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Ravi Gupta, Aakrosh Ratan, Changanamkandath Rajesh, Rong Chen, Hie Lim Kim, Richard Burhans, Webb Miller, Sam Santhosh, Ramana V Davuluri, Atul J Butte, Stephan C Schuster, Somasekar Seshagiri and George Thomas (2012). BMC Genomics, 13, 440.

With over 1.3 billion people, India is estimated to contain three times more genetic diversity than Europe. Next-generation sequencing technologies have facilitated the understanding of diversity by enabling whole genome sequencing at greater speed and lower cost. While genomes from people of European and Asian descent have been sequenced, only recently has a single male genome from the Indian subcontinent been published at sufficient depth and coverage. In this study we have sequenced and analyzed the genome of a South Asian Indian female (SAIF) from the Indian state of Kerala.

James A. Poulter, Musallam Al-Araimi, Ivan Conte, Maria M. van Genderen, Eamonn Sheridan, Ian M. Carr, David A. Parry, Mike Shires, Sabrina Carrella, John Bradbury, Kamron Khan, Phillis Lakeman, Panagiotis I. Sergouniotis, Andrew R. Webster, Anthony T. Moore, Bishwanath Pal, Moin D. Mohamed, Anandula Venkataramana, Vedam Ramprasad, Rohit Shetty, Murugan Saktivel, Govindasamy Kumaramanickavel, Alex Tan, David A. Mackey, Alex W. Hewitt, Sandro Banfi, Manir Ali, Chris F. Inglehearn, and Carmel Toomes (2013). The American Journal of Human Genetics, 93, 1143–1150.

Foveal hypoplasia and optic nerve misrouting are developmental defects of the visual pathway and only co-occur in connection with albinism; to date, they have only been associated with defects in the melanin-biosynthesis pathway. Here, we report that these defects can occur independently of albinism in people with recessive mutations in the putative glutamine transporter gene SLC38A8. Nine different mutations were identified in seven Asian and European families. Using morpholino-mediated ablation of Slc38a8 in medaka fish, we confirmed that pigmentation is unaffected by loss of SLC38A8. Furthermore, by undertaking an association study with SNPs at the SLC38A8 locus, we showed that common variants within this gene modestly affect foveal thickness in the general population. This study reveals a melanin-independent component underpinning the development of the visual pathway that requires a functional role for SLC38A8.

Halime Ekici, Shwetha D. Rao, Anders Sönnerborg, Vedam L. Ramprasad, Ravi Gupta and Ujjwal Neogi (2014). J. Antimicrob. Chemother., 69 (12), 3349-3355.

Increased trends of primary drug resistance mutations (DRMs) among treatment-naive HIV-1-infected patients in low- and middle-income countries (LMICs) and the non-availability of pre-antiretroviral therapy (ART) genotypic resistance testing (GRT) may severely affect future therapeutic outcomes. The main objective of this study was therefore to develop a simplified, cost- and labor-efficient but high-throughput GRT protocol to be applied in the large-scale surveillance of DRMs in LMICs.

Amit Chaudhuri (2014). Frontiers in Immunology, 5, 546.

The M1 and M2 states of macrophage polarization are the two extremes of a physiologic/phenotypic continuum that is dynamically influenced by environmental signals. The M1/M2 paradigm is an excellent framework to understand and appreciate some of the diverse functions that macrophages perform. Molecular analysis of mouse and human macrophages indicated that they gain M1 and M2-related functions after encountering specific ligands in the tissue environment. In this perspective, I discuss the function of recepteur d’origine nantais (RON) receptor tyrosine kinase in regulating the M2-like state of macrophage activation Besides decreasing pro-inflammatory cytokine production in response to toll-like receptor-4 activation, macrophage-stimulating protein strongly suppresses nitric oxide synthase and at the same time upregulates arginase, which is the rate limiting enzyme in the ornithine biosynthesis pathway. Interestingly, RON signaling preserved some of the characteristics of the M1 state, while still promoting the hallmarks of M2 polarization. Therefore, therapeutic modulation of RON activity can shift the activation state of macrophages between acute and chronic inflammatory states.

Lakshmi Mahadevan, Ancy Yesudas, PK Sajesh, S Revu, Prasanna Kumar, Devi Santhosh, Sam Santhosh, JM Sashikumar, VK Gopalakrishnan, Joji Boben, Changanamkandath Rajesh (2014). Indian Journal of Human Genetics, Vol. 20, Issue: 2, 175-184.

We have identified that certain variants associated with cardiovascular disease and related drug response in the five genes, especially those in VKORC1, CYP2C19 and MYBPC3, are highly prevalent in the Kerala population, with almost 2 times higher prevalence of CYP2C19*2 variant compared with other regions in the country. Since the variants chosen in this study have relevance in disease phenotype and/or drug response, and are detected at a higher frequency, this study is likely to encourage clinicians to perform genetic testing before prescribing therapy.