Pharmacogenomics and Precision medicine

SINGLE NUCLEOTIDE POLYMORPHISMS

CHARACTERIZATION OF SINGLE NUCLEOTIDE POLYMORPHISMS ASSOCIATED WITH RESPONSE TO ANTIDEPRESSANT DRUGS IN SUDANESE POPULATION

Authors name: Suaad Balla khalaf alla , Mohamed O Elsiddeig, Muntaser Eltyeb Ibrahim

Affiliation: Institute of Endemic Disease – University of Khartoum.

Background: Antidepressant drugs [AD] prescribed for major depressive disorders are associated with therapeutic failures in approximately 40% of patients after initial dosing. Pharmacogenetic (PGx) variances play a significant role in these failures and therefore, using genetic data in decision-making for population-based dosing may both enhance efficacy and reduce adverse effects. Prior knowledge of allele distributions of the (PGx) biomarkers in different countries can help towards patient stratification for most populations during the drug prescribing process. However, Allele frequency distributions for gene polymorphisms associated with [AD] response in the Sudanese population and Africa in general remains largely not characterized.

Objective: To investigate single nucleotide Polymorphisms [SNPs] affecting several pharmacodynamic and pharmacokinetic variables associated with response to [AD] in Sudanese and to compare the data with the global geographical data reported in gnomAD genome database from different ethnic populations.⁠

Design: Out of 764 SNPs in 7 candidate genes affecting response to [AD] in 242 healthy Sudanese individuals genotype data, a total of 46 SNPs chosen according to deleteriousness and clinical annotation reported in PharmGKB database. Minor allele frequency (MAF) of clinically actionable SNPs compared with gnomaAD genome population frequencies using Chi-square test.

Result: Among deleterious SNPs, nine are unreported in gnomad genome database, two SNPs were common, MAF>5%, SLC6A4 rs138004662 (8%) and ABCB1 rs2032582 (15%). Of the clinically actionable variants, 3 SNPs (ABCB1 rs1045642, rs2032582, and BDNF rs7103411) show significant differences (p-value <0.05) between Sudanese and all other populations with the lowest frequency in Sudanese. ABCB1 rs1272006 was monomorphic (that is, no variation) across all population tested. 2 SNPs (rs7103411 and rs7124442) associated with better response to citalopram is less common in Sudanese compared with other populations.

Conclusion: Since therapeutic decision relies mainly on the US FDA or European Medical Agency guidelines for dosing instructions, understanding of the inter-ethnic differences in the pharmacogenetic is critical to guide more effective global drug prescriptions, Such data will be useful for future clinical and for drug dosage recommendations in the Sudanese population.

Keywords: Antidepressant, SNP, Pharmacogenetics.

 

Presenter name: Suaad Balla Khalafalla Abdalla

Affiliations: Institute of Endemic Diseases- University of Khartoum.

 

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PHARMACOGENETICS OF FLUOROPYRAMIDINES

PHARMACOGENETICS OF FLUOROPYRAMIDINES: ANALYSIS OF DPYD SNPS IN THE SUDANESE POPULATION

Sabah Alrasheed Abdalaziz Alhaj1, Mohammed Omar Elsiddieg Abdallah2, Muntaser Ibrahim3   

  1. Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, P. O. Box 102, ArmyRoad, 11111 Khartoum, Sudan, Sabahalhaj1991@gmail.com
  2. Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, P. O. Box 102, Army Road, 11111 Khartoum, Sudan, melsiddieg@gmail.com
  3. Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, P. O. Box 102, Army Road, 11111 Khartoum, Sudan, mibrahim@iend.org

 

Aim: To contribute towards the DPYD gene database and the Pharmacogenetics Sudanese database reporting for the first time, the frequency and type of sequence variations in the DPYD gene among the Sudanese population.  Furthermore, we aim to analyze the variation spectrum in the DPYD gene by comparing the reported Sudanese frequencies with the global population’s frequencies.

