School of Bioinformatics · Genomics & transcriptomics
Clinical Genomics & Variant Interpretation
Turning a list of variants into a defensible interpretation requires annotation, population data, functional evidence and a structured framework. This course teaches that process as used in genomic medicine, for research and training purposes.
Course overview
Clinical Genomics & Variant Interpretation follows a variant from a VCF file to a classification: transcript selection and HGVS nomenclature, annotation with population frequency and predictors, and the evidence codes of the ACMG/AMP germline guidelines and the AMP/ASCO/CAP somatic tiers.
Case-based labs practise filtering exome data for rare disease and tumour data for actionable alterations, with attention to the pitfalls that cause misclassification. The course is educational: it does not qualify participants to issue clinical reports.
Learning outcomes
By the end of the course you will be able to:
- Write and read HGVS variant nomenclature against the right transcript
- Annotate variants with VEP, gnomAD, ClinVar and in-silico predictors
- Apply ACMG/AMP evidence criteria and combine them into a classification
- Prioritise candidate variants in rare-disease exomes using phenotype data
- Tier somatic variants by clinical significance
Skills you will practise
Eligibility and prerequisites
Who can apply
- Students and graduates of B.Sc., M.Sc., B.Tech., M.Tech., B.Pharm., M.Pharm., MBBS, BDS, B.V.Sc. or a PhD programme in the life sciences, biotechnology, bioinformatics, pharmacy, medicine, agriculture, chemistry, statistics or computer science
- Researchers, faculty and industry professionals moving into data-driven biology
- Final-year students may apply before their results are declared
Prerequisites
- NGS Data Analysis or equivalent
- Undergraduate genetics
Best suited to
- Genetic counsellors, clinicians and laboratory scientists in training
- Bioinformaticians supporting clinical research
- Life-science graduates aiming for genomic-medicine roles
Module-wise syllabus
6 modules. Each pairs instructor-led sessions with a hands-on lab on public data.
Topics
- Transcript choice and MANE
- HGVS for DNA and protein
- Variant types and their consequences
Topics
- Ensembl VEP
- Population frequency in gnomAD
- In-silico predictors and their limits
Topics
- Evidence codes and strengths
- Combining criteria
- ClinGen specifications
Topics
- Inheritance models and trios
- HPO phenotypes and gene prioritisation
- Reporting incidental findings
Topics
- VAF and tumour purity
- AMP/ASCO/CAP tiers
- Knowledge bases such as CIViC
Topics
- Case analysis
- Classification
- Limitations and disclaimers
Practical sessions and projects
Capstone project
Interpret a case
Work through a case from VCF to a research interpretation report, documenting the evidence behind each classification and the uncertainty that remains.
Assessed on the correctness of the analysis, the quality of the code and the reasoning in the write-up. A pass is required for the certificate.
- Variants and nomenclature
Write HGVS descriptions for a set of variants and resolve discrepancies between transcripts.
- Annotation
Annotate an exome VCF and filter it by consequence, frequency and quality.
- The ACMG/AMP framework
Classify ten variants with full evidence trails and compare with expert-curated classifications.
- Rare-disease analysis
Find the likely causal variant in a public trio exome using inheritance and phenotype.
- Somatic variants
Tier the somatic variants of a public tumour sample and justify each tier.
- Project: an interpretation report
Prepare a research interpretation report for a case, with evidence for each classification and its limits.
Software, tools and datasets
Software and tools
All software is free and open source or free for academic use. Recommended computer: 8 GB RAM, 30 GB free disk, Linux, macOS or Windows with WSL2.
Datasets
- Public trio exome data: Rare-disease prioritisation.GIAB / public trio releases
- Curated variant sets: Classification practice with known answers.ClinVar expert panels
Core reading
- Richards S et al. (2015). Standards and guidelines for the interpretation of sequence variants. Genetics in Medicine 17:405–424.
- Li MM et al. (2017). Standards and guidelines for the interpretation and reporting of sequence variants in cancer. Journal of Molecular Diagnostics 19:4–23.
Duration, format and fees
- Next cohort
- Dates are sent with your admission offer
- Timetable
- Three evening or weekend sessions a week (IST), plus a lab clinic; intensive and weekend-only schedules on request
- Payment
- Secure online payment link with your admission offer (UPI, cards, net banking). Instalments on request for fees above ₹15,000.
- Refunds
- See the refund and cancellation policy.
Instructor
The instructor for each cohort is named in your admission offer and on this page when the cohort is announced. Vedicgen instructors are selected for hands-on research or industry experience in the subject they teach, and every course is reviewed by a second subject expert.
Questions about who teaches a cohort? [email protected]
Certificate
Learners who complete the course and pass its capstone receive a Vedicgen certificate of completion for Clinical Genomics & Variant Interpretation, issued by Vivofold, stating the guided hours and skills assessed. Each certificate has a unique ID and QR code that anyone can check.
Apply for Clinical Genomics & Variant Interpretation
Apply
Send the form below. It takes about five minutes.
Review
An adviser confirms your fit and format within two working days.
Offer
You receive dates, timetable and a secure payment link.
Onboard
Set-up guide, pre-reading and joining links.
Frequently asked questions
No. The course teaches the methods used in clinical genomics for education and research. Signing clinical reports requires the professional qualifications and laboratory accreditation defined by your national regulations.
In the live cohort, modules are taught in instructor-led sessions with a weekly lab clinic where you work on real public data with help at hand; every session is recorded. The self-paced format uses the same lessons, labs and datasets with mentor review of your capstone. Both formats end with an assessed project reviewed for the code and the science.
A laptop with at least 8 GB of RAM and about 30 GB of free disk space, running Linux, macOS, or Windows with WSL2. Installation instructions are sent before the first session, and lab clinics help with any set-up problems.
Yes. Learners who complete the course and pass its assessment receive a Vedicgen certificate of completion, issued by Vivofold. Every certificate carries a unique ID and a QR code that anyone, including an employer or admissions office, can check on the certificate verification page.
Apply with the form on this page. Live and in-person cohorts run through the year; the dates, timetable and joining details of the next cohort are sent with your admission offer and listed on this page once announced. Self-paced enrolment opens as soon as your application is accepted.
Yes. No course runs longer than four weeks, and the length is customisable: choose the standard schedule, an intensive one- to two-week schedule, weekends only, or a custom timetable. Pick your preference on the application form; colleges and teams can book their own dates.
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