Our group is primarily involved in Statistical Genomics with applications to identification of genetic variants which confer susceptibility to complex diseases in humans. We use data from GWAS, transcriptomics, epigenomics, e-QTL studies, and develop techniques to accelerate discovery of variants, genes and pathways from high-throughput genomics data. For this, we apply analytic approaches such as multiple-testing, meta-analysis, pathway/enrichment analysis and integrative genomics. We are also interested in understanding the causal mechanisms underlying these variants driving disease pathogenesis and in developing ways to understand gene-gene and gene-environment interactions that is crucial for effective genomics driven personalized medicine.
Biswas S, Pal S, Majumder PP, Bhattacharjee S*. A framework for pathway knowledge driven prioritization in genome-wide association studies. Genet Epidemiol. 2020 Nov;44(8):841-853. doi: 10.1002/gepi.22345. Epub 2020 Aug 10. PMID: 32779262; PMCID: PMC7116354.
Sengupta D, Guha U, Bhattacharjee S*, Sengupta M*. Association of 12 polymorphic variants conferring genetic risk to lung cancer in Indian population: An extensive meta-analysis. Environ Mol Mutagen. 2017 Dec;58(9):688-700. doi: 10.1002/em.22149. Epub 2017 Oct 27. PMID: 29076184.
Carty CL, Bhattacharjee S, Haessler J, Cheng I, Hindorff LA, Aroda V, Carlson CS, Hsu CN, Wilkens L, Liu S, Selvin E, Jackson R, North KE, Peters U, Pankow JS, Chatterjee N, Kooperberg C. Analysis of metabolic syndrome components in >15 000 african americans identifies pleiotropic variants: results from the population architecture using genomics and epidemiology study. Circ Cardiovasc Genet. 2014 Aug;7(4):505-13. doi: 10.1161/CIRCGENETICS.113.000386. Epub 2014 Jul 14. PMID: 25023634; PMCID: PMC4142758.
Bhattacharjee S, Rajaraman P, Jacobs KB, Wheeler WA, Melin BS, Hartge P; GliomaScan Consortium, Yeager M, Chung CC, Chanock SJ, Chatterjee N. A subset-based approach improves power and interpretation for the combined analysis of genetic association studies of heterogeneous traits. Am J Hum Genet. 2012 May 4;90(5):821-35. doi: 10.1016/j.ajhg.2012.03.015. PMID: 22560090; PMCID: PMC3376551.
Bhattacharjee S, Wang Z, Ciampa J, Kraft P, Chanock S, Yu K, Chatterjee N. Using principal components of genetic variation for robust and powerful detection of gene-gene interactions in case-control and case-only studies. Am J Hum Genet. 2010 Mar 12;86(3):331-42. doi: 10.1016/j.ajhg.2010.01.026. Epub 2010 Mar 4. PMID: 20206333; PMCID: PMC2833365.
The primary area of research in our group is Statistical Genomics with applications to genomics of complex diseases such as cardiovascular diseases, neuro-psychiatric diseases and autoimmune disorders. We use GWAS data and other high-throughput omics data available in the public domain to enhance our understanding of complex disease and at the same time we develop tools and techniques that enable others to better analyse their own datasets. We also collaborate with scientists and clinicians who collect patient samples to generate their own genomics datasets on complex diseases.
Current Projects
Statistical Methods to Enhance the Power of Discovering Associations from Genome-wide Data. DBT/Wellcome Trust India Alliance Intermediate Fellowship Grant (Dec 2014-2019, Extended till: April 2021)
Education
| Year | Degree | University |
|---|---|---|
| 2008 | Ph.D | University of Pittsburgh |
| 2004 | M.Stat. | Indian Statistical Institute, Kolkata |
| 2002 | B.Stat. | Indian Statistical Institute, Kolkata |
Professional Appointments
October 2011 - June 2019 : Assistant Professor at National Institute of Biomedical Genomics, Kalyani, India
Sep 2008 - August 2011 : Research Fellow at the Biostatistics Branch of the Division of Cancer Epidemiology and Genetics, National Cancer Institute (NIH).
