35 research outputs found
Variant effect on splicing regulatory elements, branchpoint usage, and pseudoexonization: strategies to enhance bioinformatic prediction using hereditary cancer genes as exemplars
No full textIt is possible to estimate the prior probability of pathogenicity for germline disease gene variants based on bioinformatic prediction of variant effect/s. However, routinely used approaches have likely led to the underestimation and underreporting of variants located outside donor and acceptor splice site motifs that affect messenger RNA (mRNA) processing. This review presents information about hereditary cancer gene germline variants, outside native splice sites, with experimentally validated splicing effects. We list 95 exonic variants that impact splicing regulatory elements (SREs) in BRCA1, BRCA2, MLH1, MSH2, MSH6, and PMS2. We utilized a pre-existing large-scale BRCA1 functional data set to map functional SREs, and assess the relative performance of different tools to predict effects of 283 variants on such elements. We also describe rare examples of intronic variants that impact branchpoint (BP) sites and create pseudoexons. We discuss the challenges in predicting variant effect on BP site usage and pseudoexonization, and suggest strategies to improve the bioinformatic prioritization of such variants for experimental validation. Importantly, our review and analysis highlights the value of considering impact of variants outside donor and acceptor motifs on mRNA splicing and disease causation
Mutational Analysis of the GALT Gene in Filipino Patients
No full textClassic galactosemia is an inherited metabolic disorder due to mutations in the galactose-1-phosphate uridyltransferase (GALT) gene. This study describes the results of the GALT gene analysis of four unrelated Filipino patients with Classic Galactosemia. DNA extracted from dried blood spots and peripheral blood of the patients, age one month to two and a half years, underwent PCR-amplification with subsequent bidirectional sequencing of all eleven exons with their flanking intronic regions following standard protocols. Clinical data of these patients were reviewed. The patients presented with jaundice, hepatomegaly, diarrhea, vomiting, poor feeding and seizures during their neonatal period. They were diagnosed with elevated blood galactose and galactose-1-phosphate and absent GALT activity. Four missense mutations were found wherein two were previously reported (p.V168L and p.A345D) and two were novel (p.L116P and p.M178R). The most frequent mutation in our cohort is p.V168L. This study suggests that GALT mutations are ethnic-specific and that galactosemia is a heterogeneous disorder at the molecular level. The importance of early detection, immediate and proper medical management and genetic counseling of the patients and their families cannot be overemphasized
GOOD HOUSEKEEPING: LEVEL OF 5S COMPLIANCE OF HOUSEKEEPERS FROM SELECTED BED AND BREAKFAST IN TAGAYTAY CITY
No full textAbstract: Implementation of 5’S in hotels is very important because it provides an organized and efficient workplace for the employees. 5’S implementation can be applied in various industries such as hospitality particularly accommodation provider such as hotels. The researchers assess the implementation of 5’S in selected hotels in the city of Tagaytay which is a known tourist destination. The respondents in the study are the hotel employees from the selected hotels in the city of Tagaytay and survey questionnaire as the instrument of the study the result shows that most of the employees of the hotel age 21 to 30 with a gender of male, had an educational attainment of college graduate a monthly income range of P10,000 to P20,000 and is employed with the hotel for less than 1 year. The result of the 5’S assessment shows that the hotel employees often practiced Sort (Seiri), Set in Order (Seiton), Shine (Seiso) and Standard (Seiketsu) while the Sustain (Shitsuke) is sometimes practiced. The result of the relationship between the profile of the respondents and aspects of 5’S shows that there is no significant relationship.
Keywords: 5’S, Hotels, Sort, Set in Order, Shine, Standard and Sustain.
