Cell-free DNA (cfDNA) analysis has become essential in cancer diagnostics and prenatal testing. We present cfNOMe, a two-in-one method of measuring cfDNA cytosine methylation and nucleosome occupancy ...in a single assay using non-disruptive enzymatic cytosine conversion and a custom bioinformatic pipeline. We show that enzymatic cytosine conversion better preserves cfDNA fragmentation information than does bisulfite conversion. Whereas previously separate experiments were required to study either epigenetic marking, cfNOMe delivers reliable results for both, enabling more comprehensive and inexpensive epigenetic cfDNA profiling. cfNOMe has the potential to advance biomarker discovery and diagnostic usage in diseases with systemic perturbations of cfDNA composition.
Counseling recurrence risks for monogenic disorders is one of the mainstays of human genetics. However, in practice, consultations concerning autosomal recessive disorders exceed the simple ...conveyance of a 25 % recurrence risk for future offspring. Medical geneticists should be aware of the multifaceted way in which autosomal recessive disorders can pose a diagnostic and counseling challenge in their daily lives and of the pitfalls they might encounter. Although the intentional or incidental detection of carrier states for autosomal recessive diseases happens more and more frequently, our current practice when clarifying their associated reproductive risks remains unsystematic and often subjectively guided. We question whether the approach of focusing on small recurrence risks for a single familial disease with extensive single-gene tests in the partner of a known carrier truly addresses the counseling needs of a couple seeking preconceptional genetic advice. Different perspectives between patients and medical practitioners (or between different medical practitioners) on “acceptable risks” or the extent to which such risks must be minimized raise the question of whether existing professional guidelines need to be clarified.
The adult phenotype of Schaaf-Yang syndrome Marbach, Felix; Elgizouli, Magdeldin; Rech, Megan ...
Orphanet journal of rare diseases,
10/2020, Letnik:
15, Številka:
1
Journal Article
Recenzirano
Odprti dostop
MAGEL2-associated Schaaf-Yang syndrome (SHFYNG, OMIM #615547, ORPHA: 398069), which was identified in 2013, is a rare disorder caused by truncating variants of the paternal copy of MAGEL2, which is ...localized in the imprinted region on 15q11.2q13. The phenotype of SHFYNG in childhood partially overlaps with that of the well-established Prader-Willi syndrome (PWS, OMIM #176270). While larger numbers of younger individuals with SHFYNG have been recently published, the phenotype in adulthood is not well established. We recruited 7 adult individuals (aged 18 to 36) with molecularly confirmed SHFYNG and collected data regarding the clinical profile including eating habits, sleep, behavior, personal autonomy, psychiatric abnormalities and other medical conditions, as well as information about the respective phenotypes in childhood. Within our small cohort, we identified a range of common features, such as disturbed sleep, hypoactivity, social withdrawal and anxiety, but also noted considerable differences at the level of personal autonomy and skills. Behavioral problems were frequent, and a majority of individuals displayed weight gain and food-seeking behavior, along with mild intellectual disability or borderline intellectual function. Classical symptoms of SHFYNG in childhood were reported for most individuals. Our findings indicate a high variability of the functional abilities and social participation of adults with SHFYNG. A high prevalence of obesity within our cohort was notable, and uncontrollable food intake was a major concern for some caregivers. The phenotypes of PWS and SHFYNG in adulthood might be more difficult to discern than the phenotypes in childhood. Molecular genetic testing for SHFYNG should therefore be considered in adults with the suspected diagnosis of PWS, if testing for PWS has been negative.
