Abstract Background As clinical genetics evolves towards the broader field of clinical genomics, the diagnostic approach to rare diseases is undergoing a paradigm shift. This transformation has significantly impacted rare disease diagnostics, increasingly done through gene panels, whole exome and whole genome sequencing. To advance beyond genomics into precision medicine and encompass the breadth of relevant clinical scenarios, a true systems shift is required that challenges conventional barriers and enables the formation of cross-disciplinary, integrated environments. Methods The Genomic Medicine Center Karolinska Rare Diseases (GMCK-RD) has, for the past 10 years, brought together healthcare and academia to enable large-scale genome sequencing in a clinical diagnostics context. Within GMCK-RD, experts from various medical disciplines collaborate closely with clinical geneticists, bioinformaticians, and researchers to integrate genome sequencing into healthcare. Results In total, 15 644 individuals with suspected rare diseases were analyzed using clinical genome sequencing, including pediatric (48%), adult (48%) and fetal (4%) samples. The overall diagnostic yield was 22.6%, providing a diagnosis for 3 538 individuals with variants in 1 570 genes. Moreover, a rare disease analysis tool suite developed and validated in house includes a bioinformatic pipeline allowing for comprehensive data analysis covering a wide range of genetic variants including SNVs, INDELs, repeat expansions, uniparental disomies, balanced and unbalanced structural variants as well as insertions of mobile elements. Results are visualized and interpreted in custom-developed decision support systems functioning as an interpretation portal as well as a knowledge-base to capture the interpretation efforts made in a structured format allowing future secondary use. Conclusions Altogether, GMCK-RD has shifted healthcare in our region towards precision diagnostics. We emphasize the need to transition from traditional clinical genetic diagnostics to a broader clinical genomics approach. Beyond this shift, we advocate integrating genomics with specialized clinical and laboratory medicine, a concept pioneered for inborn errors of metabolism (IEM) with stepwise spread to additional disease groups. In this model, a multidisciplinary unit combines screening, targeted diagnostics, individualized treatment, and long-term patient follow-up. Here we provide a road map and guide for inspiration for centers aiming to implement genome sequencing in rare disease diagnostics.

Sweden has one neonatal screening laboratory and two centers conducting diagnostic workup for inborn errors of metabolism (IEM). Next-generation sequencing (NGS) has been gradually introduced as a confirmatory diagnostic test in the Swedish newborn screening program. Here, we describe the use of NGS in the diagnostic workup of IEM in screening-detected babies in Sweden between 2015 and 2023. During this period, 1,023,344 newborn children were screened, and 81 of 290 IEM cases were genetically confirmed using NGS. Planned improvements to the program are to perform genetic validation directly on the initial dried blood spot (DBS). As whole-genome sequencing (WGS) is superior in detecting causative genetic variants compared to Sanger sequencing, targeted NGS, and whole-exome sequencing (WES), it will likely become the method of choice more broadly in the future. A strong focus is to consolidate the nationally coordinated DBS newborn screening program, with all its individual components, including screening, targeted diagnostics, individualized treatment, and follow-up. This challenges the current regionalized organization of Swedish healthcare, which hinders close national collaboration between experts and sharing of data, as well as equal access to advanced treatments for identified patients, regardless of their place of birth.

Loss-of-function variants in the PRKN gene encoding the ubiquitin E3 ligase PARKIN cause autosomal recessive early-onset Parkinson’s disease (PD). Extensive in vitro and in vivo studies have reported that PARKIN is involved in multiple pathways of mitochondrial quality control, including mitochondrial degradation and biogenesis. However, these findings are surrounded by substantial controversy due to conflicting experimental data. In addition, the existing PARKIN-deficient mouse models have failed to faithfully recapitulate PD phenotypes. Therefore, we have investigated the mitochondrial role of PARKIN during ageing and in response to stress by employing a series of conditional Parkin knockout mice. We report that PARKIN loss does not affect oxidative phosphorylation (OXPHOS) capacity and mitochondrial DNA (mtDNA) levels in the brain, heart, and skeletal muscle of aged mice. We also demonstrate that PARKIN deficiency does not exacerbate the brain defects and the pro-inflammatory phenotype observed in mice carrying high levels of mtDNA mutations. To rule out compensatory mechanisms activated during embryonic development of Parkin -deficient mice, we generated a mouse model where loss of PARKIN was induced in adult dopaminergic (DA) neurons. Surprisingly, also these mice did not show motor impairment or neurodegeneration, and no major transcriptional changes were found in isolated midbrain DA neurons. Finally, we report a patient with compound heterozygous PRKN pathogenic variants that lacks PARKIN and has developed PD. The PARKIN deficiency did not impair OXPHOS activities or induce mitochondrial pathology in skeletal muscle from the patient. Altogether, our results argue that PARKIN is dispensable for OXPHOS function in adult mammalian tissues.

