The document discusses the genomics revolution from the perspective of a privacy researcher. It outlines the benefits of whole genome sequencing for medicine but also notes privacy concerns, as genomic data is highly sensitive and difficult to anonymize. While sequencing costs have declined drastically, enabling testing for many, it also means more sensitive personal data is being collected. The researcher describes work exploring these privacy issues, such as quantifying how relatives' privacy is affected when one genome is leaked. Techniques like differential privacy and secure computation are also discussed for how they may enable privacy-preserving genomic testing in the future.
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
This presents a number of case studies on the application on high-throughput sequencing (HTS), next generation sequencing (NGS), to biological problems ranging from human genome sequencing, identification of disease mutations, metagenomics, virus discovery, epidemic, transmission chains and viral populations. Presented at the University of Glasgow on Friday 26th June 2015.
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
This presents a number of case studies on the application on high-throughput sequencing (HTS), next generation sequencing (NGS), to biological problems ranging from human genome sequencing, identification of disease mutations, metagenomics, virus discovery, epidemic, transmission chains and viral populations. Presented at the University of Glasgow on Friday 26th June 2015.
Building bioinformatics resources for the global communityExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Building bioinformatics resources for the global community. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.
Shining a light on virus infection with high-resolution microscopyRoland Remenyi, PhD
Each year the Astbury Centre holds a research retreat to promote interdisciplinary activity, to discuss and present latest findings and to promote and encourage interdisciplinary research at the highest level. I communicated my results from a Chikungunya virus project in a 15-min presentation. Slides from this presentation are shown here.
Application of Whole Genome Sequencing in the infectious disease’ in vitro di...ExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Applications of WGS in industry. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
This lecture covers key findings to the development of genomics as a field. This first part covers briefly Mendel to knowing that DNA is the genetic material by Hershey and Chase
Viral metagenomics is the study of viral genetic material sourced directly from the environment rather than from a host or natural reservoir. The goal is to ascertain the viral diversity in the environment that is often missed in studies targeting specific potential reservoirs.
Supporting Genomics in the Practice of Medicine by Heidi RehmKnome_Inc
View the webinar at http://www.knome.com/webinar-supporting-genomics-practice-medicine. In this presentation, Dr. Heidi Rehm, Chief Laboratory Director of the Laboratory for Molecular Medicine at Partners Healthcare and one of the Principal Investigators on ClinGen, elucidates the challenges of genomics in medicine and outlined the path to integrating large scale sequencing into clinical practice.
Quantified Self On Being A Personal Genomic ObservatoryLarry Smarr
Larry Smarr's presentation on the "Quantified Self On Being A Personal Genomic Observatory", Keynote in the "Humans as Genomic Observatories" Meeting Session in the Genomics Standards Consortium, GSC 15, April 24, 2013
Building bioinformatics resources for the global communityExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Building bioinformatics resources for the global community. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.
Shining a light on virus infection with high-resolution microscopyRoland Remenyi, PhD
Each year the Astbury Centre holds a research retreat to promote interdisciplinary activity, to discuss and present latest findings and to promote and encourage interdisciplinary research at the highest level. I communicated my results from a Chikungunya virus project in a 15-min presentation. Slides from this presentation are shown here.
Application of Whole Genome Sequencing in the infectious disease’ in vitro di...ExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Applications of WGS in industry. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
This lecture covers key findings to the development of genomics as a field. This first part covers briefly Mendel to knowing that DNA is the genetic material by Hershey and Chase
Viral metagenomics is the study of viral genetic material sourced directly from the environment rather than from a host or natural reservoir. The goal is to ascertain the viral diversity in the environment that is often missed in studies targeting specific potential reservoirs.
Supporting Genomics in the Practice of Medicine by Heidi RehmKnome_Inc
View the webinar at http://www.knome.com/webinar-supporting-genomics-practice-medicine. In this presentation, Dr. Heidi Rehm, Chief Laboratory Director of the Laboratory for Molecular Medicine at Partners Healthcare and one of the Principal Investigators on ClinGen, elucidates the challenges of genomics in medicine and outlined the path to integrating large scale sequencing into clinical practice.
Quantified Self On Being A Personal Genomic ObservatoryLarry Smarr
Larry Smarr's presentation on the "Quantified Self On Being A Personal Genomic Observatory", Keynote in the "Humans as Genomic Observatories" Meeting Session in the Genomics Standards Consortium, GSC 15, April 24, 2013
Personal Genomes: what can I do with my data?Melanie Swan
Biology evolved to be just good enough to survive and genomics provides the critical next-generation toolkit for its greater exploitation. Genomics is already starting to be medically actionable and is likely to become increasingly useful over time. This presentation discusses how your genetic information is already useful today,
IRIDA's Genomic epidemiology application ontology for data standardization, integration and sharing. Presented at IMMEM XI in Estoril, Portugal, March 11 2016.
