The given slide deck was presented on the 2017 Festival of Genomics in London, UK. It depicts how latest in-memory database technology supports clinicians in finding the best treatment options incorporating genetic data.
Patient Journey in Oncology 2025: Molecular Tumour Boards in PracticeMatthieu Schapranow
The slide deck was presented at the Bio Data World Congress in Basel on Dec. 04, 2019. It shares first results from the work in the HiGHmed consortium on the use case oncology.
Gesundheit geht uns alle an: Smart Data ermöglicht passendere Entscheidungen...Matthieu Schapranow
The document discusses how Analyze Genomes provides real-time analysis of big medical data to enable precision medicine. It analyzes diverse data sources, from genomes to clinical trials, using an in-memory database. This allows identifying best treatment options, such as finding no-small cell lung cancer patients the most effective drug. Analyze Genomes also powers related digital health applications and research projects that integrate data from various healthcare partners.
AnalyzeGenomes.com: A Federated In-Memory Database Platform for Digital HealthMatthieu Schapranow
The slide deck of the presentation "AnalyzeGenomes.com: A Federated In-Memory Database Platform for Digital Health" of the 2017 BMBF All Hands Meeting in Karlsruhe are online available now.
This presentation shows application examples of the analyzegenomes.com service for precision medicine. It was presented at 2016 HIMSS conference in Las Vegas, NV
The given presentation was presented at SAPPHIRE 2017 in Orlando, FL on May 18, 2017. It highlights latest research results focusing on user-centered in-memory applications for precision medicine.
ICT Platform to Enable Consortium Work for Systems Medicine of Heart FailureMatthieu Schapranow
The slide deck "ICT Platform to Enable Consortium Work for Systems Medicine of Heart Failure" was presented on Oct 5, 2016 at the 2016 e:Med Meeting on Systems Medicine in Kiel, Germany.
The given presentation showcases examples of how artificial intelligence technology can be used to improve the patient journey in the specific medical field of oncology.
Patient Journey in Oncology 2025: Molecular Tumour Boards in PracticeMatthieu Schapranow
The slide deck was presented at the Bio Data World Congress in Basel on Dec. 04, 2019. It shares first results from the work in the HiGHmed consortium on the use case oncology.
Gesundheit geht uns alle an: Smart Data ermöglicht passendere Entscheidungen...Matthieu Schapranow
The document discusses how Analyze Genomes provides real-time analysis of big medical data to enable precision medicine. It analyzes diverse data sources, from genomes to clinical trials, using an in-memory database. This allows identifying best treatment options, such as finding no-small cell lung cancer patients the most effective drug. Analyze Genomes also powers related digital health applications and research projects that integrate data from various healthcare partners.
AnalyzeGenomes.com: A Federated In-Memory Database Platform for Digital HealthMatthieu Schapranow
The slide deck of the presentation "AnalyzeGenomes.com: A Federated In-Memory Database Platform for Digital Health" of the 2017 BMBF All Hands Meeting in Karlsruhe are online available now.
This presentation shows application examples of the analyzegenomes.com service for precision medicine. It was presented at 2016 HIMSS conference in Las Vegas, NV
The given presentation was presented at SAPPHIRE 2017 in Orlando, FL on May 18, 2017. It highlights latest research results focusing on user-centered in-memory applications for precision medicine.
ICT Platform to Enable Consortium Work for Systems Medicine of Heart FailureMatthieu Schapranow
The slide deck "ICT Platform to Enable Consortium Work for Systems Medicine of Heart Failure" was presented on Oct 5, 2016 at the 2016 e:Med Meeting on Systems Medicine in Kiel, Germany.
The given presentation showcases examples of how artificial intelligence technology can be used to improve the patient journey in the specific medical field of oncology.
The given presentation outlines services of the cloud platform "Analyze Genomes" enabling precision medicine. It was presented on the mHealth meets Diagnostics symposium in Berlin on Jun 21, 2016.
A Federated In-Memory Database Computing Platform Enabling Real-Time Analysis...Matthieu Schapranow
1) Dr. Schapranow presents a federated in-memory database computing platform called AnalyzeGenomes.com to enable real-time analysis of big medical data.
2) The platform aims to incorporate all available patient data, reference latest lab results and medical knowledge, and support interactive analysis to help clinicians make treatment decisions.
3) It uses a distributed in-memory database across nodes to combine and link heterogeneous medical data sources while addressing challenges of data privacy, locality, and volume.
The Driver of the Healthcare System in the 21st Century: Real-world Applicati...Matthieu Schapranow
The document discusses the driver of the healthcare system in the 21st century. It describes how patients, clinicians, and researchers interact and how their interactions will change. It also discusses the challenges of distributed and heterogeneous healthcare data sources, and proposes approaches like in-memory databases and real-time analysis of big medical data to address these challenges. Specific examples discussed include analyzing genomes and creating a medical knowledge cockpit to link patient specifics with international healthcare knowledge.
This presentation provides a brief overview of how in-memory database technology can be applied to support systems medicine approaches. For that, it shares real-world experiences, e.g. from the SMART project consortium funded by the German Federal Ministry of Education and Research.
