliation: Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany. Electronic address: martin.granzow@med.uni-heidelberg.de.
authors.forename: M
authors.initials: M
authors.lastname: Granzow
authors.affiliation: Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Medical Faculty Heidelberg, Heidelberg University, 69120 Heidelberg, Germany.
authors.forename: N
authors.initials: N
authors.lastname: Paramasivam
authors.affiliation: Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany.
authors.forename: K
authors.initials: K
authors.lastname: Hinderhofer
authors.affiliation: Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany.
authors.forename: C
authors.initials: C
authors.lastname: Fischer
authors.affiliation: Genomics & Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.
authors.forename: S
authors.initials: S
authors.lastname: Chotewutmontri
authors.affiliation: Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany.
authors.forename: L
authors.initials: L
authors.lastname: Kaufmann
authors.affiliation: Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany.
authors.forename: C
authors.initials: C
authors.lastname: Evers
authors.affiliation: Section of Neuropediatrics, Center for Child and Adolescent Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany.
authors.forename: U
authors.initials: U
authors.lastname: Kotzaeridou
authors.affiliation: Section of Ophthalmologic Rehabilitation, Department of Ophthalmology, University Hospital Heidelberg, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany.
authors.forename: K
authors.initials: K
authors.lastname: Rohrschneider
authors.affiliation: Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
authors.forename: M
authors.initials: M
authors.lastname: Schlesner
authors.affiliation: Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstrasse 7, 72076 Tübingen, Germany.
authors.forename: M
authors.initials: M
authors.lastname: Sturm
authors.affiliation: Genomics & Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.
authors.forename: S
authors.initials: S
authors.lastname: Pinkert
authors.affiliation: Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, 69120 Heidelberg, Germany.
authors.forename: R
authors.initials: R
authors.lastname: Eils
authors.affiliation: Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany.
authors.forename: C R
authors.initials: CR
authors.lastname: Bartram
authors.affiliation: Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstrasse 7, 72076 Tübingen, Germany.
authors.forename: P
authors.initials: P
authors.lastname: Bauer
authors.affiliation: Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany.
authors.forename: U
authors.initials: U
authors.lastname: Moog
mesh_terms: D001927:Brain Diseases / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D003241:Consanguinity; D059472:Exome; D005260:Female; D008040:Genetic Linkage; D020022:Genetic Predisposition to Disease; D006720:Homozygote; D006801:Humans; D008297:Male; D008565:Membrane Proteins / Q000235:genetics*; D009154:Mutation; D010375:Pedigree; D010744:Phosphoric Monoester Hydrolases / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D014421:Turkey
chemical_list: D008565:Membrane Proteins; C484857:PGAP1 protein, human; D010744:Phosphoric Monoester Hydrolases
keywords: Analysis pipeline; Encephalopathy; Intellectual disability; PGAP1; Retinal dystrophy; Whole Exome Sequencing