Contributors - Manoj Kumar, Sam Bhatia, Kelly Johnson, Roberto Llaras, Luis Apellaniz Fontanez, Sean Hamill, Mary Burke, Anukool A, Christina Tillbrook
Imagine having a special friend who is a genomics expert and can understand your genetic profile and can help you understand it in a simple, easy to understand way. Well, that's exactly what we built during the recent Microsoft Hackathon in September 2024.
Picture this: You visit the doctor's office, and they give you a bunch of papers filled with big, fancy words and numbers as part of your recent genomic analysis. Whoa, that can be confusing, right?
Physicians today use genomic reports to diagnose and treat a wide range of genetic conditions. These reports typically provide information about an individual's genetic makeup, including any mutations or variations that may be associated with specific diseases or disease conditions. Interpreting genomic reports can be complex and requires specialized training and expertise. Physicians typically work with genetic counselors and other specialists to help interpret and understand the information contained in these reports. In general, physicians will look for any genetic mutations or variations that are known to be associated with the patient's symptoms or family history. They will also consider the patient's overall health, medical history, and other factors when interpreting genomic reports. The interpretation of genomic reports is constantly evolving as new research and discoveries are made in the field of genetics. As a result, physicians must stay up to date with the latest advances in genomics and work closely with other experts to ensure that they are providing the most accurate and effective care possible.
That's where the CoPilot for genomic report interpretation jumps in to save the day! It's like having a secret decoder that turns all those complex things into simple stories just for you.
What is a CoPilot?
A copilot is an intelligent virtual assistant that uses large language models to facilitate natural, human-like conversational interactions. It can assist users in various tasks and decision-making processes across multiple domains within an enterprise environment. By leveraging these models, AI copilots have the capability to understand, analyze, and process vast amounts of data. Microsoft, for instance, has rebranded all of its AI-powered companions as Copilot, adding specialized monikers to each of them. These AI copilots can provide support in areas such as coding, writing, learning, and more. They are designed to understand context, provide relevant suggestions, and even generate content, making them a valuable tool in many professional settings.
This Copilot is responsible for taking the report or genomic impression from tertiary analysis as input and creating a narrative on the impression in the report in a layman language for non-experts to understand.
Watch the following video to understand how it actually works.
Following is the architecture for this hackathon project.
Health copilot was a powerapp application that different personas interacted with. The reports were stored in Azure storage. The reference for this was available as part of SharePoint List. Power Automate was used to connect to Azure form recognizer to convert from pdf to text. This text was then sent to Azure Open AI GPT 3.5 model with a specific prompt to generate response. Text analytics for health was also used to highlight medical images that were part of the report for easy reading.
Following prompt was sent to large language models in order to produce a consistent as well as understandable summary report at 5th grade level.
#### **Introduction**
Please create a report that will help patients with their
diagnosis based on the lab and genomics results. Use simple language to explain
the findings and what they mean. Be sure to explain any scientific terms you
use in a glossary at the end of the report.
#### **Section Breakdown**
1. **Your Test**
- Describe the type of test carried out in a manner easy
for a patient to understand. Mention that a small sample of their blood was
taken for the test.
2. **What We Found**
- Summarize the findings, including lab parameters seen
in the report if any. Briefly explain what was looked at in the genes without
using technical jargon.
3. **What It Means**
- Break down what the findings mean in simple terms,
focusing on mapping lab results to what was found in the genetic tests.
4. **Your Health Team's Advice**
- Provide advice on potential lifestyle changes like diet
and physical activity in a patient-friendly way, encouraging healthy habits
rather than instilling fear.
5. **Questions You Might Have**
- Anticipate and answer a couple of basic questions a
patient might have, framing it as a collaborative effort to maintain health.
6. **Glossary**
- Define any technical terms used in the report in
simple, easy-to-understand language.
#### **Guidance on Tone**
- Maintain a friendly, reassuring tone throughout the
report.
- Avoid using scary words or phrases that might cause
anxiety.
- Use encouraging language that promotes a positive
outlook and emphasizes the proactive steps the patient can take to maintain
their health.
#### **Instructions**
1. Start with a friendly greeting to make the patient
feel seen and respected.
2. For each section, provide clear, concise information
without overwhelming the reader with too much detail.
3. Use analogies or comparisons where possible to explain
complex concepts in a way that a patient can understand.
4. Include colorful illustrations or diagrams to help
explain the concepts visually (if possible).
5. Review the report to ensure it is free of medical
jargon, and replace any complex terms with simpler alternatives.
6. Conclude with a positive note, reassuring the patient
that their health team is there to support them.
#### **Review**
After drafting the report, please review it to ensure:
- The language is appropriate for a 5th-grade reading
level.
- The report conveys all necessary information without
being too detailed or technical.
- It maintains a friendly, positive tone throughout.