Title: GOOD HOUSEKEEPING: LEVEL OF 5S COMPLIANCE OF HOUSEKEEPERS FROM SELECTED BED AND BREAKFAST IN TAGAYTAY CITY
Author: Karl Angelo B. Sanchez, Lambert John D. Canoza, Mary Joy L. Sy, Mrs. Mary Daffodil Cordero
International Journal of Thesis Projects and Dissertations (IJTPD)
Vol. 10, Issue 3, July 2022 - September 2022
Page No: 60-73
Research Publish Journals
Website: www.researchpublish.com
Published Date: 23-July-2022
DOI: https://doi.org/10.5281/zenodo.6890653
Paper Download Link (Source)
https://www.researchpublish.com/papers/good-housekeeping-level-of-5s-compliance-of-housekeepers-from-selected-bed-and-breakfast-in-tagaytay-cityInternational Journal of Thesis Projects and Dissertations (IJTPD), Research Publish Journals, Website: www.researchpublish.co
Clinical, biochemical and molecular characteristics of Filipino patients with mucopolysaccharidosis type II - Hunter syndrome
No full textAbstract
Background
Mucopolysaccharidosis type II, an X-linked recessive disorder is the most common lysosomal storage disease detected among Filipinos. This is a case series involving 23 male Filipino patients confirmed to have Hunter syndrome. The clinical and biochemical characteristics were obtained and mutation testing of the IDS gene was done on the probands and their female relatives.
Results
The mean age of the patients was 11.28 (SD 4.10) years with an average symptom onset at 1.2 (SD 1.4) years. The mean age at biochemical diagnosis was 8 (SD 3.2) years. The early clinical characteristics were developmental delay, joint stiffness, coarse facies, recurrent respiratory tract infections, abdominal distention and hernia. Majority of the patients had joint contractures, severe intellectual disability, error of refraction, hearing loss and valvular regurgitation on subspecialists\u2019 evaluation. The mean GAG concentration was 506.5\ua0mg (SD 191.3)/grams creatinine while the mean plasma iduronate-2-sulfatase activity was 0.86 (SD 0.79) nmol/mg plasma/4\ua0h. Fourteen (14) mutations were found: 6 missense (42.9%), 4 nonsense (28.6%), 2 frameshift (14.3%), 1 exon skipping at the cDNA level (7.1%), and 1 gross insertion (7.1%). Six (6) novel mutations were observed (43%): p.C422F, p.P86Rfs*44, p.Q121*, p.L209Wfs*4, p.T409R, and c.1461_1462insN[710].
Conclusion
The age at diagnosis in this series was much delayed and majority of the patients presented with severe neurologic impairment. The results of the biochemical tests did not contribute to the phenotypic classification of patients. The effects of the mutations were consistent with the severe phenotype seen in the majority of the patients
variants found in classic galactosemia patients using a novel cell‐free translation method
No full textFunctional analysis of GALT variants found in classic galactosemia patients using a novel cell‐free translation method
No full textClassic galactosemia is an autosomal recessive disorder caused by deleterious variants in the galactose-1-phosphate uridylyltransferase () gene. GALT enzyme deficiency leads to an increase in the levels of galactose and its metabolites in the blood causing neurodevelopmental and other clinical complications in affected individuals. Two variants NM_000155.3:c.347T>C (p.Leu116Pro) and NM_000155.3:c.533T>G (p.Met178Arg) were previously detected in Filipino patients. Here, we determine their functional effects on the GALT enzyme through analysis and a novel experimental approach using a HeLa-based cell-free protein expression system. Enzyme activity was not detected for the p.Leu116Pro protein variant, while only 4.5% of wild-type activity was detected for the p.Met178Arg protein variant. Computational analysis of the variants revealed destabilizing structural effects and suggested protein misfolding as the potential mechanism of enzymological impairment. Biochemical and computational data support the classification of p.Leu116Pro and p.Met178Arg variants as pathogenic. Moreover, the protein expression method developed has utility for future studies of variants
ASO Author Reflections: Impact of Breast Cancer Screening Beyond Mortality Reductions
No full textASO Author Reflections is a brief invited commentary on the article, “Treatment Intensity Differences After Early-Stage Breast Cancer Diagnosis Depending on Participation in a Screening Program.” Ann Surg Oncol. 2018;25:2563–72
Exploring the role of splicing in TP53 variant pathogenicity through predictions and minigene assays