Algorithmen statt Ärzte: Algorithmen statt Ärzte: Ersetzt Big Data künftig ...Matthieu Schapranow
The document discusses whether algorithms will replace doctors in medicine. It notes that healthcare costs are rising significantly. While algorithms and health apps promise benefits like improved prevention, quality issues exist if not regulated as medical products. The document explores various use cases where algorithms already augment doctors, such as automatically segmenting tissues in scans. Citizens increasingly demand digital health services and control over their own data. The conclusion is that algorithms and doctors can work together, with algorithms handling routine tasks and doctors focusing on personal care, if challenges around regulation and data protection are addressed.
The given presentations share a specific use case from the medical field of oncology and outlines the potentials of applying artificial intelligence to it.
Processing of Big Medical Data in Personalized Medicine: Challenge or PotentialMatthieu Schapranow
Experience our AnalyzeGenomes.com services at the example of the Medical Knowledge Cockpit and how it can improve the daily work for researchers and physicians.
The document discusses challenges and opportunities presented by big medical data and describes an approach using in-memory technology. It proposes a medical knowledge cockpit that allows interactive exploration of distributed medical data sources. This would facilitate tasks like identifying relevant information for a patient's genes, finding suitable clinical trials, and interactively analyzing drug response data. The goal is to enable personalized medicine through real-time analysis of medical data from various sources.
This presentation covers the final presentation of the 2016 Festival of Genomics workshop "Big Medical Data in Precision Medicine: Challenges or Opportunities?" on Jan 19, 2016 in London.
Festival of Genomics 2016 London: Analyze Genomes: A Federated In-Memory Comp...Matthieu Schapranow
This presentation covers the "Analyze Genomes: A Federated In-Memory Computing Platform for Life Sciences" presentation of the 2016 Festival of Genomics workshop "Big Medical Data in Precision Medicine: Challenges or Opportunities?" on Jan 19, 2016 in London.
Analyze Genomes: A Federated In-Memory Database System For Life SciencesMatthieu Schapranow
1) Dr. Matthieu-P. Schapranow presented on Analyze Genomes, a federated in-memory database system for life sciences.
2) The system aims to provide real-time analysis of big medical data while maintaining sensitive data locally due to privacy and locality restrictions.
3) It incorporates local compute resources by installing worker nodes to process sensitive data locally and store results in local database instances, while being managed as part of a larger federated database system.
Slides of the 2015 Bio Data World Congress show how our analyzegenomes.com services are combined to support precision medicine in the context of modern oncology treatment.
The document proposes a federated in-memory database system for life sciences that addresses the needs of patients, clinicians, and researchers by enabling real-time analysis of big medical data while maintaining data privacy and locality. It describes key actors and a use case in cancer treatment. The proposed solution incorporates local compute resources through a federated in-memory database with a cloud service provider managing shared algorithms and master data, while sensitive patient data resides locally.
This is the presentation as shown on the 2015 Future Convention in Frankfurt, Germany on Nov 23, 2015. It shows latest research results in the field of precision medicine using the Drug Response Analysis app of the http://we.analyzegenomes.com platform.
This presentation shares a 10 minute pitch of big data potentials in the field of life sciences as presented at the 2015 CMS Global Life Science Forum on Nov 9, 2015 in Frankfurt
Festival of Genomics 2016 London: Analyze Genomes: Modeling and Executing Gen...Matthieu Schapranow
This presentation covers the "Analyze Genomes: Modeling and Executing Genome Data Processing Pipelines" presentation of the 2016 Festival of Genomics workshop "Big Medical Data in Precision Medicine: Challenges or Opportunities?" on Jan 19, 2016 in London.
Festival of Genomics 2016 London: Mining and Processing of Unstructured Medic...Matthieu Schapranow
This presentation covers the "Mining and Processing of Unstructured Medical Data" presentation of the 2016 Festival of Genomics workshop "Big Medical Data in Precision Medicine: Challenges or Opportunities?" on Jan 19, 2016 in London.
Festival of Genomics 2016 London: Challenges of Big Medical Data?Matthieu Schapranow
This presentation covers the "Challenges of Big Medical Data" presentation of the 2016 Festival of Genomics workshop "Big Medical Data in Precision Medicine: Challenges or Opportunities?" on Jan 19, 2016 in London.
Festival of Genomics 2016 London: Real-time Exploration of the Cancer Genome,...Matthieu Schapranow
This presentation covers the NCT presentation of the 2016 Festival of Genomics workshop "Big Medical Data in Precision Medicine: Challenges or Opportunities?" on Jan 19, 2016 in London.
The given presentation outlines services of the cloud platform "Analyze Genomes" enabling precision medicine. It was presented on the mHealth meets Diagnostics symposium in Berlin on Jun 21, 2016.
A Federated In-Memory Database Computing Platform Enabling Real-Time Analysis...Matthieu Schapranow
1) Dr. Schapranow presents a federated in-memory database computing platform called AnalyzeGenomes.com to enable real-time analysis of big medical data.
2) The platform aims to incorporate all available patient data, reference latest lab results and medical knowledge, and support interactive analysis to help clinicians make treatment decisions.
3) It uses a distributed in-memory database across nodes to combine and link heterogeneous medical data sources while addressing challenges of data privacy, locality, and volume.
The Driver of the Healthcare System in the 21st Century: Real-world Applicati...Matthieu Schapranow
The document discusses the driver of the healthcare system in the 21st century. It describes how patients, clinicians, and researchers interact and how their interactions will change. It also discusses the challenges of distributed and heterogeneous healthcare data sources, and proposes approaches like in-memory databases and real-time analysis of big medical data to address these challenges. Specific examples discussed include analyzing genomes and creating a medical knowledge cockpit to link patient specifics with international healthcare knowledge.
