Genomics toolkit

Introduction

What is genomics and why is it important?

Genetics usually refers to the study of single-gene disease, whereas Genomics refers to the study of the entirety of a person's DNA including genes and the DNA in between, known as the genome. Genomic Medicine is the application of Genomics to patient care.  The transformational 100,000 Genomics project sequenced 100,000 genomes, adding significantly to knowledge of cancer and rare disease, and providing more patients with a diagnosis. This was the first step towards establishing a Genomic Medicine service within the NHS and increasing the use of genomic information within routine NHS patient care in non-genomics specialties, known as 'mainstreaming'. The NHS Genomics Medicine Service was launched in 2018. 

There will be increasing provision of genomic testing within NHS routine clinical care and there is an increase in requests from the public for genomic testing via private, non-NHS, routes (direct-to-consumer testing). Increasing numbers of patients are likely to present to Primary Care, with either their or a family member's test result, and we in Primary Care will need to be able to identify those who are eligible and those who will benefit from genomic testing.

About this toolkit

The Genomics Toolkit has been developed in partnership with Health Education England Genomics Education Programme to support increasing understanding, raise awareness of Genomics Medicine and support primary care with increased knowledge of how genomics can contribute to improving patient care in a 'genomics era'.  It is a collection of resources that explain how Genomics Medicine can be incorporated in Primary Care, including training resources and audit suggestions, and providing links to relevant guidance and patient resources. The resources can be used as quick reference resources or as a package for CPD, to deliver awareness-raising and educational events, and in supporting trainees preparing for the MRCGP.

This toolkit is designed to be used by the entire clinical primary care team. The content development has been informed by the relevant RCGP Curriculum Statement, and on the findings from a Delphi survey conducted by HEE which identified knowledge, skills and attitudes in Genomics required by the primary care team.

Impact of genomics in primary care

This section provides links to resources and articles which outline the impact of Genomics within Primary Care.

• The BJGP editorial, "Genomics in routine clinical care: what does this mean for primary care?" outlines how Genomics may impact on Primary Care with Rare Disease and Common Complex Disease including Cancer which are currently the main clinical areas of impact.
• Brief video clips introduce Genomics, impact within Primary Care, and the role of the GP in management of individuals and family with rare disease.
  • Rare Disease: The GP's role (Dr Sarah Jarvis and Professor Nadeem Qureshi, GPs)
  • Genomics in Medical Specialties - Primary Care (Dr Jude Hayward, GP)
  • Introducing Genomics in Healthcare (Vivienne Parry, Science Writer and Broadcaster)
• Generation Genome: The Annual Report of the Chief Medical Officer Dame Sally Davies (2016) describes how Genomic Technologies can benefit patients, and provides recommendations for NHS Systems and Services, Research, Data and Regulation, and engaging staff and patients.
• The Topol Review (2019): Preparing the healthcare workforce to deliver the digital future, identifies Genomics, Artificial Intelligence (PDF) and Digital Medicine as the key technologies to impact on the NHS, and makes recommendations for deployment and implementation within the NHS.
• A Genomics England public dialogue, co-funded by Science Wise and delivered in partnership with Ipsos Mori: A Public dialogue on genomic medicine: time for a new social contract?. This report explores public aspirations, concerns, expectations and limits regarding delivery of genomic medicine and use of genomic data.
• Rare diseases are individually rare but collectively common, with a prevalence of 1 in 17, the majority have an underlying genetic basis. Rare diseases in general practice: recognising the zebras among the horses, provides an overview of detection and management in primary care, and the impact of genomic testing.
• Should UK primary care be an early adopter of genomic medicine. This editorial began as a debate presented at the 2017 RCGP annual conference and summarises the potential benefits and harms of genomic medicine in the context of primary care.
• Non-invasive prenatal testing: use of cell-free foetal DNA in Down Syndrome screening. An explanation and overview of non-invasive prenatal testing (NIPT) within national the national ante-natal screening programme. Results from ante-natal and new born screening programmes are mostly dealt with by midwives and health visitors, but primary care practitioners may be asked by patients to discuss results.
• Epigenetics in Primary Care explains the concept of Epigenetics and outlines how it impacts on clinical management within primary care.

Aiding genomics conversations

This section is designed to provide accessible information on key genomic terms and concepts as well as explain these potentially complex concepts to patients in the consultation. These resources can assist every Primary Care Health Professional in managing these sometimes challenging concepts and are relevant to GP Registrars preparing for the CSA.

‘Speaking Genomics' is a brief glossary containing key Genomics terminology and explaining nomenclature of Genomic test results.

• Genomics Phrasebook (PDF)

Communicating Genomics is a series of brief video clips in which three GPs give examples of how modes of inheritance and genomic test results may be explained to patients within a consultation.

• X-linked Dominant and Recessive
• Pathogenic Variants
• Autosomal Recessive Inheritance
• Autosomal Dominant Inheritance

Training resources

This section is a repository of educational and training resources.

• RCGP Curriculum Statement, Genetics in Primary Care. Three main themes which are still applicable in the genomics era: identifying patients with, or at risk of, a genetic condition; clinical management of genetic conditions; communicating genetic information.
• The RCGP Genomics in Primary Care: Four webinars, each lasting 15 minutes, can be used separately or as a package, for individual CPD in delivering tutorials or educational sessions. These contain a lot of information but are short so the individual can choose whether to watch as a brief outline, or explore information in more depth.
  • Part 1: Familial Cancer
  • Part 2: Rare Disease
  • Part 3: Non-invasive prenatal testing
  • Part 4: Ethical issues
• Podcasts: Four podcasts in the format of conversations, lasting up to 15 minutes, introduce and overview of genomics issues within primary care.
  • Podcast 1: An introduction to genomics in primary care from Helen Stokes-Lampard
  • Podcast 2: An introduction to genomics basic terminology and the potential for primary care involvement
  • Podcast 3: Potential impact of applications of genomic medicine in primary care citing the importance of family history and conditions seen though secondary care specialties
  • Podcast 4: Considerations around the ethical, social and legal implications of genomics in primary care. Discussion around direct consumer testing and pharmacogenomic

• Overview of the NHS Genomics Medicine service (PDF): comprising Genomics Medicine Centre and Regional Genetics Services, Genomic Laboratory Hubs, and the Genomic Test Directory. 

