Katja Lohmann’s research while affiliated with Universitätsklinikum Schleswig - Holstein and other places

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Publications (319)


Correction: Structural variant calling and clinical interpretation in 6224 unsolved rare disease exomes
  • Article
  • Full-text available

April 2025

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28 Reads

European Journal of Human Genetics

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Stephan Ossowski
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Fig. 3 | Study design. Figure created with BioRender.com.
Frequency of the LRRK2 p.L1795F and p.G2019S variants across ancestries in the GP2 genotyping cohort
The LRRK2 p.L1795F variant causes Parkinson’s disease in the European population

March 2025

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192 Reads

npj Parkinson s Disease

LRRK2 -PD represents the most common form of autosomal dominant Parkinson’s disease. We identified the LRRK2 p.L1795F variant in three families and six additional unrelated cases using genetic data from over 50,000 individuals. Carriers with available genotyping data shared a common haplotype. The clinical presentation resembles other LRRK2 -PD forms. Combined with published functional evidence showing strongly enhanced LRRK2 kinase activity, we provide evidence that LRRK2 p.L1795F is pathogenic.


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An improved polygenic score for Parkinson's disease partly explains variable penetrance of genetic Parkinson's disease

March 2025

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61 Reads

While genetic causes are identified in up to 15% of all Parkinson's disease (PD) patients, the remaining idiopathic PD (iPD) patients are attributed to polygenic risk, environmental and lifestyle factors, and interactions thereof. We applied five advanced polygenic score (PGS) tools to data from 1,762 iPD patients and 4,227 healthy controls of European ancestry, resulting in the development of a novel iPD-PGS with significantly improved discriminative performance compared to existing models with an AUC of 0.680 (95% confidence interval (-CI): [0.665, 0.695]). Validation in independent cohorts confirmed its robustness. Notably, patients with early-onset iPD exhibited markedly high PGS values when compared to late-onset iPD patients and healthy controls, underlining the high polygenetic burden in these individuals. We subsequently applied our novel iPD-PGS to carriers of heterozygous PRKN variants and GBA1 coding risk variants. In both cases, our findings suggest that part of the penetrance in these genetic forms of PD can be explained by the same polygenic alterations as observed mitigating iPD. The discriminative potential was greater for GBA1 than for PRKN (GBA1: AUC=0.639, 95%-CI=[0.590, 0.687], PRKN: AUC=0.594, 95%-CI=[0.501, 0.687]). Our study highlights the potential of advanced PGSs in PD research, particularly for understanding varying penetrance in genetic PD and identifying high-risk individuals.



Fig. 1 | Family pedigrees of the three probands from mainland China with a positive family history of Parkinson's disease. There is partial evidence for cosegregation (with the p.Arg1067Gln variant detected in five individuals affected with PD), however with seemingly incomplete penetrance (the youngest sibling in Family 2 [II:5] being clinically unaffected when assessed at age 63 years). The age of onset is written below each affected individual, where available.
Fig. 2 | LRRK2 kinase hyperactivity in vivo due to the presence of the LRRK2 p.Arg1067Gln (p.R1067Q) variant. Monocyte lysates were analyzed by quantitative immunoblotting (a). Quantified immunoblotting data are presented as ratios of phospho-Rab10 Thr73 /total Rab10 and total Rab10/GAPDH (b), and phospho-LRRK2 Ser935 /total LRRK2 and total LRRK2/GAPDH (c), normalized to the average
Fig. 3 | LRRK2 kinase activity of the LRRK2 p.Arg1067Gln variant compared to p.Gly2019Ser and p.Arg1441Gly in a cellular overexpression system. In vitro characterization of the LRRK2 p.Arg1067Gln variant in comparison with the common LRRK2 p.Gly2019Ser and p.Arg1441Gly variants in an established HEK293 overexpression system, followed by LI-COR Odyssey immunoblotting and quantification of LRRK2 kinase activity relative to LRRK2 wildtype (wt) (a). Three independent biological replicate transfection experiments were performed including one where cells were treated with and without the specific LRRK2 kinase inhibitor MLi-2 (200 nM for 1.5 h). Each (-) lane represents a biological replicate. LRRK2-
Fig. 4 | Structural insights into predicted impact of the LRRK2 p.Arg1067Gln variant. Overview of the inactive LRRK2 monomer (a) with detailed view of the Arg1067Gln residue in the inactive LRRK2 monomer (PDB: 8FO2) (b), LRRK2 bound to Type II inhibitor that stabilizes LRRK2 kinase domain in the inactive conformation (PDB: 8U8A) (c), and LRRK2 bound to Type I inhibitor that stabilizes LRRK2 kinase domain in the active conformation (PDB: 8TZH) (d). The interactions that Arg1067 makes with kinase domain residues Phe1883 (electrostatic backbone and potentially Pi-stacking) and Leu1884 (electrostatic backbone) in the inactive conformation are highlighted (b, c). The interaction that Arg1067 makes with kinase domain residues Glu1882 (electrostatic) in the active conformation is also illustrated (d).
Clinico-demographic features of patients harboring the LRRK2 p.Arg1067Gln variant
Clinical and functional evidence for the pathogenicity of the LRRK2 p.Arg1067Gln variant

