3^rd International Conference on Genomics & Pharmacogenomics September 21-23, 2015 San Antonio, USA

Juan Carlos A Padilla is a Graduate student currently on his fi nal semester towards his Master of Science degree in Genomics and Biotechnology from the Instituto Politécnico Nacional.

Aeromonas caviae is a rod-shaped, gram-negative, ubiquitous bacterium which has been identifi ed to be implicated in a variety of intestinal and extra-intestinal illnesses, as well as soft -tissue infections in humans. It is also one of the bacteria in the genus Aeromonas responsible for the majority (>85%) of human infections and clinical isolates, and related to the most prevalent in pediatric patients. Th e genome of Aeromonas caviae strain 429865 isolated from an infected 2 years and 4 months old patient in Mexico was sequenced using the Illumina Miseq platform according to the standard operation based on a Pair-End library and a Mate-Pair library of 5Kb fragments. Th e genome was assembled de novo into 4 contigs using SPAdes v3.5.0 and Consed v29.0. Th e length of the assembled genome was 4,700,593 bp and has an overall G+C content of 61.0%. Annotation was performed using the NMPDR’s RAST server, upon which 4,258 Coding Sequences (CDS) were identifi ed, as well as 144 RNAs. BLAST-based Average Nucleotide Identity (ANIb) analysis confi rmed that the sequenced genome belonged to the Aeromonas caviae species. OrthoMCL and Java Script Codes were utilized to determine the pan-genome (6,957 proteins) and core-genome (3,293 proteins) of 10 sequenced genomes of A. caviae. 114 unique CDS to A. caviae strain 429865’s genome were found. Various genes that could be involved in infection were identifi ed, including the genes encoding for toxins, antibiotic resistance and motility.

Zandisiwe Emilia Magwebu is a fi nal year PhD student at the University of the Western Cape in South Africa. She is a Research Intern for the South African Medical Research Council. In 2014, she was part of the Next Generation Scientist (NGS) group at Novartis Pharma, Basel, Switzerland.

The Primate Unit and Delft Animal Centre (PUDAC) of the SA MRC maintain the only research colony of captive bred Vervet monkeys in South Africa. A small percentage (7%) of this colony has congenital cataracts and was later established that the aff ected individuals had high levels of glycine in their plasma and Cerebrospinal Fluid (CSF). Although cataracts have been documented for a variety of primate species, hyperglycinemia as well as this rare and unusual association of conditions have not been reported in the literature before, and clearly need elucidation. Th e study was aimed at investigating the pharmacodynamics of Non-Ketotic Hyperglycinemia (NKH) therapy in induced and cataract individuals with hyperglycinemia (spontaneous). Twelve animals were selected for a three months study and assigned into two groups (induced and spontaneous) and a control. Blood, urine and CSF were collected in order to determine glycine levels for baseline, induction (phase 1: valproate), treatment (phase 2: sodium benzoate and dextromethorphan) and washout period. In phase 1, 50 mg/kg of valproate only induced a slight increase in glycine levels, and was not statistically signifi cant (p=0.55). However, platelets, alkaline phosphatase, alanine aminotransferase and total protein biochemistry changes were clinically signifi cant (p<0.05). In phase 2, reduction of CSF and plasma glycine levels were observed in both groups, but signifi cant change was seen in the spontaneous group (p=0.01). A dose of 50 mg/kg valproate did not show signifi cant eff ect on Vervet monkeys. However, the combination of sodium benzoate and dextromethorphan showed benefi cial eff ect in reducing glycine levels in the spontaneous group.

Ch Sushma did her Bachelor’s degree (2007) in Genetics as combination subjects, followed by Master’s degree in Genetics (2009) and joined PhD in 2011 in Department of Genetics under the supervision of Professor K Rudrama Devi. She has interest in research and especially to work on woman related cancers like breast cancer. She has collaborated with Indo American Cancer Hospitals for specimen collection and collected about 150 paired tissue specimens for the research work for submission of her thesis. Two of her manuscripts have been accepted in international journals. She has been working on 4 different gene polymorphisms and doing the correlation study with each impact on breast cancer. She has articles published in Asian Pacifi c Journal of Cancer and International journal of Biotechnology.

