Suraj Singh Nongmaithem, Ph.D.

Senior Scientist
Pharmacology & Drug Discovery Division
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Research Focus

Genetic and Epigenetics, Polygenic Risk Score (PRS), Haematological traits, Pharmacogenomics, Common Complex Diseases

Research Interest

Our lab investigates the genetic and epigenetic basis of human health and disease, with a particular focus on polygenic risk, intermediate traits, and pharmacogenomics. Many human traits and complex diseases are polygenic, arising from the combined effects of numerous genetic variants and their interactions with environmental factors. Genome-wide association studies (GWAS) have enabled the development of polygenic risk scores (PRS) – a weighted sum of trait- or disease-associated alleles carried by an individual. PRS quantify inherited genetic susceptibility and support disease risk prediction, stratification, and prognosis. Increasingly, PRS are being applied within pharmacogenomics frameworks to understand disease progression and inter-individual variability in treatment response.

A major challenge in precision medicine is the limited transferability of genetic risk models across populations as majority of genetic studies predominate with European ancestry. This issue is particularly relevant in India, which harbours extensive genetic diversity, complex ancestral structure, and distinct environmental and nutritional exposures. Our lab emphasizes population-specific and multi-ancestral approaches to understand how polygenic susceptibility interacts with environmental, nutritional, and epigenetic factors across the life course.

We focus on modifiable intermediate traits—especially haematological traits—that influence disease onset, progression, and complications. These traits often share genetic architecture with both monogenic and common complex diseases, including sickle cell disease, autoimmune disorders, and cardio-metabolic conditions, making them promising targets for risk prediction, prognosis, and therapeutic intervention. Our research explores the use of PRS derived from haematological traits to predict disease outcomes and to study their interaction with environmental exposures and epigenetic modifications.

We work in collaboration with multiple prospective Indian birth cohorts, enabling the integration of genetic data with detailed life-course information on nutrition and environmental exposures. In addition, we leverage large-scale national and international biobanks and publicly available genomic and epigenomic resources to dissect the genetic and epigenetic contributions to human health and disease. Through these integrative and population-aware approaches, our lab aims to advance equitable precision medicine and pharmacogenomics in underrepresented populations.

Credentials

  • Senior Scientist (2025-Present) CSIR-Indian Institute of Chemical Biology, Kolkata, India.
  • Project Scientist II (2022-2025) CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
  • Project Scientist I (2021-2022) CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
  • Postdoctoral Research Fellow (2019-2021) Human Genetics Department, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom.
  • Ph.D. (2019) CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
  • M.Sc. Biochemistry (2009) Manipur University, Manipur, India.

Honours & Awards

  • Lifetime member of Indian Society of Human Genetics.
  • The Indian Academy of Medical Genetics, S S Agarwal Young Scientist Award (2017).
  • The Indian Society of Human Genetics, Young Scientist Award (2016).
  • DBT International Travel Grant for Poster Presentation in 8th World Congress on DOHaD (Developmental Origins of Health and Disease) Singapore (2013).
  • GEoCoDE Fellowship for one month to visit the University of Exeter, United Kingdom (2012).
  • CSIR-Junior Research Fellow (2010).

