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clinical trial

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Enable AI driven clinical trials matching with an open-source blueprint and one click deployment
Introducing a new open-source blueprint to quickly deploy Trial Matcher chatbot experience with one click of a button.
adishachar
Aug 03, 2023 Place Healthcare and Life Sciences Blog
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Genomics workflows on secure lockdown environment using Cromwell on AKS
Healthcare organization's heightened security, privacy, and compliance requirements (HIPAA, FEDRAMP) dictate the way genomics infrastructure is set up to provide end-to-end security for the environment. Cromwell on Azure using AKS is one such pattern. We worked with one such large provider in the US that does not take security lightly. They have a tightly controlled secure Azure environment, and every deployment must pass through rigorous security and infosec reviews. As part of their partnership with Microsoft, they are in the process of migrating all their genomic workflows and solutions from on-prem and competing cloud infrastructure to Microsoft Azure in partnership with Microsoft Industry solutions healthcare service line and Microsoft Health Futures. Both parties worked on one such deployment methodology for AKS-enabled Cromwell on Azure to run one of their key genomics workflows – the TruSight Oncology 500 assay (TSO500).
manoj1116
Apr 17, 2023 Place Healthcare and Life Sciences Blog
3.1KViews
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AI driven clinical trials matching with an open-source blueprint and one click deployment","conversation":{"__ref":"Conversation:conversation:3890797"},"id":"message:3890797","revisionNum":1,"uid":3890797,"depth":0,"board":{"__ref":"Blog:board:HealthcareAndLifeSciencesBlog"},"author":{"__ref":"User:user:1124879"},"teaser@stripHtml({\"removeProcessingText\":true,\"truncateLength\":-1})":" Introducing a new open-source blueprint to quickly deploy Trial Matcher chatbot experience with one click of a button. \n \n ","introduction":"","metrics":{"__typename":"MessageMetrics","views":4497},"postTime":"2023-08-03T12:39:33.704-07:00","lastPublishTime":"2023-08-03T12:39:33.704-07:00","body@stripHtml({\"removeProcessingText\":true,\"removeSpoilerMarkup\":true,\"removeTocMarkup\":true,\"truncateLength\":-1})":" Matching patients to clinical trials is a huge challenge. Based on the World Health Organization, in 2021 there were more than 82,000 clinical trials actively recruiting participants worldwide[1], containing increasingly complicated trial eligibility criteria. Given that a patient’s clinical information can be composed of hundreds of clinical notes, requiring review and analysis by a healthcare professional, matching patients to clinical trials becomes an unsustainable process. The Trial Matcher capability in Microsoft Project Health Insights addresses this challenge – by providing a tool to effectively match patients with diverse conditions to clinical trials for which they may be eligible. This is done through analysis of patient data and the complex eligibility criteria of the relevant trials. Project Health Insights is an AI service that provides built-in AI models for key scenarios in the health domain, including clinical trial recruitment. Available in public preview, the Trial Matcher model is already deployed by several organizations worldwide to enable matching of patients to clinical trials. \n Open-source blueprint for deployment of patient-centric chatbot \n Today, we are introducing a new open-source blueprint to quickly deploy Trial Matcher chatbot experience with one click of a button. The Trial Matcher chatbot is an Azure Health Bot instance with Clinical Trial Matching template integration. The chatbot enables patients to provide relevant patient information and checks their eligibility for potential trials, and after finding matches, provides a list of clinical trials the patient may be eligible for. Using this blueprint organizations can now expedite the onboarding process and start realizing the time saving benefits of the trial matcher capability right away. \n Deployment instructions The Azure resources that will be created and deployed when using this open-source blueprint include: \n \n Azure Health bot \n Azure Language Understanding \n Azure Health Insight \n \n Follow the instructions of the Readme file to deploy the Azure Health Bot with Trial Matcher integration based on the clinical trial matching template. \n \n \n Figure 1 List of scenarios enabling Trial Matcher from Project Health Insights \n After a successful deployment, open your generated