February 2025

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53 Reads

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1 Citation

npj Parkinson s Disease

LRRK2 -related Parkinson’s disease ( LRRK2 -PD) is the most frequent form of monogenic PD worldwide, with important therapeutic opportunities, exemplified by the advancement in LRRK2 kinase inhibition studies/trials. However, many LRRK2 variants, especially those found in underrepresented populations, remain classified as variants of uncertain significance (VUS). Leveraging on Malaysian, Singaporean, and mainland Chinese PD datasets ( n = 4901), we describe 12 Chinese-ancestry patients harboring the LRRK2 p.Arg1067Gln variant, more than doubling the number of previously reported cases (total n = 23, 87% East Asian, mean age of onset: 53.9 years). We determine that this variant is enriched in East Asian PD patients compared to population controls (OR = 8.0, 95% CI: 3.0–20.9), and provide supportive data for its co-segregation with PD, albeit with incomplete penetrance. Utilizing established experimental workflows, this variant showed increased LRRK2 kinase activity, by ~2-fold compared to wildtype and higher than the p.Gly2019Ser variant. Taken together, p.Arg1067Gln should be reclassified from a VUS to pathogenic for causing LRRK2 -PD.


Fig. 1 | Flowchart of the literature search. The number of included and excluded articles at the different steps is indicated.
Fig. 2 | Mutation screening methods. Frequencies of the mutation screening methods in the included patients.
Fig. 5 | Other clinical features in the included patients. A The age at onset (AAO) distribution is shown in 10-year bands on the x-axis. The percentage of patients is displayed on the y-axis. The graph shows the distribution for all included PD patients (blue), for the patients with VUS only (gray), for the patients with the p.G2019S variant (black), and for patients with (likely) pathogenic variants (red). B Box plots for the AAO in years in the four groups, depicting medians and interquartile ranges. Outlier points are also displayed and are defined as data points that lie outside 1.5 times the interquartile range (IQR) from the lower or upper quartile boundary. C Initial signs and symptoms in the included patients with pathogenic or likely pathogenic variants. D Levodopa response quantifications in the included PD patients with pathogenic or likely pathogenic variants. The x-axis shows the six divisions of the levodopa response quantifications and the y-axis the number of patients.
Fig. 6 | Signs and symptoms in the included patients at last examination. Cardinal clinical signs and symptoms in the included PARK-LRRK2 patients with pathogenic or likely pathogenic variants.
Updated MDSGene review on the clinical and genetic spectrum of LRRK2 variants in Parkinson´s disease

February 2025

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52 Reads

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1 Citation

npj Parkinson s Disease

Pathogenic variants in the LRRK2 gene are one of the most commonly identifiable monogenic causes of Parkinson´s disease (PD, PARK-LRRK2). This systematic MDSGene literature review comprehensively summarizes published demographic, clinical, and genetic findings related to LRRK2 variants ( https://www.mdsgene.org/ ). Data on 4660 individuals with 283 different variants were curated. The median age at onset in the PD patients with available information was 56 years, notably, with approximately one-third having PD onset <50 years. Tremor was the most frequently reported initial symptom and more common than reported in other dominantly inherited forms of PD. Of the 211 potentially PD-causing variants, 25 were classified as pathogenic or likely pathogenic, and the remaining 186 (88.2%) were variants of uncertain significance. p.G2019S was the most frequently reported pathogenic variant, followed by p.R1441G and p.R1441C. This systematic review represents the most extensive database on PARK-LRRK2 to date and provides a vital resource to improve precision medicine.