This presentation provides a brief overview of how in-memory database technology can be applied to support systems medicine approaches. For that, it shares real-world experiences, e.g. from the SMART project consortium funded by the German Federal Ministry of Education and Research.
Algorithmen statt Ärzte: Algorithmen statt Ärzte: Ersetzt Big Data künftig ...Matthieu Schapranow
The document discusses whether algorithms will replace doctors in medicine. It notes that healthcare costs are rising significantly. While algorithms and health apps promise benefits like improved prevention, quality issues exist if not regulated as medical products. The document explores various use cases where algorithms already augment doctors, such as automatically segmenting tissues in scans. Citizens increasingly demand digital health services and control over their own data. The conclusion is that algorithms and doctors can work together, with algorithms handling routine tasks and doctors focusing on personal care, if challenges around regulation and data protection are addressed.
The given presentations share a specific use case from the medical field of oncology and outlines the potentials of applying artificial intelligence to it.
Processing of Big Medical Data in Personalized Medicine: Challenge or PotentialMatthieu Schapranow
Experience our AnalyzeGenomes.com services at the example of the Medical Knowledge Cockpit and how it can improve the daily work for researchers and physicians.
The document discusses challenges and opportunities presented by big medical data and describes an approach using in-memory technology. It proposes a medical knowledge cockpit that allows interactive exploration of distributed medical data sources. This would facilitate tasks like identifying relevant information for a patient's genes, finding suitable clinical trials, and interactively analyzing drug response data. The goal is to enable personalized medicine through real-time analysis of medical data from various sources.
This presentation covers the final presentation of the 2016 Festival of Genomics workshop "Big Medical Data in Precision Medicine: Challenges or Opportunities?" on Jan 19, 2016 in London.
Festival of Genomics 2016 London: Analyze Genomes: A Federated In-Memory Comp...Matthieu Schapranow
This presentation covers the "Analyze Genomes: A Federated In-Memory Computing Platform for Life Sciences" presentation of the 2016 Festival of Genomics workshop "Big Medical Data in Precision Medicine: Challenges or Opportunities?" on Jan 19, 2016 in London.
Analyze Genomes: A Federated In-Memory Database System For Life SciencesMatthieu Schapranow
1) Dr. Matthieu-P. Schapranow presented on Analyze Genomes, a federated in-memory database system for life sciences.
2) The system aims to provide real-time analysis of big medical data while maintaining sensitive data locally due to privacy and locality restrictions.
3) It incorporates local compute resources by installing worker nodes to process sensitive data locally and store results in local database instances, while being managed as part of a larger federated database system.
Slides of the 2015 Bio Data World Congress show how our analyzegenomes.com services are combined to support precision medicine in the context of modern oncology treatment.
The document proposes a federated in-memory database system for life sciences that addresses the needs of patients, clinicians, and researchers by enabling real-time analysis of big medical data while maintaining data privacy and locality. It describes key actors and a use case in cancer treatment. The proposed solution incorporates local compute resources through a federated in-memory database with a cloud service provider managing shared algorithms and master data, while sensitive patient data resides locally.
This is the presentation as shown on the 2015 Future Convention in Frankfurt, Germany on Nov 23, 2015. It shows latest research results in the field of precision medicine using the Drug Response Analysis app of the http://we.analyzegenomes.com platform.
This presentation shares a 10 minute pitch of big data potentials in the field of life sciences as presented at the 2015 CMS Global Life Science Forum on Nov 9, 2015 in Frankfurt
Festival of Genomics 2016 London: Analyze Genomes: Modeling and Executing Gen...Matthieu Schapranow
This presentation covers the "Analyze Genomes: Modeling and Executing Genome Data Processing Pipelines" presentation of the 2016 Festival of Genomics workshop "Big Medical Data in Precision Medicine: Challenges or Opportunities?" on Jan 19, 2016 in London.
Festival of Genomics 2016 London: Mining and Processing of Unstructured Medic...Matthieu Schapranow
This presentation covers the "Mining and Processing of Unstructured Medical Data" presentation of the 2016 Festival of Genomics workshop "Big Medical Data in Precision Medicine: Challenges or Opportunities?" on Jan 19, 2016 in London.
Festival of Genomics 2016 London: Challenges of Big Medical Data?Matthieu Schapranow
This presentation covers the "Challenges of Big Medical Data" presentation of the 2016 Festival of Genomics workshop "Big Medical Data in Precision Medicine: Challenges or Opportunities?" on Jan 19, 2016 in London.
Festival of Genomics 2016 London: Real-time Exploration of the Cancer Genome,...Matthieu Schapranow
This presentation covers the NCT presentation of the 2016 Festival of Genomics workshop "Big Medical Data in Precision Medicine: Challenges or Opportunities?" on Jan 19, 2016 in London.
UCSF Informatics Day 2014 - Wylie Burke, "Bioethical Issues in Genomics and E...CTSI at UCSF
This document discusses several bioethical issues related to genomics and electronic health records. It touches on the challenges of linking disparate health datasets while protecting patient privacy. It also examines the blurring lines between clinical care and research when using individuals' health information. Specifically, it raises questions around informed consent, transparency, justification for using data, and ensuring adequate confidentiality. The document also explores issues of trust in different contexts and public concerns about the use of newborn screening samples in research. Finally, it discusses developing policy around "information commons" and engaging stakeholders to help shape biorepository research standards.
