Profile
Research Interest:
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.
Selected Publications
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.
Research
The primary area of research in our group is Statistical Genomics with applications to genomics of complex diseases such as type-2 diabetes, cardiovascular disease, 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 other investigators to analysis and integration of their own datasets more efficiently. We also collaborate with scientists and clinicians who collect patient samples to generate their own genomics datasets to answer important scientific questions about complex diseases.
We have ongoing projects in the following areas:
Current Projects
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Prioritization of GWAS based on biological knowledge such as variant positional and functional annotations and gene-level knowledge from pathways and ontologies.
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Integrative Genomics: Utilizing transcriptomic studies, eQTL studies and epigenomic data to integrate with GWAS data for discovering additional genomic variants and to identify genes mediating the action of these variants.
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In-Silico Fine-Mapping and Functional Annotation: Guiding functional validation studies using statistical procedures to identify potential causal variants and regulatory variants with potential mechanisms of regulation.
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Gene-Gene and Gene-Environment Interactions: Understanding Interactions among genetic variants and between genes and environmental/lifestyle factors in the pathogenesis of complex diseases, that has a direct bearing on personalized risk assessment, therapy and/or management.
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Statistical Issues in High-throughput Genomics: We have been working towards addressing several statistical issues arising in analysis of genomics data such as
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Large-scale Multiple Testing with locally correlated genomic tests.
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Methods for large-scale genetic pleiotropy analysis.
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Variable-selection in high-dimensional settings with sparsity restrictions
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Statistical modelling of interactions between variants, genes, pathways and environmental factors.
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Computational Issues in High-Throughput Genomics: We create various software tools for methods that we develop and disseminate them freely for the genomics community. We are currently creating a user-friendly web-portal for remotely accessing, analyzing, integrating, and visualizing public domain genomic data.
Research Grant(s) as PI
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)
CV
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).
Professional Memberships
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)
Awards/Honors
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)
Invited/Special lectures
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)
Publications
- Dutta T, Sengupta S, Adhya S, Saha
A, Sengupta D, Mondal R, Bhattacharjee S*, Sengupta M*. Identification
of TNF-α as major susceptible risk locus for vitiligo: A systematic review and
meta-analysis study in Asian population. Dermatology. 2024 Feb 20. doi:
10.1159/000536480. Epub ahead of print. PMID: 38377977.
- Srikanta Goswami, Bishnupriya
Chhatriya, Moumita Mukherjee, Sukanta Ray, Kshaunish Das, Samsiddhi
Bhattacharjee, Saroj Kant Mohapatra (2023), “Comprehensive transcriptomic
analysis of tissue and serum samples of patients with benign and malignant
pancreatic head mass to find out potential biomarker”, Pancreatology, Volume
23, Issue 8, 2023, https://doi.org/10.1016/j.pan.2023.09.003.
- Chakraborty S, Sharma A, Pal S,
Sharma A, Sihota R, Bhattacharjee S, Acharya M. A quantitative trait
GWAS on lens thickness identifies novel risk loci on PTPRM in the narrow angle
individuals susceptible to PACG. Eur J Ophthalmol. 2023 Sep;33(5):1922-1930.
doi: 10.1177/11206721231160988. Epub 2023 Mar 17. PMID: 36927043.
- Debmalya Sengupta, Pramiti
Mukhopadhyay#, Souradeep Banerjee#, Kausik Ganguly, Prateek Mascharak, Noyonika
Mukherjee, Sangeeta Mitra, Samsiddhi
Bhattacharjee, Ritabrata Mitra, Abhijit Sarkar, Tamohan Chaudhuri, Gautam
Bhattacharjee, Somsubhra Nath, Susanta Roychoudhury, Mainak Sengupta (2023):
“Identifying polymorphic cis-regulatory variants as risk markers for lung
carcinogenesis and chemotherapy responses in tobacco smokers from Eastern
India”. Sci Rep. 2023 Mar
10;13(1):4019. doi: 10.1038/s41598-023-30962-9.
- 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. Genet Epidemiol.
2020 Nov;44(8):841-853. doi: 10.1002/gepi.22345. Epub 2020 Aug 10. PMID:
32779262
- 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]
- S Biswas, S., Pal, S., & Bhattacharjee,
S*. (2017). A Regression-based Framework for Scalable Pathway-guided Search
in Genome-wide Association Studies. bioRxiv, 241265.
- 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. doi: 10.1371/journal.pone.0171689. eCollection
2017
- Sujay Datta, Xiao-Qin Xia, Samsiddhi
Bhattacharjee, and Zhenyu Jia: Advances in Statistical Medicine. Computational and Mathematical Methods in
Medicine, vol. 2014, Article ID 316153, 2 pages, 2014.
doi:10.1155/2014/316153
- 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.
- 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: 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.
- 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.
- F Gu, R M Pfeiffer, S
Bhattacharjee, S S Han, P R Taylor, S Berndt, H Yang, A J Sigurdson, J
Toro, L Mirabello, M H Greene, N D Freedman, C C Abnet, S M Dawsey,NHu, Y-L
Qiao, T Ding, A V Brenner, M Garcia-Closas, R Hayes, L A Brinton, J Lissowska,
N Wentzensen, C Kratz, L E Moore, R G Ziegler, W-H Chow, S A Savage, L
Burdette, M Yeager, S J Chanock, N Chatterjee, M A Tucker, A M Goldstein and X
R Yang: Common genetic variants in the 9p21 region and their associations with
multiple tumours. Br J Cancer 2013 Apr
2;108(6):1378-86.
- Max Leenders, Samsiddhi
Bhattacharjee, et. al., Rachael Z. Stolzenberg-Solomon:
Polymorphisms in genes related to one-carbon metabolism are not related to
pancreatic cancer in PanScan and PanC4. Cancer
Causes Control 2013 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.
- Samsiddhi Bhattacharjee, Chia-Ling Kuo, Nandita Mukhopadhyay, Guy N. Brock, Daniel E.
Weeks and Eleanor Feingold: Robust score statistics for QTL linkage analysis, Am J Hum Genet 2008 Mar;82(3):567-582.
- Nandita Mukhopadhyay,
Indrani Halder, Samsiddhi Bhattacharjee,
Daniel E. Weeks: Two-dimensional linkage analyses of rheumatoid arthritis, BMC Proceedings 2007 Dec; I (Suppl
I):568.
- Haydar Sengul, Samsiddhi Bhattacharjee, Eleanor
Feingold, Daniel E. Weeks: The elusive goal of pedigree weights, Genet Epidemiol 2007 Jan;31(1):51-65.
-
Saurabh Ghosh, Samsiddhi Bhattacharjee, Gourab Basu, Sandip Pal, Partha P
Majumder: 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
Lab members
Ph.D. Students:
Prasun Panja
Kallol Datta
Gaurav R. Amale
Diptanil Biswas
Graduated:
Shrayashi Biswas