Background Long-read sequencing is increasingly used to uncover structural variants in the human genome, both functionally neutral and deleterious. Structural variants occur more frequently in ...regions with a high homology or repetitive segments, and one rearrangement may predispose to additional events. Bartter syndrome type 3 (BS 3) is a monogenic tubulopathy caused by deleterious variants in the chloride channel gene CLCNKB, a high proportion of these being large gene deletions. Multiplex ligation-dependent probe amplification, the current diagnostic gold standard for this type of mutation, will indicate a simple homozygous gene deletion in biallelic deletion carriers. However, since the phenotypic spectrum of BS 3 is broad even among biallelic deletion carriers, we undertook a more detailed analysis of precise breakpoint regions and genomic structure. Methods Structural variants in 32 BS 3 patients from 29 families and one BS4b patient with CLCNKB deletions were investigated using long-read and synthetic long-read sequencing, as well as targeted long-read sequencing approaches. Results We report a ~3 kb duplication of 3'-UTR CLCNKB material transposed to the corresponding locus of the neighbouring CLCNKA gene, also found on ~50 % of alleles in healthy control individuals. This previously unknown common haplotype is significantly enriched in our cohort of patients with CLCNKB deletions (45 of 51 alleles with haplotype information, 2.2 kb and 3.0 kb transposition taken together, p=9.16x10.sup.-9). Breakpoint coordinates for the CLCNKB deletion were identifiable in 28 patients, with three being compound heterozygous. In total, eight different alleles were found, one of them a complex rearrangement with three breakpoint regions. Two patients had different CLCNKA/CLCNKB hybrid genes encoding a predicted CLCNKA/CLCNKB hybrid protein with likely residual function. Conclusions The presence of multiple different deletion alleles in our cohort suggests that large CLCNKB gene deletions originated from many independently recurring genomic events clustered in a few hot spots. The uncovered associated sequence transposition haplotype apparently predisposes to these additional events. The spectrum of CLCNKB deletion alleles is broader than expected and likely still incomplete, but represents an obvious candidate for future genotype/phenotype association studies. We suggest a sensitive and cost-efficient approach, consisting of indirect sequence capture and long-read sequencing, to analyse disease-relevant structural variant hotspots in general. Keywords: Bartter syndrome type 3, Salt-wasting tubulopathy, Long-read sequencing, Target enrichment, CLCNKA, CLCNKB, Structural variant, Risk haplotype, Next-generation sequencing, HiFi-sequencing
Lipopolysaccharide-responsive and beige-like anchor protein (LRBA) deficiency is characterized by autoimmunity, chronic diarrhea, and immunodeficiency. Minor renal manifestations have been found in a ...few patients, but kidney disease has not been systematically studied and may remain underdiagnosed in this highly variable entity.
Our patient initially presented with pancytopenia, enteropathy, hypogammaglobulinemia, and failure to thrive at the age of 15 months. Chronic kidney disease was diagnosed at 6 years. A renal biopsy taken at 11 years of age showed interstitial nephritis. The patient progressed rapidly to end-stage renal disease (ESRD) and underwent kidney transplantation at the age of 12 years. Bronchiolitis obliterans, post-transplant lymphoproliferative disease (PTLD), and chronic rejection complicated the post-transplant management. Graft loss required reinstitution of hemodialysis within 3 years. After negative results of different targeted sequencing strategies, exome sequencing identified a homozygous nonsense mutation (p.Q1010
) in the
gene more than 21 years after the patient's initial presentation.
We report here the development of ESRD and long-term follow-up in a patient with LRBA deficiency. A molecular diagnosis in rare (kidney) disease like LRBA deficiency bears many advantages over a descriptive diagnosis. A precise diagnosis may result in improved (symptomatic) treatment and allows differentiating treatment- and procedure-related complications from manifestations of the primary disease.
Zusammenfassung
Hintergrund
Die Grundlage der arteriellen Hypertonie bei der überwiegenden Mehrzahl der Patienten ist multifaktorieller, zum großen Teil umweltbedingter Genese und derzeit in der ...Routinediagnostik nicht sinnvoll molekulargenetisch untersuchbar. Bei einem kleinen Teil der Patienten (<1 %) ist die arterielle Hypertonie aber Folge hereditärer, monogener Defekte. Hierzu gehören das Liddle-Syndrom, familiärer Hyperaldosteronismus, apparenter Mineralkortikoidexzess und Pseudohypoaldosteronismus. Diese und andere hereditäre Hypertonien gehen pathomechanistisch auf Störungen in den renalen Regelkreisen der Elektrolyt- und Volumenhomöostase zurück.
Ziel der Arbeit
Die bekannten Typen der hereditären Hypertonien sollen verständlich und schematisch erläutert werden. Besonderer Fokus liegt dabei auch auf dem klinischen Bild der jeweiligen Unterformen sowie der therapeutischen Konsequenz, die sich in dieser Krankheitsgruppe direkt aus dem molekulargenetischen Befund ergeben kann. Eine Auswahl weiterer genetischer Syndrome mit arterieller Hypertonie als Begleit- oder Spätsymptom wird zusammenfassend behandelt.
Fazit
Die korrekte Diagnose eines Betroffenen mit einer Form der hier beschriebenen hereditären Hypertonien ermöglicht eine gezielte und effektive medikamentöse Therapie auf Basis der inzwischen insgesamt gut verstandenen jeweiligen Pathomechanismen.
Zusammenfassung
Hintergrund
Die Grundlage der arteriellen Hypertonie bei der überwiegenden Mehrzahl der Patienten ist multifaktorieller, zum großen Teil umweltbedingter Genese und derzeit in der ...Routinediagnostik nicht sinnvoll molekulargenetisch untersuchbar. Bei einem kleinen Teil der Patienten (<1 %) ist die arterielle Hypertonie aber Folge hereditärer, monogener Defekte. Hierzu gehören das Liddle-Syndrom, familiärer Hyperaldosteronismus, apparenter Mineralkortikoidexzess und Pseudohypoaldosteronismus. Diese und andere hereditäre Hypertonien gehen pathomechanistisch auf Störungen in den renalen Regelkreisen der Elektrolyt- und Volumenhomöostase zurück.
