The GALNS p.P77R variant is a probable Gujarati-Indian founder mutation causing Mucopolysaccharidosis IVA syndrome
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ABSTRACT:
PROVIDER: PRJEB51874 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR9451600_1.fastq.gz | Fastqsanger.gz | |||
| ERR9451600_2.fastq.gz | Fastqsanger.gz | |||
| ERR9451610_1.fastq.gz | Fastqsanger.gz | |||
| ERR9451610_2.fastq.gz | Fastqsanger.gz | |||
| ERR9451620_1.fastq.gz | Fastqsanger.gz |
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Project description:BackgroundMucopolysaccharidosis IVA (Morquio syndrome A, MPS IVA) is an autosomal recessive lysosomal storage disorder caused due to biallelic variants in the N-acetylgalactoseamine-6-sulfate sulfatase (GALNS) gene. The mutation spectrum in this condition is determined amongst sub-populations belonging to the north, south and east India geography, however, sub-populations of west Indian origin, especially Gujarati-Indians, are yet to be studied. We aimed to analyse the variants present in the GLANS gene amongst the population of Gujarat by sequencing all exons and exon-intron boundaries of the GALNS gene in patients from 23 unrelated families.ResultsWe report 11 variants that include eight missense variants: (p.L36R, p.D39G, p.P77R, p.C79R, pP125L, p.P151L, p.G255A and p.L350P), one splice site variant: (c.121-7C > G), one small insertion: (c.1241_1242insA, p.I416HfsTer2) and one small deletion: (c.839_841delACA). Of these, three missense variants (p.D39G, p.G255A and p.L350P), one splice site and the two indels mentioned above are novel. Interestingly, we observed a higher than anticipated prevalence of p.P77R variant in our cohort (n = 14/25, 56%). Haplotype analysis in cases with p.P77R variant and 63 ethnicity matched healthy population controls suggested a 4 SNP haplotype block present in cases compared to controls (likelihood ratio test p-value = 1.16 × 10-13), thereby suggesting p.P77R variant as a founder variant in the Gujarati-Indian population. Furthermore, age of mutation analysis suggested the variant to have arisen approximately 450 years ago in the population.Conclusionp.P77R variant in the GLANS gene is likely to be a founder variant in MPS IVA patients of Gujarati-Indian ancestry and appeared approximately 450 years ago in the population. To our knowledge, this is the first variant to be posited as a founder variant in the GLANS gene in patients with MPS IVA syndrome.
| S-EPMC9210747 | biostudies-literature
Project description:Mucopolysaccharidoses (MPS) type IVA is a lysosomal storage disease that mainly affects the skeletal system and is caused by a deficiency of the enzyme N-acetylgalactosamine-6-sulfatase (GALNS). The condition can mistakenly be diagnosed as a primary skeletal dysplasia such as spondylo-epiphyseal dysplasia, which shares many similar phenotypic features. Here, we utilised whole exome sequencing to make the diagnosis of MPS IVA in a resource poor country. We report for the first time the identification of a biallelic GALNS missense variant (c.697G>A, p.Asp233Asn) in the Pakistani population and highlight the potential contribution that academic institutions can make in rare disease diagnosis in the absence of a developed clinical genetic service.
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Project description:Mucopolysaccharidosis IVA (MPS IVA; Morquio A syndrome) is an autosomal recessive lysosomal storage disorder resulting from a deficiency of N-acetylgalactosamine-6-sulfate sulfatase (GALNS) activity. Diagnosis can be challenging and requires agreement of clinical, radiographic, and laboratory findings. A group of biochemical genetics laboratory directors and clinicians involved in the diagnosis of MPS IVA, convened by BioMarin Pharmaceutical Inc., met to develop recommendations for diagnosis. The following conclusions were reached. Due to the wide variation and subtleties of radiographic findings, imaging of multiple body regions is recommended. Urinary glycosaminoglycan analysis is particularly problematic for MPS IVA and it is strongly recommended to proceed to enzyme activity testing even if urine appears normal when there is clinical suspicion of MPS IVA. Enzyme activity testing of GALNS is essential in diagnosing MPS IVA. Additional analyses to confirm sample integrity and rule out MPS IVB, multiple sulfatase deficiency, and mucolipidoses types II/III are critical as part of enzyme activity testing. Leukocytes or cultured dermal fibroblasts are strongly recommended for enzyme activity testing to confirm screening results. Molecular testing may also be used to confirm the diagnosis in many patients. However, two known or probable causative mutations may not be identified in all cases of MPS IVA. A diagnostic testing algorithm is presented which attempts to streamline this complex testing process.