Background: Pharmacogenetics and pharmacogenomics (PGx) researches aim to elucidate the genetic basis for the inter-individual differences in drug response. fluoropyrimidines are among the most frequently prescribed anticancer drugs. Variant analysis of DPYD gene that codes for their key catabolism enzyme may help to predict fluoropyrimidine-related severe toxicity.

Methods: Publicly available genotype array data were analyzed for 242 Sudanese individuals encompassing 18 sub-populations. We reported the frequencies of DPYD variants that had >20 CADD score for further functional analysis. In addition, a total of 38 clinically relevant variants from the DPYD PharmGKB database were extracted and looked for in our data to report their frequencies and compare them with global populations from the gnomAD database.

Results: Of the 1219 variants analyzed, 11 have CADD score > 20. Of the 38 variants, 6 were found in our study population and significant statistical differences were found in the distribution of most of these variants when compared to the global population’s frequencies.

Conclusions: Different variation spectrum is found in the DPYD variants among Sudanese compared with other global populations. Further pharmacogenetic studies are required to investigate and document pharmacogenetic variants in DPYD and other metabolizing enzymes genes to help impact clinical practice.

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Pharmacogenetics of Artemether-Lumefantrine Combination Therapy

The pharmacogenetics of Artemether-Lumefantrine Combination Therapy for Uncomplicated Plasmodium falciparum Malaria in Sudan

 

Hamad Alneel Albagir Ahmed Ali 1, Muntaser Ibrahim 2*

1Department of Microbiology, International University of Africa

2Institute of Endemic Diseases, University Of Khartoum

*Corresponding Author

Emails: hamadalbagir@gmail.com1, Mibrahim@iend.org2*

 

Abstract

Background: Artemether-lumefantrine combination currently recommended as first-line treatment for uncomplicated Plasmodium falciparum malaria in Sudan and substrates of Cytochrome P450 enzymes.

Significant inter-individual variability in the disposition of these drugs has been documented, suggesting the possibility of the influence of genetic factors. It is; therefore, important to obtain the pharmacogenetic profile (or spectrum) of the population in Sudan with respect to these combinations and thereby enable practitioners to predict treatment outcome. The aim of this study was to determine the presence of Cytochrome P450 variant alleles (CYP2C8*2, CYP2C8*3, CYP2B6*6, CYP3A4*1B, CYP3A5*3, and CYP3A5*6 ) in Sudan where malaria is endemic.

Methods: Whole exome sequence data for 55 healthy Sudanese individuals were analyzed to determine

the  allele frequencies of the variants known to impact  artemether-lumefantrine combination.

Results: Allele frequencies of the variants: CYP2C8*2 (rs11572103), CYP2C8*3(rs10509681-

rs11572080), CYP2B6*6 (rs3745274), CYP3A4*1B (rs2740574), CYP3A5*3 (rs776746), CYP3A5*6

(rs10264272)  were found to be 0.081, 0.045, 0.081, 0.354, 0.009, 0.200 and 0.136 respectively.

Conclusion: Prevalence of CYP2C8*2, CYP2C8*3, CYP3A5*3, CYP3A5*6 and CYP2B6*6 variants are common while CYP3A4*1B variants are rare in the Sudanese Exome Data. The frequencies documented in this study are comparable to data acquired from earlier studies on African populations. Pharmacogenomics data, such as that exhibited in this paper, produce a basis for further studies on the impact of polymorphism in Artemether-lumefantrine combination safety and efficacy.

Keywords: Cytochrome P450, Artemisinin-lumefantrine combination therapy, Sudan, uncomplicated

Plasmodium falciparum malaria.

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DELETION OF GLUTATHIONE S-TRANSFERASE THETA 1

DELETION OF GLUTATHIONE S-TRANSFERASE THETA 1 IN FOUR SUDANESE ETHNIC GROUPS

Anadil Ahmed Alsubki Alhassan1, Muntaser  Eltayeb Ibrahim2

1 Department of Molecular Biology, Institute of endemic disease, Qasr street, Khartoum, Sudan,  anadilalsubki@gmail.com

2Department of Molecular Biology, Institute of endemic disease, Qasr street, Khartoum, Sudan,mibrahim@iend.org

 Background: Glutathione S-transferases (GSTs) are drug-metabolizing enzymes important in the transformation of xenobiotics, carcinogens, oxygen free radicals and drugs. Pharmacogenomics researches suggested interethnic variation in GST allele’s frequencies. Polymorphisms of GST genes contribute to susceptibility to cancer, environmental risk factors and variability in pharmacotherapy responses.

