Kornak, Uwe

[["dc.bibliographiccitation.artnumber","btac418"],["dc.bibliographiccitation.journal","Bioinformatics"],["dc.contributor.author","May, Vinzenz"],["dc.contributor.author","Koch, Leonard"],["dc.contributor.author","Fischer-Zirnsak, Björn"],["dc.contributor.author","Horn, Denise"],["dc.contributor.author","Gehle, Petra"],["dc.contributor.author","Kornak, Uwe"],["dc.contributor.author","Beule, Dieter"],["dc.contributor.author","Holtgrewe, Manuel"],["dc.contributor.editor","Birol, Inanc"],["dc.date.accessioned","2022-07-01T07:35:00Z"],["dc.date.available","2022-07-01T07:35:00Z"],["dc.date.issued","2022"],["dc.description.abstract","Abstract Motivation While the identification of small variants in panel sequencing data can be considered a solved problem, the identification of larger, multi-exon copy number variants (CNVs) still poses a considerable challenge. Thus, CNV calling has not been established in all laboratories performing panel sequencing. At the same time such laboratories have accumulated large data sets and thus have the need to identify copy number variants on their data to close the diagnostic gap. Results In this manuscript we present our method clearCNV that addresses this need in two ways. First, it helps laboratories to properly assign data sets to enrichment kits. Based on homogeneous subsets of data, clearCNV identifies CNVs affecting the targeted regions. Using real-world data sets and validation, we show that our method is highly competitive with previous methods and preferable in terms of specificity. Availability The software is available for free under a permissible license at {{https://github.com/bihealth/clear-cnv}} Supplementary information Supplementary data are available at Bioinformatics online."],["dc.identifier.doi","10.1093/bioinformatics/btac418"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/112064"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-581"],["dc.relation.eissn","1460-2059"],["dc.relation.issn","1367-4803"],["dc.title","ClearCNV: CNV calling from NGS panel data in the presence of ambiguity and noise"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2068"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","American Journal of Medical Genetics Part A"],["dc.bibliographiccitation.lastpage","2076"],["dc.bibliographiccitation.volume","182"],["dc.contributor.author","Suter, Aude‐Annick"],["dc.contributor.author","Santos‐Simarro, Fernando"],["dc.contributor.author","Toerring, Pernille Mathiesen"],["dc.contributor.author","Abad Perez, Angela"],["dc.contributor.author","Ramos‐Mejia, Rosario"],["dc.contributor.author","Heath, Karen E."],["dc.contributor.author","Huckstadt, Victoria"],["dc.contributor.author","Parrón‐Pajares, Manuel"],["dc.contributor.author","Mensah, Martin Atta"],["dc.contributor.author","Hülsemann, Wiebke"],["dc.contributor.author","Holtgrewe, Manuel"],["dc.contributor.author","Mundlos, Stefan"],["dc.contributor.author","Kornak, Uwe"],["dc.contributor.author","Bartsch, Oliver"],["dc.contributor.author","Ehmke, Nadja"],["dc.date.accessioned","2021-04-14T08:26:20Z"],["dc.date.available","2021-04-14T08:26:20Z"],["dc.date.issued","2020"],["dc.identifier.doi","10.1002/ajmg.a.61735"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/81910"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-399"],["dc.relation.eissn","1552-4833"],["dc.relation.issn","1552-4825"],["dc.title","Variable pulmonary manifestations in Chitayat syndrome: Six additional affected individuals"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.contributor.author","Holtgrewe, Manuel"],["dc.contributor.author","Stolpe, Oliver"],["dc.contributor.author","Nieminen, Mikko"],["dc.contributor.author","Mundlos, Stefan"],["dc.contributor.author","Knaus, Alexej"],["dc.contributor.author","Kornak, Uwe"],["dc.contributor.author","Seelow, Dominik"],["dc.contributor.author","Segebrecht, Lara"],["dc.contributor.author","Spielmann, Malte"],["dc.contributor.author","Fischer-Zirnsak, Björn"],["dc.contributor.author","Boschann, Felix"],["dc.contributor.author","Scholl, Ute"],["dc.contributor.author","Ehmke, Nadja"],["dc.contributor.author","Beule, Dieter"],["dc.date.accessioned","2020-06-24T12:24:18Z"],["dc.date.available","2020-06-24T12:24:18Z"],["dc.date.issued","2020"],["dc.identifier.doi","10.1101/2020.01.27.921965"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/66713"],["dc.title","VarFish - Collaborative and Comprehensive Variant Analysis for Diagnosis and Research"],["dc.type","preprint"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.contributor.author","Holtgrewe, Manuel"],["dc.contributor.author","Stolpe, Oliver"],["dc.contributor.author","Nieminen, Mikko"],["dc.contributor.author","Mundlos, Stefan"],["dc.contributor.author","Knaus, Alexej"],["dc.contributor.author","Kornak, Uwe"],["dc.contributor.author","Seelow, Dominik"],["dc.contributor.author","Segebrecht, Lara"],["dc.contributor.author","Spielmann, Malte"],["dc.contributor.author","Fischer-Zirnsak, Björn"],["dc.contributor.author","Boschann, Felix"],["dc.contributor.author","Scholl, Ute"],["dc.contributor.author","Ehmke, Nadja"],["dc.contributor.author","Beule, Dieter"],["dc.date.accessioned","2020-06-24T12:23:57Z"],["dc.date.available","2020-06-24T12:23:57Z"],["dc.date.issued","2020-04-27"],["dc.description.abstract","VarFish is a user-friendly web application for the quality control, filtering, prioritization, analysis, and user-based annotation of DNA variant data with a focus on rare disease genetics. It is capable of processing variant call files with single or multiple samples. The variants are automatically annotated with population frequencies, molecular impact, and presence in databases such as ClinVar. Further, it provides support for pathogenicity scores including CADD, MutationTaster, and phenotypic similarity scores. Users can filter variants based on these annotations and presumed inheritance pattern and sort the results by these scores. Variants passing the filter are listed with their annotations and many useful link-outs to genome browsers, other gene/variant data portals, and external tools for variant assessment. VarFish allows users to create their own annotations including support for variant assessment following ACMG-AMP guidelines. In close collaboration with medical practitioners, VarFish was designed for variant analysis and prioritization in diagnostic and research settings as described in the software's extensive manual. The user interface has been optimized for supporting these protocols. Users can install VarFish on their own in-house servers where it provides additional lab notebook features for collaborative analysis and allows re-analysis of cases, e.g. after update of genotype or phenotype databases."],["dc.identifier.doi","10.1093/nar/gkaa241"],["dc.identifier.pmid","32338743"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/66711"],["dc.language.iso","en"],["dc.relation.eissn","1362-4962"],["dc.relation.issn","0305-1048"],["dc.title","VarFish: comprehensive DNA variant analysis for diagnostics and research"],["dc.type","journal_article"],["dc.type.internalPublication","no"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","Journal of Inherited Metabolic Disease"],["dc.contributor.author","Vogt, Guido"],["dc.contributor.author","El Choubassi, Naji"],["dc.contributor.author","Herczegfalvi, Ágnes"],["dc.contributor.author","Kölbel, Heike"],["dc.contributor.author","Lekaj, Anja"],["dc.contributor.author","Schara, Ulrike"],["dc.contributor.author","Holtgrewe, Manuel"],["dc.contributor.author","Krause, Sabine"],["dc.contributor.author","Horvath, Rita"],["dc.contributor.author","Schuelke, Markus"],["dc.contributor.author","Hübner, Christoph"],["dc.contributor.author","Mundlos, Stefan"],["dc.contributor.author","Roos, Andreas"],["dc.contributor.author","Lochmüller, Hanns"],["dc.contributor.author","Karcagi, Veronika"],["dc.contributor.author","Kornak, Uwe"],["dc.contributor.author","Fischer‐Zirnsak, Björn"],["dc.date.accessioned","2021-04-14T08:29:24Z"],["dc.date.available","2021-04-14T08:29:24Z"],["dc.date.issued","2021"],["dc.identifier.doi","10.1002/jimd.12341"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/82890"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-399"],["dc.relation.eissn","1573-2665"],["dc.relation.issn","0141-8955"],["dc.title","Expanding