Harnessing genomic and bioinformatic data to broaden understanding of leukaemia across continents
Background/Aim: Leukaemia is a malignant disease of blood cells found in the bone marrow, which can be divided into acute lymphocytic leukaemia and myelocytic leukaemia. Current management of acute leukaemia still uses chemo therapy as the main therapy but has many side effects, therefore a new appr...
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Medical Society of the Republic of Srpska, Banja Luka, University of Banja Luka. Faculty of Medicine
2024-01-01
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| Series: | Scripta Medica |
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| Online Access: | https://scindeks-clanci.ceon.rs/data/pdf/2490-3329/2024/2490-33292406717G.pdf |
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| author | Gumelar Gugun Ulfa Mia Maria Amukti Danang Prasetyaning Irham Lalu Muhammad Yuliani Sapto Adikusuma Wirawan Khairi Sabiah Darmawi Darmawi Chong Rockie Ates Ilker Singh Dilpreet Chavan Aditya Ashok |
| author_facet | Gumelar Gugun Ulfa Mia Maria Amukti Danang Prasetyaning Irham Lalu Muhammad Yuliani Sapto Adikusuma Wirawan Khairi Sabiah Darmawi Darmawi Chong Rockie Ates Ilker Singh Dilpreet Chavan Aditya Ashok |
| author_sort | Gumelar Gugun |
| collection | DOAJ |
| description | Background/Aim: Leukaemia is a malignant disease of blood cells found in the bone marrow, which can be divided into acute lymphocytic leukaemia and myelocytic leukaemia. Current management of acute leukaemia still uses chemo therapy as the main therapy but has many side effects, therefore a new approach is needed to identify genetic factors involved in leukaemia. The aim of this study was to investigate gene variations that have potential pathogenic properties in leukaemia. Methods: This study used genome-wide association study (GWAS) data obtained from the National Human Genome Research Institute (NHGRI) to search for genomic variants associated with leukaemia. The data was then screened using SNPnexus to detect potentially protein-damaging variants. Furthermore, the gene expression of these variants was analysed using the GTEx portal. Results: Of the 2115 genomic variants found, four were deleterious, namely rs12140153, rs140386498, rs757110 and rs2066827, representing four different genes, namely PATJ, MINDY1, ABCC8 and CDKN1B. Alterations in the expression of PATJ, MINDY1, CDKN1B and ABCC8 genes affect the brain and leukaemia development. PATJ maintains brain cell integrity, MINDY1 regulates gene expression, CDKN1B controls the cell cycle and ABCC8 regulates glucose levels. Their deregulation is associated with neurological dysfunction and leukaemia. Variation in allele frequencies showed differences between continents, with rs757110 and rs2066827 having higher expression than rs12140153 and rs140386498. Variant gene expression also varied between tissues, with rs757110 and rs2066827 showing higher expression than rs12140153 and rs140386498. Conclusion: This study successfully identified four genomic variants by harnessing a genomic and bioinformatic database, which are associated with leukemia and demonstrated variations in gene distribution and expression across different populations and tissues. |
| format | Article |
| id | doaj-art-aa48bcda4acf4bf7ab0db63e4b3a479e |
| institution | Kabale University |
| issn | 2490-3329 2303-7954 |
| language | English |
| publishDate | 2024-01-01 |
| publisher | Medical Society of the Republic of Srpska, Banja Luka, University of Banja Luka. Faculty of Medicine |
| record_format | Article |
| series | Scripta Medica |
| spelling | doaj-art-aa48bcda4acf4bf7ab0db63e4b3a479e2025-02-05T13:19:48ZengMedical Society of the Republic of Srpska, Banja Luka, University of Banja Luka. Faculty of MedicineScripta Medica2490-33292303-79542024-01-0155671772510.5937/scriptamed55-517202490-33292406717GHarnessing genomic and bioinformatic data to broaden understanding of leukaemia across continentsGumelar Gugun0https://orcid.org/0009-0008-9351-0590Ulfa Mia Maria1https://orcid.org/0009-0002-7577-3537Amukti Danang Prasetyaning2https://orcid.org/0000-0002-4256-6534Irham Lalu Muhammad3https://orcid.org/0000-0002-0091-4887Yuliani Sapto4https://orcid.org/0000-0002-8454-2370Adikusuma Wirawan5https://orcid.org/0000-0001-9165-690XKhairi Sabiah6https://orcid.org/0000-0002-4412-1176Darmawi Darmawi7https://orcid.org/0000-0001-5018-2381Chong Rockie8https://orcid.org/0000-0001-6736-9687Ates Ilker9https://orcid.org/0000-0001-5791-7694Singh Dilpreet10https://orcid.org/0000-0001-8286-3800Chavan