Utilizing Science & Technology and Innovation for Development A Genome Wide Association Study for Type 2 Diabetes Susceptibility Gene and Treatment in Jordanian Population of Arab Descent Marriott Hotel- Amman, August 13th, 2015

Project Team Principle Investigator: Dr. Laith AL-Eitan/Jordan University of Science and Technology/Biotechnology and Genetic Department /Jordan Co-Investigator: Dr. Motasem Ismail/ Molecular Biology and Genetics Laboratory/United Arab Emirates Co-Investigator: Dr. Basima Almoman/Jordan University of Science and Technology/Clinical Pharmacy Department /Jordan Co-Investigator: Dr. Nesreen Saadeh/Jordan University of Science and Technology/Internal Medicine Department/Department /Jordan Co-Investigator: Dr. Rami Alkhatib /Jordan University of Science and Technology/Biotechnology and Genetic Department /Jordan Co-Investigator: Dr. Nour Abdo/ Public Health/ Jordan University of Science and Technology/Jordan

Brief Description Type 2 Diabetes The prevalence of Type 2 Diabetes (T2D) in the Jordanian Population is steadily increasing, posing a major public health problem. Metformin In T2D treatment management, Metformin is a safe and effective first line in type 2 diabetes (T2D) therapy. pharmacogenomic Recent pharmacogenomic (PGx) studies indicate that genetic polymorphisms of drug-metabolizing enzymes and transporters should be taken into consideration.

Justifications Type 2 Diabetes To date, no genome wide screen genetic factors of Type 2 Diabetes among the Jordanian population nor any other Arab populations. Illumina's Human 660W-Quad-BeadChip Towards this, the first Genome Wide Association Study in Jordanian population of Arab origin will be performed using Illumina's Human 660W-Quad-BeadChip. genetic susceptibility regions on Chromosomes 3, 6, 8, 9, 10, 11, 16, and 17 for diabetes and its treatment. Work in Caucasians has previously defined genetic susceptibility regions on Chromosomes 3, 6, 8, 9, 10, 11, 16, and 17 for diabetes and its treatment. the first GWAS study with metformin response and efficacy in this ethnic group, and with the clinical status with a sample from Jordan. To the best of our knowledge, this will be the first GWAS study to examine the relationship between these polymorphisms of interest within multiple genes and their relation with metformin response and efficacy in this ethnic group, and with the clinical status with a sample from Jordan.

Objectives The main Objectives are: (DNA profiling) genome-wide Single Nucleotide Polymorphism To measure genetic ancestry (DNA profiling) in the Jordanian Population of Arab population using genome-wide Single Nucleotide Polymorphism (SNP) arrays. To study specific diseases that are common to populations of this region Type 2 Diabetes such as Type 2 Diabetes (T2D). susceptibility its treatment To detect genes influencing susceptibility to T2D and its treatment in Jordanian population of Arab descent.22

Scope of work/Duration Estimated Budget Scope of work: three directions This Research proposal has three directions and its aims as following: Genome wide association study (GWAS) Illumina Human 660 Quad chip array and Luminex chip array Conducting Genome wide association study (GWAS) using a case- control based association test using the Illumina Human 660 Quad chip array and Luminex chip array a Genome-Wide Association Study (GWAS "Body Mass Index" (BMI) and "Waist Circumference" (WC). Identifying factors that result in obesity, and its association with T2D by conducting a Genome-Wide Association Study (GWAS) and specifically assessing genetic associations with "Body Mass Index" (BMI) and "Waist Circumference" (WC). responsiveness to treatment for certain drug such as metformin and the clinical status. Evaluating and identifying factors that will be associated with responsiveness to treatment for certain drug such as metformin and the clinical status. Duration: 36 months (each scope: 12 months) 166,000 JD Estimated Budget : 166,000 JD

Methodology of Implementation diabetic patients of Arab descent healthy controls from ethnically homogenous population of Arab d Blood samples will be collected from diabetic patients of Arab descent and healthy controls from ethnically homogenous population of Arab descent. DNA sample specialized kit. DNA sample will be extracted according to the standard method using specialized kit. the Illumina Human 660 Quad chip array Luminex chip array A genome wide association study (GWAS) using the Illumina Human 660 Quad chip array and Luminex chip array will be conducted. SPSS The patients’ data and their related genotyping results will be coded and entered into SPSS (version 19). Haploview® software Haplotype analysis will be performed using Haploview® software (version 4.2). Permutation (n=100,000) adjustment for multiple testing will be performed in Haploview (Barrett et al., 2005).

