Dr Peter J Freeman

Lecturer in Healthcare Sciences (Clinical Bioinformatics)

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Overview

Peter Freeman (Formerly Causey-Freeman) is a lecturer in healthcare sciences (Clinical Bioinformatics, Genomics) at the University of Manchester, UK. As a member of the Manchester Academy for Healthcare Science Education, his main teaching role is teaching UK National Health Service scientists, and other clinical scientists how to use bioinformatics to determine whether genetic variants are pathogenic or not. He also teaches on a wider Masters programme and online PGCert in genomic medicine and co-leads the unit Introduction to programming for the PGCert and NHS STP programmes https://tinyurl.com/y45upaoe

His research focus is in the discipline of translational bioinformatics in healthcare, particularly concentrating on improving the robustness and consistency of data shared in databases and clinical literature used in genomic diagnostics, in particular the naming of sequence variants. His Free and Open-Source software, VariantValidator https://variantvalidator.org/ is widely regarded as the most accurate variant description validation software and is used in diagnostic labs and research institutions world-wide. VariantValidator was recognised as World-Leading research by the Research Excellence Framework REF 2021 https://twitter.com/VariantValidatr/status/1524725459455557633

In 2020 VariantValidator was endorsed by the Human Genome Organisation (HUGO) Reporting of Sequence Variants Working Group, and Peter was made a member of this group. Peter is very excited about the opportunities that have arisen thanks to the Human Genome Organisation (HUGO) Reporting of Sequence Variants Working Group’s efforts. They have enabled him to work with major partners, including clinical journals, to begin collaborative harmonisation efforts intended to eliminate miss-naming of sequence variants in clinical literature and databases. VariantValidator is being used as key "translation engine" providing resources that seamlessly converts variant descriptions between the different formats used in different databases and literature, making it easier for clinicians to rapidly identify sequence variant data in clinical literature and clinical databases by eliminating discrepancies in the naming of the data. 

Although it is “early days” Peter’s hopes that this collaborative effort will substantially reduce the time clinicians take when performing literature and database searchers and will help to tackle the diagnostic odyssey where it currently takes on average 5 years to diagnose a rare genetic illness at the molecular level.  During this time, patients and their families find it difficult to access effective support and treatment which improve the quality of life for patients and may also save lives. Tackling this odyssey became a poignant personal challenge for Peter in 2021 and he has first-hand experience of the challenges families face trying to access support. Peter is now taking steps to become an advocate for patients and families with genetic illnesses, providing both personal experience of the difficulties alongside the extensive knowledge of laboratory and computational genomics that he has developed over the last 20 or so years. In 2022 Peter was delighted to be offered the post of Patient Editor (and Section editor) at the Elsevier journal, Genetics in Medicine. In this role he helps to plan strategies for effective patient representation in journal entries and also provides specialist scientific knowledge in the field of genomics bioinformatics. 

After completing his PhD in 2007 at the University of Leicester, he became a post-doctoral researcher at Leicester specialising in empirical genome analysis techniques and developing novel methods to improve Next Generation Sequencing techniques.

In 2015, he switched career paths from laboratory work into the bioinformatics space. He developed genomic sequence variant nomenclature software called VariantValidator. VariantValidator is endorsed as a gold-standard sequence variant description tool by world leading biomedical journals including Human Mutation and Genetics in Medicine. VariantValidator is integrated into genomic analysis and diagnostic pipelines including packages created by the Global Alliance for Genomics and Health, UKs NHS and Leiden Open Variant Database (LOVD). VariantValidator is also endorsed by genomics Quality Assurance bodies in the UK, USA and EU. 

In late 2018, Peter was made a member of the HGVS Sequence Variant Nomenclature working group and was also awarded an honorary lectureship at the University of Leicester where he actively contributes to ongoing research.

In March 2019 Peter moved to the University of Manchester to apply his knowledge of quality standards in genomic sequence variation classification into teaching and research around genomic medicine.

In 2020 Peter was appointed a member of the Human Genome Organisation (HUGO) Reporting of Sequence Variants Working Group who are driving improved standards of sequence variant reporting in biomedical journals. 

Memberships of committees and professional bodies

Member of:

External positions

Patient Editor (Genetics in Medicine), Elsevier BV

18 Apr 2022 → …

Section Editor (Genetics in Medicine), Elsevier BV

18 Apr 2022 → …

Honorary Lecturer, University of Leicester

18 Jan 2019 → …

Education / academic qualifications

  • 2008 - Doctor of Philosophy, Genetics, University of Leicester (2003 - 2007)
  • 2002 - Bachelor of Science, Molecular Biology, The University of Manchester (1999 - 2002)

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