Thank you for helping to create a report that respects
and empowers our young patients by providing them with the information they
need in a way they can understand!
---
[Start of text]
Text extracted from complex genomics reports
[End of text]
Sample output from the model using the above prompt.
Dear Sarah Taylor,
We hope this report finds you well. We have conducted a test to help diagnose your condition and provide you with valuable information. Below, we have summarized the findings and explained what they mean in simple terms. If you have any questions, please don't hesitate to reach out to your health team.
Section 1: Your Test
We conducted a test called FoundationOne®Liquid which involved taking a small sample of your blood. This test uses next generation sequencing to identify genomic alterations related to your condition.
Section 2: What We Found
Based on the test results, we found some biomarker and genomic findings related to your diabetes type 1. Autoantibodies to other antigens have been reported, but they occur infrequently and are not used for prediction. We also found some genomic alterations, including HLA-DR3 & HLA-DR4 combined, CTLA4 +49G>A and CT60, and IL2RA rs2104286, rs12722489, and rs11594656. These variations were found in a certain percentage of the population.
Section 3: What It Means
The presence of HLA-DR3 and HLA-DR4 alleles is associated with an increased risk of type 1 diabetes. Treatment strategies for type 1 diabetes typically involve insulin therapy, diet management, regular exercise and monitoring of blood glucose levels Immunomodulatory agents can also be used to prevent or delay the onset of type 1 diabetes.
For patients with CTLA4 alterations, immunomodulatory agents can be used to prevent or delay the onset of type 1 diabetes. These agents work by modulating the immune system to prevent the destruction of insulin-producing beta cells in the pancreas. Other potential treatment strategies include standard therapies for type 1 diabetes, such as insulin therapy, diet management, regular exercise and monitoring of blood glucose levels.
Patients with IL2RA alterations can also benefit from immunomodulatory agents to prevent or delay the onset of type 1 diabetes. These agents work by modulating the immune system to prevent the destruction of insulin-producing beta cells in the pancreas.
Section 4: Your Health Team's Advice
We advise you to work closely with your healthcare provider to develop a personalized plan for managing your risk of developing type 1 diabetes. These include insulin therapy, diet management, regular exercise, and monitoring your blood glucose levels. These proactive steps can contribute to better overall health and help you maintain stable blood sugar levels. Your healthcare provider can also discuss the potential use of immunomodulatory agents and other treatment options based on your specific situation. Remember, your health team is here to support you every step of the way.
Section 5: Questions You Might Have
You may have some questions about your diagnosis and the recommended lifestyle changes. We anticipate a few common questions you might have:
Q: What lifestyle changes can I make to manage my risk of developing type 1 diabetes?
A: Maintaining a healthy diet, engaging in regular physical activity, and monitoring your blood glucose levels can help manage your risk of developing type 1 diabetes. It's important to work with your healthcare provider to develop a personalized plan that suits your needs.
Q: Are there any experimental treatments available for type 1 diabetes?
A: Cell transplantation is an experimental treatment that involves transplanting insulin producing cells from a donor pancreas into a patient with type 1 diabetes. However, this procedure is not widely available and should be discussed with your healthcare provider.
Q: How can I manage my diet effectively?
A: Your healthcare team can provide you with a personalized diet plan that takes into account your specific needs and preferences. They can guide you on portion sizes, food choices, and meal timings to help you maintain stable blood sugar levels.
Q: What types of physical activity are recommended?
A: Engaging in regular physical activity, such as walking, swimming, or cycling, can have a positive impact on your overall health and help manage diabetes. Your healthcare team can provide guidance on the appropriate level of activity for you and any precautions you should take.
Section 6: Glossary
To ensure you understand all the terms used in this report, we have included a glossary at the end. It provides simple, easy-to-understand definitions of any technical terms used.
- Autoantibodies: Antibodies produced by the immune system that mistakenly target and attack the body's own cells or tissues.
- Genomic alterations: Changes or variations in the DAN sequence that can affect the function of genes.
- HLA-DR3 & HLA-DR4: Specific genetic variations associated with an increased risk of type 1 diabetes.
- CTLA4: A gene involved in regulating the immune response.
- IL2RA: A gene that encodes a protein involved in the immune response.
- Immunomodulatory agents: Medications that modify or regulate the immune system's response.
- Insulin therapy: Treatment involving the use of insulin to manage blood glucose levels in individuals with diabetes.
- Diet management: Making healthy food choices and following a balanced diet to maintain blood glucose levels.
- Regular exercise: Engaging in physical activity to improve overall health and manage blood glucose levels.
- Monitoring of blood glucose levels: Regularly checking blood glucose levels to ensure they are within a healthy range.
We hope this report helps you better understand your diagnosis and the steps you can take to manage your health. Remember, your health team is always available to answer any further questions you may have. Stay positive and take proactive steps towards a healthier lifestyle.
Best regards,
[Your Name]