Ziel der Arbeit
Die bekannten Typen der hereditären Hypertonien sollen verständlich und schematisch erläutert werden. Besonderer Fokus liegt dabei auch auf dem klinischen Bild der jeweiligen Unterformen sowie der therapeutischen Konsequenz, die sich in dieser Krankheitsgruppe direkt aus dem molekulargenetischen Befund ergeben kann. Eine Auswahl weiterer genetischer Syndrome mit arterieller Hypertonie als Begleit- oder Spätsymptom wird zusammenfassend behandelt.
Fazit
Die korrekte Diagnose eines Betroffenen mit einer Form der hier beschriebenen hereditären Hypertonien ermöglicht eine gezielte und effektive medikamentöse Therapie auf Basis der inzwischen insgesamt gut verstandenen jeweiligen Pathomechanismen.
Innate immunity triggers responsible for viral control or hyperinflammation in COVID‐19 are largely unknown. Here we show that the SARS‐CoV‐2 spike protein (S‐protein) primes inflammasome formation ...and release of mature interleukin‐1β (IL‐1β) in macrophages derived from COVID‐19 patients but not in macrophages from healthy SARS‐CoV‐2 naïve individuals. Furthermore, longitudinal analyses reveal robust S‐protein‐driven inflammasome activation in macrophages isolated from convalescent COVID‐19 patients, which correlates with distinct epigenetic and gene expression signatures suggesting innate immune memory after recovery from COVID‐19. Importantly, we show that S‐protein‐driven IL‐1β secretion from patient‐derived macrophages requires non‐specific monocyte pre‐activation in vivo to trigger NLRP3‐inflammasome signaling. Our findings reveal that SARS‐CoV‐2 infection causes profound and long‐lived reprogramming of macrophages resulting in augmented immunogenicity of the SARS‐CoV‐2 S‐protein, a major vaccine antigen and potent driver of adaptive and innate immune signaling.
SYNOPSIS
SARS‐CoV‐2 infection leads to hyperinflammatory syndromes in a subset of patients. We show that human primary macrophages require genome‐wide transcriptional modifications for pro‐inflammatory signaling upon stimulation with the SARS‐CoV‐2 surface glycoprotein (S‐protein).
The SARS‐CoV‐2 spike protein drives NRLP3 inflammasome activation in COVID‐19 patient derived macrophages.
Macrophages from SARS‐CoV‐2 naïve individuals fail to process and subsequently secrete IL‐1β upon stimulation with the S‐protein.
The S‐protein is a pathogen‐associated molecular pattern (PAMP) requiring macrophage pre‐activation for NLRP3 inflammasome formation.
Inflammasome activation and IL‐1β signaling represent attractive targets for pharmacological interventions in severe COVID‐19.
SARS‐CoV‐2 infection leads to hyperinflammatory syndromes in a subset of patients. We show that human primary macrophages require genome‐wide transcriptional modifications for pro‐inflammatory signaling upon stimulation with the SARS‐CoV‐2 surface glycoprotein (S‐protein).
Primary hyperoxaluria type 2 is a rare inherited disorder of glyoxylate metabolism causing nephrocalcinosis, renal stone formation and ultimately kidney failure. Previously, primary hyperoxaluria ...type 2 was considered to have a more favorable prognosis than primary hyperoxaluria type 1, but earlier reports are limited by low patient numbers and short follow up periods. Here we report on the clinical, genetic, and biochemical findings from the largest cohort of patients with primary hyperoxaluria type 2, obtained by a retrospective record review of genetically confirmed cases in the OxalEurope registry, a dataset containing 101 patients from eleven countries. Median follow up was 12.4 years. Median ages at first symptom and diagnosis for index cases were 3.2 years and 8.0 years, respectively. Urolithiasis was the most common presenting feature (82.8% of patients). Genetic analysis revealed 18 novel mutations in the GRHPR gene. Of 238 spot-urine analyses, 23 (9.7%) were within the normal range for oxalate as compared to less than 4% of 24-hour urine collections. Median intra-individual variation of 24-hour oxalate excretion was substantial (34.1%). At time of review, 12 patients were lost to follow-up; 45 of the remaining 89 patients experienced chronic kidney disease stage 2 or greater and 22 patients had reached stage 5. Median renal survival was 43.3 years, including 15 kidney transplantations in 11 patients (1 combined with liver transplantation). Renal outcome did not correlate with genotype, biochemical parameters or initially present nephrocalcinosis. Thus, primary hyperoxaluria type 2 is a disease with significant morbidity. Accurate diagnosis by 24-hour urine analysis and genetic testing are required with careful follow-up.
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