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)

BackgroundHomocystinuria (HCU) is a rare metabolic disease that affects many organs, including the eyes. Aims: to assess visual functions, ocular characteristics, visual quality of life and time from the onset of ocular manifestations to HCU-diagnosis in patients with HCU.Material and methodsEighteen patients underwent ophthalmological examinations and visual quality of life questionnaires.ResultsBest corrected decimal visual acuity was median 1.0 (range amaurosis - 1.3) right eye and 1.0 (range amaurosis -1.3) left eye. Five patients presented with severe myopia as first HCU manifestation, duration to HCU diagnosis was mean 13.6 years (range 2-25). Two patients had suffered ectopia lentis as first HCU manifestation, HCU diagnosis was established mean 8.0 years (range 7-9) later. One patient had suffered both from thrombosis and ectopia lentis prior to diagnosis. Another four patients suffered thromboembolic events before diagnosis. Median VFQ-25 composite score was 93 (68-98).ConclusionsThe prevalence of myopia, ectopia lentis and monocular blindness was high in HCU-patients, which was reflected in their visual quality of life. Diagnosis was often delayed after the first ocular manifestation, increasing the risk of other severe non-ocular complications.

Introduction: Brain calcifications are frequent findings on imaging. In a small proportion of cases, these calcifications are associated with pathogenic gene variants, hence termed primary familial brain calcification (PFBC). The clinical penetrance is incomplete and phenotypic variability is substantial. This paper aims to characterize a Swedish PFBC cohort including 25 patients: 20 from seven families and five sporadic cases. Methods: Longitudinal clinical assessment and CT imaging were conducted, abnormalities were assessed using the total calcification score (TCS). Genetic analyses, including a panel of six known PFBC genes, were performed in all index and sporadic cases. Additionally, three patients carrying a novel pathogenic copy number variant in SLC20A2 had their cerebrospinal fluid phosphate (CSF-Pi) levels measured. Results: Among the 25 patients, the majority (76%) displayed varying symptoms during the initial assessment including motor (60%), psychiatric (40%), and/or cognitive abnormalities (24%). Clinical progression was observed in most patients (78.6%), but there was no significant difference in calcification between the first and second scans, with mean scores of 27.3 and 32.8, respectively. In three families and two sporadic cases, pathogenic genetic variants were identified, including a novel finding, in the SLC20A2 gene. In the three tested patients, the CSF-Pi levels were normal. Conclusions: This report demonstrates the variable expressivity seen in PFBC and includes a novel pathogenic variant in the SLC20A2 gene. In four families and three sporadic cases, no pathogenic variants were found, suggesting that new PFBC genes remain to be discovered.

Background: Fabry disease (FD) is an X-linked inherited lysosomal storage disease that is caused by deficient activity of the enzyme alpha-galactosidase A. Cardiovascular magnetic resonance (CMR) imaging can detect cardiac sphingolipid accumulation using native T1 mapping. The kidneys are often visible in cardiac CMR native T1 maps; however, it is currently unknown if the maps can be used to detect sphingolipid accumulation in the kidneys of FD patients. Therefore, the aim of this study was to evaluate if cardiac-dedicated native T1 maps can be used to detect sphingolipid accumulation in the kidneys. Methods: FD patients (n = 18, 41 +/- 10 years, 44% (8/18) male) and healthy subjects (n = 38, 41 +/- 16 years, 47% (18/38) male) were retrospectively enrolled. Native T1 maps were acquired at 1.5T using modified Look-Locker inversion recovery research sequences. Native T1 values were measured by manually delineating regions of interest (ROI) in the renal cortex, renal medulla, heart, spleen, blood, and liver. Endo- and epicardial borders were delineated in the myocardium and averaged across all slices. Blood ROIs were placed in the left ventricular blood pool in the midventricular slice. Results: There were no differences in native T1 between the FD patients and the healthy subjects in the renal cortex (1034 +/- 88 ms vs 1056 +/- 59 ms, p = 0.29), blood (1614 +/- 111 ms vs 1576 +/- 100 ms, p = 0.22), spleen (1143 +/- 45 ms vs 1132 +/- 70 ms, p = 0.54), or liver (568 +/- 49 ms vs 557 +/- 47 ms, p = 0.41). Native myocardial T1 was lower in FD patients compared to healthy subjects (951 +/- 79 vs 1006 +/- 38, p<0.01), and higher in the renal medulla (1635 +/- 144 vs 1514 +/- 81, p<0.01). Conclusion: Compared to healthy subjects, patients with FD and cardiac involvement showed no differences in native T1 of the renal cortex. FD patients had higher native T1 in the renal medulla, which is not totally explained by differences in blood native T1 but may reflect a hyperfiltration state in the development of renal failure. The findings suggest that sphingolipid accumulation in the renal cortex in FD patients could not be detected with cardiac-dedicated research native T1 maps.