Hasso Plattner gave this presentation about how in-memory technology can support analysis of big medical data at the 2013 World Health Summit in Berlin. It consists real-world examples showing latest results of partners, such as the Hasso Plattner Institute, Stanford, Charité, and SAP. For background details, please refer to http://we.analyzegenomes.com
The document discusses modern medical technologies including MRI scanners and remote surgery. MRI scanners use strong magnets and radio waves to produce detailed images of the body without exposing patients to radiation. Remote surgery allows surgeons to operate on patients from long distances using robotic arms, enabling life-saving procedures in remote areas. It can be used cooperatively with an assistant surgeon present with the patient or for teaching purposes from a distance.
This document discusses emerging technologies in healthcare including:
1) Earlier diagnosis, less invasive treatments, and shorter hospital stays which can lower costs.
2) Demographic changes and rising healthcare costs increasing focus on quality improvement.
3) Emerging technologies like nanotechnology, bionics, regenerative medicine, and mobile/wearable devices that could transform diagnosis, treatment and healthcare delivery.
4) Applications of these technologies including drug delivery, imaging, disease detection, prosthetics and more personalized/preventative care models.
The document discusses the World Health Organization's (WHO) strategy on traditional medicine. It defines traditional medicine as health practices incorporating plant, animal and mineral-based medicines, spiritual therapies, and exercises used to maintain well-being and treat illness. The WHO strategy from 2002-2005 aims to integrate traditional medicine into national healthcare systems, provide guidance on safety, efficacy and quality, ensure access, and promote rational use. It addresses developing standards for herbal medicines, monitoring safety, protecting traditional knowledge, and training guidelines.
This document discusses personalized medicine and provides an outline of topics covered. It defines personalized medicine as tailoring medical treatment to an individual's characteristics. Key areas discussed include pharmacogenetics, how genes and genetic variations affect drug responses, and examples of genetic screening and biomarkers used in drug labeling. The document also addresses challenges in implementing personalized medicine and steps needed like educating healthcare professionals in pharmacogenomics.
Forum on Personalized Medicine: Challenges for the next decadeJoaquin Dopazo
Bioinformatics and Big Data in the era of Personalized Medicine
10th Anniversary Instituto Roche Forum on Personalized Medicine: Challenges for the next decade.
Santiago de Compostela (Spain), September 25th 2014
Genomic Medicine: Personalized Care for Just PenniesHealth Catalyst
The document discusses the progress and future of genomic medicine. The cost of sequencing a human genome has declined drastically from $100 million to an expected cost of just pennies by 2020. This will enable more personalized care based on a patient's genomic profile. Genomic analysis is already improving diagnosis and treatment for various diseases like rare genetic disorders and cancer. In the future, genomic data combined with sensor data will generate huge amounts of healthcare data and further advance personalized medicine.
Personalized medicine (PM) aims to individualize treatment based on a person's genes, environment, and lifestyle. It involves analyzing a person's genetic, genomic, and clinical information to make predictions about disease susceptibility, progression, and best treatment options. PM is not just about genetics but also considers natural variations in how individuals metabolize and respond to drugs. Through molecular analysis of biomarkers, PM can classify disease subtypes and subgroups that respond differently to therapies. The goals of PM are to enable more informed healthcare decisions, improve outcomes through targeted therapies, reduce side effects, focus on prevention over reaction, allow for earlier intervention, and reduce costs through a more personalized approach.
Ayurveda is a traditional system of medicine native to India that is based on balancing the three doshas (bodily humors) of vata, pitta, and kapha. The earliest Ayurvedic texts date back to 1500 BC and are found in Hindu scriptures like the Atharvaveda and Suśruta Saṃhitā. Ayurveda views health as a balance of physical, mental and emotional well-being. Diagnosis evaluates the doshas, and treatments emphasize herbal medicines, yoga, and lifestyle. The goal is to ensure proper functioning of the body's channels to prevent disease.
10 tech trends in healthcare are discussed including:
1. Smartphones have been widely adopted in clinical care and applications leverage smartphone hardware.
2. Wi-Fi adoption has increased with more connected devices on healthcare networks than wired ones.
3. Bring your own device (BYOD) policies are required to manage personal devices on hospital networks.
4. Government mandates have forced investment in IT and applications and have potential for big data analysis.
This document discusses personalized medicine and how genetic variations between individuals can impact disease susceptibility and drug response. It provides examples of how single nucleotide polymorphisms can influence conditions like heart disease and impact drug metabolism pathways involving cytochrome P450 enzymes. The document also discusses challenges like implementing pharmacogenomic testing, ensuring privacy of genetic data, and determining appropriate coverage and costs of personalized medicine approaches.
Festival of Genomics 2016 London: Analyze Genomes: Real-world ExamplesMatthieu Schapranow
This presentation covers the "Analyze Genomes: Real-world Examples" presentation of the 2016 Festival of Genomics workshop "Big Medical Data in Precision Medicine: Challenges or Opportunities?" on Jan 19, 2016 in London.
The document summarizes Dr. Matthieu-P. Schapranow's presentation at the Festival of Genomics in Boston on turning big medical data into precision medicine. It describes an in-memory database approach that enables real-time analysis of heterogeneous medical data sources. This allows clinicians and researchers to interactively explore patient data, clinical trials, pathways, and literature to obtain personalized treatment recommendations. The system was designed using a human-centered methodology to ensure usability, effectiveness, and feasibility for precision medicine applications.