Single-Cell Sequencing for Drug Discovery: Applications and Challengesinside-BigData.com
In this deck from DOE CSGF 2019, Sarah Middleton from GlaxoSmithKline presents: Single-Cell Sequencing for Drug Discovery: Applications and Challenges.
"Most gene expression studies have been performed on “bulk” tissue samples, consisting of millions of cells of various types and functions mixed together. Although such research is extremely useful for comparing general characteristics of tissues – for example, before and after therapeutic drug treatment – they are limited in their ability to inform on the characteristics and responses of different cell types within the tissue. More recently, advances in techniques for single-cell RNA sequencing have made it possible to profile gene expression in individual cells on a large scale, opening up the possibility to explore the heterogeneity of expression within and across cell types. This exciting technology is now being applied to almost every tissue in the human body, with some experiments generating expression profiles for more than 100,000 cells at a time. However, several roadblocks still stand in the way of making full use of this information, including issues related to missing data and scaling up existing bioinformatics analytical tools. Here, I will discuss some of the ways single-cell RNA-sequencing is being used to improve drug discovery and development, as well as some of the challenges we currently face. I’ll also highlight a new approach I am developing to help overcome some of these challenges."
Watch the video: https://wp.me/p3RLHQ-lkw
Learn more: https://www.krellinst.org/csgf/conf/2019/agenda
Sign up for our insideHPC Newsletter: http://insidehpc.com/newsletter
Smart TV Buyer Insights Survey 2024 by 91mobiles.pdf91mobiles
91mobiles recently conducted a Smart TV Buyer Insights Survey in which we asked over 3,000 respondents about the TV they own, aspects they look at on a new TV, and their TV buying preferences.
"Impact of front-end architecture on development cost", Viktor TurskyiFwdays
I have heard many times that architecture is not important for the front-end. Also, many times I have seen how developers implement features on the front-end just following the standard rules for a framework and think that this is enough to successfully launch the project, and then the project fails. How to prevent this and what approach to choose? I have launched dozens of complex projects and during the talk we will analyze which approaches have worked for me and which have not.
Builder.ai Founder Sachin Dev Duggal's Strategic Approach to Create an Innova...Ramesh Iyer
In today's fast-changing business world, Companies that adapt and embrace new ideas often need help to keep up with the competition. However, fostering a culture of innovation takes much work. It takes vision, leadership and willingness to take risks in the right proportion. Sachin Dev Duggal, co-founder of Builder.ai, has perfected the art of this balance, creating a company culture where creativity and growth are nurtured at each stage.
UiPath Test Automation using UiPath Test Suite series, part 3DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 3. In this session, we will cover desktop automation along with UI automation.
Topics covered:
UI automation Introduction,
UI automation Sample
Desktop automation flow
Pradeep Chinnala, Senior Consultant Automation Developer @WonderBotz and UiPath MVP
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
Connector Corner: Automate dynamic content and events by pushing a buttonDianaGray10
Here is something new! In our next Connector Corner webinar, we will demonstrate how you can use a single workflow to:
Create a campaign using Mailchimp with merge tags/fields
Send an interactive Slack channel message (using buttons)
Have the message received by managers and peers along with a test email for review
But there’s more:
In a second workflow supporting the same use case, you’ll see:
Your campaign sent to target colleagues for approval
If the “Approve” button is clicked, a Jira/Zendesk ticket is created for the marketing design team
But—if the “Reject” button is pushed, colleagues will be alerted via Slack message
Join us to learn more about this new, human-in-the-loop capability, brought to you by Integration Service connectors.
And...
Speakers:
Akshay Agnihotri, Product Manager
Charlie Greenberg, Host
Search and Society: Reimagining Information Access for Radical FuturesBhaskar Mitra
The field of Information retrieval (IR) is currently undergoing a transformative shift, at least partly due to the emerging applications of generative AI to information access. In this talk, we will deliberate on the sociotechnical implications of generative AI for information access. We will argue that there is both a critical necessity and an exciting opportunity for the IR community to re-center our research agendas on societal needs while dismantling the artificial separation between the work on fairness, accountability, transparency, and ethics in IR and the rest of IR research. Instead of adopting a reactionary strategy of trying to mitigate potential social harms from emerging technologies, the community should aim to proactively set the research agenda for the kinds of systems we should build inspired by diverse explicitly stated sociotechnical imaginaries. The sociotechnical imaginaries that underpin the design and development of information access technologies needs to be explicitly articulated, and we need to develop theories of change in context of these diverse perspectives. Our guiding future imaginaries must be informed by other academic fields, such as democratic theory and critical theory, and should be co-developed with social science scholars, legal scholars, civil rights and social justice activists, and artists, among others.
