# Vessel > Vendor-neutral programs that build the capability to run molecular tumor boards, from liquid biopsy to treatment decision. Faculty from European cancer centres. Public Ghost content for AI and LLM tooling. This file includes a bounded export of public pages first, then recent public posts. Append `.md` to any post or page URL to get the content in Markdown (for example, `/example-post.md`). ## Pages ### Welcome to Vessel URL: https://www.vesseldna.com/signin/ Last updated: 2023-11-03T12:50:14.000Z _No content available._ ### Welcome to Vessel - Where Professionals meet to Accelerate Precision Oncology URL: https://www.vesseldna.com/signup/ Last updated: 2023-11-03T12:51:34.000Z Membership includes a seat in monthly live calls, and access to our immediately applicable content. _This page is for subscribers only._ ### Subscribe URL: https://www.vesseldna.com/subscribe/ Last updated: 2023-11-03T12:51:59.000Z _This page is for subscribers only._ ### Your North Star in the Transformation of Precision Oncology URL: https://www.vesseldna.com/membership/ Last updated: 2022-11-05T08:32:15.000Z [READY TO APPLY FOR MEMBERSHIP](https://www.vesseldna.com/vessel-application/) ### How the Vessel Membership works Once you have gone through the application process, Vessel membership offers a number of deep dive briefings and participation in our live calls and Q&A sessions. We'll also be offering ways to access our peer network primarily via our career programs, which we are currently establishing. ### Apply to Vessel Why the application instead of a simple sign up form? We're serious about moving the needle when it comes to implementing precision oncology approaches in the clinic now -- and not years down the road. That's why we're looking for serious members to join the platform. Ideally, you strive to be a member that contributes to this community and want to actively participate in conversation so that we can drive adoption of the latest technologies. This is why we kindly ask you to provide some details about yourself. It only takes 40 seconds or less to fill out these 4 questions! ### Vessel Programs We work with leading companies as well as leaders at companies and institutions, identifying patterns on how they create value, produce impact and implement novel solutions to improving precision oncology. Vessel programs are designed to teach you the skill of understanding and working with current and future molecular approaches - and maybe even more importantly - we'll provide you with the confidence and competence to introduce these approaches at your institutions. ## Membership Criteria Vessel is a community of geneticists, pathologists, oncologists, genome researchers/biologists, bioinformaticians, nurses, students and other health care professionals. Together, we strive to enable state-of-the-art precision oncology approaches throughout the entire patient journey, driving the adoption of precision medicine by hospitals, payers and providers. ### What we look for in potential members - Precision medicine-related role - Relevant company or industry - Ambitious individuals willing to contribute and go the extra mile ### Have any questions? E-mail us at support@vessel.com or simply apply below [Apply For Membership](https://www.vesseldna.com/vessel-application/) ### Account URL: https://www.vesseldna.com/account/ Last updated: 2023-11-03T12:52:14.000Z _This page is for subscribers only._ ### SME URL: https://www.vesseldna.com/sme/ Last updated: 2024-06-12T11:51:19.000Z _No content available._ ### Join Vessel Now URL: https://www.vesseldna.com/join-vessel-now-sign/ Last updated: 2023-11-03T12:52:45.000Z _No content available._ ### Alpha Version - NGS Dissertation Seminar URL: https://www.vesseldna.com/alpha-version/ Last updated: 2023-11-03T12:53:23.000Z _This page is for subscribers only._ ### You're Offline. URL: https://www.vesseldna.com/offline/ Last updated: 2023-11-03T12:54:28.000Z It looks like you're currently offline. Try to get your connection back up ### Where Professionals Meet to Accelerate Precision Oncology URL: https://www.vesseldna.com/home/ Last updated: 2023-11-13T05:27:26.000Z ### What You Get as a Vessel Member Vessel Membership includes guidance and community. Monthly calls, demos and content releases. But it's not just about the resources. It's about the people. By becoming a Vessel member, you'll be joining a community of ambitious professionals who are all striving for the same thing: to make a real difference in the world of precision oncology. You'll have the chance to connect with and learn from your peers, share best practices, and work together to drive the adoption of precision medicine. ### Guidance and Community With Vessel, you'll get access to all the guidance and community resources you need to take your practice to the next level. From ongoing walk-throughs and demos to live calls and case studies, we've got you covered. - **Access immediatelyapplicable content** - **Focus on bridging the gap of precision medicine and clinical application** - **Meet ambitious peers and network** ### Ongoing walk throughs, demos and summaries to accelerate precision oncology practice - **Ongoing virtual and in depth walk-throughs of workflows, analyses and diverse products** - **Live calls, demos and case studies** - **Accelerate precision oncology practices** Apply to Vessel today! [Apply For Membership](https://www.vesseldna.com/vessel-application/) As a member of Vessel, you will have access to guidance and community resources. These include access to immediately applicable content, focus on bridging the gap between precision medicine and clinical application, and the opportunity to meet and network with ambitious peers. The platform also offers ongoing walk-throughs, demos, and summaries to help accelerate precision oncology practices, as well as live calls, demos, and case studies. These resources are intended to help members accelerate their precision oncology practices and stay up-to-date on the latest developments in the field. ### The only clinician's handbook for ctDNA you'll ever need URL: https://www.vesseldna.com/a-clinicians-handbook-for-ctdna/ Last updated: 2025-03-02T08:11:28.000Z - **Understand which panel makes sense for your patient.** - **How is ctDNA detected from plasma?** - **Understand what tumor fraction means.** - **Learn how to interpret copy number data.** - **Get a grasp on variant interpretation.** - **Understand the latest bioinformatics behind future plasma DNA applications.