the clinical and molecular spectrum of ATP6V1A related metabolic cutis laxa"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","115219"],["dc.bibliographiccitation.journal","Bone"],["dc.bibliographiccitation.volume","133"],["dc.contributor.author","Ehmke, Nadja"],["dc.contributor.author","Cusmano-Ozog, Kristina"],["dc.contributor.author","Koenig, Rainer"],["dc.contributor.author","Holtgrewe, Manuel"],["dc.contributor.author","Nur, Banu"],["dc.contributor.author","Mihci, Ercan"],["dc.contributor.author","Babcock, Holly"],["dc.contributor.author","Gonzaga-Jauregui, Claudia"],["dc.contributor.author","Overton, John D"],["dc.contributor.author","Xiao, Jing"],["dc.contributor.author","Martinez, Ariel F"],["dc.contributor.author","Muenke, Maximilian"],["dc.contributor.author","Balzer, Alexander"],["dc.contributor.author","Jochim, Judith"],["dc.contributor.author","El Choubassi, Naji"],["dc.contributor.author","Fischer-Zirnsak, Björn"],["dc.contributor.author","Huber, Céline"],["dc.contributor.author","Kornak, Uwe"],["dc.contributor.author","Elsea, Sarah H"],["dc.contributor.author","Cormier-Daire, Valérie"],["dc.contributor.author","Ferreira, Carlos R"],["dc.date.accessioned","2020-06-23T10:10:24Z"],["dc.date.available","2020-06-23T10:10:24Z"],["dc.date.issued","2020-04"],["dc.description.abstract","Catel-Manzke syndrome is characterized by the combination of Pierre Robin sequence and radial deviation, shortening as well as clinodactyly of the index fingers, due to an accessory ossification center. Mutations in TGDS have been identified as one cause of Catel-Manzke syndrome, but cannot be found as causative in every patient with the clinical diagnosis. We performed a chromosome microarray and/or exome sequencing in three patients with hand hyperphalangism, heart defect, short stature, and mild to severe developmental delay, all of whom were initially given a clinical diagnosis of Catel-Manzke syndrome. In one patient, we detected a large deletion of exons 1-8 and the missense variant c.1282C > T (p.Arg428Trp) in KYNU (NM_003937.2), whereas homozygous missense variants in KYNU were found in the other two patients (c.989G > A (p.Arg330Gln) and c.326G > C (p.Trp109Ser)). Plasma and urine metabolomic analysis of two patients indicated a block along the tryptophan catabolic pathway and urine organic acid analysis showed excretion of xanthurenic acid. Biallelic loss-of-function mutations in KYNU were recently described as a cause of NAD deficiency with vertebral, cardiac, renal and limb defects; however, no hand hyperphalangism was described in those patients, and Catel-Manzke syndrome was not discussed as a differential diagnosis. In conclusion, we present unrelated patients identified with biallelic variants in KYNU leading to kynureninase deficiency and xanthurenic aciduria as a very likely cause of their hyperphalangism, heart defect, short stature, and developmental delay. We suggest performance of urine organic acid analysis in patients with suspected Catel-Manzke syndrome, particularly in those with cardiac or vertebral defects or without mutations in TGDS."],["dc.identifier.doi","10.1016/j.bone.2019.115219"],["dc.identifier.pmid","31923704"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/66656"],["dc.language.iso","en"],["dc.relation.eissn","1873-2763"],["dc.relation.issn","8756-3282"],["dc.title","Biallelic variants in KYNU cause a multisystemic syndrome with hand hyperphalangism"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]