What are today's challenges of big medical data and how can we use the immense data to turn it into potentials, e.g. for precision medicine. Get insights in application examples, where big medical data are incorporated and how in-memory database technology can enable it instantaneous analysis.
Introduction to High-performance In-memory Genome Project at HPI Matthieu Schapranow
The document discusses challenges of big data processing for personalized medicine. It describes the vision of using large amounts of diverse medical data like genomes, medical records, clinical trials, and research papers to enable personalized preventative care and more effective therapies for patients. The speaker then outlines their approach using in-memory databases and analytics to enable interactive analysis of this data. Examples discussed include tools for researchers to analyze genomes, clinicians to find comparable patient cases, and patients to identify relevant clinical trials.
Enabling Real-time Genome Data Research with In-memory Database Technology (S...Matthieu Schapranow
Dr. Schapranow presented on using in-memory database technology to enable real-time genome data research. Key points include:
- Current genome analysis takes 4-6 weeks but in-memory technology can accelerate it to minutes or less.
- The High-Performance In-Memory Genome project aims to analyze a patient's full genomic and medical record data during a doctor's visit.
- Tests on SAP HANA showed genome analyses like variant calling and allele counting were 82-600x faster than traditional methods.
- The in-memory approach enables interactive exploration of patient cohorts and pathways to better understand treatment effectiveness.
1) In-memory applications are revolutionizing oncology research by enabling fast access and analysis of large amounts of individual patient data, clinical trials data, research findings, and more.
2) Researchers are developing tools that incorporate all available individual patient information, reference latest lab results and medical knowledge, and allow interactive analysis to help clinicians personalize cancer treatment in real time.
3) Key challenges include analyzing and combining distributed heterogeneous medical data sources rapidly. Technologies using in-memory databases aim to address this by enabling analysis of large datasets in seconds.
Enabling Real-Time Genome Data Research with In-Memory Database Technology (I...Matthieu Schapranow
This document discusses enabling real-time genome data research using in-memory database technology. It describes how in-memory databases can perform genomic analyses like variant calling and clustering of patient cohorts much faster than traditional disk-based approaches. The document outlines several research topics like improving data preparation pipelines and integrating genetic pathways. It also presents results showing how an in-memory database loaded a large genome dataset and was able to perform queries 82-600 times faster than conventional tools. The future potential for combining genomic and clinical data in real-time to help researchers, clinicians and patients is also discussed.
The document summarizes a presentation on the Norwegian clinical genetics analysis platform "genAP". Key points include:
- "genAP" aims to develop an ICT infrastructure for centralized storage of human genome data to allow distributed use nationally and potentially internationally.
- It seeks to efficiently analyze sensitive genome data through existing tools and integrate genome data into clinical diagnostics and treatment.
- Challenges include standardizing analyses, conveying complex information to clinicians, ensuring data security and privacy, and navigating research versus clinical applications.
- Examples provided automation of variant analysis, a decision support system for drug dosages, and plans for future clinical pilots.
The document provides an overview of several agricultural databases and genome research programs. It discusses the National Center for Biotechnology Information (NCBI) and databases it maintains, including GenBank, PubMed, PubChem, dbSNP, and others. It also describes other plant-focused databases like Gramene, GrainGenes, PlantGDB, TIGR, UK CropNet, and databases for specific crops like MaizeDB, TAIR, Rice Genome Research Program, and the US Wheat Genome Project. Genome assembly and analysis software is also briefly mentioned.
This document provides an overview of the November 2000 issue of JALA (Journal of Analytical Laboratories Automation). It describes the development of a novel robotic system for the New York Cancer Project biorepository in collaboration with the Medical Automation Research Center. The biorepository receives 50-100 blood samples per day which are processed robotically to extract, quantify, aliquot and store DNA, plasma and RNA to be accessible to investigators. The robotic system aims to provide rapid random access to the hundreds of thousands of DNA samples stored for high-throughput analysis in studies of gene-environment interactions and cancer risk.
Examining gene expression and methylation with next gen sequencingStephen Turner
Slides on RNA-seq and methylation studies using next-gen sequencing given at the University of Miami Hussman Institute for Human Genomics "Genetic Analysis of Complex Human Diseases" course in 2012 (http://hihg.med.miami.edu/educational-programs/analysis-of-complex-human-diseases/genetic-analysis-of-complex-human-diseases/)
Evolution of Knowledge Discovery and Management inscit2006
The document discusses the evolution of knowledge discovery and management over time. It outlines how knowledge discovery has progressed from early efforts using simulated data due to lack of large real-world datasets, to today where there is no shortage of complex real-world problems and data available. Key areas evolving now include automated data analysis, integration of tools and databases, and handling different data types like text and images. While expert systems showed early promise but had limited results, knowledge discovery has led to valuable applications through continued academic and industrial research.
The document discusses Zhiyong Lu's work at the National Center for Biotechnology Information (NCBI) developing text mining and natural language processing tools to help biocuration and biomedical research. Some key points:
- Lu leads teams that develop machine learning algorithms and tools for biomedical literature mining, clinical text analysis, and medical image analysis.
- Popular tools developed include PubTator, tmVar, DNorm, and deep learning models for chest X-ray and retinal image analysis.
- The tools have been applied to tasks like curation of PubMed, UniProt, and other databases and have received positive user feedback.
- Lu has also led several BioCreative challenges
This presentation covers the agenda of the 2016 Festival of Genomics workshop "Big Medical Data in Precision Medicine: Challenges or Opportunities?" on Jan 19, 2016 in London.