| S-EPMC3590423 | biostudies-literature
Project description:Cancer is predominantly a somatic disease. A mutant allele found in cancer cell genome is considered somatic when it is absent in paired normal genome and dbSNP, the most comprehensive public SNP database. However, dbSNP inadequately represents several non-Caucasian populations including that from the Indian subcontinent, posing a limitation in cancer genomic analyses of data from these populations. We present TMC-SNPdb, as the first open source freely accessible (through ANNOVAR), flexible and upgradable SNP database from whole exome data of 62 normal samples derived from cancer patients of Indian origin, representing 114,309 unique germline variants. TMC-SNPdb is presented with a companion subtraction tool that can be executed with command line option or an easy-to-use graphical user interface (GUI) with the ability to deplete additional Indian population specific SNPs over and above that possible with dbSNP and 1000 Genomes databases. Using an institutional generated whole exome data set of 132 samples of Indian origin, we demonstrate that TMC-SNPdb reduced 42%, 33% and 28% false positive somatic events post dbSNP depletion in Indian origin tongue, gallbladder, and cervical cancer samples, respectively. Beyond cancer somatic analyses, we anticipate utility of TMC-SNPdb in several Mendelian germline diseases.
2018-06-06 | E-MTAB-4618 | biostudies-arrayexpress
Project description:Mucopolysaccharidosis IVA (MPS IVA; Morquio A: OMIM 253000) is a lysosomal storage disease with an autosomal recessive trait caused by the deficiency of N-acetylgalactosamine-6-sulfate sulfatase. Deficiency of this enzyme leads to accumulation of specific glycosaminoglycans (GAGs): chondroitin-6-sulfate (C6S) and keratan sulfate (KS). C6S and KS are mainly produced in the cartilage. Therefore, the undegraded substrates are stored primarily in cartilage and in its extracellular matrix (ECM), leading to a direct impact on cartilage and bone development, and successive systemic skeletal dysplasia. Chondrogenesis, the earliest phase of skeletal formation, is maintained by cellular interactions with the ECM, growth and differentiation factors, signaling pathways, and transcription factors in a temporal-spatial manner. In patients with MPS IVA, the cartilage is disrupted at birth as a consequence of abnormal chondrogenesis and/or endochondral ossification. The unique skeletal features are distinguished by a disproportional short stature, odontoid hypoplasia, spinal cord compression, tracheal obstruction, pectus carinatum, kyphoscoliosis, platyspondyly, coxa valga, genu valgum, waddling gait, and laxity of joints. In spite of many descriptions of these unique clinical features, delay of diagnosis still happens. The pathogenesis and treatment of systemic skeletal dysplasia in MPS IVA remains an unmet challenge. In this review article, we comprehensively describe historical aspect, property of GAGs, diagnosis, screening, pathogenesis, and current and future therapies of MPS IVA.