The incidence of breast cancer in India is on the rise and is rapidly becoming the number one cancer in females pushing the cervical cancer to the second spot. It is reported that one in 22 women in India is likely to suff er from breast cancer during her lifetime. Breast cancer is not only acquired but can also be inherited. Women who have fi rst-degree relative diagnosed to have breast cancer increase their risk of acquiring breast cancer. Further studies have added many candidate genes. KRAS (proto-oncogene) is one such gene reported in BCGD. It is implicated in 20-75% of colorectal cancer 80-90% of pancreatic cancer and a lesser frequency with other cancers. Mutations in KRAS gene causes constitutively active signaling function leading to cell proliferation and cancer. Most of these KRAS mutations are localized on codon 12 and to a lesser degree at codons 61. A study on mutational analysis of human breast cancer cell lines has revealed 18% of association of KRAS gene mutations. Studies from diff erent parts of the world have reported a strong contribution of KRAS gene mutations in breast cancer. In the present study, around 150 paired (tumor and normal) tissue samples, diagnosed for breast cancer would be analyzed for KRAS gene mutations. An equal number of blood samples would be analyzed of the same patients to understand germinal mutations of KRAS gene mutations. PCR-RFLP method will be employed to analyze clinically relevant mutations whereas PCR-SSCP analysis will be employed to detect unknown mutations. All the samples suspected for mutations by SSCP analysis will be confi rmed by direct sequencing. Th e relation between overall survival of patients with breast cancer and KRAS gene mutations can be established. Th e possible role of KRAS gene mutations in disease prognosis of breast cancer can be understood. Th e KRAS gene mutations are detected in both male and female breast cancer patients and have been shown to have KRAS gene mutations. Th e signifi cant correlation of KRAS gene mutations in age and gender are analyzed. All the above cases are analyzed to screen full KRAS gene. Th e paraffi n embedded block tissues are screened for the histo-pathological studies.

Sunaina Gautam has completed PhD from Department of Zoology, University of Lucknow, India. Presently, she has joined as a Post-Doctoral Fellow in the Department of Biochemistry, King’s George Medical University Lucknow, India under the D S Kothari Post-Doc Fellowship Scheme. She has published 10-11 papers in national and international reputed journals. She won a few prizes including Young Scientist Award in conference organized by the Zoological Society of India. She co-supervised the dissertation work of MSc students and was also involved in various conferences and workshops organized by our laboratory. She has a keen interest to pursue her future studies to understand the fundamental aspects of the complex diseases at molecular level and its prevention

Type II Diabetes Mellitus (T2DM) is now considered to be a serious disease that is always associated with long-term and life-threatening complications, attributed deaths and economic burden to nations. Several Single Nucleotide Polymorphisms (SNPs) in CD36 gene have been found to be associated with metabolic syndrome and HDL metabolism, both predictors of the risk of heart disease and T2DM. We studied eleven SNPs in entire CD36 gene and their association with 100 each of control subjects and T2DM. Th e haplotypic analysis of few signifi cant SNPs was carried out in individuals from families with diabetic history in order to evaluate its utility in disease prediction. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCRRFLP) was used for genotyping. Ten families with a family history of diabetes were identifi ed and blood samples were collected from as many family members as possible. Genotyping of three SNPs viz. rs1761667 (G>A) in exon 1 A, rs3211938 (T>G) in exon 10 and rs3212018 (16 bp del) in exon 14 was performed in all samples. In our study on North Indian population, SNP G>A (rs1761667) genotypes showed a highly signifi cant association (p<0.001) and 1264T>G (rs3211938) showed mild signifi cant for T2DM (p=0.045). Moreover, individuals having a ‘GATTC1’ haplotype might be at risk of developing T2DM (p<0.001) and therefore might be susceptible to related complications. In addition of it, ‘A’ ‘G’ and ‘G’ alleles of SNPs rs1761667 (G>A), rs3211938 (T>G) and rs1984112 (T>G), respectively tend to have increased BMI. Such studies may be helpful for disease prediction in individuals at risk of T2DM and could be used as a genetic marker.

Zhiyao Chen has completed his PhD from Nanjing University in China. He has been a Clinical Pharmacist in The First Affi liated Hospital of Soochow University from 2013. He has nearly 10 years research experience in Pharmacogenomics and has published more than 10 papers in reputed journals.

Purpose: Th e goal of the current study is to determine whether an easily detectable biomarker can be used to replace HLA-B*5801 allele testing for the prediction of allopurinol-induced Severe Cutaneous Adverse Reactions (SCARs) in a cohort of Chinese patients. Methods: Six SNPs (including rs9263726) and the HLA-B*5801 were analyzed in 17 patients with allopurinol-induced SCARs and in 151 control patients (including 31 allopurinol-tolerant patients and 120 healthy subjects). SNPs were analyzed by pyrosequencing and HLA-B*5801 was evaluated by sequencing-based techniques. Consistency between sequencing-based HLA-B*5801 testing and pyrosequencing-based rs9263726 testing were further evaluated in 75 individuals that possessed a copy of the HLA-B*5801 allele and 187 individuals that did not possess the allele. Results: A signifi cant association with allopurinol-induced SCARs were found at rs9263726 (OR=108.8) and HLA-B*5801 (OR=108.8), and the occurrence of these was found to be in absolute linkage disequilibrium (D’=1.0, r2=0.92). Th e Kappa values between sequencing-based HLA-B*5801 testing and pyrosequencing-based rs9263726 testing was 0.96 (>0.75), demonstrating that the two methods were well coincident with each other. Conclusion: Th e ease of typing rs9263726 makes it an effi cient surrogate for HLA-B*5801 allele testing in the screening of patients at high risk for developing allopurinol-induced SCAR.