No full textAbstract Background TP53 variant classification benefits from the availability of large-scale functional data for missense variants generated using cDNA-based assays. However, absence of comprehensive splicing assay data for TP53 confounds the classification of the subset of predicted missense and synonymous variants that are also predicted to alter splicing. Our study aimed to generate and apply splicing assay data for a prioritised group of 59 TP53 predicted missense or synonymous variants that are also predicted to affect splicing by either SpliceAI or MaxEntScan. Methods We conducted splicing analyses using a minigene construct containing TP53 exons 2 to 9 transfected into human breast cancer SKBR3 cells, and compared results against different splice prediction methods, including correlation with the SpliceAI-10k calculator. We additionally applied the splicing results for TP53 variant classification using an approach consistent with the ClinGen Sequence Variant Interpretation Splicing Subgroup recommendations. Results Aberrant transcript profile consistent with loss of function, and for which a PVS1 (RNA) code would be assigned, was observed for 42 (71%) of prioritised variants, of which aberrant transcript expression was over 50% for 26 variants, and over 80% for 15 variants. Data supported the use of SpliceAI ≥ 0.2 cutoff for predicted splicing impact of TP53 variants. Prediction of aberration types using SpliceAI-10k calculator generally aligned with the corresponding assay results, though maximum SpliceAI score did not accurately predict level of aberrant expression. Application of the observed splicing results was used to reclassify 27/59 (46%) test variants as (likely) pathogenic or (likely) benign. Conclusions In conclusion, this study enhances the integration of splicing predictions and provides splicing assay data for exonic variants to support TP53 germline classification. Graphical abstrac
Validation of a PCR-based test for the genetic diagnosis of Filipino patients with x-linked dystonia parkinsonism (Xdp)
No full textBackground and Objective. X-linked dystonia parkinsonism (XDP, DYT3, MIM #314250) is a neurodegenerative movement disorder found endemically in the Philippines. An SVA retrotransposon insertion mutation has been described in patients with XDP, which requires Southern analysis for detection. However, this method is costly and time-consuming. Hence we developed a PCR-based method and validated it among our local population. Methods and Results. A total of 58 samples from 58 patients with a clinical diagnosis of XDP were collected. Other samples were from an obligate female carrier, two unaffected male relatives, and two patients with typical Parkinson's disease. Primers designed to amplify the SVA retrotransposon found in the DYT3-TAF1 gene (NCBI Accession Number AB191243) were used. All patients were positive for the expected 3229-bp product after PCR amplification. The normal control showed a 599-bp product, while the female carrier showed both the 3229 and 599-bp product. Subsequent RFLP analysis using SamHI verified the presence of the SVA retrotransposon insertion mutation. Conclusion. Our results show that large-scale PCR-based testing to screen for genetic diseases with a relatively high prevalence such as XDP is possible in our setting. When followed by RFLP analysis, this can provide genetic confirmation of the diagnosis of XDP and facilitate proper genetic counselling and therapy
The echo of ice letting go
No full textI. Tosca Lived a Good Life -- In the Belly of the Whale -- A New Toolbox -- Recent Blood Tests Are Indicative of a Cancer Recurrence -- What I Lost That Day in Gifford, Pennsylvania -- No More Words -- What Meaning -- Not a Fairy-Tale Ending -- Dear Becky -- I Drowned -- Half-Found John Muir Poem #4 -- River of Mercy -- II. Winter Rain -- Half-Found John Muir Poem #5 -- Spargania magnoliata -- On a Summer Day after My Son and I Witness a -- Young Man's Drowning -- What Is Gathered and What Is Lost -- Walking Home -- More Ache than the Sea -- The Anchorage Jail -- Emergency Room, Wednesday 4pm -- Inside Out -- His Sadness Is a Lake These Mountains Are Long-Extinct Volcanoes -- Near Power Creek: After a Marriage -- Looking out the Window on a Winter Morning -- Still -- Anniversary: My Parents' Marriage -- Redpolls in Winter -- III. Mythography of the Wolf's Sorrow or An Alternative Rendering of the Romulus and Remus Legend -- Trinity -- Tosca, Act V -- Here the Promise -- Only Winter -- Reincarnate -- I Bow -- Kashin-Beck Disease Is Endemic to Tibet -- Who Will Speak of Lhasa? -- Faith -- All Things Are Transient -- Dr. Anderson Called and the News Isn't Good -- This Body Is Baggage I'm Not Yet Ready to Leave Behind -- IV. This Is a Raging Wind -- Since June -- Walk on Water -- Half-Found John Muir Poem #1 -- Ge(ne)ology -- Half-Found John Muir Poem #2 -- On a Summer Day -- Sun like a Daffodil -- A Light in Winter -- Half-Found John Muir Poem #3 -- Remission -- Half-Found Li Shang-yin Poem -- Tomorrow Is a White Flag -- Unravel -- Sky Burial