Disease frequencies in affected patients with GBA1 variants
Characteristics of genetically different groups of PD patients
Classification and Genotype-Phenotype Relationships of GBA1 Variants: MDSGene Systematic Review

Movement Disorders

Depending on zygosity and the specific change, different variants in the GBA1 gene can cause Parkinson's disease (PD, PARK-GBA1) with reduced penetrance, act as genetic risk factors for PD or parkinsonism, and/or lead to Gaucher's disease (GD). This MDSGene systematic literature review covers 27,963 patients carrying GBA1 variants from 1082 publications with 794 variants, including 13,342 patients with PD or other forms of parkinsonism. It provides a comprehensive overview of demographic, clinical, and genetic findings from an ethnically diverse sample originating from 82 countries across five continents. The most frequent pathogenic or likely pathogenic variants were "N409S" (aka "N370S"; dominating among Jewish and Whites), and "L483P" (aka "L444P"; dominating among Asians and Hispanics), whereas the most common coding risk variants were "E365K" (E326K), and "T408M" (T369M) (both common among Whites). A novel finding is that early-onset PD patients were predominantly of Asian ethnicity, whereas late-onset PD patients were mainly of White ethnicity. Motor cardinal features were similar between PD patients and other forms of parkinsonism, whereas motor complications and non-motor symptoms were more frequently reported in PD patients carrying "severe" variants than in those with "risk" or "mild" variants. Cognitive decline was reported in most patients after surgical treatment, despite achieving a beneficial motor function response. Most GD patients developing PD harbored the "N409S" variant, were of Ashkenazi Jewish ethnicity, and showed a positive response to chronic levodopa treatment. With this review, we start to fill the gaps regarding genotype-phenotype correlations in GBA1 variant carriers, especially concerning PD. © 2025 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.



Overview of the Solve-RD analysis and interpretation framework and community resource established
a, Solve-RD brought together rare-disease data and expertise. Central to Solve-RD are four core ERNs relating to rare diseases; via these expert disease networks, patients with rare diseases were recruited from 43 research groups from 37 institutes in 12 European countries (Belgium, Czech Republic, Finland, France, Germany, Hungary, Italy, the Netherlands, Portugal, Slovenia, Spain and the United Kingdom) and Canada. The work involved >300 collaborators in the submission, analysis and interpretation of rare-disease data. The RD-REAL framework allows sharing of data and expertise on a continental scale, consisting of (1) expert curated data, (2) a comprehensive analysis suite and (3) a two-level (that is, molecular and clinical) expert review. The complete dataset comprises 9,645 individuals from 6,004 families and includes phenotypes in Phenopacket format (average of six HPO terms per affected individual), pedigrees and genomic data (genomes and exomes). b, Illustration of the utility of this resource to the global rare-disease community. In total, RD-REAL data of >23,000 individuals with >100 million unique genomic variants are available via RD-Connect GPAP and EGA. This represents a growing resource containing data that have been submitted since the start of Solve-RD. Interpretable data (genetic variants, phenotypes and pedigrees) are standardized and annotated, and are made available for querying, analysis and interpretation in RD-Connect GPAP for authorized users. In addition, all raw and processed data are available for download at EGA under a controlled-access model. All icons, except logos of services (GPAP; EGA) and consortia/networks (Solve-RD; European Reference Networks) that are contributors of this publication, created with Biorender.com.
Systematic reanalysis of genomic datasets for the genetic diagnosis of rare diseases
a, Flowgram of systematic analysis of 6,004 families. Yield per analysis type (genetic diagnoses by SNV/InDel and other variant types; candidate genetic diagnoses and genetic diagnoses by ad hoc expert review) are shown. For SNV/InDels, we evaluated why the 464 variants previously identified in 419 families had not been classified as disease causing. b, Chart summarizing diagnostic yield across 6,004 families in Solve-RD. c, Chart summarizing yield per disease category (ERN); the denominator is 6,004 families. d, Chart summarizing the different variant types that led to a molecular diagnosis in 506 of 6,004 families as part of the systematic reanalysis effort of Solve-RD. aDisease-causing SNVs or short insertions/deletions were identified in 419 families. bDisease-causing non-SNV variants identified in 87 families, including three cases of compound heterozygosity involving an SNV and a CNV/SV, identified through the ‘other variant type’ analyses, and are counted only under ‘New genetic diagnosis other variant types’. cIn 114 of 147 cases where we could confirm the variant identified in the ad hoc analysis, we established that it would also have been found by the standard analysis. RD, rare disease; splicing SNV/InDel, noncanonical splicing sites; WG, work group.
Examples of ‘beyond standard’ variant types by Solve-RD
a–d, Illustrative examples of previously unsolved rare-disease probands for which a new variant other than a coding SNV/InDel resulted in a new diagnosis. a, De novo CNV affecting BICRA (P0012861). b, MEI variant in COL6A2 (P0014682). c, SV in SCN11A (P0011371). d, STR expansion affecting AR (P0002409).
Example of a new discovery by Solve-RD
a,b, An example of discoveries enabled by the Solve-RD resource. a, RAB14 de novo variants in two cases from this project contribute to the establishment of a new genotype–phenotype relationship. The first individual (P0012753) presents with mild global developmental delay in the absence of any facial dysmorphism or congenital anomalies, and carries a de novo variant in RAB14 (chr9:123952916G>A; NM_016322.3:c.200C>T; p.(Thr67Met)), which is rare (not observed in gnomAD v.2.1.1), likely to be deleterious (CADD score of 29) and has been observed de novo in at least four additional individuals with developmental disorders in the literature²³. The second individual (P0012904) presents with mild ID, subtle facial dysmorphisms comprising a high, square-shaped forehead, downslant of palpebral fissures and a low-hanging columella, in the absence of congenital anomalies. The de novo variant found in this individual (chr9:123954475A>C; NM_016322.3:c.80T>G; (p.(Leu27Trp)) is also absent from gnomAD, predicted to be deleterious (CADD score of 28) and has been observed de novo in at least one additional individual with a neurodevelopmental disorder in DECIPHER (https://www.deciphergenomics.org/patient/305550/phenotypes/person/62257). The female individual reported in Decipher presents with moderate ID, facial dysmorphism consisting of large earlobes, smooth philtrum, a wide mouth and protruding tongue, short feet with congenital talipes calcaneovalgus, thick hair and an umbilical hernia. b, Salent features of the two cases in a. aa, Amino acid.
Genomic reanalysis of a pan-European rare-disease resource yields new diagnoses