Aim: To determine the prevalence of GSTT1 null genotype in different ethnic groups and if ethnicity has a role in the allelic distribution.

Individuals and method: GSTT1 null allele genotyped by Multiplex PCR in 120 healthy individuals .

Result:  Hausa and Nilotic have the highest frequencies of the null allele, Beja Bani Amir has the lowest frequency, Beja Bani Amir and Beja Hadendowa frequencies are different from each other although they belong to the same ethnic group ,however, the difference is not statistically significant by Fisher exact test.

Conclusion: Ethnic differences has no effect in GSTT1 null genotype disturbution in groups under study.

 

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CLARITHROMYCIN RESISTANCE OF CLINICAL HELICOBACTER PYLORI

DETECTION AND CLARITHROMYCIN RESISTANCE OF CLINICAL HELICOBACTER PYLORI ISOLATES IN INDIAN POPULATION

Mr. Angesom Abraham 1, 2 , Dr. Asish Kumar Mukhopadhyay 1

  1. National Institute of Cholera and Enteric Diseases Division of Bacteriology, Kolkata, India. 2. Eritrea Institute of Technology, Mai-Nefhi, Eritrea.

Aim: This study is aimed at detecting the presence of H. pylori and the resistance to clarithromycin in Indian population.

Background: Helicobacter pylori is the most bacterial infection worldwide, infecting almost half of people in developed countries and 80% of people in developing countries (Go MF, 2002).  Clarithromycin therapy is effective in eradicating Helicobacter pylori. However, the resistance of H. pylori to clarithromycin is increasingly reported and it is associated to the point mutation in the 23s rRNA gene (Versalovic et al, 1996).

Methods: Helicobacter pylori is detected in the strains by culturing, positive test for Rapid Urease Test (RUT), oxidase, catalase and positive test to Urease gene by Normal-PCR (amplifying the Urease gene). Clarithromycin resistance detected by MAMA (Mismatch Amplification Mutational Assay)-PCR (amplifying the 23s rRNA gene) and antimicrobial susceptibility test.

Results: All the 40 strains were positive for Helicobacter pylori by culture and positive to urease gene by PCR. Out of the 40 strains 36 (90 %) were sensitive to clarithromycin and 4 (10 %) were resistant to clarithromycin by the PCR (amplifying the 23s rRNA gene). In addition, the MIC method was used and the 36 strains were sensitive to the concentration of 0.125 µg/ml of clarithromycin. However, the remaining 4 (10 %) are able to grow up to >2 µg/ml, as they are resistant to the action of clarithromycin. PCR results showed consistency with CLR MIC data that is ≥ 2 µg/ml MIC value for CLR-resistant strains and MICs ≤ 0.125µg/ml for CLR-sensitive strains.

Conclusions: The resistance of Helicobacter pylori to clarithromycin antibiotic is emerging in the Indian population. As a result, researchers has to work hard on the eradication of Helicobacter pylori infection by designing a better drug (antibiotic) based on the genetic features of the bacteria.

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Rhaman Ademelu poster

GENE DIVERSITY OF IMMUNOGLOBULIN VARIABLE DOMAINS AMONG SOME ETHNIC GROUPS IN AFRICA; IMPLICATION FOR HIV VACCINE DEVELOPMENT

Ahmed Rahaman A., Adekoya Khalid and Okoli Victoria

Medical Genetics Unit, Cell Biology and Genetics Department, University of Lagos, Nigeria

