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Background: Serine residues in the protein backbone of heavily glycosylated proteoglycans are bound to glycosaminoglycans through a tetrasaccharide linker. UXS1 encodes UDP‐glucuronate decarboxylase 1, which catalyzes synthesis of UDP‐xylose, the donor of the first building block in the linker. Defects in other enzymes involved in formation of the tetrasaccharide linker cause so‐called linkeropathies, characterized by short stature, radio‐ulnar synostosis, decreased bone density, congenital contractures, dislocations, and more. Methods: Whole exome sequencing was performed in a father and son who presented with a mild skeletal dysplasia, as well as the father's unaffected parents. Wild‐type and mutant UXS1 were recombinantly expressed in Escherichia coli and purified. Enzyme activity was evaluated by LC–MS/MS. In vivo effects were studied using HeparinRed assay and metabolomics. Results: The son had short long bones, normal epiphysis, and subtle metaphyseal changes especially in his legs. The likely pathogenic heterozygous variant NM_001253875.1(UXS1):c.557T>A p.(Ile186Asn) detected in the son was de novo in the father. Purified Ile186Asn‐UXS1, in contrast to the wild‐type, was not able to convert UDP‐glucuronic acid to UDP‐xylose. Plasma glycosaminoglycan levels were decreased in both son and father. Conclusion: This is the first report linking UXS1 to short‐limbed short stature in humans. [ABSTRACT FROM AUTHOR]

Abstract Background Serine residues in the protein backbone of heavily glycosylated proteoglycans are bound to glycosaminoglycans through a tetrasaccharide linker. UXS1 encodes UDP‐glucuronate decarboxylase 1, which catalyzes synthesis of UDP‐xylose, the donor of the first building block in the linker. Defects in other enzymes involved in formation of the tetrasaccharide linker cause so‐called linkeropathies, characterized by short stature, radio‐ulnar synostosis, decreased bone density, congenital contractures, dislocations, and more. Methods Whole exome sequencing was performed in a father and son who presented with a mild skeletal dysplasia, as well as the father's unaffected parents. Wild‐type and mutant UXS1 were recombinantly expressed in Escherichia coli and purified. Enzyme activity was evaluated by LC–MS/MS. In vivo effects were studied using HeparinRed assay and metabolomics. Results The son had short long bones, normal epiphysis, and subtle metaphyseal changes especially in his legs. The likely pathogenic heterozygous variant NM_001253875.1(UXS1):c.557T>A p.(Ile186Asn) detected in the son was de novo in the father. Purified Ile186Asn‐UXS1, in contrast to the wild‐type, was not able to convert UDP‐glucuronic acid to UDP‐xylose. Plasma glycosaminoglycan levels were decreased in both son and father. Conclusion This is the first report linking UXS1 to short‐limbed short stature in humans.

Background: Automation has been introduced into variant interpretation, but it is not known how automated variant interpretation performs on a stand‐alone basis. The purpose of this study was to evaluate a fully automated computerized approach. Method: We reviewed all variants encountered in a set of carrier screening panels over a 1‐year interval. Observed variants with high‐confidence ClinVar interpretations were included in the analysis; those without high‐confidence ClinVar entries were excluded. Results: Discrepancy rates between automated interpretations and high‐confidence ClinVar entries were analyzed. Of the variants interpreted as positive (likely pathogenic or pathogenic) based on ClinVar information, 22.6% were classified as negative (variants of uncertain significance, likely benign or benign) variants by the automated method. Of the ClinVar negative variants, 1.7% were classified as positive by the automated software. On a per‐case basis, which accounts for variant frequency, 63.4% of cases with a ClinVar high‐confidence positive variant were classified as negative by the automated method. Conclusion: While automation in genetic variant interpretation holds promise, there is still a need for manual review of the output. Additional validation of automated variant interpretation methods should be conducted. [ABSTRACT FROM AUTHOR]

Abstract Background Automation has been introduced into variant interpretation, but it is not known how automated variant interpretation performs on a stand‐alone basis. The purpose of this study was to evaluate a fully automated computerized approach. Method We reviewed all variants encountered in a set of carrier screening panels over a 1‐year interval. Observed variants with high‐confidence ClinVar interpretations were included in the analysis; those without high‐confidence ClinVar entries were excluded. Results Discrepancy rates between automated interpretations and high‐confidence ClinVar entries were analyzed. Of the variants interpreted as positive (likely pathogenic or pathogenic) based on ClinVar information, 22.6% were classified as negative (variants of uncertain significance, likely benign or benign) variants by the automated method. Of the ClinVar negative variants, 1.7% were classified as positive by the automated software. On a per‐case basis, which accounts for variant frequency, 63.4% of cases with a ClinVar high‐confidence positive variant were classified as negative by the automated method. Conclusion While automation in genetic variant interpretation holds promise, there is still a need for manual review of the output. Additional validation of automated variant interpretation methods should be conducted.

Background: Noninvasive prenatal diagnosis (NIPD) based on cell‐free DNA (cfDNA) has been introduced into the clinical application for some monogenic disorders but not for tuberous sclerosis (TSC) yet, which is an autosomal dominant disease caused by various variations in TSC1 or TSC2 gene. We aimed to explore the feasibility of NIPD on TSC. Methods: We recruited singleton pregnancies at risk of TSC from 14 families with a proband child. Definitive NIPD for TSC was performed using targeted next‐generation sequencing of cfDNA in parallel with maternal white blood cell DNA (wbcDNA). The NIPD results were validated by amniocentesis or postnatal gene testing and follow‐up of the born children. Results: Missense mutations, nonsense mutations, frameshift mutations, and splice‐site variants which were obtained through de‐novo, maternal, or paternal inheritance were included. The mean and minimum gestational weeks of NIPD were 17.18 ± 5.83 and 8 weeks, respectively. The NIPD results were 100% consistent with the amniocentesis or postnatal gene testing and follow‐up of the born children. Conclusion: This study demonstrates that NIPD based on cfDNA is feasible for TSC, but required to be confirmed with more samples. Studies on TSC can contribute to the application and promotion of NIPD for monogenic disorders. [ABSTRACT FROM AUTHOR]

Abstract Background Noninvasive prenatal diagnosis (NIPD) based on cell‐free DNA (cfDNA) has been introduced into the clinical application for some monogenic disorders but not for tuberous sclerosis (TSC) yet, which is an autosomal dominant disease caused by various variations in TSC1 or TSC2 gene. We aimed to explore the feasibility of NIPD on TSC. Methods We recruited singleton pregnancies at risk of TSC from 14 families with a proband child. Definitive NIPD for TSC was performed using targeted next‐generation sequencing of cfDNA in parallel with maternal white blood cell DNA (wbcDNA). The NIPD results were validated by amniocentesis or postnatal gene testing and follow‐up of the born children. Results Missense mutations, nonsense mutations, frameshift mutations, and splice‐site variants which were obtained through de‐novo, maternal, or paternal inheritance were included. The mean and minimum gestational weeks of NIPD were 17.18 ± 5.83 and 8 weeks, respectively. The NIPD results were 100% consistent with the amniocentesis or postnatal gene testing and follow‐up of the born children. Conclusion This study demonstrates that NIPD based on cfDNA is feasible for TSC, but required to be confirmed with more samples. Studies on TSC can contribute to the application and promotion of NIPD for monogenic disorders.