Consultant - Forensic Genetics Trainer
Purpose of the Consultancy
The purpose of the consultancy is to strengthen capacity of lab staff in the context of COVID-19 pandemic by providing on the job training of trainers (TOT) on the use of Genetic Analyzer performing the followings for the staff of Central Public Health Lab (CPHL) in Kabul, Afghanistan.
- Human mitochondrial DNA (mtD ) sequencing analysis and data interpretation
- Introduction of gene panels for SNPs, haplotype, InDels and copy number expressions analysis including data/result analysis
- DNA re/sequencing analysis of X-chromosome, Y-Chromosome and autosomal chromosomes analysis and data interpretation
- Touch DNA analysis and data interpretation
- Paternity testing (using PrepFiler DNA extraction and/or equal kit for extracting DNA from (whole blood, bone, hair, and touch DNA samples) and quantifying extracting DNA by both of the following kits identifying male:female ration
- Quantifiler Duo quantification kit along with result analysis (Complete procedure)
- Quantifiler Trio along with result analysis (Complete procedure)
And data analysis by the following kits
- Globalfiler kit including results and data analysis along with related/required software.
- Y-filer kit along with data and analysis
- Analysing autosomal STRs including data analysis
- Analysing X-STRs including data analysis
- SNaPshot kit including generating data, data analysis and result interpretation
Afghanistan has been at a heightened risk of large-scale community transmission in the initial stage of the COVID-19 pandemic. Since January 2020, an approximately 300,000 Afghans have returned from Iran - the epicentre of COVID-19 in the region. Protracted conflict, high poverty rates, a challenged health system and public services contribute significantly to the COVID-19 epidemic in country. The first case of COVID-19 in Afghanistan was reported on February 24. As of 1st September 2020, there are 38,196 confirmed COVID-19 cases in Afghanistan across all 34 provinces and 1,406 total death. Initially there was no testing capacity in country. However, laboratory testing sites have now been established in 11 locations by WHO through World Bank (WB) fund with the capacity of doing 2500 tests per day. Recently, under the Pandemic Emergency Fund for world bank, it is aimed to procure two Genetic Analyser machines for the CPHL lab at Kabul, Afghanistan. The capacity of the lab staff to use these machines is limited, therefore, the consultant will be hired to provide on the job trainings to enhance the capacity of the lab staff for the efficient use of these machine.
Work to be performed
- Practically performing research fields mentioned in the purpose of the consultancy.
- Develop SOPs for research fields mentioned in the purpose of the consultancy.
- Perform sequencing.
- Provide lectures and hands-on training covering all aspects on sequencing from principles of primer design to assembling and curating sequence data that can be used in further analysis
- Provide training on sequence assembly and alignments, phylogenetic reconstructions and data interpretation”
- Provide training on uploading the generated sequencing data to the Global database like GISAID, GENBANK etc.
- Provide continues the job trainings for two months on Genetic Analyzer machine to the lab staff of Central Public Health Lab (CPHL)
- Provide on the-job trainings for two months on Real Time PCR machine at CPHL for the lab staff of Kabul and provinces (cover all processes).
- Conduct continues on-job trainings for two months on Conventional PCR at the CPHL for the lab staff of Kabul and provinces (if required).
- Evaluate the skills that trainees acquired during the training regarding the use of Genetic Analyzer machine, Real Time PCR, Conventional PCR and strengthen the skills based on the results of evaluation
- Provide on the job guidance on the related biosafety measures and how to decontaminate a lab when required.
- Deliverable 1. Report of the trainings and key recommendations
- Deliverable 2. SOPs for research fields mentioned in the purpose of the consultancy
- Deliverable 3. Report of genome sequencing of COVID-19
- Qualifications required:
- At least 5 years of experience using molecular biology techniques including sequencing analysis, gene expressions, cancer research, SNPs, InDels and copy number variations analysis, experience in inherited diseases research including forensic DNA paternity testing analysis both manual and through dedicated software using global filer, Y-filer, quantification trio and duo kits.
- Field research publications are required.
- Expert in gene sequencing, SNPs, InDels, mitochondrial DNA and SNaPshot data analysis
- Skills / Technical skills and knowledge:
- Gene sequencing, cancer research, reproductive health inherited diseases and forensic genetics DNA research and data analysis and result interpretation.
- Demonstrated ability in strategic planning, effective report writing and program development
- Ability to establish and maintain effective working relationships within a team with multi-cultural backgrounds in a multi-disciplinary management service environment.
Fluency in English language (Reading, writing, and speaking) is required.
Place of assignment
Kabul, Afghanistan (Visa is required)
The selected Consultant will be expected to provide a medical certificate of fitness for work.