| S-EPMC5293636 | biostudies-literature
Project description:Mucopolysaccharidosis type IVA (MPS IVA, or Morquio syndrome type A) is an inherited metabolic lysosomal disease caused by the deficiency of the N-acetylglucosamine-6-sulfate sulfatase enzyme. The deficiency of this enzyme accumulates the specific glycosaminoglycans (GAG), keratan sulfate, and chondroitin-6-sulfate mainly in bone, cartilage, and its extracellular matrix. GAG accumulation in these lesions leads to unique skeletal dysplasia in MPS IVA patients. Clinical, radiographic, and biochemical tests are needed to complete the diagnosis of MPS IVA since some clinical characteristics in MPS IVA are overlapped with other disorders. Early and accurate diagnosis is vital to optimizing patient management, which provides a better quality of life and prolonged life-time in MPS IVA patients. Currently, enzyme replacement therapy (ERT) and hematopoietic stem cell transplantation (HSCT) are available for patients with MPS IVA. However, ERT and HSCT do not have enough impact on bone and cartilage lesions in patients with MPS IVA. Penetrating the deficient enzyme into an avascular lesion remains an unmet challenge, and several innovative therapies are under development in a preclinical study. In this review article, we comprehensively describe the current diagnosis, treatment, and management for MPS IVA. We also illustrate developing future therapies focused on the improvement of skeletal dysplasia in MPS IVA.
| S-EPMC7073202 | biostudies-literature
Project description:RNA-seq data of founder mice pancreatic islets
2021-07-27 | GSE180364 | GEO
Project description:Mucopolysaccharidosis IVA (MPS IVA; Morquio A syndrome) is caused by a deficiency of the N-acetylgalactosamine-6-sulfate-sulfatase (GALNS) enzyme, leading to the accumulation of glycosaminoglycans (GAG), keratan sulfate (KS) and chondroitin-6-sulfate (C6S), mainly in cartilage and bone. This lysosomal storage disorder (LSD) is characterized by severe systemic skeletal dysplasia. To this date, none of the treatment options for the MPS IVA patients correct bone pathology. Enzyme replacement therapy with elosulfase alpha provides a limited impact on bone growth and skeletal lesions in MPS IVA patients. To improve bone pathology, we propose a novel gene therapy with a small peptide as a growth-promoting agent for MPS IVA. A small molecule in this peptide family has been found to exert biological actions over the cardiovascular system. This work shows that an AAV vector expressing a C-type natriuretic (CNP) peptide induces bone growth in the MPS IVA mouse model. Histopathological analysis showed the induction of chondrocyte proliferation. CNP peptide also changed the pattern of GAG levels in bone and liver. These results suggest the potential for CNP peptide to be used as a treatment in MPS IVA patients.
| S-EPMC10298227 | biostudies-literature
Project description:Mucopolysaccharidosis IVA (OMIM 253000; also known as Morquio A syndrome) is associated with skeletal, airway, and hearing abnormalities. Cochlear implantation is an effective intervention for patients with severe-to-profound hearing loss. Patients can gain substantial improvement in auditory performance, speech perception, and their quality of life from cochlear implantation. Although severe progressive sensorineural hearing loss is a common feature of mucopolysaccharidosis IVA, no detailed description of cochlear implantation for mucopolysaccharidosis IVA has been reported. To review the effectiveness and special considerations associated with cochlear implantation in patients with mucopolysaccharidosis IVA, we here report the case of cochlear implantation in mucopolysaccharidosis IVA by a multidisciplinary team. A retrospective chart review was conducted on a 34-year-old female with mucopolysaccharidosis IVA, who received a cochlear implant. Audiometric thresholds, speech perception scores, and cochlear implant processor mapping information were reviewed during the first 12 months following cochlear implantation. The results of audiological tests indicate improved hearing thresholds as well as remarkable enhancement of speech perception skills over 12 months of cochlear implant use. Cochlear implantation improved auditory performance in a mucopolysaccharidosis IVA patient with postlingually severe-to-profound sensorineural hearing loss. The benefits of cochlear implantation could be meaningful for other Morquio patients with progressive hearing loss, although the risks of surgery and anesthesia should be carefully considered by a multidisciplinary team of experts during the cochlear implant candidacy process.
| S-EPMC6719565 | biostudies-literature
Project description:Founder mice islet RNA profiling
| PRJNA747994 | ENA