American Society of Human Genetics (2005 to 2008), American Statistical Association (2007-2011), ENAR-International Biometric Society (2008-2011), Indian Society of Human Genetics (since 2012), Calcutta Consortium of Human Genetics (since 2012), National Network for Mathematical and Computational Biology (since 2015)
Year Award
2010 Statistics in Epidemiology Young Investigator Award (Joint Statistical Meetings, 2010)
2011 Outstanding Research Paper by a Fellow (Division of Cancer Epidemiology and Genetics, 2010-11)
2014 Wellcome Trust/DBT India-Alliance Intermediate Fellowship (May, 2014)
| 2015 | Indo-US Conference cum Workshop on “Big Data Analysis and Translation in Disease Biology (JNU, New Delhi, India, 2015): “Statistical Methods for Integrative Analysis of Genome-wide Data” |
| 2016 | NIBMG-UChicago Workshop on “Big Data Analysis in BioMedical Genomics” (NIBMG, Kalyani, India), “Integration of Pathways and Gene-Expression Data in GWAS.” |
| 2018 | Symosium on “Accelerating Biology 2018: Digitizing Life” (C-DAC Pune): Invited talk “Statistical and Computational Tools for Scalable Integrative Analysis of Genome-wide Data”. |
| 2019 | Indian Society of Human Genetics, 44th Annual Meeting (Hosted by NIBMG & Kalyani University, Kalyani, WB, India): “Meta-analysis and Its Applications in Genomics of Diseases”. |
| 2019 | Center for Advanced Faculty Training on "Modern Statistical Techniques in Genetics", ICAR-Indian Agricultural Statistics Research Institute, (New Delhi): “Statistical and computational methods for analysis of genome-wide association (GWAS) studies.” |
Invited/Special lectures
Year Institute/meeting, Title of the talk
Past Major Projects
Pathway-driven Prioritization of GWAS (2014-2019)
Genetic Association for Heterogeneous traits and subtypes (2010-2014)
Gene-Gene Interactions in Presence of Population Stratification. (2008-2010)
Score Tests for QTL (Quantitative Trait Locus) Linkage Analysis. (2006-2008)
Suhas Ganesh, Alekhya Vemula, Samsiddhi Bhattacharjee, Kezia Mathew, Dhruva Ithal, Karthick Navin, Ravi Kumar Nadella, Biju Viswanath, Patrick F. Sullivan, The ADBS Consortium, Sanjeev Jain, Meera Purushottam (2022). “Whole exome sequencing in dense families suggests genetic pleiotropy amongst Mendelian and complex neuropsychiatric syndromes”. Sci Rep 12, 21128 (2022). https://doi.org/10.1038/s41598-022-25664-7
Chakraborty S, Sharma A, Bagchi I, Pal S, Bhattacharyya C, Gupta V, Maitra A, Bhattacharjee S, Sharma A, Sihota R, Acharya M. (2021): A genomewide association study on individuals with occludable angles identifies potential risk loci for intraocular pressure. J Genet. 2021;100:69.
Sengupta, D., Banerjee, S., Mukhopadhyay, P., Mitra, R., Chaudhuri, T., Sarkar, A., Bhattacharjee, G., Nath, S., Roychoudhury, S., Bhattacharjee, S.* and Sengupta, M.* (2021): A comprehensive meta-analysis and a case–control study give insights into genetic susceptibility of lung cancer and subgroups. Scientific Reports, 2021, 11(1), pp.1-16.
Pandit, Bhaswati, Samsiddhi Bhattacharjee, and Bornali Bhattacharjee. "Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India." Infection, Genetics and Evolution 90 (2021): 104734.
Sudipta Chakraborty, Anshul Sharma, Arundhati Sharma, Ramanjit Sihota, Samsiddhi Bhattacharjee, Moulinath Acharya (2020): A Haplotype-based genomic analysis reveals novel association of CNTNAP5 genic region with primary angle closure glaucoma. Journal of Biosciences 46, no. 1 (2021): 1-9.
Kavya Vipparthi; Ankit K Patel; Subhashis Ghosh; Subrata Das; Chitrarpita Das; Koyeli Das; Anwesha Sarkar; Venu Thatikonda; Biswajoy Pal; Arun S Remani; Neeraj Arora; Mayur Parihar; Maleppillil V Vijayakumar; Manoj K Bhat; Ramanamurthy Boppana; Samsiddhi Bhattacharjee; Nidhan K Biswas; Pattatheyil Arun; Rajeev Sharan; Sandeep Singh (2020): Two novel cell culture models of buccal mucosal oral cancer from patients with no risk-habits of tobacco smoking or chewing. Oral Oncology 113 (2020): 105131.
Bishnupriya Chhatriya, Moumita Mukherjee, Sukanta Ray, Barsha Saha , Somdatta Lahiri, Sandip Halder, Indranil Ghosh, Sujan Khamrui, Kshaunish Das, Samsiddhi Bhattacharjee, Saroj Kant Mohapatra and Srikanta Goswami (2020): Transcriptome analysis identifies putative multi-gene signature distinguishing benign and 1 malignant pancreatic head mass. J Transl Med. 2020;18(1):420. Published 2020 Nov 7. doi:10.1186/s12967-020-02597-1
Shrayashi Biswas, Soumen Pal, Partha P. Majumder, Samsiddhi Bhattacharjee* (2020): A Framework for Pathway Knowledge Driven Prioritization in Genome-wide Association Studies. Genetic Epidemiology (In Press)
Debmalya Sengupta, Souradeep Banerjee, Pramiti Mukhopadhyay, Udayan Guha, Kausik Ganguly, Samsiddhi Bhattacharjee, Mainak Sengupta (2020): A meta-analysis and in silico analysis of polymorphic variants conferring breast cancer risk in the Indian subcontinent. Future Oncol. 2020 Aug 1. doi: 10.2217/fon-2020-0333. Epub ahead of print. PMID: 32744066.