Gaining Time – Real-time Analysis of Big Medical Data SAP Technology
Growing volumes of diverse medical data from sources like genomes, proteomes, clinical records, medical sensors and clinical trials are creating new opportunities for innovation in medicine. SAP HANA is enabling real-time analysis of this big medical data through its ability to process large volumes of data in memory at rapid speeds. This allows for new scenarios like genome variant analysis across large populations in parallel, building proteomics-based cancer diagnostic pipelines interactively, and providing unified access to clinical data from different sources. Multidisciplinary teams combining clinical, research, technical and business expertise are needed to develop new collaborative approaches that are viable and can help drive improvements in areas like personalized healthcare and clinical decision making.
tranSMART Community Meeting 5-7 Nov 13 - Session 3: transmart’s application t...David Peyruc
tranSMART Community Meeting 5-7 Nov 13 - Session 3: tranSMART’s Application to Clinical Biomarker Discovery Studies in Sanofi
Sherry Cao, Sanofi
This presentation will discuss challenges we are encountering in clinical biomarker discovery
study and how we are using tranSMART to help to address them.
- Video recording of this lecture in English language: https://youtu.be/Pt1nA32sdHQ
- Video recording of this lecture in Arabic language: https://youtu.be/uFdc9F0rlP0
- Link to download the book free: https://nephrotube.blogspot.com/p/nephrotube-nephrology-books.html
- Link to NephroTube website: www.NephroTube.com
- Link to NephroTube social media accounts: https://nephrotube.blogspot.com/p/join-nephrotube-on-social-media.html
Does Over-Masturbation Contribute to Chronic Prostatitis.pptxwalterHu5
In some case, your chronic prostatitis may be related to over-masturbation. Generally, natural medicine Diuretic and Anti-inflammatory Pill can help mee get a cure.
5-hydroxytryptamine or 5-HT or Serotonin is a neurotransmitter that serves a range of roles in the human body. It is sometimes referred to as the happy chemical since it promotes overall well-being and happiness.
It is mostly found in the brain, intestines, and blood platelets.
5-HT is utilised to transport messages between nerve cells, is known to be involved in smooth muscle contraction, and adds to overall well-being and pleasure, among other benefits. 5-HT regulates the body's sleep-wake cycles and internal clock by acting as a precursor to melatonin.
It is hypothesised to regulate hunger, emotions, motor, cognitive, and autonomic processes.
10 Benefits an EPCR Software should Bring to EMS Organizations Traumasoft LLC
The benefits of an ePCR solution should extend to the whole EMS organization, not just certain groups of people or certain departments. It should provide more than just a form for entering and a database for storing information. It should also include a workflow of how information is communicated, used and stored across the entire organization.
1. AnalyzeGenomes.com: When time matters…
Dr. –Ing. Matthieu-P. Schapranow
Festival of Genomics, London, UK
Jan 31, 2017
2. What is the Hasso Plattner Institute, Potsdam, Germany?
Dr. Schapranow, Festival
of Genomics, Jan 31,
2017
When time matters...
2
3. From Raw Genome Data to Analysis
Dr. Schapranow, Festival
of Genomics, Jan 31,
2017
When time matters...
■ DNA Sequencing: Transformation of
analogues DNA into digital format
■ Alignment: Reconstruction of complete
genome with snippets
■ Variant Calling: Identification of genetic
variants
■ Data Annotation: Linking genetic variants
with research findings
3
4. ■ Purpose: Transformation of analogous DNA into digital format (A/D converter)
■ Input: Chunks of DNA
■ Output: DNA reads in digital form, e.g. in FASTQ format
1. DNA Sequencing
Dr. Schapranow, Festival
of Genomics, Jan 31,
2017
When time matters...
44peaks.app
5. ■ FASTQ format used for further processing
■ One read is a quart-tuple of:
1. Sequence identifier / description
2. Raw sequence
3. Strand / direction
4. Quality values per sequenced base
1. Output of Sequencing
Dr. Schapranow, Festival
of Genomics, Jan 31,
2017
When time matters...
5
6. ■ Purpose: Mapping of DNA reads to a reference
■ Input:
□ DNA reads := Sequence of nucleotides with a length of 100 bp up to some 1 kbp
□ Reference genome := Blueprint for alignment of DNA reads
■ Output: Mapped DNA reads
■ Bear in mind:
□ Less fraction in DNA reads, i.e. longer reads, allows more precise alignment
□ Reference from same origin improves mapping quality
2. Alignment
Overview
Dr. Schapranow, Festival
of Genomics, Jan 31,
2017
When time matters...
6
7. ■ Purpose: Variant Calling := Detect variations within a genome
■ Input:
□ Mapped DNA reads, i.e. output of alignment process
□ Reference genome
■ Output: List of variants
■ Bear in mind:
□ Read depth at posi:= Number of nucleotides storing information about pos i
3. Variant Calling
Overview
Dr. Schapranow, Festival
of Genomics, Jan 31,
2017
When time matters...
7
8. ■ Purpose:
□ Assess impact of genetic changes
□ Understand gene function and possible medical therapy options
■ Input: List of genetic variants
■ Output: Details about certain genetic locus
4. Genetic Annotations
Dr. Schapranow, Festival
of Genomics, Jan 31,
2017
When time matters...
