IDEAS home Printed from https://ideas.repec.org/a/epw/ejmed0/v2y2020i5id40487.html

Identification of Mutation in Exon2 of the NKX2.5 Gene in Bangladeshi Pediatric Patients with Congenital Hypothyroidism

Author

Listed:
  • Marjia Khatun
  • Sagana Shahreen Chowdhury
  • Toufiq Hasan Khan
  • Laila Anjuman Banu

Abstract

Context and rationale: Congenital hypothyroidism is a prevalent endocrine disease that may occur due to the alteration in the sequence of nucleotides of the NKX2.5 gene. Though congenital hypothyroidism is quite common among the Bangladeshi pediatric population, there are few studies on the genetic basis of this disease. Objective: This study aimed to identify any mutation in the exon2 of the NKX2.5 gene in Bangladeshi pediatric patients with congenital hypothyroidism. Methods: Forty (40) Bangladeshi pediatric patients with congenital hypothyroidism were recruited, the sociodemographic data were collected and analyzed, DNA was isolated, quantity and quality of DNA were checked, polymerase chain reaction (PCR) was done, the amplicons were visually validated by gel electrophoresis and cycle sequencing was done by Sanger sequencing. The raw chromatogram data were analyzed and compared with the NCBI database by BLAST (Basic Local Alignment Search Tool) search. Results: Sanger sequencing revealed two types of alteration in the nucleotide sequence. Nine patients showed substitutions (c.1051G>T) and eight patients showed deletions (c.1143 delT-), and both substitution and deletion were present in four patients. This substitution and deletion occurred in the Sequence Tagged Site (STS) of the exon2 of the NKX2.5 gene and these are new variants and not reported in NCBI database. Conclusion: In the present study, two types of variants were identified. So, further study to find out mutational status among Bangladeshi children might be helpful in enriching the database of mutational spectra of pediatric patients with congenital hypothyroidism.

Suggested Citation

  • Marjia Khatun & Sagana Shahreen Chowdhury & Toufiq Hasan Khan & Laila Anjuman Banu, 2020. "Identification of Mutation in Exon2 of the NKX2.5 Gene in Bangladeshi Pediatric Patients with Congenital Hypothyroidism," European Journal of Medical and Health Sciences, European Open Science, vol. 2(5), September.
    • Handle: RePEc:epw:ejmed0:v:2:y:2020:i:5:id:40487
    DOI: 10.24018/ejmed.2020.2.5.487
    as

