Data-mining approach for screening of rare genetic elements associated with predisposition of prostate cancer in South-Asian populations

Muhammad Zubair Mahboob 1 , Arslan Hamid 2 , Nada Mushtaq 1 , Sana Batool 3 , Hina Batool 3 , Nadia Zeeshan 4 , Muhammad Ali 5 , Kalsoom Sughra 4  and Naeem Mahmood Ashrafhttp://orcid.org/https://orcid.org/0000-0003-3614-0702 4
  • 1 University of Gujrat, Department of Biochemistry and Biotechnology, Gujrat, Pakistan
  • 2 University of Stuttgart, Department of Sciences, Stuttgart, Germany
  • 3 University of the Punjab, School of Biological Sciences, Lahore, Pakistan
  • 4 University of Gujrat – Hafiz Hayat Campus, Department of Biochemistry and Biotechnology, Gujrat, Pakistan
  • 5 Department of Biotechnology, Abbottabad Campus, COMSATS Institute of Information Technology, Abbottabad, Pakistan
Muhammad Zubair Mahboob
  • University of Gujrat, Department of Biochemistry and Biotechnology, Gujrat, Pakistan
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, Arslan Hamid, Nada Mushtaq
  • University of Gujrat, Department of Biochemistry and Biotechnology, Gujrat, Pakistan
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, Sana Batool, Hina Batool, Nadia Zeeshan
  • University of Gujrat – Hafiz Hayat Campus, Department of Biochemistry and Biotechnology, Gujrat, Pakistan
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, Muhammad Ali
  • Department of Biotechnology, Abbottabad Campus, COMSATS Institute of Information Technology, Abbottabad, Pakistan
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, Kalsoom Sughra
  • Corresponding author
  • University of Gujrat – Hafiz Hayat Campus, Department of Biochemistry and Biotechnology, Gujrat, Pakistan
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and Naeem Mahmood AshrafORCID iD: https://orcid.org/0000-0003-3614-0702

Abstract

Objective

Prostate cancer (PCa) is a complex heterogeneous disease and a major health risk to men throughout the world. The potential tumorigenic genetic hallmarks associated with PCa include sustaining proliferative signaling, resisting cell death, aberrant androgen receptor signaling, androgen independence, and castration resistance. Despite numerous comprehensive genome-wide association studies (GWAS), certain genetic elements associated with PCa are still unknown. This situation demands more systematic GWAS studies in different populations. This study presents a computational strategy for identification of novel and uncharacterized genetic factors associated with incidence of PCa in South Asian populations.

Materials and methods

Genome-wide association studies (GWAS) catalog and Gene Expression Omnibus (GEO) furnished PCa-related genetic studies. Database for Annotation, Visualization and Integrated Discovery (DAVID) functionally annotated these genes and wANNOVAR separated South Asian (SAS) populations – specific genetic factors at MAF threshold <0.05.

Results

The study reports 195 genes as potential contributors to prostate cancer in SAS populations. Some of identified genes are PYGO2, RALBP1, RFX5, SLC22A3, VPS53, HMCN1 and KIF1C.

Conclusion

The identified genetic elements may assist in development of population-specific screening and management strategies for PCa. Moreover, this approach may also be used to retrieve potential genetic elements associated with other types of cancers.

    • Supplementary Material
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Turkish Journal of Biochemistry (TJB), official journal of Turkish Biochemical Society, is issued electronically every 2 months. The main aim of the journal is to support the research and publishing culture by ensuring that every published manuscript has an added value and thus providing international acceptance of the “readability” of the manuscripts published in the journal.

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