** Hi there, we're the authors of the publication below that you probably just read. As stated, we believe that especially young oncologists' careers will benefit greatly from learning about the fundamentals of genomics and liquid biopsy profiling early on. So without much further ado, let's get right to it. [A clinician’s handbook for using ctDNA throughout the patient journey - Molecular CancerBackground The promise of precision cancer medicine presently centers around the genomic sequence of a patient’s tumor being translated into timely, actionable information to inform clinical care. The analysis of cell-free DNA from liquid biopsy, which contains circulating tumor DNA (ctDNA) in patie…![](https://molecular-cancer.biomedcentral.com/static/img/favicons/bmc/apple-touch-icon-582ef1d0f5.png)BioMed CentralSamantha O. Hasenleithner![](https://media.springernature.com/w200/springer-static/cover/journal/12943.jpg)](https://molecular-cancer.biomedcentral.com/articles/10.1186/s12943-022-01551-7?ref=vesseldna.com) Whether ordering ctDNA testing from your local lab or an industry provider, it is important to know the steps taken before trying to implement the genomic findings into clinical care. 💡 Which panel makes sense for my patient? 💡 Can I collect the sample while my patient is undergoing therapy? 💡 How is ctDNA detected from plasma? 💡 How should I interpret copy number data? 💡 What does low tumor fraction mean? 💡 The report shows an actionable mutation, but the variant allele frequency is very low. What does this mean? Vessel offers [career programs](https://www.vesseldna.com/membership/) and projects through wet and dry lab processes, as well as an interpretation tutorial from real-world cases studies using ctDNA profiling (Hasenleithner & Speicher, *Molecular Cancer* 2022). ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/03/image-8.png) ### Real-world case studies We're going to work on two use cases for ctDNA analysis throughout the patient journey: (1) **Identification of actionable targets from ctDNA in patients with advanced cancer** ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/03/image-12.png) and (2) **Disease monitoring** ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/03/image-13.png) Before we dive into the real-world cases, let's take a "meta" look at the procedures involved in the interpretation of cfDNA-based data. ### From whole blood to clinical report (a high-level overview) There are a number of pre-analytical sampling handling factors that influence downstream analysis of cell-free DNA (cfDNA). It helps to be aware of these factors when working with cfDNA testing, as they may significantly affect the integrity, purity and yield of a sample. ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/03/image-14.png) Previous works have detailed the influence of pre-analytical factors, such as the choice of blood collection tubes, which may have varying stabilization reagents, sample storage conditions and duration, centrifugation steps for plasma separation, cfDNA purification, quantification and characterization, as well as library preparation protocols. ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/03/image-15.png) Example literature evaluating the influence of pre-analytical factors on cfDNA analyses In this regard, several collaborative efforts are working to evaluate these findings, devise the criteria for standardizing liquid biopsy workflows, put these into context for providers and end users of cfDNA assays, and to bridge the gap between academia and industry to enable the translation of research findings into clinical implementation: | Initiative | Source | | ----------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | CANCER-ID | [https://www.cancer-id.eu/](https://www.cancer-id.eu/?ref=vesseldna.com) (project completed) | | The European Liquid Biopsy Society (ELBS) | [https://www.uke.de/english/departments-institutes/institutes/tumor-biology/european-liquid-biopsy-society-elbs/index.html](https://www.uke.de/english/departments-institutes/institutes/tumor-biology/european-liquid-biopsy-society-elbs/index.html?ref=vesseldna.com) | | BLOODPAC | [https://www.bloodpac.org/](https://www.bloodpac.org/?ref=vesseldna.com) | Once cfDNA has been successfully isolated and quantified, a library preparation and subsequent sequencing strategy must be selected. The *strategy will vary depending on the type of ctDNA signal you are trying to measure* and, of course, so too will the price of sequencing. ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/03/image-16.png) The clinical question/goal dictates the appropriate library preparation and sequencing strategy. For example, are you only interested in detecting somatic copy number alterations (SCNA)? If that is the case, an untargeted, shallow whole-genome sequencing (sWGS) approach would suffice. Do you have *a priori* knowledge of the patient's tumor and would like to selectively track these mutations through liquid biopsy monitoring? This would indicate the use of a targeted, personalized approach. Are you looking to identify regions of open chromatin to infer tissue-of-origin of cfDNA fragments? For this purpose, a whole-genome sequencing (WGS) approach at higher coverage would be the most suitable. However, it is important to be aware that not every alteration in a patient's sample will be detected by every approach and assay sensitivity is variable. ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/03/image-17.png) After sequencing has been performed, imaging data from the sequencer are converted into base calls, which are then converted into sample-specific raw data. The sequencing reads and quality scores are stored in the universal FASTQ format. ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/03/image-18.png) What does a FASTQ data file look like when you open it? ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/03/image-19.png) The FASTQ format has 4 lines of data per sequence: ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/03/image-20.png) Data stored in FASTQ format The reads stored in the FASTQ file do not contain any positional information. How can we predict the locus from which the read originates? This is done through a step called read alignment, or mapping. Essentially, the reads are mapped to a reference genome using an alignment software. ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/03/image-21.png) Genomic variance is derived through the comparison with the reference genome. Harvesting the ctDNA signal from the alignment data varies dramatically, depending on the sequencing strategy and clinical question, and is conducted with various computational pipelines. For example, the process of mutation detection (SNVs + InDels) is called variant calling. This differs from e.g. copy number or structural variant calling, which requires a different computational strategy. Similarly, fragmentomics-based approaches require specially tailored algorithms depending on the feature being harvested. This entire workflow of NGS data analysis, i.e. bioinformatics, is one of the most decisive aspects of ctDNA testing, yet it represents the step most lacking in transparency for clinicians. The "black box" of bioinformatics serves as the backbone for much uncertainty when it comes to understanding and trusting data generated by next-generation sequencing. ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/03/image-24.png) Interpretation of data from liquid biopsy is potentially the most complex step in the ctDNA testing workflow, especially as it requires expertise about bioinformatics-related limitations as well as cancer knowledgebases. ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/03/image-26.png) For example, the following questions must be answered when interpreting copy number or mutation data: ❔ Which alterations are pathogenic? Which are unknown? ❔ Is this a potential germline variant? Should genetic counseling be recommended? ❔ How do these genomic alterations relate to the tumor type at hand? What is the frequency of this alteration in which types of cancer? ❔ Are any of these alterations known resistance markers? ❔ Did I not detect any alterations in my sample because of a limit of detection issue? ❔ Does the variant allele frequency reflect the tumor content of the plasma sample? ❔ Do any of these alterations represent actionable targets? What are the drugs that match to these targets? Answering these questions requires a careful, comprehensive interpretation process. Molecular geneticists and genome scientists have the experience to mine the various publicly available variant databases to derive conclusions about potential germline variants, pathogenicity, and clinical actionability. Ultimately, the goal is to construct a report for oncologists with only the most clinically relevant patient-specific information displayed clearly and concisely such that a clinician may quickly and accurately differentiate between actionable targets, resistance markers, and alterations with little or no evidence of clinical relevance. ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/03/image-25.png) Combining variant annotation and interpretation with treatment decision-making within the context of a specific tumor type is a complex process. In this regard, several commercial providers have begun to launch a variety of clinical decision support tools that convert the molecular information obtained via NGS into a clinical-grade report describing treatment options and clinical trials matched to the patient's genomic profile. In the future, once standardized, such solutions may streamline genomic interpretation workflows and provide labs with the opportunity to scale their services, as they eliminate the manual labor associated with deriving clinical evidence from cancer knowledgebases, drug regulatory agencies, published literature, and clinical trial registries. *Example clinical decision support tools:* ℹ️ NAVIFY Mutation Profiler ℹ️ PierianDx ℹ️ Alissa Interpret ℹ️ QCI Interpret ℹ️ CureMatch ℹ️ OncoKDM Relevant literature evaluating such tertiary NGS analysis tools and oncogenomic reporting: | Literature | | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Katsoulakis E, Duffy JE, Hintze B, Spector NL, Kelley MJ. Comparison of Annotation Services for Next-Generation Sequencing in a Large-Scale Precision Oncology Program. JCO Precis Oncol. 2020;4\. [https://doi.org/10.1200/PO.19.00118](https://doi.org/10.1200/PO.19.00118?ref=vesseldna.com). eCollection 2020. | | Perakis SO, Weber S, Zhou Q, Graf R, Hojas S, Riedl JM, et al. Comparison of three commercial decision support platforms for matching of next-generation sequencing results with therapies in patients with cancer. ESMO Open. 2020;5(5):e000872–2020–000872. | | Yaung SJ, Krishna S, Xi L, Ju C, Palma JF, Schmid M. Assessment of a Highly Curated Somatic Oncology Database to Aid in the Interpretation of Clinically Important Variants in Next-Generation Sequencing Results. J Mol Diagn. 2020 Nov;22(11):1356-1366\. doi: 10.1016/j.jmoldx.2020.08.004\. Epub 2020 Sep 19\. PMID: 32961319. | | Boichard A, Richard SB, Kurzrock R. The Crossroads of Precision Medicine and Therapeutic Decision-Making: Use of an Analytical Computational Platform to Predict Response to Cancer Treatments. Cancers (Basel). 2020 Jan 9;12(1):166\. doi: 10.3390/cancers12010166\. PMID: 31936627; PMCID: PMC7017109. | | Yaung SJ, Pek A. From Information Overload to Actionable Insights: Digital Solutions for Interpreting Cancer Variants from Genomic Testing. Journal of Molecular Pathology. 2021; 2(4):312-318\. [https://doi.org/10.3390/jmp2040027](https://doi.org/10.3390/jmp2040027?ref=vesseldna.com) | | Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, et al. A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. Nat Genet. 2020;52(4):448–57. | | Reisle, C., Williamson, L.M., Pleasance, E. et al. A platform for oncogenomic reporting and interpretation. Nat Commun13, 756 (2022). [https://doi.org/10.1038/s41467-022-28348-y](https://doi.org/10.1038/s41467-022-28348-y?ref=vesseldna.com) | However, it is impossible to remove the need for expert human insight for the interpretation of molecular profiling results within the context of the individual patient. As the frontline leaders of precision cancer medicine, oncologists must ultimately make the final decision based on all available evidence as to which treatment plan best suits his/her patient. In this regard, the concept of the molecular tumor board (MTB) has demonstrated its importance in standardizing the processing of patient history, clinical data, and NGS profiling results for treatment decision-making. With an MTB infrastructure, clinics can harvest the diverse expertise from oncologists, pathologists, geneticists, variant scientists, bioinformaticians and clinical trial coordinators to ensure a reproducible yet personalized analysis workflow for the patient in question, not to mention devise innovative research approaches. ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/03/image-27.png) --- This was just a taste. Like what you see? Subscribe for deeper dives with programs tailored to the following topics: - Biology of cell-free DNA (release, clearance, half-life, detection levels across tumor entities, etc.) - Pre-analytics (choosing a blood collection tube, centrifugation, storage, extraction, quantification) - Library preparation approaches - Sequencing approaches - Intro to bioinformatics basics - Analysis approaches to detection of: tumor fraction, fragment size, SCNAs, mutations, epigenetic alterations and open chromatin - Fragmentomics applications - Interpretation of data from liquid biopsy - Clinical decision support tools - Breakdown of more individual case studies Start now to make liquid biopsy a routine tool in your precision medicine portfolio. Click below to subscribe to our content. ## Welcome to Vessel ### where professionals meet to accelerate precision oncology [Ready to join](https://www.vesseldna.com/vessel-application/) We are a precision oncology community whose goal it is to make state-of-the-art personalized care available to the majority of patients. It's our aim to educate patients and enable clinicians to implement state-of-the-art precision oncology approaches throughout the entire patient journey, driving the adoption of precision medicine by hospitals, payers and providers. ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/03/vesselblog.png) Strengthen your understanding of the molecular profiling data generated by the latest next-generation sequencing technology that informs your patient care right here at [Vessel](https://www.vesseldna.com/vessel-application/). ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/03/image.png) ### Vessel Application URL: https://www.vesseldna.com/vessel-application/ Last updated: 2023-11-03T12:54:45.000Z ## Join the community that accelerates precision oncology Precision oncology asks for polymath proficiency across multiple knowledge domains. We focus on bridging the gap of precision medicine and clinical application, enabling clinicians to fulfil on the promise of early precision medicine. > "Vessel is the “connective tissue" between clinicians, industry, patients and their families." ### Application received URL: https://www.vesseldna.com/thank-you-for-your-application/ Last updated: 2024-05-20T18:43:00.000Z ## Thank you for your application We will be reviewing your application as soon as possible and will get back to you via e-mail. ## What to expect next After review of your application, you'll get an e-mail from us with your account credentials and further instructions [Back to the Vessel Blog](https://www.vesseldna.com/blog/) ### Terms of Service URL: https://www.vesseldna.com/terms/ Last updated: 2026-06-12T15:21:35.000Z *Last updated: 12 June 2026* ## 1\. Provider Vessel FlexCo Kranewittergasse 20, 8042 Graz, Austria Company Register Number: 629078 s Commercial Register Court: Commercial Court of Graz VAT ID: ATU80912158 Email: [office@vesseldna.com](mailto:office@vesseldna.com) ## 2\. Scope These Terms of Service govern your use of the website vesseldna.com (the "Website"), including the program configurator tool, blog content, and contact forms. By accessing the Website, you agree to these terms. ## 3\. Nature of Services Vessel provides precision oncology education and implementation programs for healthcare institutions and their industry partners. **Important distinctions:** - The Website provides general information about Vessel's services. It does not constitute medical advice, clinical guidance, or diagnostic recommendations. - Program concepts generated by the configurator tool are **non-binding illustrations** designed to give prospective clients a preliminary view of what a program could include. They do not constitute offers, contracts, or commitments by either party. - Final program scope, curriculum, faculty, and investment are determined through a formal program assessment and are subject to a separate written agreement. ## 4\. Program Configurator The program configurator allows users to explore program options and generate non-binding program concepts. - **No binding offer**: Generated concepts are informational only. A binding agreement requires execution of a separate written contract. - **Pricing ranges**: Where investment ranges are shown, they are indicative and based on general parameters. Actual pricing is determined during program scoping. - **Shareable links**: Program concepts can be shared via URL. These URLs contain the information you entered (name, organization, email, configuration). By sharing a link, you acknowledge that anyone with the URL can view this information. - **Data handling**: Information entered in the configurator is processed in your browser. Vessel does not store configurator submissions on its servers. See our [Privacy Policy](https://www.vesseldna.com/privacy/) for details. ## 5\. Educational Purpose All content on this Website, including program descriptions, blog posts, and generated program concepts, is provided for **educational and informational purposes only**. - Content does not constitute medical advice or clinical recommendations - Program curricula are designed to build institutional capabilities, not to promote specific pharmaceutical products or therapies - Vessel programs are developed independently by clinical faculty without promotional influence from pharmaceutical sponsors ## 6\. Intellectual Property All content on the Website, including text, graphics, logos, designs, and software, is the intellectual property of Vessel FlexCo and is protected by applicable copyright and trademark laws. - You may not reproduce, distribute, or publicly display Website content without prior written consent - Program concepts generated by the configurator may be shared internally within your organization for evaluation purposes - The Vessel name, logo, and brand elements may not be used without authorization ## 7\. Testimonials Where testimonials are displayed on the Website or in generated program concepts, they are from actual program participants. They reflect individual experiences and may not be representative of every participant's outcomes. Institution names may be generalized for confidentiality. All testimonials are shared with documented consent. ## 8\. Third-Party Services The Website uses third-party services including Typeform (contact forms), PostHog (analytics), Ghost (content management), and CookieYes (cookie consent). Your use of these services is subject to their respective terms and privacy policies. ## 9\. Limitation of Liability To the fullest extent permitted by Austrian law: - Vessel FlexCo is not liable for indirect, incidental, or consequential damages arising from the use of the Website - Information on the Website is provided "as is" without warranties of any kind regarding accuracy, completeness, or fitness for a particular purpose - Vessel FlexCo's total liability is limited to direct damages and shall not exceed the amount paid by you to Vessel, if any The above limitations do not apply to damages arising from injury to life, body, or health, or to damages caused intentionally or through gross negligence, or to any other liability that cannot be excluded or limited under mandatory Austrian law. ## 10\. Applicable Law and Jurisdiction These Terms are governed by the laws of the Republic of Austria, excluding its conflict-of-law rules and the UN Convention on Contracts for the International Sale of Goods. Where the user is an entrepreneur within the meaning of the Austrian Commercial Code (UGB), a legal entity under public law, or has no general place of jurisdiction in Austria, any disputes arising from or in connection with these Terms shall be subject to the exclusive jurisdiction of the competent courts in Graz, Austria. Mandatory consumer protection provisions, including §14 KSchG, remain unaffected. ## 11\. Confidentiality