Specialty Content

Genomics and Molecular Pathology specialty

Genomics has changed faster than any other specialty since the NHS Genomic Medicine Service (GMS) launch. Our coverage focuses on NGS workflow, variant interpretation, and NHS GMS panels.

Where the content lives

• The Genomics Laboratory — /genomics-lims — the full laboratory simulation: Worklist, Bench, Interpret, Learn. Sequencing and quality metrics, the bioinformatics pipeline, ACMG/AMP classification with the CanVIG-UK points bands, somatic oncogenicity tiering, and the reporting decision itself
• Specialty page — /genomics-interviews — guides, simulators and case studies, with the link into the Interview Explorer question bank (Bands 2 to 8)
• Clinical Scientist Genomics day-in-life — /biomedical-sciences/clinical-scientist-genomics-day-in-life
• Genomics training courses overview — /biomedical-sciences/genomics-training-biomedical-scientists-uk-courses
• Result Interpretation (genomics) — open /result-interpretation and click the Genomics card — variant interpretation, ACMG classification, NHS GMS panels
• Molecular Diagnostics PCR training — /biomedical-sciences/molecular-diagnostics-pcr-training-biomedical-scientists
• Specialist Portfolio (Molecular / Genomics) — /portfolio → choose the Genetics & Genomics discipline card, then select Specialist Diploma in the AI Assistant tab

Key competencies covered

• Next-generation sequencing (NGS) — workflow, QC metrics (coverage, depth, GC bias), library preparation
• Sanger sequencing — confirmatory, low-throughput variant verification
• Variant interpretation — the ACMG/AMP 2015 combining rules and the ClinGen Bayesian points system the CanVIG-UK bands apply (Benign / Likely Benign / VUS / Likely Pathogenic / Pathogenic). The two frameworks disagree on a minority of criterion combinations; the simulation shows both answers where they differ
• NHS GMS panels — common panels for cancer (somatic), rare disease (germline), and pharmacogenomics
• Copy number variation (CNV) — array CGH, NGS-based CNV calling
• Bioinformatics pipelines — basic concepts, validation
• Quality metrics in genomics — read depth, allele frequency, on-target rate
• MDT participation — communicating variant significance to clinicians and counsellors

Career path note

Genomics in the NHS is increasingly led by Clinical Scientists (via the STP route) rather than Biomedical Scientists. Both routes exist:

• Biomedical Scientist route — IBMS-accredited degree → HCPC BMS registration → specialty (often Histology or Haematology first) → Genomics via Specialist Portfolio
• Clinical Scientist route — STP at NSHCS (3-year programme) → HCPC Clinical Scientist registration in Genomics

See /biomedical-sciences/how-to-become-clinical-scientist for the Clinical Scientist pathway.

Bands progression

• Band 5 (£32,073-£39,043) — qualified BMS performing routine molecular assays under supervision
• Band 6 (£39,959-£48,117) — specialist NGS workflows, supervised variant interpretation, training
• Band 7 (£49,387-£56,515) — independent variant interpretation, MDT contribution, audit
• Band 8 — Principal / Consultant Clinical Scientist; reports to commissioning

Standards alignment

• ACMG/AMP 2015 variant classification, with the ClinGen sequence variant interpretation recommendations that followed it — including the withdrawal of PP5 and BP6 in 2018 and the recommendation that PM2 be applied at supporting strength
• ACGS Best Practice Guidelines for Variant Classification, 2026 v3 (July 2026)
• CanVIG-UK points bands: Pathogenic ≥10, Likely Pathogenic 6–9, Likely Benign −1 to −5, Benign ≤−6
• NHS England Genomic Medicine Service specifications
• Genomics England PanelApp — current panel content
• UKAS ISO 15189:2022 for laboratory accreditation
• AGNC (Association of Genetic Nurses and Counsellors) MDT guidance
• UK NEQAS for Molecular Genetics scheme requirements

Common interview question themes (Band 5-7)

• "Walk me through how you would classify a missense variant using ACMG"
• "What QC metrics do you monitor on an NGS run, and what thresholds trigger a re-run?"
• "How would you handle a VUS in a clinically actionable gene?"
• "Describe how a panel is validated for a new condition"
• "How does the NHS GMS commissioning work, and what does it mean for our service?"

A good preparation stack: Result Interpretation → Molecular Diagnostics PCR training → Practice Tests filtered to Genomics + your Band → AI Interview Coach.