instance of Azure Health Bot, and go to the management portal. Under Scenario Management, you will see several scenarios that power the clinical trials matching from Project Health Insights that were automatically ingested by the blueprint into your Azure Health Bot instance. To engage with the matching experience, start a chat conversation by clicking on the chat icon in the blue task bar on top to the right, and ask for clinical trials. For example, you can ask the chatbot: ‘find clinical trials in Arizona for a 24-year-old female with lung cancer’. The chatbot will use Azure AI Language Understanding that was ingested in your LU resource by the blueprint to recognize the pre-built intent in the words \"find clinical trials\", and extract the relevant clinical trial characteristics to look for from your request. The data provided in this case includes patient age (24), patient sex (female), patient medical condition (lung cancer), and preferred trial location (Arizona). \n \n \n \n Figure 2 Example chatbot conversation for clinical trial matching \n \n To improve the patient qualification process, additional details can be captured by asking the patient for further information. Your chatbot does that by generating a question and waiting for user input. After receiving the needed response, the Azure Health Bot sends a request to the Trial Matcher model, receives a trials list, and uses the response to start asking additional questions about the patient's condition to enable the Trial Matcher model to perform a more accurate qualification and narrow down the list of clinical trials the patient could be eligible for. \n \n After a few iterations of questions and additional information provided by the user, you’ll be provided with a list of clinical trials that are relevant according to the clinical data and preferences that were provided. The model also provides a list of ineligible trials with reasons (one or more) for ineligibility so that the patient may assess this information independently. \n \n Important \n Trial Matcher is a capability provided “AS IS” and “WITH ALL FAULTS.” Trial Matcher isn't intended or made available for use as a medical device, clinical support, diagnostic tool, or other technology intended to be used in the diagnosis, cure, mitigation, treatment, or prevention of disease or other conditions, and no license or right is granted by Microsoft to use this capability for such purposes. This capability isn't designed or intended to be implemented or deployed as a substitute for professional medical advice or healthcare opinion, diagnosis, treatment, or the clinical judgment of a healthcare professional, and should not be used as such. The customer is solely responsible for any use of Trial Matcher. \n \n Get started today. \n \n Follow the guidelines in the Readme file to deploy the Azure Health Bot with Trial Matcher integration and then to start a chat conversation using the bot to experience patient centric workflow microsoft/ClinicalTrialsBlueprint: Setup the resources for provisioning Clinical Trials search (github.com) \n Learn more about Project Health Insights and Trial Matcher \n Project Health Insights | Microsoft Learn Trial Matcher documentation - Project Health Insights | Microsoft Learn \n \n [1] Percent of trials with enrollment year preceding registration year (1999-2022) (who.int) ","body@stripHtml({\"removeProcessingText\":true,\"removeSpoilerMarkup\":true,\"removeTocMarkup\":true,\"truncateLength\":-1})@stringLength":"5824","kudosSumWeight":3,"repliesCount":0,"readOnly":false,"images":{"__typename":"AssociatedImageConnection","edges":[{"__typename":"AssociatedImageEdge","cursor":"MjUuMXwyLjF8b3wyNXxfTlZffDE","node":{"__ref":"AssociatedImage:{\"url\":\"https://techcommunity.microsoft.com/t5/s/gxcuf89792/images/bS0zODkwNzk3LTQ5NDkyOWkzRUI4NTM5ODA4RjU3NUNF?revision=1\"}"}},{"__typename":"AssociatedImageEdge","cursor":"MjUuMXwyLjF8b3wyNXxfTlZffDI","node":{"__ref":"AssociatedImage:{\"url\":\"https://techcommunity.microsoft.com/t5/s/gxcuf89792/images/bS0zODkwNzk3LTQ5NDkzMGlGMjVERERGREZDQjZFNTlC?revision=1\"}"}},{"__typename":"AssociatedImageEdge","cursor":"MjUuMXwyLjF8b3wyNXxfTlZffDM","node":{"__ref":"AssociatedImage:{\"url\":\"https://techcommunity.microsoft.com/t5/s/gxcuf89792/images/bS0zODkwNzk3LTQ5NDkzMWlFNEIzMzIxRTI0MENBNkI4?revision=1\"}"}}],"totalCount":3,"pageInfo":{"__typename":"PageInfo","hasNextPage":false,"endCursor":null,"hasPreviousPage":false,"startCursor":null}},"videos":{"__typename":"VideoConnection","edges":[],"totalCount":0,"pageInfo":{"__typename":"PageInfo","hasNextPage":false,"endCursor":null,"hasPreviousPage":false,"startCursor":null}},"coverImage":null,"coverImageProperties":{"__typename":"CoverImageProperties","style":"STANDARD","titlePosition":"BOTTOM","altText":""}},"Conversation:conversation:3711366":{"__typename":"Conversation","id":"conversation:3711366","topic":{"__typename":"BlogTopicMessage","uid":3711366},"lastPostingActivityTime":"2023-04-17T10:23:33.859-07:00","solved":false},"User:user:1556564":{"__typename":"User","uid":1556564,"login":"manoj1116","registrationData":{"__typename":"RegistrationData","status":null},"deleted":false,"avatar":{"__typename":"UserAvatar","url":"https://techcommunity.microsoft.com/t5/s/gxcuf89792/images/dS0xNTU2NTY0LTQzMTE4OWlCQjJERUI2QTVEOTMwMTM5"},"id":"user:1556564"},"AssociatedImage:{\"url\":\"https://techcommunity.microsoft.com/t5/s/gxcuf89792/images/bS0zNzExMzY2LTQzMTUyM2kxN0JDNUU0MzU4MjZEQkMz?revision=8\"}":{"__typename":"AssociatedImage","url":"https://techcommunity.microsoft.com/t5/s/gxcuf89792/images/bS0zNzExMzY2LTQzMTUyM2kxN0JDNUU0MzU4MjZEQkMz?revision=8","title":"cover page.jpg","associationType":"TEASER","width":1585,"height":887,"altText":null},"AssociatedImage:{\"url\":\"https://techcommunity.microsoft.com/t5/s/gxcuf89792/images/bS0zNzExMzY2LTQzMTIwMWlEQjcxOTNDNDg3MzJBQUEw?revision=8\"}":{"__typename":"AssociatedImage","url":"https://techcommunity.microsoft.com/t5/s/gxcuf89792/images/bS0zNzExMzY2LTQzMTIwMWlEQjcxOTNDNDg3MzJBQUEw?revision=8","title":"Blog-architecture-png.png","associationType":"BODY","width":1587,"height":621,"altText":null},"BlogTopicMessage:message:3711366":{"__typename":"BlogTopicMessage","subject":"Genomics workflows on secure lockdown environment using Cromwell on AKS","conversation":{"__ref":"Conversation:conversation:3711366"},"id":"message:3711366","revisionNum":8,"uid":3711366,"depth":0,"board":{"__ref":"Blog:board:HealthcareAndLifeSciencesBlog"},"author":{"__ref":"User:user:1556564"},"teaser@stripHtml({\"removeProcessingText\":true,\"truncateLength\":-1})":" \n Healthcare organization's heightened security, privacy, and compliance requirements (HIPAA, FEDRAMP) dictate the way genomics infrastructure is set up to provide end-to-end security for the environment. Cromwell on Azure using AKS is one such pattern. \n \n We worked with one such large provider in the US that does not take security lightly. They have a tightly controlled secure Azure environment, and every deployment must pass through rigorous security and infosec reviews. As part of their partnership with Microsoft, they are in the process of migrating all their genomic workflows and solutions from on-prem and competing cloud infrastructure to Microsoft Azure in partnership with Microsoft Industry solutions healthcare service line and Microsoft Health Futures. \n \n Both parties worked on one such deployment methodology for AKS-enabled Cromwell on Azure to run one of their key genomics workflows – the TruSight Oncology 500 assay (TSO500). ","introduction":"","metrics":{"__typename":"MessageMetrics","views":3066},"postTime":"2023-01-10T17:55:52.500-08:00","lastPublishTime":"2023-04-17T10:23:33.859-07:00","body@stripHtml({\"removeProcessingText\":true,\"removeSpoilerMarkup\":true,\"removeTocMarkup\":true,\"truncateLength\":-1})":" Healthcare organizations now have some of the strictest controls, network security and infosec requirements while running workloads in the cloud. When dealing with healthcare data, there are heightened security, privacy, and compliance requirements (HIPAA, FEDRAMP) that the organization’s infosec team impose that any of their cloud-based solutions will have to meet. These requirements dictate the way genomics infrastructure is set up to provide end-to-end security for the environment. \n \n We worked with one such large provider in the US that does not take security lightly. They have a tightly controlled secure Azure environment, and every deployment must pass through rigorous security and infosec reviews. As part of their partnership with Microsoft, they are in the process of migrating all their genomic workflows and solutions from on-prem and competing cloud infrastructure to Microsoft Azure in partnership with Microsoft Industry solutions healthcare service line and Microsoft Health Futures. \n \n Both parties worked on one such deployment methodology for AKS-enabled Cromwell on Azure to run one of their key genomics workflows – the TruSight Oncology 500 assay (TSO500). TSO500 is a next-generation sequencing (NGS) assay from Illumina that enables in-house comprehensive genomic profiling of tumor samples. It supports identification of all relevant DNA and RNA variants implicated in various solid tumor types. Cromwell is a workflow management system for scientific workflows, orchestrating the computing tasks needed for genomics