Program concepts, pricing information, and proposal content generated through the configurator or provided in formal proposals are intended exclusively for evaluation purposes within the recipient's organization and should not be disclosed to third parties without prior written consent from Vessel FlexCo. Binding confidentiality obligations are established in the separate written agreements governing each program. ## 12\. Severability Should any provision of these Terms be or become invalid or unenforceable in whole or in part, the validity of the remaining provisions shall not be affected. The invalid or unenforceable provision shall be replaced by a valid provision that most closely reflects its economic purpose. ## 13\. Changes to These Terms We reserve the right to modify these Terms at any time. Changes take effect upon publication on the Website. Continued use of the Website after changes constitutes acceptance of the revised Terms. ### Welcome to Vessel URL: https://www.vesseldna.com/welcome-to-vessel/ Last updated: 2024-11-13T11:59:25.000Z _This page is for subscribers only._ ### The Role of the Pathologist in NGS URL: https://www.vesseldna.com/the-role-of-the-pathologist-in-ngs/ Last updated: 2022-09-04T09:45:33.000Z ## Let's move beyond just tissue provision... to a more active role in your molecular profiling workflows. We are looking to move you beyond just tissue provision to a more active role in your molecular profiling workflows. Working with next-generation sequencing can be a bit daunting and we are here to make it easy to get started. In a series of 4 calls, we’re going to take you through the end-to-end workflow of NGS - covering every step in more detail than we could possibly do in a public talk. We’ll do one call per week for about 4 weeks. Before every call, we’ll take upfront questions and will answer them on the calls or shortly after. We’ll be sure not to miss anything! - In week 1 we will introduce QC of tissue for NGS - Week 2 covers different library preparation approaches and sequencing strategies - In week 3 we’re getting into basic bioinformatics and data analysis - Finally in week 4, we will close out with some basics in data interpretation If this sounds like something you’d be interested in, you can sign up below. We’ll ask for your name and e-mail and will then follow up with you personally with the next steps. --- ### Bringing CGP to Greek Pathology URL: https://www.vesseldna.com/bringing-cgp-to-greek-pathology/ Last updated: 2023-03-31T18:33:21.000Z _This page is for subscribers only._ ### Tag URL: https://www.vesseldna.com/tag/ Last updated: 2022-09-05T08:58:15.000Z _This page is for subscribers only._ ### Vessel Slack Community Guidelines URL: https://www.vesseldna.com/vessel-slack-community/ Last updated: 2023-11-03T12:55:46.000Z _This page is for subscribers only._ ### Tags URL: https://www.vesseldna.com/tags/ Last updated: 2022-09-04T11:32:12.000Z _This page is for subscribers only._ ## Posts ### Navigating the clinical ctDNA testing landscape: Assays, applications & approvals throughout the cancer patient journey URL: https://www.vesseldna.com/navigating-the-clinical-ctdna-testing-landscape/ Last updated: 2024-02-04T15:07:59.000Z Are you new to ctDNA testing strategies? Fear not! With this walk-through, we will guide you through some high-level concepts to help orient yourself in the current clinical landscape. _This post is for subscribers only._ ### VB04 - Let's interpret some variants (1) URL: https://www.vesseldna.com/vb04-variant-interpretation/ Last updated: 2023-10-23T12:05:25.000Z ## Brief synopsis In this briefing, we walk you through a step-by-step process of the resources you can access to assess variant pathogenicity and actionability, including what information to harvest and how to interpret it. Here, we use a gene amplification as an example and provide you with an exercise at the end to practice on your own. A follow-up tutorial and more examples will follow soon. ## VB04 recording ## See our past briefings [BriefingsOverview 💡Vessel Briefings are short sessions that are intended to not take too much time out of your busy schedule, but that still allow our community to interact on important topics. With this format, we will present case studies, do live Q&As and tackle problems that we all share![](https://www.vesseldna.com/assets/icon-192x192.png?v=0fad5241ee)VesselDieter Hasenleithner![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/11/Vessel-2.png)](https://www.vesseldna.com/briefings/) ### Understanding and estimating tumor fraction from plasma cell-free DNA URL: https://www.vesseldna.com/understanding-and-estimating-tumor-fraction-from-plasma-cell-free-dna/ Last updated: 2023-09-06T10:13:50.000Z In this brief tutorial, we will describe the basics of estimation and analysis of tumor fraction from plasma. ### Brief background Liquid biopsy is a non-invasive and simple alternative to surgical biopsies that helps clinicians discover a wide range of information about a tumor through a simple blood sample. Liquid biopsies rely on the detection of circulating tumor cells (CTCs), cell-free DNA (cfDNA), which in patients with cancer includes circulating tumor DNA (ctDNA), RNA, proteins, lipids, and metabolites present in biofluids of patients. ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2023/04/image.png) A simple blood draw, a wealth of information In principle, bodily fluids other than plasma, such as cerebrospinal fluid, urine, saliva, stool, pleural fluid, and ascites, can also be analyzed, but here we are only going to focus on blood and only on cfDNA, as cfDNA profiling is increasingly being used to guide cancer care in the clinic. ### I am not working with cfDNA. Why should I care about cfDNA approaches? The increasing prevalence of cancer, rising preference for non-invasive procedures, various advantages of liquid biopsy over standard tissue biopsy, favorable government initiatives, and growing public and private interest are factors that are fueling the growth of the cfDNA field. Even though you might not be actively working with liquid biopsy right now at your institution, this approach is going to be central to future precision oncology approaches. Whether you are a pathologist, oncologist, or molecular biologist involved in molecular profiling workflows, getting to know the fundamentals of liquid biopsy will help you navigate the growing field of personalized cancer care and how to integrate these analyses into your existing workflows. Particularly as an oncologist, harnessing liquid biopsy technology will provide you with another tool in your arsenal to help treat patients and guide clinical-decision making, particularly when tissue is inadequate or unavailable altogether. There are numerous established and ongoing efforts to incorporate cfDNA testing throughout the cancer patient journey, owing to many promising emerging NGS-based technologies. ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2023/04/image-1.png) In the future, cell-free DNA testing may be applied to anywhere throughout the patient journey. ### Liquid biopsy in a nutshell *Taken from Hasenleithner & Speicher, Molecular Cancer 2022\. Please see original text for references.* In addition to their eased access, liquid biopsies may capture the tumoral spatial heterogeneity not observed from traditional single-site biopsy genotyping, as they may enable the detection of DNA shed from both clonal and subclonal sites within multiple metastatic lesions. An array of studies has established the general concordance between aberrations detected in ctDNA and tumor tissue, ranging approximately between 70 and 90%. Some discordance between mutations identified in primary tumor tissue and ctDNA is to be expected, which can be attributed to tumor heterogeneity or evolution, sampling bias, time lapses between sample acquisition, differences in sensitivity of the sequencing assays applied, or even different sequencing platforms. However, with suitable and validated workflows, the potential applications of ctDNA are far-reaching, including diagnosing cancers earlier than traditional imaging, customizing treatments detected via genotyping, associating DNA levels with response to treatment, identifying mechanisms of resistance to therapies and measuring minimal residual disease after treatment. As new evidence of analytical validity, clinical validity as well as utility continues to accumulate for these applications, strategies and requirements for the integration of ctDNA analysis workflows into clinical oncology programs are taking form. ### Some basics about cfDNA and ctDNA from the plasma of patients with cancer In patients with cancer, the cfDNA in plasma is derived from both tumor and normal cells. The majority of DNA in the bloodstream originates from “healthy” white blood cells, with lower amounts of apoptotic or necrotic cancer cells releasing their ctDNA into the circulation. Other DNA populations originate from cells of the tumor microenvironment as well as other non-cancer cells, such as endothelial and immune cells from various parts of the body. For a deeper dive into what is currently known about the biology and release of cfDNA, check out this comprehensive work ([PMID: 32359482](https://pubmed.ncbi.nlm.nih.gov/32359482/?ref=vesseldna.com)). However, what you really need to know is that if you analyze DNA taken from a liquid biopsy, the tumor signal that you want to detect (ctDNA) is masked by the signal from the DNA of other healthy cells. Furthermore, the amount of ctDNA that lands in the bloodstream is influenced by many factors. For example, smaller, earlier-stage tumors shed less DNA into the circulation and the amount of shedding differs across tumor types. This means that tumor-derived DNA is only a small fraction of the DNA harvested from the bloodstream, which of course has implications for which assay you choose to employ downstream. For more details about this, see [Hasenleithner & Speicher 2022](https://molecular-cancer.biomedcentral.com/articles/10.1186/s12943-022-01551-7?ref=vesseldna.com). ### The factors that influence tumor fraction in plasma Tumor fraction from plasma, which is defined as the fractional proportion of tumor DNA relative to total cfDNA, is dependent on multiple factors. These primarily include: Biological factors associated with tumor DNA shedding, such as: - tumor volume and tumor surface area - vascularization - tumor cell growth and death rates - mitotic and metabolic activity - cell morphology Clinical factors, such as: - tumor type (some tumors are “good” shedders \[e.g. CRC\], some are “poor” shedders \[e.g. RCC\]) - active tumor proliferation (more aggressive cancers tend to shed more DNA into the bloodstream) - disease stage (localized, i.e. early-stage vs. metastatic, i.e. late-stage) - overall tumor burden - current clinical response (progressive disease, stable disease, partial or complete response to treatment) - Patient-specific factors such as fasting status or physical activity prior to blood collection - Technical/pre-analytic factors such as blood collection tubes, transport, and sample processing However, it is very important to note here that, at present, not all factors influencing tumor fraction in plasma are currently known. It is very likely that additional factors that influence tumor content will be identified in the future. ### Tumor fraction from plasma is critical for understanding and interpreting your results You can probably begin to appreciate why negative results from liquid biopsy testing need to be interpreted with caution. Failure to detect a genomic alteration from plasma may simply be related to the low tumor fraction represented in plasma (although failure to detect mutations may also be a result/limitation of the selected assay, such as its breadth or sensitivity). Furthermore, if you have access to serial samples, monitoring the changes in ctDNA levels in conjunction with treatment may help you determine if the patient is responding to therapy or not. The tumor content of a sample is especially important when interpreting variant allele frequencies (VAFs) from an NGS report. For these reasons, determining the cfDNA tumor fraction has become an essential feature of cfDNA molecular profiling. Results that are not provided with the tumor fraction of that sample are limited and must be interpreted with caution. ### What are the current approaches to measuring tumor fraction from cfDNA? There are several methods described in the literature or those that are currently in commercial use to derive tumor fraction. Click on the name of the approach to direct you to the associated literature/source. Here, we will briefly list some examples, but will go into detail about two main approaches used both in research and the clinic. _This post is for subscribers only._ ### VB03 - Getting to know HRD testing URL: https://www.vesseldna.com/vb03-getting-to-know-hrd-testing/ Last updated: 2023-11-03T12:46:56.000Z ## Brief Synopsis For this Briefing, we asked Prof. Ellen Heitzer and Georgios Vlachos from the Institute of Human Genetics, Medical University of Graz to share their experience in working with homologous recombination deficiency (HRD) testing. Join us to familiarize yourself with the concepts and approaches central to performing this type of testing and why it is important for precision oncology. Hope to see you there! Join us on Wednesday, February 15th, 2023\. 