    Download full text from publisher

    File URL: https://eu-opensci.org/index.php/ejmed/article/view/40487
    File Function: Abstract page
    Download Restriction: no
    File URL: https://eu-opensci.org/index.php/ejmed/article/download/40487/9032
    File Function: Full text
    Download Restriction: no
    File URL: https://libkey.io/10.24018/ejmed.2020.2.5.487?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Joseph K. Pickrell & John C. Marioni & Athma A. Pai & Jacob F. Degner & Barbara E. Engelhardt & Everlyne Nkadori & Jean-Baptiste Veyrieras & Matthew Stephens & Yoav Gilad & Jonathan K. Pritchard, 2010. "Understanding mechanisms underlying human gene expression variation with RNA sequencing," Nature, Nature, vol. 464(7289), pages 768-772, April.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Sora Yoon & Seon-Young Kim & Dougu Nam, 2016. "Improving Gene-Set Enrichment Analysis of RNA-Seq Data with Small Replicates," PLOS ONE, Public Library of Science, vol. 11(11), pages 1-16, November.
    2. Faisal Shahla & Tutz Gerhard, 2017. "Missing value imputation for gene expression data by tailored nearest neighbors," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 16(2), pages 95-106, April.
    3. Tang Clara S. & Ferreira Manuel A. R., 2012. "GENOVA: Gene Overlap Analysis of GWAS Results," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(3), pages 1-15, February.
    4. Claudia Giambartolomei & Damjan Vukcevic & Eric E Schadt & Lude Franke & Aroon D Hingorani & Chris Wallace & Vincent Plagnol, 2014. "Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics," PLOS Genetics, Public Library of Science, vol. 10(5), pages 1-15, May.
    5. repec:plo:pgen00:1002078 is not listed on IDEAS
    6. Jiapei Yuan & Yang Tong & Le Wang & Xiaoxiao Yang & Xiaochuan Liu & Meng Shu & Zekun Li & Wen Jin & Chenchen Guan & Yuting Wang & Qiang Zhang & Yang Yang, 2024. "A compendium of genetic variations associated with promoter usage across 49 human tissues," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    7. Thanh Nguyen & Asim Bhatti & Samuel Yang & Saeid Nahavandi, 2016. "RNA-Seq Count Data Modelling by Grey Relational Analysis and Nonparametric Gaussian Process," PLOS ONE, Public Library of Science, vol. 11(10), pages 1-18, October.
    8. Urmo Võsa & Tõnu Esko & Silva Kasela & Tarmo Annilo, 2015. "Altered Gene Expression Associated with microRNA Binding Site Polymorphisms," PLOS ONE, Public Library of Science, vol. 10(10), pages 1-24, October.
    9. Asta Laiho & Laura L Elo, 2014. "A Note on an Exon-Based Strategy to Identify Differentially Expressed Genes in RNA-Seq Experiments," PLOS ONE, Public Library of Science, vol. 9(12), pages 1-12, December.
    10. Pingting Ying & Can Chen & Zequn Lu & Shuoni Chen & Ming Zhang & Yimin Cai & Fuwei Zhang & Jinyu Huang & Linyun Fan & Caibo Ning & Yanmin Li & Wenzhuo Wang & Hui Geng & Yizhuo Liu & Wen Tian & Zhiyong, 2023. "Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human cancer risk," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    11. Lulu Shang & Wei Zhao & Yi Zhe Wang & Zheng Li & Jerome J. Choi & Minjung Kho & Thomas H. Mosley & Sharon L. R. Kardia & Jennifer A. Smith & Xiang Zhou, 2023. "meQTL mapping in the GENOA study reveals genetic determinants of DNA methylation in African Americans," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    12. Hui Jiang & Tianyu Zhan, 2017. "Unit-Free and Robust Detection of Differential Expression from RNA-Seq Data," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 9(1), pages 178-199, June.
    13. Xiaodong Cai & Juan Andrés Bazerque & Georgios B Giannakis, 2013. "Inference of Gene Regulatory Networks with Sparse Structural Equation Models Exploiting Genetic Perturbations," PLOS Computational Biology, Public Library of Science, vol. 9(5), pages 1-13, May.
    14. Chuan Gao & Ian C McDowell & Shiwen Zhao & Christopher D Brown & Barbara E Engelhardt, 2016. "Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering," PLOS Computational Biology, Public Library of Science, vol. 12(7), pages 1-39, July.
    15. Kensuke Yamaguchi & Kazuyoshi Ishigaki & Akari Suzuki & Yumi Tsuchida & Haruka Tsuchiya & Shuji Sumitomo & Yasuo Nagafuchi & Fuyuki Miya & Tatsuhiko Tsunoda & Hirofumi Shoda & Keishi Fujio & Kazuhiko , 2022. "Splicing QTL analysis focusing on coding sequences reveals mechanisms for disease susceptibility loci," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    16. Alexandra C Nica & Leopold Parts & Daniel Glass & James Nisbet & Amy Barrett & Magdalena Sekowska & Mary Travers & Simon Potter & Elin Grundberg & Kerrin Small & Åsa K Hedman & Veronique Bataille & Jo, 2011. "The Architecture of Gene Regulatory Variation across Multiple Human Tissues: The MuTHER Study," PLOS Genetics, Public Library of Science, vol. 7(2), pages 1-9, February.
    17. David Lamparter & Rajat Bhatnagar & Katja Hebestreit & T Grant Belgard & Alice Zhang & Victor Hanson-Smith, 2020. "A framework for integrating directed and undirected annotations to build explanatory models of cis-eQTL data," PLOS Computational Biology, Public Library of Science, vol. 16(6), pages 1-27, June.
    18. Jean Francois Lefebvre & Emilio Vello & Bing Ge & Stephen B Montgomery & Emmanouil T Dermitzakis & Tomi Pastinen & Damian Labuda, 2012. "Genotype-Based Test in Mapping Cis-Regulatory Variants from Allele-Specific Expression Data," PLOS ONE, Public Library of Science, vol. 7(6), pages 1-15, June.
    19. Nicoló Fusi & Oliver Stegle & Neil D Lawrence, 2012. "Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies," PLOS Computational Biology, Public Library of Science, vol. 8(1), pages 1-9, January.
    20. Bin Wang, 2020. "A Zipf-plot based normalization method for high-throughput RNA-seq data," PLOS ONE, Public Library of Science, vol. 15(4), pages 1-15, April.
    21. Jin Hyun Ju & Sushila A Shenoy & Ronald G Crystal & Jason G Mezey, 2017. "An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci," PLOS Computational Biology, Public Library of Science, vol. 13(5), pages 1-26, May.

    More about this item

    Keywords

    ;
    ;
    ;
    ;
    ;

    JEL classification:

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:epw:ejmed0:v:2:y:2020:i:5:id:40487. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Support (email available below). General contact details of provider: https://eu-opensci.org/index.php/ejmed .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.