An increasing number of women with urea cycle disorders (UCDs) are reaching child-bearing age and becoming pregnant. Improved diagnostics and increased awareness of inherited metabolic diseases has also led to more previously undetected women being diagnosed with a UCD during or shortly after pregnancy. Pregnancy increases the risk of acute metabolic decompensation with hyperammonemia-which can occur in any trimester, and/or the postpartum period, and may lead to encephalopathy, psychosis, coma, and even death, if not diagnosed promptly and treated appropriately. There are also (theoretical) concerns that a maternal UCD, or its treatment, may cause potential risks for the unborn child. Currently evidence on management and outcome of pregnancies in UCDs is limited to case reports and there are no clear guidelines. In order to inform management and investigate outcomes of pregnancies in women with a UCD, we performed a retrospective review of published cases and analyzed data collected from an international online survey. We conclude that, although risk during the intra- and postpartum period exists, multidisciplinary management by an experienced team and a prospective plan usually result in successful pregnancy, labor, delivery, and postpartum period. No deaths were reported in mothers managed accordingly. With the exception of male neonates with Ornithine Transcarbamylase deficiency, the clinical outcome of children born to mothers with UCDs appears positive, although follow-up is limited. The outcome for women presenting with a first acute metabolic decompensation during pregnancy or postpartum is less favorable. Deaths were associated with diagnostic delay/late management of hyperammonemia in previously undiagnosed women.

Background Fabry disease (FD) is an X-linked lysosomal disease, in which diagnosis is often established several years after onset of symptoms. Ocular manifestations can occur in childhood and be a clue to earlier diagnosis. The aim was to report ocular outcome and visual quality of life (QoL) in patients with FD. Material and methods FD-patients recruited from Karolinska University Hospital underwent ophthalmological examinations including best corrected visual acuity (BCVA), refraction, biomicroscopy, optical coherence tomography, keratometry, review of medical records and QoL Inventories. A total severity score (TSS), as estimated via Fabry Stabilization Index, was calculated. Results Twenty-six FD-patients (16 men) mean age 36.4 years (range 5.0-63.5 years) were included. BCVA was median 1.0 (range 0.5-1.6). Conjunctival blood vessel tortuosity occurred in 15/26 patients, chemosis in 2/26 patients, cornea verticillata in 23/26 patients, lens opacities in 19/26 patients, and tortuous or dilated retinal vessels in 20/25 patients. Group-wise comparisons of adult patients showed no differences regarding age, TSS, or ocular parameters. Overall, TSS was correlated to age (r = 0.53, p = 0.02). A linear regression model showed that age and sex explained 38% of the variance in TSS. Keratometry did not reveal corneal ectasia in any of the 12 patients examined. VFQ 25 in 15 patients showed a high median composite score, 93.6 (range: 78.1-100). Conclusions BCVA in FD-patients was good despite corneal and lens pathology. Ocular variables did not show an association with TSS in adult patients. Corneal or lens opacities should also lead to a suspicion of FD in children.