5PM CET/6PM EET Please join the conversation and post your comments, thoughts and questions below leading up to the briefing. ## VB03 Recording _This post is for subscribers only._ ### VB02 - Concordance of genomic results between tissue and liquid testing URL: https://www.vesseldna.com/vb02-concordance-of-genomic-results-between-tissue-and-liquid-testing/ Last updated: 2024-06-03T16:49:14.000Z ### Brief synopsis The concordance between tissue and circulating tumor DNA testing is well-established. However, clinicians may be confronted with discrepant results, especially when performing tissue and liquid testing in parallel, and interpretation may not be so straightforward. In this Vessel Briefing, we will address some basic concepts and provide case studies to raise awareness about this factor that affects treatment decisions. Join us on January 12th, 2023\. 5PM CET/6PM EET Please join the conversation and post your comments, thoughts and questions below leading up the the briefing. _This post is for subscribers only._ ### VB01 - Two CGP case studies from liquid biopsy URL: https://www.vesseldna.com/vb01-vessel-briefing/ Last updated: 2024-02-04T14:56:47.000Z In our first Vessel Briefing on December 14th, we will go over a couple of liquid biopsy case studies where CGP was used to derive clinically relevant information. Some good questions were posted in our Slack community. We decided to move them over here into the discussion thread below, especially since they are related to the case studies we will present in the first Vessel Briefing. Please join the conversation and post your comments, thoughts and questions below leading up to the briefing. _This post is for subscribers only._ ### Fall 2022 dates - Bringing CGP to Greek pathology URL: https://www.vesseldna.com/fall-2022-focus-group/ Last updated: 2024-05-25T05:13:48.000Z _This post is for subscribers only._ ### Bringing CGP to Greek Pathology URL: https://www.vesseldna.com/bringing-cgp-to-greek-pathology-2/ Last updated: 2022-11-13T18:57:40.000Z _This post is for subscribers only._ ### How exactly does a Vessel program work? URL: https://www.vesseldna.com/how-exactly-does-such-a-program-work/ Last updated: 2024-02-04T12:25:23.000Z Get the low down of what to expect during the program and how to engage with your peers. _This post is for subscribers only._ ### Getting Started URL: https://www.vesseldna.com/getting-started/ Last updated: 2023-11-03T12:48:39.000Z _This post is for subscribers only._ ### ctDNA profiling case studies URL: https://www.vesseldna.com/ctdna-profiling/ Last updated: 2023-04-17T17:59:52.000Z ## Introduction In this condensed tutorial, we want to walk you through real-world cases as presented in our[ *Molecular Cancer* review](https://molecular-cancer.biomedcentral.com/articles/10.1186/s12943-022-01551-7?ref=vesseldna.com) (original Figure 3 from the review). The cases here represent scenarios in which the goal was to identify actionable targets from plasma. In the next set of case studies to be launched, we will walk through the other 3 cases (original Figure 4 in the review), which were scenarios in which we performed serial monitoring via shallow whole-genome sequencing (sWGS) alone to follow the patient’s clinical course. --- ### Getting started Let’s start with Case 1 in Figure 1 below. ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/06/image.png) Figure 1\. Use cases for ctDNA analysis throughout the cancer patient journey: identification of actionable targets in patients with advanced cancer. **A** Representation of 3 real-world cases of patients with confirmed progressive disease where liquid biopsy was justified to identify actionable targets. **B** Basic decision tree for this use case and the interpretation of detected alterations from liquid biopsy NGS data. The cases in (**A**) are mapped at the corresponding position that reflects the individual scenario. In the description of Case 1 below, we will describe an overview of the NGS workflow and our methods that apply to all cases presented here so that you have an idea as to how the data were generated. ## Case 1 **White and dark blue boxes**: Without going into too much detail about the patient’s history, we are just going to provide a brief summary. Here we have a case of a 65-year old female with a lung adenocarcinoma who is a current smoker with COPD. At the time of diagnosis, this patient had already presented with multiple metastases, including in the lung and spleen. As is routine, a tissue biopsy of her primary tumor was sent for genomic profiling and did not reveal any alterations in the canonical genes *ALK*, *ROS*, *EGFR* or *BRAF*. Immunohistochemistry revealed a positive staining for PD-L1 of 30%, for which the patient was later started on nivolumab. After several months of treatment, the tumor progressed and the patient subsequently underwent a series of treatment lines without tumor shrinkage. She was then provided with best supportive care. **Dark green box:** Due to further clinical progression, the patient was asked to undergo re-biopsy to obtain more recent tumor tissue for molecular profiling. The patient declined this option and was then offered molecular profiling via liquid biopsy, to which she agreed. In our experience, patients are very willing to donate blood, whereas re-biopsy tends to be met with less willingness. **Light green box:** Two vials of blood of approximately 10mL each were sent to us in PAXgene ccfDNA tubes for analysis. After DNA extraction, we employed our standard AVENIO ctDNA Expanded Panel (Roche), which contains 77 genes in the U.S. National Comprehensive Cancer Network (NCCN) Guidelines as well as emerging cancer biomarkers. As this assay represents comprehensive genomic profiling (CGP), we can detect all four classes of alterations: SNVs, indels, select fusions and select copy number alterations (to see which genes and regions are covered with this panel, see this [list of targets](https://sequencing.roche.com/content/dam/rochesequence/worldwide/resources/brochure-avenio-ctdna-tumor-tissue-expanded-kit-gene-list-SEQ100327.pdf?ref=vesseldna.com)). Just so you have an idea about the duration of the wet and dry lab workflows, here is a rough estimation of the number of hours/days needed: *Table 1\. General durations of each step in the wet/dry lab workflows.* | **Workflow** | **Step** | **Duration** | | ----------------------------------------- | ------------------------------------------------------------------------------------------- | ---------------- | | Wet lab | DNA isolation | \~2 hours | | Library preparation | 3 days | | | Library quantification | \~2 hours | | | Sequencing enriched library | \~1.5 days | | | Sequencing whole-genome library | 14-17 hours | | | Dry lab | Secondary data analysis (variant detection, tumor fraction estimation, copy number calling) | approx. 12 hours | | Tertiary data analysis and interpretation | up to 4 hours | | This most critical step is the interpretation of the detected variants, which we will touch upon later on. 