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De novo copy number variations in candidate genomic regions in patients of severe autism spectrum disorder in Vietnam (2024)
Journal Article
Bui, H. T. P., Huy Do, D., Ly, H. T. T., Tran, K. T., Le, H. T. T., Nguyen, K. T., …Nguyen, L. T. (in press). De novo copy number variations in candidate genomic regions in patients of severe autism spectrum disorder in Vietnam. PloS one, 19(3), e0290936. https://doi.org/10.1371/journal.pone.0290936

Autism spectrum disorder (ASD) is a developmental disorder with a prevalence of around 1% children worldwide and characterized by patient behaviour (communication, social interaction, and personal development). Data on the efficacy of diagnostic test... Read More about De novo copy number variations in candidate genomic regions in patients of severe autism spectrum disorder in Vietnam.

Whole exome sequencing reveals novel candidate genes in familial forms of Glaucomatous Neurodegeneration (2023)
Journal Article
Narta, K., Teltumbade, M., Vishal, M., Sadaf, S., Faruq, M., Jama, H., …Mukhopadhyay, A. (2023). Whole exome sequencing reveals novel candidate genes in familial forms of Glaucomatous Neurodegeneration. Genes, 14(2), 495. https://doi.org/10.3390/genes14020495

Glaucoma is the largest cause of irreversible blindness with a multifactorial genetic etiology. This study explores novel genes and gene networks in familial forms of primary open angle glaucoma (POAG) and primary angle closure glaucoma (PACG) to ide... Read More about Whole exome sequencing reveals novel candidate genes in familial forms of Glaucomatous Neurodegeneration.

Whole exome-sequencing of vitiligo lesions indicate lower burden of somatic variations: implications in risk for non-melanoma skin cancers (2022)
Journal Article
Gupta, I., Shankrit, S., Narta, K., Ghazi, M., Grover, R., Pandey, R., …Natarajan, V. (2022). Whole exome-sequencing of vitiligo lesions indicate lower burden of somatic variations: implications in risk for non-melanoma skin cancers. Journal of Investigative Dermatology, https://doi.org/10.1016/j.jid.2022.11.018

Genetic depigmentary conditions such as albinism with complete loss of epidermal pigmentation pose a higher risk for cutaneous malignancies ( Lekalakala et al., 2015 ). By analogy, clinical management for photoprotection of the acquired depigmented s... Read More about Whole exome-sequencing of vitiligo lesions indicate lower burden of somatic variations: implications in risk for non-melanoma skin cancers.

Diagnostic and prognostic potential of MiR-379/656 MicroRNA cluster in molecular subtypes of breast cancer (2021)
Journal Article
Lal, M., Ansari, A., Agrawal, A., & Mukhopadhyay, A. (2021). Diagnostic and prognostic potential of MiR-379/656 MicroRNA cluster in molecular subtypes of breast cancer. Journal of Clinical Medicine, 10(18), e4071. https://doi.org/10.3390/jcm10184071

Introduction: Breast cancer is the most frequently diagnosed cancer globally and is one of the most important contributors to cancer-related deaths. Earlier diagnosis is known to reduce mortality, and better biomarkers are needed. MiRNA clusters ofte... Read More about Diagnostic and prognostic potential of MiR-379/656 MicroRNA cluster in molecular subtypes of breast cancer.

Human brain shows recurrent non-canonical microRNA editing events enriched for seed sequence with possible functional consequence (2020)
Journal Article
Paul, D., Ansari, A., Lal, M., & Mukhopadhyay, A. (2020). Human brain shows recurrent non-canonical microRNA editing events enriched for seed sequence with possible functional consequence. Non-Coding RNA, 6(2), e21. https://doi.org/10.3390/ncrna6020021

RNA editing is a post-transcriptional modification, which can provide tissue-specific functions not encoded in DNA. Adenosine-to-inosine is the predominant editing event and, along with cytosine-to-uracil changes, constitutes canonical editing. The r... Read More about Human brain shows recurrent non-canonical microRNA editing events enriched for seed sequence with possible functional consequence.