PHP Frameworks: I want to break free (IPC Berlin 2024)Ralf Eggert
In this presentation, we examine the challenges and limitations of relying too heavily on PHP frameworks in web development. We discuss the history of PHP and its frameworks to understand how this dependence has evolved. The focus will be on providing concrete tips and strategies to reduce reliance on these frameworks, based on real-world examples and practical considerations. The goal is to equip developers with the skills and knowledge to create more flexible and future-proof web applications. We'll explore the importance of maintaining autonomy in a rapidly changing tech landscape and how to make informed decisions in PHP development.
This talk is aimed at encouraging a more independent approach to using PHP frameworks, moving towards a more flexible and future-proof approach to PHP development.
GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using Deplo...James Anderson
Effective Application Security in Software Delivery lifecycle using Deployment Firewall and DBOM
The modern software delivery process (or the CI/CD process) includes many tools, distributed teams, open-source code, and cloud platforms. Constant focus on speed to release software to market, along with the traditional slow and manual security checks has caused gaps in continuous security as an important piece in the software supply chain. Today organizations feel more susceptible to external and internal cyber threats due to the vast attack surface in their applications supply chain and the lack of end-to-end governance and risk management.
The software team must secure its software delivery process to avoid vulnerability and security breaches. This needs to be achieved with existing tool chains and without extensive rework of the delivery processes. This talk will present strategies and techniques for providing visibility into the true risk of the existing vulnerabilities, preventing the introduction of security issues in the software, resolving vulnerabilities in production environments quickly, and capturing the deployment bill of materials (DBOM).
Speakers:
Bob Boule
Robert Boule is a technology enthusiast with PASSION for technology and making things work along with a knack for helping others understand how things work. He comes with around 20 years of solution engineering experience in application security, software continuous delivery, and SaaS platforms. He is known for his dynamic presentations in CI/CD and application security integrated in software delivery lifecycle.
Gopinath Rebala
Gopinath Rebala is the CTO of OpsMx, where he has overall responsibility for the machine learning and data processing architectures for Secure Software Delivery. Gopi also has a strong connection with our customers, leading design and architecture for strategic implementations. Gopi is a frequent speaker and well-known leader in continuous delivery and integrating security into software delivery.
State of ICS and IoT Cyber Threat Landscape Report 2024 previewPrayukth K V
The IoT and OT threat landscape report has been prepared by the Threat Research Team at Sectrio using data from Sectrio, cyber threat intelligence farming facilities spread across over 85 cities around the world. In addition, Sectrio also runs AI-based advanced threat and payload engagement facilities that serve as sinks to attract and engage sophisticated threat actors, and newer malware including new variants and latent threats that are at an earlier stage of development.
The latest edition of the OT/ICS and IoT security Threat Landscape Report 2024 also covers:
State of global ICS asset and network exposure
Sectoral targets and attacks as well as the cost of ransom
Global APT activity, AI usage, actor and tactic profiles, and implications
Rise in volumes of AI-powered cyberattacks
Major cyber events in 2024
Malware and malicious payload trends
Cyberattack types and targets
Vulnerability exploit attempts on CVEs
Attacks on counties – USA
Expansion of bot farms – how, where, and why
In-depth analysis of the cyber threat landscape across North America, South America, Europe, APAC, and the Middle East
Why are attacks on smart factories rising?
Cyber risk predictions
Axis of attacks – Europe
Systemic attacks in the Middle East
Download the full report from here:
https://sectrio.com/resources/ot-threat-landscape-reports/sectrio-releases-ot-ics-and-iot-security-threat-landscape-report-2024/
UiPath Test Automation using UiPath Test Suite series, part 4DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 4. In this session, we will cover Test Manager overview along with SAP heatmap.
The UiPath Test Manager overview with SAP heatmap webinar offers a concise yet comprehensive exploration of the role of a Test Manager within SAP environments, coupled with the utilization of heatmaps for effective testing strategies.
Participants will gain insights into the responsibilities, challenges, and best practices associated with test management in SAP projects. Additionally, the webinar delves into the significance of heatmaps as a visual aid for identifying testing priorities, areas of risk, and resource allocation within SAP landscapes. Through this session, attendees can expect to enhance their understanding of test management principles while learning practical approaches to optimize testing processes in SAP environments using heatmap visualization techniques
What will you get from this session?
1. Insights into SAP testing best practices
2. Heatmap utilization for testing
3. Optimization of testing processes
4. Demo
Topics covered:
Execution from the test manager
Orchestrator execution result
Defect reporting
SAP heatmap example with demo
Speaker:
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
Kubernetes & AI - Beauty and the Beast !?! @KCD Istanbul 2024Tobias Schneck
As AI technology is pushing into IT I was wondering myself, as an “infrastructure container kubernetes guy”, how get this fancy AI technology get managed from an infrastructure operational view? Is it possible to apply our lovely cloud native principals as well? What benefit’s both technologies could bring to each other?
