Dan Frampton Email and Phone Number

Bioinformatician with 15+ years experience in pathogen genomics.Genpax is revolutionising infectious disease investigation with IDEM, our groundbreaking surveillance tool using whole genome sequencing analysis. IDEM uses precision genomics to uncover the true relationship between bacterial isolates, offering a comprehensive solution to strain identification and outbreak management.

Working to embed real-time NGS within a hospital setting for virus outbreak response and surveillance, and leading multidisciplinary teams for the development of reporting and visualisation frameworks for clinicians and virologists at UCLH and external clinical partners. Management of junior bioinformaticians, providing support and training. Key achievements include:• The ICONIC virus genome assembly pipeline is now run daily at UCL/UCLH as part of the hospital’s COVID-19 response, notably underpinning our recent work investigating the genomic characteristics and clinical effect of B.1.1.7 on disease severity [Ref. 1]. • Overseeing the computational and information governance requirements involved in establishing APDU UCLH as a COVID-19 Genomics UK Consortium (COG-UK) sequencing site, to share UCLH sequenced SARS-CoV-2 genomes and their associated metadata with the broader scientific community.• Developing a rapid NGS diagnostic test for multiple drug resistance in tuberculosis (manuscript under review).• Validation of the MinION portable sequencer for real-time influenza diagnostics and infection control within a clinical setting.• Developing a dashboard in collaboration with colleagues at AHRI (Durban, South Africa) to visualise geospatial distribution of drug resistance mutations (DRMs) across KwaZulu-Natal for ~2000 HIV patient samples.• Delivery of online training in NGS and molecular epidemiology to HIV clinicians in Russia as part of the REACH project.• Awarded 2019 UCL Global Engagement funding to collaborate with colleagues in Fiocruz, Brazil, to investigate patterns in influenza seasonality and vaccine efficacy across Brazil via NGS data analysis.• Invitations to speak at several national and international meetings and to give specialist seminars, notably most recently IMMEM (Sept 2019), ICG-13 (BGI/CNGB annual conference, Oct 2018), COG-UK (Sept 2020, March 2021) and University Hospital Basel (Dec 2019).

Leading the development of an automated high-throughput genome assembly pipeline at UCL for the ICONIC and PANGEA projects (£multi-million multi-site virus NGS projects, linking genomic and clinical data for ~20k samples from UK clinics and sub-Saharan African HIV cohorts, respectively) to aid individualised treatment and assist infection control.Key achievements include: • The pipeline is now run daily at UCL/UCLH as part of the hospital’s COVID-19 response, notably underpinning our recent work investigating the genomic characteristics and clinical effect of B.1.1.7 on disease severity [Ref. 1]. Previously it has been used to identify and report a rapidly emerging subclade of H3N2 influenza in Dec-Jan 2016-17 in near real-time [Ref. 2] and as part of several HIV surveillance studies in London [e.g. Ref. 3].• Developing and implementing an in-house algorithm and reporting system to assist clinicians resolve transmission clusters via phylogenetic and clinical data analysis: now an integral part of UCLH Infection Control. This has been used to characterise several viral outbreaks [e.g. Ref. 4] and also to estimate the rate of nosocomial spread of influenza within the hospital [Ref. 5].• Leading pipeline optimisation and roll-out at partner hospital sites in the UK (UCLH and Barts) and abroad (MRC Uganda, Shanghai Jiao Tong University School of Medicine) on HPC clusters and local servers. This formed part of a collaboration with Intel Health and Life Sciences’ EMEA Innovation Team, published in an Intel White Paper [Ref. 6].• Much of the initial pipeline development involved collaboration with teams at the Wellcome Trust Sanger Institute: I was a Visiting Worker there from 2015-18.• The ICONIC pipeline won the Institute of Engineering and Technology (IET) Healthcare Technologies award in 2018 for its translation of a research methodology into routine clinical settings in the UK and abroad.

Working alongside molecular biologists to develop and apply a broad selection of NGS approaches and computational biological techniques to pathogen research, including:• Differential gene expression analysis of both host and viral transcripts to generate gene signatures and identify key pathways involved in varicella zoster virus (VZV) infection of keratinocytes [Ref 7. https://doi.org/10.1371/journal.ppat.1003896]• Mapping dog transcriptomes to corresponding methylomes to identify dysregulated pathways in canine transmissible venereal tumour (CTVT), to better understand the molecular mechanisms behind and gene signatures associated with tumour regression [Ref 8. https://doi.org/10.1016/j.ccell.2018.03.003]• Applying graph theoretical techniques to analyse B-cell receptor repertoires using short reads to estimate relative levels of sequence variants [Ref 9. https://doi.org/10.1371/journal.ppat.1004552]• Developing a cross-platform microarray database with browser support, to facilitate meta-analysis by mapping probes to transcripts on local datasets.

Following several years of collaborative research with clinicians at UCLH, I was awarded an honorary contract to continue and further develop this work with the Advanced Pathogens Diagnostic Unit (APDU), a clinicial microbiology team linked to UCLH Virology.Working alongside the relevant clinical teams, this has enabled me to directly link Next Generation Sequencing outputs to clinical and epidemiological data from patient electronic healthcare records (EHRs) from within the "NHS firewall", greatly improving "sample-to-report" turnaround times whilst maintaining patient confidentiality with strict data governance and ethical frameworks.

Providing bioinformatics support for UCL-based researchers.Analysis, QC and report design for collaborators microarray data sets.Developing and delivering a 5-day training course with practical sessions in transcriptomics and proteomics.

Drug absorption and metabolic stability screening of novel pharmaceutical compounds.Growing Caco-2 cells for drug absorption assays via aseptic technique.Lab transfer from Dagenham to Paris (Spring 2000) and setting up new laboratories in Paris (Summer 2000).