Resources

The GenomeAsia 100K Project enables genetic discoveries across Asia

Nature, volume 576, pages106–111 (2019)

Jeffrey D. Wall, Eric W. Stawiski, Aakrosh Ratan, Hie Lim Kim, Changhoon Kim, Ravi Gupta, Kushal Suryamohan, Elena S. Gusareva, Rikky Wenang Purbojati, Tushar Bhangale, Vadim Stepanov, Vladimir Kharkov, Markus S. Schröder, Vedam Ramprasad, Jennifer Tom, Steffen Durinck, Qixin Bei, Jiani Li, Joseph Guillory, Sameer Phalke, Analabha Basu, Jeremy Stinson, Sandhya Nair, Sivasankar Malaichamy, Nidhan K. Biswas, John C. Chambers, Keith C. Cheng, Joyner T. George, Seik Soon Khor, Jong-Il Kim, Belong Cho, Ramesh Menon, Thiramsetti Sattibabu, Akshi Bassi, Manjari Deshmukh, Anjali Verma, Vivek Gopalan, Jong-Yeon Shin, Mahesh Pratapneni, Sam Santhosh, Katsushi Tokunaga, Badrul M. Md-Zain, Kok Gan Chan, Madasamy Parani, Purushothaman Natarajan, Michael Hauser, R. Rand Allingham, Cecilia Santiago-Turla, Arkasubhra Ghosh, Santosh Gopi Krishna Gadde, Christian Fuchsberger, Lukas Forer, Sebastian Schoenherr, Herawati Sudoyo, J. Stephen Lansing, Jonathan Friedlaender, George Koki, Murray P. Cox, Michael Hammer, Tatiana Karafet, Khai C. Ang, Syed Q. Mehdi, Venkatesan Radha, Viswanathan Mohan, Partha P. Majumder, Somasekar Seshagiri, Jeong-Sun Seo, Stephan C. Schuster & Andrew S. Peterson

The underrepresentation of non-Europeans in human genetic studies so far has limited the diversity of individuals in genomic datasets and led to reduced medical relevance for a large proportion of the world’s population. Population-specific reference genome datasets as well as genome-wide association studies in diverse populations are needed to address this issue. Here we describe the pilot phase of the GenomeAsia 100K Project. This includes a whole-genome sequencing reference dataset from 1,739 individuals of 219 population groups and 64 countries across Asia.

  https://www.nature.com/articles/s41586-019-1793-z

Irreversible Electroporation Combined with Checkpoint Blockade and TLR7 Stimulation Induces Antitumor Immunity in a Murine Pancreatic Cancer Model

Journal of Cancer Immunology Research, 7(10): 1714-1726, October 2019

Jayanth S. Shankara Narayanan, Partha Ray, Tomoko Hayashi, Thomas C. Whisenant, Diego Vicente, Dennis A. Carson, Aaron M. Miller, Stephen P. Schoenberger and Rebekah R. White

Irreversible electroporation (IRE) is a nonthermal ablation technique that is used clinically in selected patients with locally advanced pancreatic cancer, but most patients develop recurrent distant metastatic disease. We hypothesize that IRE can induce an in situ vaccination effect by releasing tumor neoantigens in an inflammatory context. Using an immunocompetent mouse model, we demonstrated that IRE alone produced complete regression of subcutaneous tumors in approximately 20% to 30% of mice.

  https://cancerimmunolres.aacrjournals.org/content/7/10/1714#ref-21

Unmasking tumor heterogeneity and clonal evolution by single-cell analysis

Journal of Cancer Metastasis and Treatment, 4:47, 31 August 2018

Xiaoshan Shi, Papia Chakraborty, Amitabha Chaudhuri

The intratumoral heterogeneity orchestrated by the tumor intrinsic and extrinsic mechanisms enable cancers to persist and spread notwithstanding the use of aggressive interventional therapies. The heterogeneity is revealed at multiple levels – at the level of individual tumor cells, in the cellular composition of tumor infiltrates and in the chemical microenvironment in which the cells reside. Deconvoluting the complex nature of the cell types present in the tumor, along with the homo and heterotypic interactions between different cell types can produce novel insights of biological and clinical relevance.

  https://jcmtjournal.com/article/view/2770

A neoepitope derived from a novel human germline APC gene mutation in familial adenomatous polyposis shows selective immunogenicity

PLoS ONE, 13:9, 26 September 2018

Snigdha Majumder, Rakshit Shah, Jisha Elias, Yogesh Mistry, Karunakaran Coral, Priyanka Shah, Anand Kumar Maurya, Bharti Mittal, Jason K. D’Silva, Sakthivel Murugan, Lakshmi Mahadevan, Rekha Sathian, V. L. Ramprasad, Papia Chakraborty, Ravi Gupta, Amitabha Chaudhuri, Arati Khanna-Gupta

Familial adenomatous polyposis (FAP) is an inherited condition arising from genetic defects in the Adenomatous polyposis coli (APC) gene. Carriers with mutations in the APC gene develop polyps in the colon and rectum which if not managed, transition into colon cancer. In this study, we identified a novel germline mutation in the APC gene in members of an FAP-affected (Familial adenomatous polyposis) family.

  https://www.ncbi.nlm.nih.gov/pubmed/30256815
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