💡 *If you want to see what sample processing, library preparation and sequencing looks like, take a look at our wet lab video tutorials*. Let’s take a look at how we derived the NGS results, which are split up into *“Tumor fraction”*, *“Known and pathogenic variants”*, and *“Non-actionable variants and VUS”*. Here is a breakdown of the main steps to generate the data: ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/06/cgp_new.png) Figure 2. After DNA extraction from plasma, we begin with comprehensive genomic profiling via the AVENIO ctDNA Expanded panel. This means that using a single assay, i.e. one single DNA source, we can detect the 4 classes of alterations - base substitutions, - insertions and deletions, - somatic copy number alterations (SCNA) and - structural rearrangements. After adapter ligation and amplification, we can obtain a library of all original cfDNA fragments that were present in the sample, as there was no selection of target regions at this step (here referred to as the whole-genome library). Some of this DNA library is then processed further in the protocol using targeted enrichment. With this hybrid capture-based targeted approach, select regions within the library are captured using long, biotinylated oligonucleotide baits, or probes. These biotinylated baits have been designed to hybridize to regions of interest (here the regions within the 77 genes listed [here](https://sequencing.roche.com/content/dam/rochesequence/worldwide/resources/brochure-avenio-ctdna-tumor-tissue-expanded-kit-gene-list-SEQ100327.pdf?ref=vesseldna.com)) within the fragmented cfDNA and streptavidin is subsequently used to separate the baits bound to target DNA from other fragments which were not bound. Each of these libraries, i.e. whole-genome and enriched, are sequenced separately for different purposes. The whole-genome library is sequenced at low coverage, as a shallow coverage of 0.1x suffices for the calling of copy numbers and estimation of tumor fraction. For variant detection, we must sequence the enriched library at high coverage \~5000x in order to ensure reliable variant detection at low allelic frequencies. Once we have our estimated tumor content (provided as a % ), SCNAs of interest, and true variants, we can combine all of this pertinent information into a clinical report and provide an integrated interpretation of the results. ### Tumor fraction calculation Below, you will learn why the estimation of tumor content in plasma is essential to the interpretation of copy number changes and the variant allele frequencies detected in your sample. To derive tumor fraction, we employ the publicly available [ichorCNA algorithm developed and maintained by the Broad Institute](https://github.com/broadinstitute/ichorCNA/wiki?ref=vesseldna.com). ichorCNA uses a probabilistic model, implemented as a hidden Markov model (HMM), to simultaneously segment the genome, predict large-scale copy number alterations, and estimate the tumor fraction of shallow whole-genome sequencing data. It is optimized for low coverage (\~0.1x) sequencing of samples and has been benchmarked using patient and healthy donor cfDNA samples. ichorCNA has a limit of detection of 3%, meaning that liquid biopsy samples with a ctDNA fraction of < 3% indicate lowly detectable levels or the absence of tumor-derived DNA. To run the algorithm, we use our shallow whole-genome sequencing dataset (described in “Known and pathogenic variants”) as an input. Below is the graphical output of the algorithm alongside the tumor fraction estimation for this patient sample in Case 1: ![](https://storage.ghost.io/c/2f/bc/2fbc0957-2405-4d2a-bf9f-1dca3d1d146f/content/images/2022/06/case1.png) Figure 3\. ichorCNA profile depicting genome-wide copy number alterations and estimated tumor fraction Here you will see a standard copy number plot with the chromosomes on the x-axis and the copy number log2 ratios for each bin in the genome on the y-axis. The color mapping is: - 1 copy (i.e. loss) = dark green - 2 copies = blue - 3 copies (i.e. gain) = brown - 4+ copies (i.e. amplification) = red Notice the high-level amplifications detected on chromosomes 1 and 18\. You can see the estimation of tumor content provided as a fraction. Here, we see that the algorithm calculated a tumor content of 16.69%, or roughly 17%. This value is carried over to our final clinical report. For a more details about data interpretation from ichorCNA, the [Github Wiki](https://github.com/broadinstitute/ichorCNA/wiki/Interpreting-ichorCNA-results?ref=vesseldna.com) page provides more information. ### Detection of somatic copy number alterations (SCNAs) _This post is for subscribers only._ ### Our Mission URL: https://www.vesseldna.com/our-mission/ Last updated: 2024-02-04T12:34:12.000Z ### Here is what Vessel is all about Our mission is to educate patients and enable clinicians to implement state-of-the-art precision oncology approaches throughout the entire patient journey, driving the adoption of precision medicine by hospitals, payers and providers. Vessel is your trusted advisor for end-to-end consulting in molecular tumor profiling. We focus on [bridging the gap](https://www.vesseldna.com/membership/) of precision medicine and clinical application. We are the “connective tissue" between clinicians, industry, patients and their families. *Here is the deal:* If you want to employ precision oncology approaches, you need to accept and overcome the fact that precision oncology asks for polymath-like proficiency across multiple knowledge domains. If you ever have asked yourself questions like: - How can I adopt precision oncology at my hospital? - How does next-generation sequencing (NGS) work and what exactly is bioinformatics? - When should I use liquid biopsy and how can I interpret the results? - How do I know if my plasma sample contains circulating tumor DNA (ctDNA)? - How can I better understand the latest early detection strategies that are based on complex new approaches, especially those that are based on multi-dimensional data and artificial intelligence (AI)? - What is the field of fragmentomics and how can I apply this to my liquid biopsy strategies? - What can I do with whole-genome sequencing and is it ready for the clinic? - How can I use NGS to answer my research question? Then this is the right place for you. Remove the barriers of implementing precision oncology approaches through our [Vessel Programs](https://www.vesseldna.com/membership/), together with our partners, by signing up below. ### Why the application form you ask? We are looking for serious members to join our platform. We aim to share a lot of insight and information that are immediately applicable to your workplace. In order to do this, we expect you to share some personal information as well as to bring the willingness to contribute and actively participate in this community. We sincerely hope to see you join and promise never to spam you or share your information with anyone else.