8
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
chr7 140753336 rs113488022 T A 61 PASS NS=1 GT 0/1
9. ■ Manual, time-consuming Internet search, e.g. publications, annotations, guidelines
■ International consortiums provide fragmented information
■ Missing linkage across individual data sources
■ Annotations vary in completeness and correctness
4. Challenges
Today
Dr. Schapranow, Festival
of Genomics, Jan 31,
2017
When time matters...
9
11. 4. Interpretation of Annotations: BRAF Gene
Kegg
Dr. Schapranow, Festival
of Genomics, Jan 31,
2017
When time matters...
11
12. 4. Interpretation of Annotations: BRAF gene
GeneCards
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13. 4. Interpretation of Annotations: BRAF Gene
PubMed
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14. Simplified Clinical Oncology Process (1/2)
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Simplified Clinical Oncology Process (1/2)
15. Simplified Clinical Oncology Process (1/2)
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Simplified Clinical Oncology Process (2/2)
16. ■ Can we enable clinicians to take their therapy decisions:
□ Incorporating all available patient specifics,
□ Referencing latest lab results and worldwide medical knowledge, and
□ In an interactive manner during their ward round?
Our Motivation
Turn Precision Medicine Into Clinical Routine
When time matters...
16
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17. Use Case: Precision Oncology
Identification of Best Treatment Option for Cancer Patient
■ Patient: 48 years, female, non-smoker, smoke-free environment
■ Diagnosis: Non-Small Cell Lung Cancer (NSCLC), stage IV
■ Markers: KRAS, EGFR, BRAF, NRAS, (ERBB2)
1. Remove tumor through surgery
2. Send tumor sample to laboratory for DNA extraction
3. Sequence complete DNA of sample results in 750 GB of raw genome data
4. Process raw genome data, e.g. alignment, variant calling, and annotate
5. Identify relevant variants using international medical knowledge
6. Support decision making, e.g. link to de-identified historic cases
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19. Our Vision
Medical Board Incorporating Latest Medical Knowledge
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20. The Challenge
Distributed Heterogeneous Data Sources
20
Human genome/biological data
600GB per full genome
15PB+ in databases of leading institutes
Prescription data
1.5B records from 10,000 doctors and
10M Patients (100 GB)
Clinical trials
Currently more than 30k
recruiting on ClinicalTrials.gov
Human proteome
160M data points (2.4GB) per sample
>3TB raw proteome data in ProteomicsDB
PubMed database
>23M articles
Hospital information systems
Often more than 50GB
Medical sensor data
Scan of a single organ in 1s
creates 10GB of raw dataCancer patient records
>160k records at NCT
When time matters...
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21. ■ Requirements
□ Managed services
□ Reproducibility
□ Real-time data analysis
■ Restrictions
□ Data privacy
□ Data locality
□ Volume of big medical data
Software Requirements in Life Sciences
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http://stevedempsen.blogspot.de/2013/08/agile-software-requirements-comic.html
22. Project Time Line
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2009 2010 2011 2012 2013 2014 2015
SAP HANA
launched Oncolyzer SORMAS
Drug Response
Analysis
Enterprise
Software
Medical
Knowledge
Cockpit
Analyze
Genomes
Platform
IMDB
Research
2016 2017
A R
T
+
T
RAM
S
+
S
M
23. Dr. Schapranow, Festival
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Our Approach: AnalyzeGenomes.com
In-Memory Computing Platform for Big Medical Data
23
In-Memory Database
When time matters...
24. Dr. Schapranow, Festival
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Our Approach: AnalyzeGenomes.com
In-Memory Computing Platform for Big Medical Data
24
In-Memory Database
Combined and Linked Data
Genome
Data
Cellular
Pathways
Genome
Metadata
Research
Publications
Pipeline and
Analysis Models
Drugs and
Interactions
When time matters...
Indexed
Sources
25. Dr. Schapranow, Festival
of Genomics, Jan 31,
2017
Our Approach: AnalyzeGenomes.com
In-Memory Computing Platform for Big Medical Data
25
In-Memory Database
Extensions for Life Sciences
Data Exchange,
App Store
Access Control,
Data Protection
Fair Use
Statistical
Tools
Real-time
Analysis
App-spanning
User Profiles
Combined and Linked Data
Genome
Data
Cellular
Pathways
Genome
Metadata
Research
Publications
Pipeline and
Analysis Models
Drugs and
Interactions
When time matters...
Indexed
Sources
26. Dr. Schapranow, Festival
of Genomics, Jan 31,
2017
Our Approach: AnalyzeGenomes.com
In-Memory Computing Platform for Big Medical Data
26
In-Memory Database
Extensions for Life Sciences
Data Exchange,
App Store
Access Control,
Data Protection
Fair Use
Statistical
Tools
Real-time
Analysis
App-spanning
User Profiles
Combined and Linked Data
Genome
Data
Cellular
Pathways
Genome
Metadata
Research
Publications
Pipeline and
Analysis Models
Drugs and
Interactions
When time matters...
Drug Response
Analysis
Pathway Topology
Analysis
Medical
Knowledge CockpitOncolyzer
Clinical Trial
Recruitment
Cohort
Analysis
...