Background We report the findings from 4437 individuals (3219 patients and 1218 relatives) who have been analyzed by whole genome sequencing (WGS) at the Genomic Medicine Center Karolinska-Rare Diseases (GMCK-RD) since mid-2015. GMCK-RD represents a long-term collaborative initiative between Karolinska University Hospital and Science for Life Laboratory to establish advanced, genomics-based diagnostics in the Stockholm healthcare setting. Methods Our analysis covers detection and interpretation of SNVs, INDELs, uniparental disomy, CNVs, balanced structural variants, and short tandem repeat expansions. Visualization of results for clinical interpretation is carried out in Scout-a custom-developed decision support system. Results from both singleton (84%) and trio/family (16%) analyses are reported. Variant interpretation is done by 15 expert teams at the hospital involving staff from three clinics. For patients with complex phenotypes, data is shared between the teams. Results Overall, 40% of the patients received a molecular diagnosis ranging from 19 to 54% for specific disease groups. There was heterogeneity regarding causative genes (n = 754) with some of the most common ones being COL2A1 (n = 12; skeletal dysplasia), SCN1A (n = 8; epilepsy), and TNFRSF13B (n = 4; inborn errors of immunity). Some causative variants were recurrent, including previously known founder mutations, some novel mutations, and recurrent de novo mutations. Overall, GMCK-RD has resulted in a large number of patients receiving specific molecular diagnoses. Furthermore, negative cases have been included in research studies that have resulted in the discovery of 17 published, novel disease-causing genes. To facilitate the discovery of new disease genes, GMCK-RD has joined international data sharing initiatives, including ClinVar, UDNI, Beacon, and MatchMaker Exchange. Conclusions Clinical WGS at GMCK-RD has provided molecular diagnoses to over 1200 individuals with a broad range of rare diseases. Consolidation and spread of this clinical-academic partnership will enable large-scale national collaboration.

Abstract Funding Acknowledgements Type of funding sources: Public Institution(s). Main funding source(s): Karolinska Institutet Swedish Heart and Lung foundation Introduction Fabry disease (FD) is a lysosomal disease that causes accumulation of sphingolipids, which untreated may leadto hypertrophic cardiomyopathyand renal failure. Cardiovascular magnetic resonance imaging (CMR) can detect sphingolipid accumulationin the heart, using native T1 mapping. The kidneys are often visible in clinically acquired native T1 maps, however it is currently unknown if clinically acquired native T1 maps of the heart also can be used to detect sphingolipid accumulation in the kidneysin FD patients. Purpose To evaluate if clinically acquired native T1 maps using CMR can be used to detect sphingolipid accumulation in the kidneysin FD patients. Methods FD patients (n = 18, 41 ± 10 years, 44 % male) and healthy volunteers (n = 41, 26 ± 5 years, 49 % male) were retrospectively enrolled. Native T1 maps were acquired with a 1.5 T scanner (Magnetom Aera, Siemens Healthineers, Erlangen, Germany) usinga modified look locker inversion recovery (MOLLI) sequence with a 5s(3s)3s sampling scheme (Siemens WIP 1041). The native T1 maps were analysed using Segment (Medviso AB, Lund, Sweden). Native T1 values were measured by manually delineating regions of interest (ROI), conservatively placed with a minimum gap of 1 pixel between adjacent structures, in the renal cortex, renal medulla, myocardium, spleen, blood, and liver. Renal cortex ROIs were delineated in all slices where the renal cortex was visible and averaged across all slices. Renal medulla, spleen, and liver ROIs were drawn in the slice where most parenchyma was visible. Endo- and epicardial borders were delineated in all slices of the myocardium and averaged across all slices. Blood ROIs were placed in the midventricular slice, Figure 1. Results There were no differences in native T1 values between the patients and the healthy volunteers in the renal cortex (1034 ± 88 vs 1038 ± 51 ms, p = 0.89), blood (1632 ± 123 vs 1600 ± 104 ms, p = 0.94), spleen (1143 ± 45 vs 1134 ± 77 ms, p = 0.64) or liver (569 ± 49 vs 576 ± 45 ms, p = 0.57), and did not change when analysed with regards to sex, Figure 2. Native T1-values were lower in the myocardium of the patients compared to the healthy volunteers (937 ± 53 vs 1019 ± 35 ms, p = 0.01), and higher in the renal medulla (1635 ± 144 vs 1523 ± 70 ms, p = 0.01). Conclusions Compared to healthy volunteers, patients with FD and myocardial involvement have no differences in native T1 of the renal cortex. FD patients have higher native T1 in the renal medulla, which cannot be explained by differences in blood native T1. The findings suggest that clinically acquired native T1-maps cannot be used to detect sphingolipid accumulation in the renal cortex in FD patients.

Hyperornithinemia-hyperammonemia-homocitrullinuria syndrome, a rare inherited urea cycle disorder, can remain undiagnosed for decades and suddenly turn into an acute life-threatening state. Adult presentation of hyperornithinemia-hyperammonemia-homocitrullinuria syndrome has rarely been described, but is potentially underdiagnosed in the emergency room. In the case of acute hyperammonemia, prompt diagnosis is essential to minimize the risk of brain damage and death.