Patents & Publications

  1. Suraj S Nongmaithem, Amitabh Biswas, Swaroop Iyer, Jandhayala Vyshnavi, Archana Wath, Giriraj R Chandak, Dipty Jain. Development of a Clinical Severity Score for Indian Sickle Cell Anaemia Patients. medRxiv 2025.10.07.25337518; doi: https://doi.org/10.1101/2025.10.07.25337518.
  2. Kumar L, Nongmaithem S, Kumar S, Thangaraj K. Investigating the demographic history of Sindhi population inhabited in West Coast India. Human Genomics. 2025 Sep 30;19(1):111. https://doi.org/10.1186/s40246-025-00822-w.
  3. Ajay Deepak Verma*, Suraj S Nongmaithem*, Challapalli Mounika, Swetha Ramachandran, Anushri Umesh, Giriraj R Chandak. Zebrafish Model of tcn2 Deletion Reveals New Molecular Insights into the Role of Vitamin B12 in Embryonic Development. Journal of Analytical Techniques and Research. 6 (2024): 78-89. https://www.doi.org/10.26502/jatr.45.
  4. Ken Suzuki et al. Genetic drivers of heterogeneity in type 2 diabetes pathophysiology. Nature. 2024 Mar;627(8003):347-357. https://doi.org/10.1038/s41586-024-07019-6.
  5. Prachand Issarapu, Manisha Arumalla, Hannah R. Elliott, Suraj S. Nongmaithem, Alagu Sankareswaran, Modupeh Betts, Sara Sajjadi, Noah J. Kessler, Swati Bayyana, Sohail R. Mansuri, Maria Derakhshan, G. V. Krishnaveni, Smeeta Shrestha, Kalyanaraman Kumaran, Chiara Di Gravio, Sirazul A. Sahariah , Eleanor Sanderson, Caroline L. Relton, Kate A. Ward, Sophie E. Moore, Andrew M Prentice , Karen A. Lillycrop, Caroline H. D. Fall, Matt J. Silver, Giriraj R. Chandak, the EMPHASIS study group. DNA methylation at the suppressor of cytokine signaling 3 (SOCS3) gene influences height in childhood. Nature Communications 14, 5200 (2023). https://doi.org/10.1038/s41467-023-40607-0.
  6. Kanoni, S., Graham, S.E., Wang, Y. et al. Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis. Genome Biology 23, 268 (2022). https://doi.org/10.1186/s13059-022-02837-1.
  7. Shweta Ramdas, et al. A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids. American Journal of Human Genetics 109, 1366–1387, August 4, 2022. https://doi.org/10.1016/j.ajhg.2022.06.012.
  8. Loic Yengo et al. A Saturated Map of Common Genetic Variants Associated with Human Height from 5.4 Million Individuals of Diverse Ancestries. Nature 610, 704–712, 2022. https://doi.org/10.1038/s41586-022-05275-y.
  9. Lorenzo Bomba, Klaudia Walter, Qi Guo, Praveen Surendran, Kousik Kundu, Suraj Nongmaithem, Mohd Anisul Karim, Isobel D Stewart, Claudia Langenberg, John Danesh, Emanuele Di Angelantonio, David J Roberts, Willem H Ouwehand, INTERVAL study; Ian Dunham, Adam S Butterworth, Nicole Soranzo. Whole-exome sequencing identifies rare genetic variants associated with human plasma metabolites. American Journal of Human Genetics 109, 1038–1054, June 2, 2022. https://doi.org/10.1016/j.ajhg.2022.04.009.
  10. Suraj S. Nongmaithem, Robin N. Beaumont, Akshay Dedaniya, Andrew R. Wood, Babatunji-William Ogunkolade, Zahid Hassan, Ghattu V. Krishnaveni, Kalyanaraman Kumaran, Ramesh D. Potdar, Sirazul A. Sahariah, Murali Krishna, Chiara Di Gravio, Inder D. Mali, Alagu Sankareswaran, Akhtar Hussain, Biswajit W. Bhowmik, Abdul Kalam A. Khan, Bridget A. Knight, Timothy M. Frayling, Sarah Finer, Caroline H.D. Fall, Chittaranjan S. Yajnik, Rachel M. Freathy, Graham A. Hitman, Giriraj R. Chandak. Babies of South Asian and European Ancestry Show Similar Associations With Genetic Risk Score for Birth Weight Despite the Smaller Size of South Asian Newborns. Diabetes 1 April 2022; 71 (4): 821–836. https://doi.org/10.2337/db21-0479.
  11. Mahajan, A., et al. Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation. Nature Genetics 54, 560–572 (2022). https://doi.org/10.1038/s41588-022-01058-3.
  12. Anna V Mikhaylova, et al. Whole-genome sequencing in diverse subjects identifies genetic correlates of leukocyte traits: The NHLBI TOPMed program. American Journal of Human Genetics, 2021 Oct 7;108 (10):1836-1851. https://doi:10.1016/j.ajhg.2021.08.007.
  13. Suraj S. Nongmaithem, Charudatta V. Joglekar, Ghattu V. Krishnaveni, Sirazul A. Sahariah, Meraj Ahmad, Swetha Ramachandran, Meera Gandhi, Harsha Chopra, Anand Pandit, Ramesh D. Potdar, Caroline H.D. Fall, Chittaranjan S. Yajnik, Giriraj R. Chandak. GWAS identifies population-specific new regulatory variants in FUT6 associated with plasma B12 concentrations in Indians. Human Molecular Genetics, 1 July 2017, 26(13) 2551–2564, https://doi.org/10.1093/hmg/ddx071.
  14. Meraj Ahmad, Suraj S Nongmaithem, G V Krishnaveni, Caroline HD Fall, Chittaranjan S Yajnik, Giriraj R Chandak. Lack of replication of association of THSD7A with obesity. International Journal of Obesity 40, 725–726 (2016). https://doi.org/10.1038/ijo.2016.15. (Impact factor 5.09)
  15. Ashutosh Singh Tomar, Divya Sri Priyanka Tallapragada, Suraj S Nongmaithem, Smeeta Shrestha, Chittaranjan S. Yajnik, Giriraj R Chandak. Intrauterine Programming of Diabetes and Adiposity. Current Obesity Reports 4, 418–428 (2015). https://doi.org/10.1007/s13679-015-0175-6.
  16. Joshi, P., et al. Directional dominance on stature and cognition in diverse human populations. Nature 523, 459–462 (2015). https://doi.org/10.1038/nature14618.
  17. Chittaranjan S Yajnik, Giriraj R Chandak, Charudatta Joglekar, Prachi Katre, Dattatray S Bhat, Suraj N Singh, Charles S Janipalli, Helga Refsum, Ghattu Krishnaveni, Sargoor Veena, Clive Osmond, Caroline HD Fall. Maternal homocysteine in pregnancy and offspring birthweight: epidemiological associations and Mendelian randomization analysis. International Journal of Epidemiology, Volume 43, Issue 5, October 2014, Pages 1487–1497, https://doi.org/10.1093/ije/dyu132.
  18. Gagandeep Kaur Walia, Vipin Gupta, Aastha Aggarwal, Mohammad Asghar, Frank Dudbridge, Nicholas Timpson, Nongmaithem Suraj Singh, M. Ravi Kumar, Sanjay Kinra, Dorairaj Prabhakaran, K. Srinath Reddy, Giriraj Ratan Chandak, George Davey Smith, Shah Ebrahim (2014) Association of Common Genetic Variants with Lipid Traits in the Indian Population. PLoS ONE 9(7): e101688. https://doi.org/10.1371/journal.pone.0101688.
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