Srinivas Baskari is a PhD Scholar in Osmania University. He qualifi ed Basic Science Research Fellowship (BSR) in 2013. He also qualifi ed GATE in 2012 with 87 percentile. He worked in a project on “Isolation and Characterization of Active Compound with Signifi cant Anti-Bacterial Activity Extracted from Radish” under Dr Uma in JNTU at Hyderabad as a part of MSc thesis.

Progression of breast cancers is oft en dependent on hormones. Previous reports have demonstrated that elevated levels of human Growth Hormone (hGH) and/or autocrine hGH expression contributes to breast cancer progression. Th e association between hormone (Estrogen, progesterone) and NF-κB p65 has been investigated by diff erent scientists with controversial results in ER-positive and ER-negative cell lines. In the present investigation, role of autocrine production of human Growth Hormone (hGH) in the proliferation of mammary carcinoma cells (MCF-7) in vitro and molecular mechanisms responsible for metastatic growth of breast cancer was studied. For this we were stably transfected with an expression plasmid encoding the hGH gene in to MCF-7 cells and these cells (designated MCF-hGH) synthesized hGH in the cell and secreted hGH to the medium. For control purposes, a MCF cell line was generated (MCF-MUT) in which the start codon of the hGH gene was disabled and these cells transcribed the hGH gene without translation to hGH protein. Th e MCF-hGH cells increased the transcription factor NF-κB p65 which modulates the expression of genes involved in cell proliferation, diff erentiation, apoptosis and metastasis. Our results indicate that the autocrine Growth Hormone (GH) increases NF-κB p65 activity in breast cancer cell lines by RT-PCR data and western blot when compared with MCF-MUT cells. In addition to that, GH-dependent increase in NF-κB p65 expression results in loss of P- and E-cadherins in breast cancer cell line. Th is substantiate the hypothesis that certain breast cancer cells rely on NF-κB p65 for aberrant cell proliferation and simultaneously avoid apoptosis thus implicating activated NF-κB p65 as a therapeutic target for breast cancers. Taken fi ndings together further our understanding of the complex actions of autocrine hGH and NF-κB p65 in Epithelial Mesenchymal Transition (EMT) of breast cancer has to be investigated.

Doreen Duri is a 27-year old Biomedical Scientist employed by the University of Zimbabwe in the Department of Chemical Pathology. She completed an Honours Degree in Medical Laboratory Sciences from the University of Zimbabwe in 2012 and is currently a graduate student at the same university. She is a budding researcher actively involved in antiretroviral drugs pharmacogenetics research.

Given the high prevalence of HIV/AIDS in sub-Saharan Africa, and the elusive search for a cure, understanding the pharmacogenetics of currently used drugs is critical in populations from the most aff ected regions. Compared to Asian and Caucasian populations, African population groups are more genetically diverse, making it diffi cult to extrapolate fi ndings from one ethnic group to another. Th is study aimed to investigate the role of genetic variation in CYP2B6 (c.516G>T and c.983T>C) single nucleotide polymorphisms on plasma nevirapine levels among HIV-infected adult Zimbabwean patients. Using a crosssectional study, patients on nevirapine-containing HAART, having reached steady state (more than six weeks on treatment) were recruited to participate. Blood samples were collected aft er patients provided consent and samples were used to extract DNA for genetic analysis or to measure plasma nevirapine levels. Genetic analysis was carried out using PCR and RFLP or SNaPshot for the two single nucleotide polymorphisms; CYP2B6 c.516G>T and c.983T>C, while LC-MS/MS was used in analysing nevirapine concentration. CYP2B6 c.516G>T and c.983T>C signifi cantly predicted plasma nevirapine concentration with the c.516T and c.983T being associated with elevated plasma nevirapine concentrations. Comparisons of the variant allele frequencies observed in this group to those reported in some African, Caucasian and Asian populations showed signifi cant diff erences. We conclude that pharmacogenetics of nevirapine can be creatively used to determine patients who are likely to develop nevirapine-associated side eff ects as well as too low plasma concentrations for viral suppression.