January 2025

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418 Reads

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4 Citations

Nature Medicine

Genetic diagnosis of rare diseases requires accurate identification and interpretation of genomic variants. Clinical and molecular scientists from 37 expert centers across Europe created the Solve-Rare Diseases Consortium (Solve-RD) resource, encompassing clinical, pedigree and genomic rare-disease data (94.5% exomes, 5.5% genomes), and performed systematic reanalysis for 6,447 individuals (3,592 male, 2,855 female) with previously undiagnosed rare diseases from 6,004 families. We established a collaborative, two-level expert review infrastructure that allowed a genetic diagnosis in 506 (8.4%) families. Of 552 disease-causing variants identified, 464 (84.1%) were single-nucleotide variants or short insertions/deletions. These variants were either located in recently published novel disease genes (n = 67), recently reclassified in ClinVar (n = 187) or reclassified by consensus expert decision within Solve-RD (n = 210). Bespoke bioinformatics analyses identified the remaining 15.9% of causative variants (n = 88). Ad hoc expert review, parallel to the systematic reanalysis, diagnosed 249 (4.1%) additional families for an overall diagnostic yield of 12.6%. The infrastructure and collaborative networks set up by Solve-RD can serve as a blueprint for future further scalable international efforts. The resource is open to the global rare-disease community, allowing phenotype, variant and gene queries, as well as genome-wide discoveries.


Citations (63)


... A large number of LRRK2 variants, numbering almost 200, are presently classified as variants of uncertain significance (VUS) (see https://www.mdsgene.org) 12 . Although in some cases co-occurrence with PD has been reported, data have been lacking from extended pedigrees (to assess co-segregation of the variant with disease), large case-control samples, and/or functional assays in model systems, to enable a more definitive determination of the pathogenicity of these VUS. ...

Reference:

Clinical and functional evidence for the pathogenicity of the LRRK2 p.Arg1067Gln variant
Updated MDSGene review on the clinical and genetic spectrum of LRRK2 variants in Parkinson´s disease

npj Parkinson s Disease

... Since these calls support relatively large genetic events (>100 kb), we clinically assessed them in the complete human genome. In contrast, clinical interpretation of SV calls corresponding to characterized deletions, inversions, duplications, and insertions (size <100 kb) was restricted to events that reside in genes within recently curated ERN-specific gene lists (Laurie et al. 2025). ...