 Identification of vaccine-compatible antibodies capable of eliciting absolute protection against HIV infection is a global quest. Africa representation in the antibody gene databases is however low and may have implications in the global development of a quality and efficient HIV vaccine. Sequencing of immunoglobulin heavy chain variable domain (IGHV) was performed on 28 HIV infected subjects in Zulu ethnic group of South Africa, 123 novel alleles were identified and at least 8 were functional against HIV infection. This suggests that novel functional immunoglobulin gene variants are embedded in Africa population. We therefore want to explore antibody gene diversity in Nigeria being the largest population in Africa and with diverse heterogeneous ethnic groups. Illumina MiSeq will be used to sequence the entire rearranged antigen naïve variable chain gene repertoires in 105 subjects from three major ethnic groups of Nigeria; Yoruba, Hausa and Igbo. IgDiscover bioinformatics tool will be used to identify novel and known germline variable and joining antibody gene segments. Expected outcome of this extended study includes identification of large and diverse alleles, bulk of which may be missing in the public immunoglobulin databases. Novel alleles will further be assessed for functional HIV antigenic responses. This study will contribute to general knowledge of antibody especially towards utilization for a quality HIV vaccine development and other infectious diseases. It will also be of great importance to the Antibodyomics project which is aimed to provide holistic and cross-sectional information on human antibodies especially against HIV infection.

Presenter: Mr. Rahaman Ademolu Ademolu

Medical Genetics Unit, Cell Biology and Genetics Department, University of Lagos, Nigeria

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Kafayath FABIYI poster

TITLE : EXPLORATION OF THE ANTIBACTERIAL AND CHEMICAL POTENTIAL OF SOME BENINESE PHARMACOPOIEA TRADITIONAL PLANTS

Boris Lègba,1 Victorien Dougnon, 2 Kafayath Fabiyi,2 Jerrold Agbankpè,2 Gildas Hounmanou,2 Alidah Aniambossou,2 Edna Hounsa,2 Affousssath Amadou,2 Phénix Assogba,2 Honoré Bankolé,2 Jacques Dougnon,2 Lamine Baba-Moussa1

1Laboratory in Biology and Molecular Typing in Microbiology, Faculty of Sciences and Techniques, 2Research Unit in Applied Microbiology and Pharmacology of Natural Substances, Research Laboratory in Applied Biology, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, Cotonou, Benin

ABSTRACT :

Aim: This study aims to evaluate the antibacterial and chemical properties of some medicinal plants used in the fight against enteropathogens in Benin.

Background: Infections caused by enteropathogens are serious forms of infectious pathology. They are a major public health problem that causes millions of deaths a year.

Methods : Aqueous and ethanolic extracts of Senna siamea, Uvaria chamae, Lantana camara and Phyllantus amarus were tested on 10 bacterial strains. Well diffusion technique, coupled with the microdilution determination of Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (CMB) was used for antibacterial testing. The larval cytotoxicity was evaluated by using Artemia salina crustacean larvae. flavonoids and polyphenols were also assayed by the method using aluminum trichloride (AlCl3) and the method using the folin-Ciocalteu reagent, respectively.

Results : The results of the study revealed that extracts had an effective antibacterial activity at 100 mg/mL, with MIC between 100 and 25 mg/mL and CMB between 100 and 50 mg/mL. The inhibition diameters of the extracts varied between 7.5 and 21 mm. The ethanolic extract of Phyllantus amarus leaves showed the best antibacterial activity. None of the extracts tested was found to be cytotoxic at the dose of 20 mg/mL. The aqueous Uvaria chamae root extract has the highest polyphenol content (231.896552±0.27586207 in μg EAG/100 mg extract), whereas the aqueous leaf extract of Uvaria chamae is the richest in flavonoids (41.061082 0.43180737 in μg ER/100 mg of extract).

Conclusions: These interesting results can be used in the development of improved traditional medicines against enteropathogens.

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IBIWUMI USMAN poster

 

HIGHER RATES OF VIRAL SUPPRESSION AMONG HIV POSITIVE PAEDIATRIC PATIENTS USING MULTI-MONTH ART DELIVERY MODEL IN SOUTH-WESTERN NIGERIA

Authors & Affiliations: I.N Usman1 & S.O Usman2

1Department of Public Health, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria.

2Department of Chemical Pathology, Nnamdi Azikiwe University, Awka, Anambra State, Nigeria.

