Genetics & Biotechnology

Bioinformatics Analysis Pipeline

Required. Real bioinformatics analysis on a named public dataset from NCBI, Ensembl, or equivalent: BLAST sequence alignment, multiple sequence alignment (MUSCLE or MAFFT), phylogenetic tree construction (PhyML or IQ-TREE), variant annotation (Ensembl VEP or ClinVar), or RNA-seq differential expression (DESeq2 or edgeR). Submitted code must be independently runnable. Reviewed by a geneticist or bioinformatician who examines parameter choices and asks why specific settings were chosen over alternatives. All tools and data are free.

Genetic Data Interpretation

Required. Interpret real genetic data from a named public source: annotate variants using ClinVar and Ensembl VEP (both free), interpret a GWAS result from a published study tracing a named variant through statistical and functional evidence, or analyse sequencing results for a named genetic question. Document the evidence base for each interpretation claim. Reviewer presents an unseen variant of uncertain significance and asks you to classify it using ACMG/AMP criteria — requiring real-time reasoning, not recall. Builds on bioinformatics analysis (seq 10).

Biotechnology Application Case Analysis

Elective. Case analysis of a specific named biotechnology application: a named CRISPR therapy in clinical trials (ClinicalTrials.gov registry), a named synthetic biology product, or a named agricultural biotech product with a published safety assessment. Three dimensions: (1) scientific validity — what does the evidence actually show? (2) regulatory status — what approvals exist and what gaps remain? (3) ethical implications — contested trade-offs with an explicitly named ethical framework. Reviewer challenges whether the evidence you cited is sufficient to support your efficacy conclusions.

Genetics Ethics and Policy Analysis

Elective. Analyse a real genetics ethics case using an explicitly named ethical framework: DTC genetic testing regulation (named product + jurisdiction), gene drive proposals (named ecosystem + target species), germline editing policy (named national framework vs. ISSCR 2021 guidelines), or prenatal genetic diagnosis policy (named condition + jurisdiction). Apply the framework explicitly — not just describe it — and reach a substantive conclusion. Reviewer challenges with a real counter-example requiring reasoning about a specific case you may not have prepared for.

Write and Publish a Research Paper

Elective capstone. A full genetics or bioinformatics research paper accepted by a peer-reviewed journal or conference. The peer review system provides external adversarial verification. The research paper builds on the bioinformatics pipeline (seq 10) and interpretation (seq 20) — the analysis becomes the Methods and Results of a publishable paper. Not a separate investigation.

Free access to BLAST (sequence alignment), GenBank (sequence repository), SRA (short read archive), ClinVar (variant significance database), and dbSNP (SNP database). Use for the bioinformatics analysis step (BLAST alignment on a named public sequence) and the genetic data interpretation step (ClinVar variant annotation). The authoritative free resource for sequence data and clinical variant databases.

Free access to annotated genomes from hundreds of species, variant annotations via the Ensembl Variant Effect Predictor (VEP — free web tool and API), and downloadable genome sequence data. Use for the bioinformatics analysis step (genome-scale alignment and annotation) and the genetic data interpretation step (VEP annotation of your variant set). VEP is the standard tool for variant functional consequence prediction in published research.

Free registry of all clinical trials registered in the United States, including CRISPR therapies, gene therapies, and biotechnology products. Use for the biotechnology case analysis step — find a named IND for a specific CRISPR therapy, read the study protocol, and analyse the scientific validity and regulatory status. Each trial has a unique NCT number for citation.

Free online access to a rigorous textbook on bioinformatics algorithms — sequence alignment, phylogenetics, genome assembly, and more. Use to understand the mathematical foundations of the tools you use in the bioinformatics analysis step: knowing what BLAST's Smith-Waterman alignment is actually computing lets you make informed parameter choices and explain them to a reviewer.