analysis. Originally developed by the Broad Institute, Cromwell is also used in the GATK Best Practices genome analysis pipeline. Cromwell supports running scripts at various scales, including your local machine, a local computing cluster, and on the cloud. \n \n Cromwell on Azure configures all Azure resources needed to run workflows through Cromwell on the Azure cloud and uses the GA4GH TES (Task execution service) backend for orchestrating the tasks that create a workflow. The installation sets up a VM host to run the Cromwell server and uses Azure Batch to spin up virtual machines that run each task in a workflow. Cromwell workflows can be written using either the WDL or the CWL scripting languages. \n \n To improve security posture and to meet our customer’s requirement of running all workloads on environment with PaaS (Platform as a service) services, we teamed up to deploy and test Cromwell on Azure running on customer's Azure Kubernetes Service (AKS) environment. \n The deployment is available as part of Cromwell on Azure release 3.2. Once deployed, Cromwell on Azure with AKS configures the following Azure resources: \n \n Azure Kubernetes Service – Runs Cromwell, TES, TriggerService container AKS pods. Blobfuse is used to mount the default storage account as a local file system available to the containers. Also created are an OS and data disk, network interface, public IP address, virtual network, and network security group. \n Batch account - The Azure Batch account is used by TES to spin up the virtual machines that run each task in a workflow. \n Storage account - The Azure Storage account is mounted to the containers using blobfuse, which enables Azure Block Blobs to be mounted as a local file system available to the containers. By default, it includes the following Blob containers - configuration, Cromwell-executions, Cromwell-workflow-logs, inputs, outputs, and workflows. \n Application Insights - This contains logs from TES and the Trigger Service to enable debugging. \n Cosmos DB - This database is used by TES and includes information and metadata about each TES task that is run as part of a workflow. \n \n To improve the security posture, the following were evaluated in deployment in customer’s Azure environment: \n \n Locking subnet that hosts batch pool node for any inbound traffic using NSG configuration – This will prevent unauthorized access to batch pool nodes. In future, this will be simplified and made more secure using the public preview feature for simplified compute node communication. Simplified compute node communication helps reduce security risks by removing the requirement to open ports for inbound communication from the internet. \n Azure batch pool startup task to download the Prisma docker image on each new batch pool node. This startup script will run the Prisma docker image and authenticate using the credentials in key vault. This image will be up and running prior to any other Cromwell task execution hence checking docker images for security vulnerabilities before execution. \n Additionally, private links were enabled to connect to storage accounts outside the virtual network that hosts Cromwell on Azure. \n \n This architecture will act as a key pattern for the customer’s other prominent genomics workflows running on Azure cloud platform. \n \n Microsoft’s Industry solutions healthcare service line, Microsoft Health Futures, 3Cloud and Customer’s IT teams worked together to deploy this solution on their Azure tenant. The deployment was successfully tested on several sample runs with 80+ DNA and RNA samples. This architecture allows for execution of TSO500 workflows in parallel for multiple samples at a time on Azure batch pool nodes, gaining time and cost efficiencies. Downstream to this workflow is to further analyze the processed genome files to be leveraged with their other genomics applications and dashboards. The biomarkers resulting from this analysis are used during virtual molecular tumor board. The data generated from this process is paired with oncology patient level characteristics structured using Microsoft OncoPhenotype services (currently also available as APIs in private preview) to provide patient-specific clinical trials recommendations to multiple end users including pathologists and oncologists within the molecular tumor board, clinical trials research nurses and coordinators, their internal next generation sequencing reports, and genomics researchers. \n \n If you are a customer needing more information, support, or guidance related to the content in this blog, we recommend you reach out to your Microsoft sales representative. 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