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Genomics overview

Genomics is the study of an organism’s genome – its genetic material – and how that information is applied. All living things, from single-celled bacteria, to multi-cellular plants, animals and humans, have a genome – and ours is made up of DNA.


Training resources

The following training resources are available:

Genomics Education Programme:

North Thames Genomic Laboratory Hub:

South East Genomic Medicine Service Alliance:

Miscellaneous

Learning and Development Hub

Workshops

Lynch syndrome mainstreaming training programme

They are six 2 hour workshops delivered as part of the mainstreaming training for Lynch syndrome. It has been developed by Laura Monje-Garcia, National Lead Nurse for the Lynch syndrome project.

Programme outline:

  • Workshop 1: taking a family history & drawing a family pedigree
  • Workshop 2: confidentiality and ethics
  • Workshop 3: the consultation
  • Workshop 4: exercise
  • Workshop 5: final documents and full consultation practice with regional Lynch syndrome nurse
  • Workshop 6: clinic set-up - activities for clinic set-up should start alongside Workshop 1 as it can be a lengthy process (3 months average). Your regional Lynch syndrome nurse and cancer alliance can provide support for this.

The Lynch syndrome mainstreaming training programme uses the Health Education England (HEE) Genomic Education Programme (GEP) competency frameworks:

  1. Facilitating genomic testing competencies - it covers 'informed consent.' You will go through all the points during the workshops, but if you are not sure about something, ask your regional Lynch syndrome nurse. This is a reference document and is not intended to be used as an assessment tool.
  2. Communicating germline genomics results: a competency framework - this is a reference document and is not intended to be used as an assessment tool. 
  • Workshop 1: Drawing a family pedigree
    For this workshop you will need to complete the National Lynch Sydrome project's colorectal cancer option 2 training.

    This training is for multidisciplinary team (MDT) members to help them identify patients likely to have Lynch syndrome and refer these patients to genetic testing.

    Find out about the workshop

    View workshop supporting documents


    You should also start your clinic set-up process. Find out more about the clinic set-up process.

    Additional resources:

  • Workshop 2: Confidentiality & Ethics

    This workshop will review:


    Confidentiality in Genomics

    Read the Consent and confidentiality in genomic medicine medicine document by the Royal College of Physicians.

    • Most of the confidentiality points discussed in this booklet refer to predictive genetic testing but it is recommended that you read point 4.2 and case studies
    • Save it in a safe place as a reference document.

    Ethics

    • This will be discussed by the regional lynch syndrome nurse through a presentation
    • They will help you identify when ethnical situations arise, generally related to "non-disclosure" of information within the family
    • Main message: there are several forums to discuss ethical issues in Genomics. You can start by discussing with your multidisciplinary team (MDT), in document, and highlight to clinical genetics or specialised services so they can deal with them.

  • Workshop 3: The Consultation (Part 1)

    As part of your tutorials you will be able to see a full consultation by one of the Regional Lynch syndrome nurses.

    1. After, discuss the consultation and break it down into sections. This is so its easier for you select an agenda when you have your consultation and know the essentials that need to be covered. The consultation will follow the structure of this flowchart.
    2. The information that you need to discuss is covered in the RM Partner's information leaflet for patients with Endometrial Cancer
    3. To find your own way to explain Lynch syndrome, read the RM Partners’ patient information webpage as it’s easy to understand, and uses a language patients will be able to understand as well (Reviewed carefully by Lynch syndrome UK)
    4. Save all the documents available through this training in a folder where you can find them easily as you will need them later.
  • Workshop 3: The Consultation (Part 2)

    Please, watch these recommended videos that will help you find your own style to have your genetic counselling consultation: 

    1. To see how others explain the 3 possible results of genetic testing watch these short videos (max. 2.5 minutes). They will give you ideas about how you would like to explain this yourself 
    2. Other short related videos available through the genomics education programme 
    3. To understand how are genetic variants classified 
    4. What is a genome video 
    5. Autosomal dominant inheritance 
    6. How is genomics used in cancer?
  • Workshop 4: Consultation in action - finding your style

    The consultation in sections: finding your own style

    Write down how would you like to explain each section of the consultation. Send it over your Lynch syndrome nurse for feedback before or after practising the different sections of the consultation.

    Exercise: think about what you would cover during your consultation in these scenarios

    1st scenario: Maria has been diagnosed with CRC at 42. Her tumour sample IHC result showed loss of PMS2. She had a successful surgery and she is well. She works in genetics so you don’t need to teach your patient about genetics.

    • How would you explain Lynch syndrome?
    • How would you go through the 3 possible results?

    2nd scenario: John has been diagnosed with CRC at the age of 55y. He had surgery but had to have additional chemotherapy which will start in 1 month. He works as a health care assistant in your hospital. His IHC result showed loss of MLH1 & PMS2. MLH1 promoter Hypermethylation was absent. He understands genetics but he is not an expert.

    • Would you go through what DNA is?
    • How would you explain Lynch syndrome?
    • How would you explain the 3 possible results?

    3rd scenario: Jennifer has been diagnosed with CRC at the age of 36y. She had surgery but the cancer has metastasized to her liver and kidneys. She is going to have palliative chemo but she hasn’t got a start date yet. She hasn’t finished school and used to work in McDonalds, but due to her illness she is unemployed now. She would like to go back to work and study to finish her A levels. McDonalds can sponsor her for her A levels course. Her IHC show loss of MSH6. She is not very familiar with what DNA is but some understanding from the mainstream media. She looks depressed.

    • Would you go through what DNA is?
    • How would you explain Lynch syndrome?
    • How would you explain the 3 possible results?
    • Do you need to consider her emotional wellbeing?
  • Workshop 5: Full consultation & final documents

    Full consultation:You will have the opportunity to practice your full consultation

    • You will practice with your regional Lynch syndrome nurse using your own style which you developed and have already written down.

    Go through these documents

    A couple of documents to save and that you might find helpful before you start your clinic.

    • Family history questionnaire
    • Example of mainstreaming letter

    Make sure that you have your regions:

    1. Record of discussion form
    2. Germline genetic testing blood request form
    3. Your SOP has been approved by your team, cancer alliance representative, and clinical genetics department.
  • Workshop 6: Clinic set-up

    Activities for clinic set up should start alongside Workshop 1 as it can be tenthly process (3 months on average). Your regional Lynch syndrome nurse and cancer alliance can provide support for this.

    Find out more about clinic set-up

Related pages

Counselling and consent

Checklist

  • Has the patient had enough information and time to consider testing and its consequences?
  • Have the conversation and consent form been documented, recorded and stored according to local policy? Always document consultation as a written letter to the patient and sharing correspondence with the GP.
  • Has the patient been provided with:
    • Record of Discussion Form to sign (this is the consent form: one copy for patient, one for notes)
    • Patient information leaflets
    • Contact details of the clinical team
    • GMS test request form (if using phlebotomy services for blood sampling)
  • Has the patient been informed of logistical procedures including:
    • How the test will be conducted
    • When and how to expect results
    • How to access support whilst waiting for results

Frequently asked questions

  • What is 'Mainstreaming'?

    Mainstreaming Genomic testing means delivering a genetic test for patients diagnosed with a colorectal cancer who meet the standardised criteria set out in the National Genomic Test Directory.

    This is a simple blood test that can be ordered by the Colorectal Cancer Team instead of being outsourced/referred onto an external clinical genetics team.

    The results of the test are ‘actioned’ by the Colorectal Multidisciplinary Team, which include referring the patient to clinical genetics if it is necessary (see ‘When and How do I refer to Clinical Genetics?’ FAQ).

  • Why do we need 'Mainstreaming'?

    Testing within the cancer team speeds up results, reduces the number of healthcare professionals the patient has to interact with and reduces the hospital appointments they have to navigate during a stressful time.

    It ensures the patient can access relevant treatment in a timely manner based on their results.

    The patient will be offered counselling and consent for this blood test in the days after their diagnosis (vs seeing genetics—in many places this is a waiting list of more than 3 months).

  • What is the difference between a Germline and a Somatic Change?

    Germline mutations are inherited genetic changes that are present in the DNA of every cell in the body, including sperm and egg cells. These mutations can be passed down from generation to generation and can increase the risk of developing certain diseases, including cancer.

    Somatic mutations, on the other hand, are genetic changes that occur in non-germline cells during a person's lifetime.

    These mutations are not present in every cell of the body and cannot be passed down to offspring. Somatic mutations can occur due to a variety of factors, including exposure to environmental toxins, aging, and errors that occur during DNA replication.

  • How will the results of a positive test for FAP Syndrome affect treatment?

    Surgeries:

    • colectomy with ileo-rectal / distal sigmoid anastomosis
    • restorative proctocolectomy (St Mark's Polyposis Guidelines, 2022)

    Surveillance:

    • dependent on risk reducing surgeries undertaken
    • 1-3 yearly colonoscopy: commencing 12-14 years old (BSG Guidelines 2019)
  • Lynch Syndrome: How do I and when do I need to refer to Genetics Services?

    Always following results: discuss your results in the result forum allocated to you by your Lynch syndrome nurse for safety netting to discuss recommendations for your patients, which will include: cancer prevention programme and surveillance recommendations if VUS or negative.

    You can use the quick referral letter.

    Refer to local clinical genetics team, usually using a standardised form via email that will be accessible via your nearest Genomics Laboratory website. Enclose the following in your referral:

    • Attach histopathology reports
    • Attach minutes from cancer MDT meeting
    • Attach family pedigree
    • Call and inform patient they will receive an appointment for genetic referral.

    If the result is Negative or VUS the case might be virtually reviewed and your patient might not receive an appointment. You will find out when you discuss your results in your results forum.

  • How do I and when do I need to refer to Genetics Services?
    • When patient has a postively identified pathogenic variant.
    • When a patient has a variant of uncertain significance (VUS).
    • When a patient has a negative result, but a significant family history.
    • When a patient has a negative result, but presents with cancer at a young age (less than 50 years).
    • When you are not sure!

    Refer to local genetics team, usually using a standardised form via email that will be accessible via your nearest Genomics Laboratory Hub website.

  • How do I calculate a patient’s risk?

    Consider using validated tools recommended and developed by Genetics services such as:

    • QGenome
    • Modified Amsterdam Criteria.
  • How do I counsel a patient?

    Please read the genomics toolkit r208 conversation and consent guide to find out more.

Resources and reading list

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