Genetic landscape of autism spectrum disorder in Vietnamese children (2020)
Journal Article
Tran, K., Le, V., Bui, H., Do, D., Ly, H., Nguyen, H., …Nguyen, L. (2020). Genetic landscape of autism spectrum disorder in Vietnamese children. Scientific reports, 10(1), 5034. https://doi.org/10.1038/s41598-020-61695-8

Autism spectrum disorder (ASD) is a complex disorder with an unclear aetiology and an estimated global prevalence of 1%. However, studies of ASD in the Vietnamese population are limited. Here, we first conducted whole exome sequencing (WES) of 100 ch... Read More about Genetic landscape of autism spectrum disorder in Vietnamese children.

Fusion transcripts in normal human cortex increase with age and show distinct genomic features for single cells and tissues (2020)
Journal Article
Mehani, B., Narta, K., Paul, D., Raj, A., Kumar, D., Sharma, A., …Mukhopadhyay, A. (2020). Fusion transcripts in normal human cortex increase with age and show distinct genomic features for single cells and tissues. Scientific reports, 10(1), 1368. https://doi.org/10.1038/s41598-020-58165-6

Fusion transcripts can contribute to diversity of molecular networks in the human cortex. In this study, we explored the occurrence of fusion transcripts in normal human cortex along with single neurons and astrocytes. We identified 1305 non-redundan... Read More about Fusion transcripts in normal human cortex increase with age and show distinct genomic features for single cells and tissues.

Identification of miR-379/miR-656 (C14MC) cluster downregulation and associated epigenetic and transcription regulatory mechanism in oligodendrogliomas (2018)
Journal Article
Kumar, A., Nayak, S., Pathak, P., Purkait, S., Malgulawar, P., Sharma, M., …Sarkar, C. (2018). Identification of miR-379/miR-656 (C14MC) cluster downregulation and associated epigenetic and transcription regulatory mechanism in oligodendrogliomas. Journal of Neuro-Oncology, 139(1), 23-31. https://doi.org/10.1007/s11060-018-2840-6

Introduction Although role of individual microRNAs (miRNAs) in the pathogenesis of gliomas has been well studied, their role as a clustered remains unexplored in gliomas. Methods In this study, we performed the expression analysis of miR-379/... Read More about Identification of miR-379/miR-656 (C14MC) cluster downregulation and associated epigenetic and transcription regulatory mechanism in oligodendrogliomas.

Novel internal regulators and candidate miRNAs within miR-379/miR-656 miRNA cluster can alter cellular phenotype of human glioblastoma (2018)
Journal Article
Nayak, S., Aich, M., Kumar, A., Sengupta, S., Bajad, P., Dhapola, P., …Sarkar, C. (2018). Novel internal regulators and candidate miRNAs within miR-379/miR-656 miRNA cluster can alter cellular phenotype of human glioblastoma. Scientific reports, 8(2018), #7673. https://doi.org/10.1038/s41598-018-26000-8

Clustered miRNAs can affect functioning of downstream pathways due to possible coordinated function. We observed 78-88% of the miR-379/miR-656 cluster (C14MC) miRNAs were downregulated in three sub-types of diffuse gliomas, which was also corrobora... Read More about Novel internal regulators and candidate miRNAs within miR-379/miR-656 miRNA cluster can alter cellular phenotype of human glioblastoma.

A-to-I editing in human miRNAs is enriched in seed sequence, influenced by sequence contexts and significantly hypoedited in glioblastoma multiforme (2017)
Journal Article
Paul, D., Sinha, A., Ray, A., Lal, M., Nayak, S., Sharma, A., …Mukhopadhyay, A. (2017). A-to-I editing in human miRNAs is enriched in seed sequence, influenced by sequence contexts and significantly hypoedited in glioblastoma multiforme. Scientific reports, 7(2466), https://doi.org/10.1038/s41598-017-02397-6

Editing in microRNAs, particularly in seed can significantly alter the choice of their target genes. We show that out of 13 different human tissues, different regions of brain showed higher adenosine to inosine (A-to-I) editing in mature miRNAs. Thes... Read More about A-to-I editing in human miRNAs is enriched in seed sequence, influenced by sequence contexts and significantly hypoedited in glioblastoma multiforme.