Indexed
Sources
27. Combined column
and row store
Map/Reduce Single and
multi-tenancy
Lightweight
compression
Insert only
for time travel
Real-time
replication
Working on
integers
SQL interface on
columns and rows
Active/passive
data store
Minimal
projections
Group key Reduction of
software layers
Dynamic multi-
threading
Bulk load
of data
Object-
relational
mapping
Text retrieval
and extraction engine
No aggregate
tables
Data partitioning Any attribute
as index
No disk
On-the-fly
extensibility
Analytics on
historical data
Multi-core/
parallelization
Real-Time Data Analysis
In-Memory Database Technology
+
++
+
+
P
v
+++
t
SQL
x
x
T
disk
27
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28. Managed Services provided by
Federated In-Memory Database System (FIMDB)
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Node i
WorkerWorkerWorker
IMDB
Node j
WorkerWorkerWorker
IMDB
Node k
WorkerWorkerWorker
IMDB
Scheduler
Node m
WorkerWorkerWorker
IMDB
Relay
Node n
WorkerWorkerWorker
IMDB
...
Cloud Service Provider
(Shared Algorithms and Public Reference Data)
Hospital or Research Department
(Sensitive/Patient Data)
VPN
UDP
TCP
Shared File System (Pool) Shared File System (Pool)
...
Shared File System (Global)
29. From Raw Genome Data to Analysis
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■ DNA Sequencing: Transformation of
analogues DNA into digital format
■ Alignment: Reconstruction of complete
genome with snippets
■ Variant Calling: Identification of genetic
variants
■ Data Annotation: Linking genetic variants
with research findings
29
30. Reproducibility
Modeling of Data Analysis Pipelines
1. Design time (researcher, process expert)
□ Definition of parameterized process model
□ Uses graphical editor and jobs from repository
2. Configuration time (researcher, lab assistant)
□ Select model and specify parameters, e.g. aln opts
□ Results in model instance stored in repository
3. Execution time (researcher)
□ Select model instance
□ Specify execution parameters, e.g. input files
When time matters...
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31. App Example:
Cloud-based Services for Processing of DNA Data
■ Control center for processing of raw DNA data, such as
FASTQ, SAM, and VCF
■ Personal user profile guarantees privacy of uploaded
and processed data
■ Supports reproducible research process by storing all
relevant process parameters
■ Implements prioritized data processing and fair use, e.g.
per department or per institute
■ Supports additional service, such as data annotations,
billing, and sharing for all Analyze Genomes services
■ Honored by the 2014 European Life Science Award
When time matters...
Standardized Modeling and
runtime environment for
analysis pipelines
31
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32. Real-time Data Analysis and
Interactive Exploration
App Example:
Identification of Optimal Chemotherapy
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of Genomics, Jan 31,
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Smoking status,
tumor classification
and age
(1MB - 100MB)
Raw DNA data
and genetic variants
(100MB - 1TB)
Medication efficiency
and wet lab results
(10MB - 1GB)
32
Patient-specific
Data
Tumor-specific
Data
Compound
Interaction Data
■ Honored by the 2015 PerMediCon Award
35. Dr. Schapranow, Festival
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cetuximab might be more
beneficial for the current case
36. ■ Query-oriented search interface
■ Seamless integration of patient specifics, e.g. from EMR
■ Parallel search in international knowledge bases, e.g. for biomarkers, literature,
cellular pathway, and clinical trials
App Example:
Medical Knowledge Cockpit for Patients and Clinicians
When time matters...
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37. Dr. Schapranow, Festival
of Genomics, Jan 31,
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Medical Knowledge Cockpit for Patients and Clinicians
Pathway Topology Analysis
■ Search in pathways is limited to “is a certain
element contained” today
■ Integrated >1,5k pathways from international
sources, e.g. KEGG, HumanCyc, and WikiPathways,
into HANA
■ Implemented graph-based topology exploration and
ranking based on patient specifics
■ Enables interactive identification of possible
dysfunctions affecting the course of a therapy
before its start
When time matters...
Unified access to multiple formerly
disjoint data sources
Pathway analysis of genetic
variants with graph engine
37
38. Dr. Schapranow, Festival
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2017
■ Interactively explore relevant publications, e.g. PDFs
■ Improved ease of exploration, e.g. by highlighted medical terms and relevant
concepts
Medical Knowledge Cockpit for Patients and Clinicians
Publications
When time matters...
38
39. Real-time Assessment of Clinical Trial Candidates
■ Switch from trial-centric to patient-centric clinical trials
■ Real-time matching and clustering of patients and
clinical trial inclusion/exclusion criteria
■ No manual pre-screening of patients for months:
In-memory technology enables interactive pre-
screening process
■ Reassessment of already screened or already
participating patient reduces recruitment costs
When time matters...
Assessment of patients
preconditions for clinical trials
39
Dr. Schapranow, Festival
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40. ■ For patients
□ Identify relevant clinical trials and medical experts
□ Become an informed patient
■ For clinicians
□ Identify pharmacokinetic correlations
□ Scan for similar patient cases, e.g. to evaluate therapy efficiency
■ For researchers
□ Enable real-time analysis of medical data, e.g. assess pathways
to identify impact of detected variants
□ Combined mining in structured and unstructured data, e.g. publications,
diagnosis, and EMR data
What to Take Home?
Learn more and test-drive it yourself: AnalyzeGenomes.com
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When time matters...
41. Keep in contact with us!
Dr. Schapranow, Festival
of Genomics, Jan 31,
2017
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Dr.-Ing. Matthieu-P. Schapranow
Program Manager E-Health & Life Sciences
Hasso Plattner Institute
August-Bebel-Str. 88
14482 Potsdam, Germany
schapranow@hpi.de
http://we.analyzegenomes.com/