• Care pathway for assessment and care of people with a family history of breast cancer (PDF) : based on NICE guideline CG164 ‘Familial Breast Cancer:  classification, care and managing breast cancer and related risks in people with a family history of breast cancer’. 

Types of Genomic Testing

• Micro-Array Testing (PDF)

• Predictive and Diagnostic Testing (PDF)

• Somatic and Germline DNA (PDF)

• Genomic Sequencing (PDF): from sample collection to interpretation, this Health Education England Genomics Education Programme infographic lays out the roadmap for genomic testing (last reviewed September 2018 (Click to enlarge). 

• The Gen-Equip project: a European funded project which comprises online learning modules, webinars, practical tools, and patient stories.

• MOOC: The Genomics Era: The Future of Genetics in Medicine. A more in-depth educational resource, a free on-line MOOC comprising two hours per week for five weeks. It is aimed all NHS healthcare professionals, providing a grounding in genomic medicine, genomic technologies, patient diagnosis, treatment and disease prevention.

• Health Education England Genomics Education Programme
  • Resource page: includes video clips, disease summaries, genomics in clinical specialties.
  • Taught courses: information regarding CPPD modules, PGDip, PGCert, MSc in Genomic Medicine.

Ethics and genomics

Disease summaries

• Familial Hypercholesterolaemia: Nice Guidelines
• Hereditary Haemochromatosis
• Alpha-1-antitrypsin deficiency
• Hereditary Haemorrhagic Telangiectasia and Imperial College

• General resources from Health Education England on their Genomics Education Programme
• RCGP Genetic Haemochromatosis eLearning module
• RCGP Communicating Genomics
  • X-linked Dominant and Recessive
  • Pathogenic Variants
  • Autosomal Recessive Inheritance
  • Autosomal Dominant Inheritance

Guidance

NICE guidance

Familial Breast Cancer – includes sections on management in primary care, contraception and HRT, and chemoprophylactic Tamoxifen and Anastrazole.

• Familial breast cancer: NICE Guidance
• Familial hypercholesterolaemia: NICE Pathways

British Gastroenterology Society Guidance

Section Guidance On Large Bowel Surveillance For Individuals With A Family History Indicating A Moderate Risk PP15-16, outlines family histories which should be referred to secondary care, and those who should be cared for in primary care.

UKMEC

includes guidance for breast conditions, family history of breast cancer, and carriers of known gene mutations.

• UK Medical Eligibility Criteria for Contraceptive Use
• UK Medical Eligibility Criteria For Contraceptive Use – Full book

Neurofibromatosis Society guidance for review of NF1 patients in primary care. Managing chronic genetic conditions in practice.

• Guidance: Ferner RE, Huson SM, Thomas N, et al. Guidelines for the diagnosis and management of individuals with neurofibromatosis 1. J Med Genet. 2007;44(2):81–88. doi:10.1136/jmg.2006.045906

RCGP Position statement on Direct-to-consumer testing (PDF).

Audit and quality improvement guidance

• Case-finding in familial hypercholesterolaemia
• RCGP QI guide
• RCGP appraisal and revalidation guidance

Consent and confidentiality in genomic medicine guidance: illustrates consent and confidentiality issues through discussion of case scenarios.

Research

• RCGP Research Ready
• Preparing primary and community care NHS organisations for genomic research - an NIHR Clinical Research Network (CRN) a joint paper
• The 100,000 genome project, an exemplar of a hybrid research model between Genomics England and the NHS.
  
• Pharmacogenetics and the stratified medicine network talks and presentations
• Facilitating Ethical Preparedness in Genomic Medicine
• Ethics and consent FAQ advice from Genomics England for the 100,000 Genomes project

Patient resources

Cancer websites

These all include information about cancer family history, and linked genes, including when people should seek advice from their GP. They also include information regarding suspicious symptoms and lifestyle advice to reduce risk, supporting self-care.

• MacMillan: Cancer Genetics Resources
• Cancer research UK: Family History and Inherited Cancer Genes
• Ovacome: Testing for the BRCA Gene Fault

Chemo-prevention for women with no history of breast cancer

NICE decision aids:  these are aimed at women who are at above-population risk of developing breast cancer, who have been assessed as eligible by secondary or tertiary care for chemoprophylactic Tamoxifen or Anastrazole.  They include useful information and comparison tables to help women make choices regarding whether or which medication to consider.

• Chemo-prevention: NICE tamoxifen decision aid
• Chemoprophylaxis: UK Cancer Genetics Group Leaflets

Rare Disease websites

Genetic Alliance is an umbrella organisation for 200 organisations, including Rare Disease UK, and Syndromes Without A Name, and support groups for individual rare diseases.  These provide information and support for patients and families affected by a genetic condition and are also a source of information and practical advice for healthcare professionals.

Unique is a charity supporting and informing families with a rare chromosome disorder, and some single gene disorders. 

Unique also has a list of guides for healthcare professionals for individual chromosomal disorders (including deletions and duplications) in English and other languages.