Human brain harbors single nucleotide somatic variations in functionally relevant genes possibly mediated by oxidative stress (2016)
Journal Article
Sharma, A., Ansan, A., Kumari, R., Pandey, R., Rehman, R., Mehani, B., …Mukhopadhyay, A. (2017). Human brain harbors single nucleotide somatic variations in functionally relevant genes possibly mediated by oxidative stress. F1000Research, 5, 2520. https://doi.org/10.12688/f1000research.9495.3

Somatic variation in DNA can cause cells to deviate from the preordained genomic path in both disease and healthy conditions. Here, using exome sequencing of paired tissue samples, we show that the normal human brain harbors somatic single base va... Read More about Human brain harbors single nucleotide somatic variations in functionally relevant genes possibly mediated by oxidative stress.

Genetic association and stress mediated down-regulation in trabecular meshwork implicates MPP7 as a novel candidate gene in primary open angle glaucoma (2016)
Journal Article
Vishal, M., Sharma, A., Kaurani, L., Alfano, G., Mookerjee, S., Narta, K., …Mukhopadhyay, A. (2016). Genetic association and stress mediated down-regulation in trabecular meshwork implicates MPP7 as a novel candidate gene in primary open angle glaucoma. BMC Medical Genomics, 9(15), https://doi.org/10.1186/s12920-016-0177-6

Background: Glaucoma is the largest cause of irreversible blindness affecting more than 60 million people globally. The disease is defined as a gradual loss of peripheral vision due to death of Retinal Ganglion Cells (RGC). The RGC death is largely... Read More about Genetic association and stress mediated down-regulation in trabecular meshwork implicates MPP7 as a novel candidate gene in primary open angle glaucoma.

Altered expression and editing of miRNA-100 regulates iTreg differentiation (2015)
Journal Article
Negi, V., Paul, D., Das, S., Bajpai, P., Singh, S., Mukhopadhyay, A., …Ghosh, B. (2015). Altered expression and editing of miRNA-100 regulates iTreg differentiation. Nucleic Acids Research, 43(16), 8057-8065. https://doi.org/10.1093/nar/gkv752

RNA editing ofmiRNAs, especially in the seed region, adds another layer to miRNA mediated gene regulation which can modify its targets, altering cellular signaling involved in important processes such as differentiation. In this study, we have ex... Read More about Altered expression and editing of miRNA-100 regulates iTreg differentiation.

Evaluation of genetic association of the INK4 locus with primary open angle glaucoma in East Indian population (2014)
Journal Article
angle glaucoma in East Indian population. Scientific reports, 4, 5115. https://doi.org/10.1038/srep05115

INK4 locus at chromosome 9p21 has been reported to be associated with primary open angle glaucoma (POAG) and its subtypes along with the associated optic disc parameters across the populations of European, Japanese and African ancestries. The locus e... Read More about Evaluation of genetic association of the INK4 locus with primary open angle glaucoma in East Indian population.

Gene-rich large deletions are overrepresented in POAG patients of Indian and Caucasian origins (2014)
Journal Article
Kaurani, L., Vishal, M., Kumar, D., Sharma, A., Mehani, B., Sharma, C., …Mukhopadhyay, A. (2014). Gene-rich large deletions are overrepresented in POAG patients of Indian and Caucasian origins. https://doi.org/10.1167/iovs.14-14339

PURPOSE: Large copy number variations (CNV) can contribute to increased burden for neurodegenerative diseases. In this study, we analyzed the genome-wide burden of large CNVs > 100 kb in primary open angle glaucoma (POAG), a neurodegenerative diseas... Read More about Gene-rich large deletions are overrepresented in POAG patients of Indian and Caucasian origins.

Genome-wide analysis identifies common CNVs associated with primary open angle glaucoma (2014)
Journal Article
Kaurani, L., Vishal, M., Kumar, D., Mehani, B., Sharma, C., Sharma, A., …Mukhopadhyay, A. (2014). Genome-wide analysis identifies common CNVs associated with primary open angle glaucoma. Molecular Cytogenetics, 7, Article 131. https://doi.org/10.1186/1755-8166-7-s1-p131

Background Copy number variation (CNV) is one of the major factors contributing to genomic diversity and diseases. Glaucoma is a major neurodegenerative disease causing irreversible vision loss across the globe. We wanted to analyze the impact of co... Read More about Genome-wide analysis identifies common CNVs associated with primary open angle glaucoma.