Aditya Ashok11https://orcid.org/0009-0009-2391-9056Universitas Ahmad Dahlan, Faculty of Pharmacy, Yogyakarta, IndonesiaUniversitas Ahmad Dahlan, Faculty of Pharmacy, Yogyakarta, IndonesiaUniversitas Ahmad Dahlan, Faculty of Pharmacy, Yogyakarta, IndonesiaUniversitas Ahmad Dahlan, Faculty of Pharmacy, Yogyakarta, IndonesiaUniversitas Ahmad Dahlan, Faculty of Pharmacy, Yogyakarta, IndonesiaUniversity of Muhammadiyah Mataram, Department of Pharmacy, Mataram, IndonesiaCibinong Science Centre, National Research and Innovation Agency (BRIN), Research Organisation for Electronics and Informatics, Research Centre for Computing, Cibinong, IndonesiaUniversitas Riau, Faculty of Medicine, Department of Histology, Pekanbaru, IndonesiaUniversity of California, Department of Chemistry and Biochemistry, Los Angeles, Los Angeles, CA, USAAnkara University, Faculty of Pharmacy, Department of Toxicology, Tandogan, Ankara, TurkeyChandigarh University, University Institute of Pharma Sciences, Gharuan, Mohali, IndiaCalifornia State University, College of Science, East Bay, Hayward, CA, USABackground/Aim: Leukaemia is a malignant disease of blood cells found in the bone marrow, which can be divided into acute lymphocytic leukaemia and myelocytic leukaemia. Current management of acute leukaemia still uses chemo therapy as the main therapy but has many side effects, therefore a new approach is needed to identify genetic factors involved in leukaemia. The aim of this study was to investigate gene variations that have potential pathogenic properties in leukaemia. Methods: This study used genome-wide association study (GWAS) data obtained from the National Human Genome Research Institute (NHGRI) to search for genomic variants associated with leukaemia. The data was then screened using SNPnexus to detect potentially protein-damaging variants. Furthermore, the gene expression of these variants was analysed using the GTEx portal. Results: Of the 2115 genomic variants found, four were deleterious, namely rs12140153, rs140386498, rs757110 and rs2066827, representing four different genes, namely PATJ, MINDY1, ABCC8 and CDKN1B. Alterations in the expression of PATJ, MINDY1, CDKN1B and ABCC8 genes affect the brain and leukaemia development. PATJ maintains brain cell integrity, MINDY1 regulates gene expression, CDKN1B controls the cell cycle and ABCC8 regulates glucose levels. Their deregulation is associated with neurological dysfunction and leukaemia. Variation in allele frequencies showed differences between continents, with rs757110 and rs2066827 having higher expression than rs12140153 and rs140386498. Variant gene expression also varied between tissues, with rs757110 and rs2066827 showing higher expression than rs12140153 and rs140386498. Conclusion: This study successfully identified four genomic variants by harnessing a genomic and bioinformatic database, which are associated with leukemia and demonstrated variations in gene distribution and expression across different populations and tissues.https://scindeks-clanci.ceon.rs/data/pdf/2490-3329/2024/2490-33292406717G.pdfleukaemiagenome-wide association studypolymorphism, single nucleotidegenespatjmindy1abcc8cdkn1b |
| spellingShingle | Gumelar Gugun Ulfa Mia Maria Amukti Danang Prasetyaning Irham Lalu Muhammad Yuliani Sapto Adikusuma Wirawan Khairi Sabiah Darmawi Darmawi Chong Rockie Ates Ilker Singh Dilpreet Chavan Aditya Ashok Harnessing genomic and bioinformatic data to broaden understanding of leukaemia across continents Scripta Medica leukaemia genome-wide association study polymorphism, single nucleotide genes patj mindy1 abcc8 cdkn1b |
| title | Harnessing genomic and bioinformatic data to broaden understanding of leukaemia across continents |
| title_full | Harnessing genomic and bioinformatic data to broaden understanding of leukaemia across continents |
| title_fullStr | Harnessing genomic and bioinformatic data to broaden understanding of leukaemia across continents |
| title_full_unstemmed | Harnessing genomic and bioinformatic data to broaden understanding of leukaemia across continents |
| title_short | Harnessing genomic and bioinformatic data to broaden understanding of leukaemia across continents |
| title_sort | harnessing genomic and bioinformatic data to broaden understanding of leukaemia across continents |
| topic | leukaemia genome-wide association study polymorphism, single nucleotide genes patj mindy1 abcc8 cdkn1b |
| url | https://scindeks-clanci.ceon.rs/data/pdf/2490-3329/2024/2490-33292406717G.pdf |
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