Patel, A.K., Vipparthi, K., Thatikonda, V., Arun, I., Bhattacharjee, S., Sharan, R., Arun, P. and Singh, S. (2018). A subtype of cancer-associated fibroblasts with lower expression of alpha-smooth muscle actin suppresses stemness through BMP4 in oral carcinoma. Oncogenesis, 7(10), p.78.
Sengupta, D., Guha, U., Mitra, S., Ghosh, S., Bhattacharjee, S.*, Sengupta, M.* (2018). Meta-Analysis of Polymorphic Variants Conferring Genetic Risk to Cervical Cancer in Indian Women Supports CYP1A1 as an Important Associated Locus. Asian Pacific Journal of Cancer Prevention, 19(8), 2071-2081. doi: 10.22034/APJCP.2018.19.8.2071 [*Corresponding Authors]
Sengupta D, Guha U, Bhattacharjee S*, Sengupta M*: Association of 12 polymorphic variants conferring genetic risk to lung cancer in Indian population: An extensive meta-analysis. Environ Mol Mutagen. 2017 Dec;58(9):688-700. doi: 10.1002/em.22149. Epub 2017 Oct 27. [*Corresponding Authors]
Bhushan A, Ghosh S, Bhattacharjee S, Chinnaswamy S: Confounding by Single Nucleotide Polymorphism rs117648444 (P70S) Affects the Association of Interferon Lambda Locus Variants with Response to Interferon-α-Ribavirin Therapy in Patients with Chronic Genotype 3 Hepatitis C Virus Infection. J Interferon Cytokine Res. 2017 Aug;37(8):369-382. doi: 10.1089/jir.2017.0002. Epub 2017 Jul 20.
Mukhopadhyay S, Thatoi PK, Pandey AD, Das BK, Ravindran B, Bhattacharjee S , Mohapatra SK. Transcriptomic meta-analysis reveals up-regulation of gene expression functional in osteoclast differentiation in human septic shock. PLoS One. 2017 Feb 15;12(2):e0171689. PMID: 28199355.
Li WQ, Pfeiffer RM, Hyland PL, Shi J, Gu F, Wang Z, Bhattacharjee S, Luo J, Xiong X, Yeager M, Deng X, Hu N, Taylor PR, Albanes D, Caporaso NE, Gapstur SM, Amundadottir L, Chanock SJ, Chatterjee N, Landi MT, Tucker MA, Goldstein AM, Yang XR: Genetic polymorphisms in the 9p21 region associated with risk of multiple cancers. Carcinogenesis 2014 Dec;35(12):2698-705.
Datta S, Xia XQ, Bhattacharjee S, Jia Z, Advances in statistical medicine; Comput Math Methods Med; 2014:316153; [Epub 2014 Nov 9]
Cara L. Carty, Samsiddhi Bhattacharjee, Jeff Haessler, Iona Cheng, Lucia A. Hindorff, Vanita Aroda, Christopher S. Carlson, Chun-Nan Hsu, Lynne Wilkens, Simin Liu, Elizabeth Selvin, Rebecca Jackson, Kari E. North, Ulrike Peters, James S. Pankow, Nilanjan Chatterjee and Charles Kooperberg: Comparative Analysis of Metabolic Syndrome Components in over 15,000 African Americans Identifies Pleiotropic Variants: Results from the PAGE Study. Circ Cardiovasc Genet. published online July 14, 2014.
Sreedhar Chinnaswamy, Snehajyoti Chatterjee, Ramachandran Boopathi, Shuvolina Mukherjee, Samsiddhi Bhattacharjee and Tapas K. Kundu: A single nucleotide polymorphism associated with hepatitis C virus infections located in the distal region of the IL28B promoter influences NF-kB-mediated gene transcription. PLoS ONE 2013 Oct 8;8(10):e75495.