 

Background:

In Nigeria where drug resistance testing is rarely performed and poor adherence is blamed for treatment failure, programmatic approaches to preventing & handling these are thus essential. This study was aimed at determining and monitoring HIV/AIDS disease progression using viral load to provide prognostic information and evaluate patients for viral suppression using the World Health Organization (WHO) guideline strategies.

Methods:

This study was an observational longitudinal prospective cohort study of subjects living with HIV already initiated on antiretroviral therapy for at least six months, enrolled in health facilities across Ondo & Ekiti States, Western Nigeria, during a 12-month observation period (January – December 2017). All data were statistically analyzed, using Statistical Package for the Social Sciences (SPSS) version 23.0.

Results:

A total of 3920 (1005 males & 2915 females) subjects mostly between 25 – 54 years, with a mean age of 39.35 ± 10.41 years. 3086 (78.7%) of the subjects had viral suppression of <1000 RNA copies per ml. The 834 subjects went through intensive adherence counseling for three months and viral load test repeated three further months after, which made 3377 (86.1%) subjects have <1000 RNA copies per ml.

 

TABLE 1 – Chi square result showing influence of current ARV therapy regimen, ARV therapy adherence & WHO clinical staging on viral load outcome

VARIABLES                                         χ²                     df               Critical value          Decision

ARV therapy adherence influence           236.42              1                3.84                        Rejected

on viral load outcome

FIGURE I

FIGURE II

Conclusion:

HIV treatment enhanced adherence counseling is key to the achieving viral suppression and determine infection prognosis, thus, routine viral load monitoring will ultimately help in HIV/AIDS disease progression follow up and reduce treatment failure tendencies. This will help more patients stay on first line regimen and prolong their life expectancy, indicating that the UNAIDS last 90 target is achievable.

 

 

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CAROLINE SIMIYU poster

POLYMORPHISMS OF THE HUMAN DRUG METABOLISM GENE CYP2B6 AMONG HIV INFECTED CHILDREN IN NAIROBI, KENYA

 

Caroline Simiyu1,2, Elijah Songok2, Raphael Lihana2, Fred Wamunyokoli1

 

Jomo Kenyatta University of Agriculture and Technology1

Kenya Medical Research Institute2

 

Aim:

This study aims to determine polymorphisms in the human drug metabolism gene CYP2B6 among HIV infected children in Nairobi, Kenya.

 

Background:

 

Advent of antiretroviral therapy (ART) as a standard of care has significantly reduced morbidity and mortality due to HIV/AIDS globally. However, individual differences in tolerance and toxicity to ART have been observed in multiple populations resulting in poor adherence and development of drug resistance. Genetic polymorphism in antiretroviral drug metabolism enzyme and transporter genes has been indicated to significantly contribute to ART outcome. Non-nucleoside reverse transcriptase inhibitors efavirenz and nevirapine which are widely used in sub Saharan Africa countries have been shown to have a high inter-individual variability in their pharmacokinetics. Low plasma levels are associated with treatment failure while high plasma levels result in toxicities. CYP2B6 plays a role in metabolism of efavirenz and nevirapine. Polymorphisms of CYP2B6 affect therapeutic outcome of efavirenz and nevirapine. These gene variants are common among people of African ancestry thus understanding the status of CYP2B6 polymorphisms in the African population is critical to ensure an effective therapy outcome.

 

 

 Method:

The study will be conducted on 200 HIV infected children in the Lea Toto cohort. DNA will be obtained from blood samples after which amplification by PCR will be conducted for the CYP2B6 gene. The resulting amplicon will be sequenced using illumina MiSeq and, thereafter, analysis using bioinformatics tools.

 

Results/ Expected outcome:

This proposed study will provide data on the status of CYP2B6 polymorphisms among HIV infected children in Kenya and the association with ART treatment failure. This will inform on decisions to include screening for CYP2B6 polymorphisms as part of the national HIV treatment policy.

 

Conclusion:

Understanding the status of CYP2B6 polymorphisms in the African population is critical to ensure an effective antiretroviral therapy outcome.

 

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