Expected output genetic structure variations Highlighting for the first time the genetic structure variations in type 2 Diabetic patients in Arab descent from sample from Jordan. PGx in response to metformin therapy and treatment efficacy. A better understanding for the role of PGx in response to metformin therapy and treatment efficacy. PGx into routine practice personalized medicine Facilitating the integration of PGx into routine practice in the field of diabetes care as preliminary step to assist the introduction of personalized medicine. specific diseases T2D Allowing the study of specific diseases that are common to populations of this region such as T2D

Impact identify high-risk individuals to both individuals and society If genetic profiling could be used Successfully to identify high-risk individuals, this would result in substantial benefits to both individuals and society. high risk genotypesdelay the onset of diseaseslow its progressionreduce the ultimate severity of the condition Targeting preventive measures towards individuals with high risk genotypes could delay the onset of disease, slow its progression, and reduce the ultimate severity of the condition. substantial improvements in quality of life for affected individuals and a reduction in healthcare costs. This would result in substantial improvements in quality of life for affected individuals and a reduction in healthcare costs.

Sustainability genes individual's response to drugs Basically, pharmacogenetic encompasses the involvement of genes in an individual's response to drugs.

drug discovery research, the genetic basis of pharmacokinetics and pharmacodynamics, new drug development, patient genetic testing and clinical patient management. The field of pharmacogenetic covers a vast area including basic drug discovery research, the genetic basis of pharmacokinetics and pharmacodynamics, new drug development, patient genetic testing and clinical patient management. development or sustainability outcome (Personalized Medicine) the success of therapies and reduce the incidence of adverse side effects. Ultimately, the development or sustainability outcome of this project may be to predict a patient's genetic response to a specific drug as a means of delivering the best possible medical treatment for patients in the future according to the personal genetic level (Personalized Medicine). By predicting the drug response of an individual in this project, it will be possible to increase the success of therapies and reduce the incidence of adverse side effects. Sustainability

Action Plan Stage # 1: Stage # 1: Ordering Reagents, Kits, consumables, instruments: Schedule: Schedule: After 5 months after the proposal acceptance and receiving the funds. This stage will include the literature Work as well. Project Direction A: Project Direction A: A Genome Wide Search for Type 2 Diabetes Susceptibility Genes in Jordanian population of Arab decent Stage 1: Stage 1: Collecting blood samples and clinical data (Clinical data form attached) from healthy individuals and T2DM patients Stage 2: Stage 2: Extracting DNA from both subjects (T2DM patients and healthy indivuals) and quantifying the DNA concentration and assessing the DNA quality using a NanoDrop 1000® spectrophotometer Stage 3: Stage 3: Building a clean data sets for both clinical data and DNA samples for both subjects

Schedule: Schedule: 1 year after the proposal acceptance and receiving the funds and Reagents, Kits, Consumables Stage 4: Stage 4: Conducting GWAS analysis either at Princess Haya Biotechnology Centre or sending the samples overseas for analysis Schedule: Schedule: 4 months after the clean data sets established Stage 5: Stage 5: Standard biological molecular methods such as Taqman® SNP genotyping assay, DNA sequencing using Genetic Analyser 310, and restriction fragment length polymorphism (RFLP) will be employed for genotyping in the current study to confirm the quality of the Genome Wide Scan Genotyping technology for certain SNPs within specific genes. Action Plan

Schedule: Schedule: 10 months after DNA extraction and building a clean DNA data set. Stage 6: Stage 6: Data, bioinformatics and statistical analysis Stage 7: Stage 7: Writing manuscript for publication Schedule: Schedule: 3 months following the genome wide scan analysis and SNPs confirmations Action Plan

Project Direction B: Project Direction B: A Genome-Wide Association Study Examining Obese Factors in Jordanian population of Arab Decent with a History of Type 2 Diabetes Stage 1: Stage 1: Data, bioinformatics and statistical analysis and interpretation. Stage 2: Stage 2: Writing manuscript for publication. Schedule: Schedule: 3 months following the data and bioinformatics analysis Action Plan

Project Directions C: Project Directions C: A Pharmacogenetic Approach Using Genome Wide Association Study to Search for Type 2 Diabetes Susceptibility Genes and Treatment Stage 1: Stage 1: Data, bioinformatics and statistical analysis and interpretation. Stage 2: Stage 2: Writing manuscript for publication. Schedule: Schedule: 3 months following the data and bioinformatics analysis Action Plan