Gu F, Pfeiffer RM, Bhattacharjee S, Han SS, Taylor PR, Berndt S, Yang H, Sigurdson AJ, Toro J, Mirabello L, Greene MH, Freedman ND, Abnet CC, Dawsey SM, Hu N, Qiao YL, Ding T, Brenner AV, Garcia-Closas M, Hayes R, Brinton LA, Lissowska J, Wentzensen N, Kratz C, Moore LE, Ziegler RG, Chow WH, Savage SA, Burdette L, Yeager M, Chanock SJ, Chatterjee N, Tucker MA, Goldstein AM, Yang XR: Common genetic variants in the 9p21 region and their associations with multiple tumours. Br J Cancer 2013 Jan 29. doi: 10.1038/bjc.2013.7. [Epub ahead of print]
Leenders M, Bhattacharjee S, Vineis P, Stevens V, Bueno-de-Mesquita HB, Shu XO, Amundadottir L, Gross M, Tobias GS, Wactawski-Wende J, Arslan AA, Duell EJ, Fuchs CS, Gallinger S, Hartge P, Hoover RN, Holly EA, Jacobs EJ, Klein AP, Kooperberg C, Lacroix A, Li D, Mandelson MT, Olson SH, Petersen G, Risch HA, Yu K, Wolpin BM, Zheng W, Agalliu I, Albanes D, Boutron-Ruault MC, Bracci PM, Buring JE, Canzian F, Chang K, Chanock SJ, Cotterchio M, Gaziano JM, Giovanucci EL, Goggins M, Hallmans G, Hankinson SE, Hoffman-Bolton JA, Hunter DJ, Hutchinson A, Jacobs KB, Jenab M, Khaw KT, Kraft P, Krogh V, Kurtz RC, McWilliams RR, Mendelsohn JB, Patel AV, Rabe KG, Riboli E, Tjønneland A, Trichopoulos D, Virtamo J, Visvanathan K, Elena JW, Yu H, Zeleniuch-Jacquotte A, Stolzenberg-Solomon RZ: Polymorphisms in genes related to one-carbon metabolism are not related to pancreatic cancer in PanScan and PanC4. Cancer Causes Control 2013, Jan 19. Mar;24(3):595-602.
Samsiddhi Bhattacharjee, Preetha Rajaraman, Kevin B Jacobs, William A Wheeler, Beatrice S Melin, Patricia Hartge, GliomanScan Consortium, Meredith Yeager, Charles C Chung, Stephen J Chanock, Nilanjan Chatterjee: A subset-based approach improves power and interpretation for the combined-analysis of genetic association studies of heterogeneous traits. Am J Hum Genet 2012, May 4;90(5):821-835.
Idan Menashe, Dennis Maeder, Montserrat Garcia-Closas, Jonine D. Figueroa, Samsiddhi Bhattacharjee, Melissa Rotunno, Peter Kraft, David J. Hunter, Stephen J. Chanock, Philip S. Rosenberg, and Nilanjan Chatterjee: Pathway analysis of breast cancer genome wide association study highlights three pathways and one canonical signaling cascade. Cancer Res. 2010 Jun 1;70(11):4453-9. Epub 2010 May 11.
Samsiddhi Bhattacharjee, Zhaoming Wang, Julia Ciampa, Peter Kraft, Stephen Chanock, Kai Yu, Nilanjan Chatterjee: Using Principal Components of Genetic Variation for Robust and Powerful Detection of Gene-Gene Interactions in Case-Control and Case-Only Studies, Am J Hum Genet 2010 Mar 12;86(3):331-42.
Brian J. Henson, Samsiddhi Bhattacharjee, Dawn O’Dee, Eleanor Feingold, Susanne M. Gollin: The Expression of miR-125b and miR-100 in OSCC and Their Contribution to Malignancy, Genes Chromosomes Cancer. 2009 Jul;48(7):569-82.
Bhattacharjee S, Kuo CL, Mukhopadhyay NM, Brock GN, Weeks DE , Feingold EF: Robust score statistics for QTL linkage analysis, Am J Hum Genet 2008 Mar;82(3):567-582.
Sengul H, Bhattacharjee S, Feingold E, Weeks DE: The elusive goal of pedigree weights, Genet Epidemiol. 2007 Jan;31(1):51-65.
Nandita Mukhopadhyay, Indrani Halder, Samsiddhi Bhattacharjee, Daniel E. Weeks: Two-dimensional linkage analyses of rheumatoid arthritis, BMC Proceedings, 2007 Dec; I (Suppl I):568.
Ghosh S, Bhattacharjee S, Basu G, Pal S, Majumder PP: Linkage mapping of a complex trait in the New York population of the GAW14 simulated dataset: a multivariate phenotype approach, BMC Genet. 2005 Dec 30;6 Suppl 1:S19
Software
GKnowMTest (https://github.com/sbstatgen/GKnowMTest): R package for pathway knowledge-based prioritization of GWAS results.
TMVNSIM (https://cran.r-project.org/web/packages/tmvnsim/index.html): R package for importance sampling from the truncated multivariate normal distribution (2015).
ASSET (http://www.bioconductor.org/packages/release/bioc/html/ASSET.html): R package for combined analysis of heterogeneous traits and disease subtypes (2012).
Ph.D. Students:
Krittika Bhattacharyya
Kallol Datta
Submitting Thesis:
Shrayashi Biswas