Autoimmune polyendocrine syndrome type 1 (APS1) is a rare monogenic autoimmune disorder caused by mutations in the autoimmune regulator (AIRE) gene. High titer autoantibodies are a characteristic feature of APS1 and are often associated with particular disease manifestations. Pituitary deficits are reported in up to 7% of all APS1 patients, with immunoreactivity to pituitary tissue frequently reported. We aimed to isolate and identify specific pituitary autoantigens in patients with APS1. Immunoscreening of a pituitary cDNA expression library identified endothelin-converting enzyme (ECE)-2 as a potential candidate autoantigen. Immunoreactivity against ECE-2 was detected in 46% APS1 patient sera, with no immunoreactivity detectable in patients with other autoimmune disorders or healthy controls. Quantitative-PCR showed ECE-2 mRNA to be most abundantly expressed in the pancreas with high levels also in the pituitary and brain. In the pancreas ECE-2 was co-expressed with insulin or somatostatin, but not glucagon and was widely expressed in GH producing cells in the guinea pig pituitary. The correlation between immunoreactivity against ECE-2 and the major recognized clinical phenotypes of APS1 including hypopituitarism was not apparent. Our results identify ECE-2 as a specific autoantigen in APS1 with a restricted neuroendocrine distribution.

Inherited metabolic diseases usually present in the neonatal period or before school age. A growing portion of the disorders can be treated successfully, and an increasing number of patients are now treated in adult medicine. Several of the disorders also exist as attenuated variants without distinct symptoms in childhood. They can present as an acute onset event during metabolic stress in adulthood. We describe three patients with acute clinical decompensation in adulthood with severe sequelae and propose investigations to help diagnose such patients. One patient was unconscious from ammonia intoxication and developed severe neurological sequelae because of a defect in the urea cycle. A second patient had seizures caused by a defect in the conversion of homocysteine to methionine, resulting in lack of S-adenosylmethionine. A third patient had a stroke and grossly elevated homocysteine caused by undiagnosed homocystinuria. Recently there have been dramatic improvements in diagnostic methods, and new therapies are continuously being developed. Knowledge of these disorders is therefore of increasing importance also in adult medicine.

Autoimmune polyendocrine syndrome type 1 (APS1) is a rare monogenic autoimmune disorder caused by mutations in the autoimmune regulator (AIRE) gene. High‐titre autoantibodies are a characteristic feature of APS1 and are often associated with particular disease manifestations. Pituitary deficits are reported in approximately 7% of APS1 patients, with immunoreactivity to pituitary tissue frequently described. Using APS1 patient serum to immunoscreen a pituitary cDNA expression library, testis specific, 10 (TSGA10) was isolated. Immunoreactivity against TSGA10 was detected in 5/99 (5.05%) patients with APS1, but also in 5/135 (3.70%) systemic lupus erythematosus (SLE) patients and 1/188 (0.53%) healthy controls. TSGA10 autoantibodies were not detected in the serum from patients with any other autoimmune disease. Autoantibodies against TSGA10 were detectable from a young age in 4/5 positive APS1 patients with autoantibody titres remaining relatively constant over time. Furthermore, real‐time PCR confirmed TSGA10 mRNA to be most abundantly expressed in the testis and also showed moderate and low expression levels throughout the entire body. TSGA10 should be considered as an autoantigen in a subset of APS1 patients and also in a minority of SLE patients. No recognizable clinical phenotype could be found to correlate with positive autoantibody reactivity.

The distal region on the short arm of chromosome 9 is of special interest for scientists interested in sex development as well as in the clinical phenotype of patients with the 9p deletion syndrome, characterized by mental retardation, trigonocephaly and other dysmorphic features. Specific genes responsible for different aspects of the phenotype have not been identified. Distal 9p deletions have also been reported in patients with 46,XY sex reversal, with or without 9p deletion syndrome. Within this region the strongest candidates for the gonadal dysgenesis phenotype are the DMRT genes; however, the genetic mechanism is not clear yet. Multiple ligation-dependent probe amplification represents a useful technique to evaluate submicroscopic interstitial or distal deletions that would help the definition of the minimal sex reversal region on 9p and could lead to the identification of gene(s) responsible of the 46,XY gonadal disorders of sex development (DSD). We designed a synthetic probe set that targets genes within the 9p23-9p24.3 region and analyzed a group of XY patients with impaired gonadal development. We characterized a deletion distal to the DMRT genes in a patient with isolated 46,XY gonadal DSD and narrowed down the breakpoint in a patient with a 46,XY del(9)(p23) karyotype with gonadal DSD and mild symptoms of 9p deletion syndrome. The results are compared with other patients described in the literature, and new aspects of sex reversal and the 9p deletion syndrome candidate regions are discussed.