Genomic reanalysis of a pan-European rare-disease resource yields new diagnoses

Nature Medicine

... While this approach may allow to identify more VUS and result in unclear diagnosis, it may allow to identify causative variants in genes beyond restricted gene panel testing. Furthermore, this approach may allow for re-analysis of data to yield future diagnosis when novel genes are identified or tools for variant detection in short read-sequencing data become available [32][33][34]. Second, the cases analyzed in this study were referred for genetic counseling and thus the cohort may be enriched for patients with a suspected family history and/or specific cancer type. For example, a relatively high number of cases in the studied cohort(s) developed breast cancer. ...

Comprehensive reanalysis for CNVs in ES data from unsolved rare disease cases results in new diagnoses

npj Genomic Medicine

... To date, more than 20 PD-causative genes have been identified. Moreover, more genetic risk genes and variants of sporadic PD phenotypes have been identified in various association studies [6,7]. The genetic variations related to PD provide much evidence for understanding the pathogenesis of PD. ...

Uncovering the genetic basis of Parkinson's disease globally: from discoveries to the clinic
  • Citing Article
  • October 2024

The Lancet Neurology

... Haplotype analysis in the seven Malaysian and Singaporean carriers, 307 Malaysian East Asian (EAS) controls, and 1220 Malaysian EAS PD patients negative for p.Arg1067Q, was performed with forty-one single nucleotide polymorphisms (SNPs) selected from Neurobooster Array (NBA) 26 , CENTOGENE, and whole exome datasets over a 140kbp interval across the p.Arg1067Gln variant. The p.Arg1067Gln variant did not appear to be located on any shared disease haplotype among the seven carriers, or on any rare sub-haplotype based on 18 of the 41 SNPs with an MAF of 0.01 (Supplementary Table 3), and the haplotypes of the seven carriers were similar to the haplotypes seen in the controls or p.Arg1067Gln-negative patients (Supplementary Table 4). ...

NeuroBooster Array: A Genome-Wide Genotyping Platform to Study Neurological Disorders Across Diverse Populations
  • Citing Article
  • September 2024

Movement Disorders

... GBA1-PD falls within this category. While this is the most common genetic cause of PD, based on the latest information coming from the ROPAD study showing a 10.4% positive GBA1 variant among 12,580 patients with PD [30], given the estimated number of patients in the USA suffering from PD being more than 1 million [31], this 10.4% falls within the definition of rare disease, which is less than 200,000 (https: //www.fda.gov/patients/rare-diseases-fda accessed on 14 February 2025). ...

Relevance of genetic testing in the gene-targeted trial era: the Rostock Parkinson's disease study

Brain

... Pathogenic variants in the LRRK2 gene are among the most common causes of autosomal dominant Parkinson's disease (PD) 1,2 and are thought to act through a gain-of-function mechanism that increases kinase activity 3 . The LRRK2 p.L1795F variant (chr12:40322386:G:T, hg38, rs111910483) has been shown to significantly enhance kinase activity, supporting its pathogenic role 4 . ...

Parkinson’s disease variant detection and disclosure: PD GENEration, a North American study
  • Citing Article
  • July 2024

Brain

... Further systematic studies in patients with rare diseases are needed to determine what reanalysis strategy is optimal and cost-effective, ideally implemented in healthcare systems, as exemplified in a recent collaborative study between German university hospitals [80]. Future advances in bioinformatics infrastructure could facilitate frequent automated reannotation of available genomic data using software-or artificial intelligence-based variant classification or interpretation [81,82] and integration with systematic phenotyping data with application programming interface (API) [83], thereby prioritizing variants for expert review. ...

Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings

Nature Genetics

... The utilization of genomic sequencing has seen a significant rise in the diagnosis of a wide array of diseases, including rare ones (40,44). In recent years, there has been a paradigm shift in diagnosing rare diseases of epigenetic origin (RDEOs) owing to the transformative impact of next-generation sequencing techniques. ...

Quality assurance for next-generation sequencing diagnostics of rare neurological diseases in the European Reference Network

European Journal of Human Genetics

... Over the past decade, the integration of WES into routine clinical diagnostics has increased due to its ability to enhance diagnostic yield. It has considerably improved the identification of genetic variants linked to diseases, making it invaluable for research and clinical applications [1][2][3][4]. However, despite becoming a firsttier genetic test [5,6], the laboratory procedure remains highly complicated and sensitive without unified standards or guidelines. ...

Structural variant calling and clinical interpretation in 6224 unsolved rare disease exomes

European Journal of Human Genetics