Let me take this questions and provide you a short journey through existing deployment models and use cases for AI software. On practical examples, we discuss what cloud/on-premise strategy we may need for applying it to our own infrastructure to get it to work from an enterprise perspective. I want to give an overview about infrastructure requirements and technologies, what could be beneficial or limiting your AI use cases in an enterprise environment. An interactive Demo will give you some insides, what approaches I got already working for real.
Accelerate your Kubernetes clusters with Varnish CachingThijs Feryn
A presentation about the usage and availability of Varnish on Kubernetes. This talk explores the capabilities of Varnish caching and shows how to use the Varnish Helm chart to deploy it to Kubernetes.
This presentation was delivered at K8SUG Singapore. See https://feryn.eu/presentations/accelerate-your-kubernetes-clusters-with-varnish-caching-k8sug-singapore-28-2024 for more details.
Software Delivery At the Speed of AI: Inflectra Invests In AI-Powered QualityInflectra
In this insightful webinar, Inflectra explores how artificial intelligence (AI) is transforming software development and testing. Discover how AI-powered tools are revolutionizing every stage of the software development lifecycle (SDLC), from design and prototyping to testing, deployment, and monitoring.
Learn about:
• The Future of Testing: How AI is shifting testing towards verification, analysis, and higher-level skills, while reducing repetitive tasks.
• Test Automation: How AI-powered test case generation, optimization, and self-healing tests are making testing more efficient and effective.
• Visual Testing: Explore the emerging capabilities of AI in visual testing and how it's set to revolutionize UI verification.
• Inflectra's AI Solutions: See demonstrations of Inflectra's cutting-edge AI tools like the ChatGPT plugin and Azure Open AI platform, designed to streamline your testing process.
Whether you're a developer, tester, or QA professional, this webinar will give you valuable insights into how AI is shaping the future of software delivery.
Software Delivery At the Speed of AI: Inflectra Invests In AI-Powered Quality
The Genomics Revolution: The Good, The Bad, and The Ugly
1. The Genomics Revolution: The
Good, The Bad, and The Ugly
(A Privacy Researcher's Perspective)
Emiliano De Cristofaro
University College London
https://emilianodc.com
2. In a nutshell
The Good
Revolution in medicine and healthcare
Genetic testing for the masses
The Bad
Collection of highly sensitive data
Very hard to anonymize / de-identify
The Ugly
Greater good vs privacy
Encryption might not be the answer
2
4. WGS Progress
History
1970s: DNA sequencing starts
1990: The “Human Genome Project” starts
2003: First human genome fully sequenced
2012: UK announces sequencing of 100K genomes
2015: USA announces sequencing of 1M genomes
$$$
$3B: Human Genome Project
$250K: Illumina (2008)
$5K: Complete Genomics (2009), Illumina (2011)
$1K: Illumina (2014) 4
5. How to read the
genome?
Genotyping
Testing for genetic
differences using a set
of markers
Sequencing
Determining the full
nucleotide order of an
organism’s genome
5
12. Privacy Researcher’s Perspective
Treasure trove of sensitive information
Ethnic heritage, predisposition to diseases
Genome = the ultimate identifier
Hard to anonymize / de-identify
Sensitivity is perpetual
Cannot be “revoked”
Leaking one’s genome ≈ leaking relatives’ genome
12
16. Aggregation
Re-identification of aggregated data
Statistics from allele frequencies can be used to
identify genetic trial participants [1]
Presence of an individual in a group can be determined by
using allele frequencies and his DNA profile [2]
[1] R. Wang et al. “Learning Your Identity and Disease from Research Papers:
Information Leaks in Genome Wide Association Study.” ACM CCS, 2009
[2] N. Homer et al. Resolving individuals contributing trace amounts of DNA to highly
complex mixtures using high-density SNP genotyping microarrays. PLoS Genetics,
4, Aug. 2008 16
17. Kin Privacy
Quantifying how much privacy do relatives lose
when one’s genome is leaked?
M. Humbert et al., “Addressing the Concerns of the Lacks Family:
Quantification of Kin Genomic Privacy.” Proceedings of ACM CCS, 2013
Also read: “Routes for
breaching genetic privacy”
Y. Erlich and A. Narayanan,
Nature Review Genetics
Vol. 15, No. 6, 2014
19. Ethnographic Studies in WGS
Semi-structured interviews with 16 participants
Assessing perception of genetic tests, attitude toward WGS
programs, as well as perception of privacy/ethical issues
(Some) Preliminary results
1. Preferred method is through doctors not companies
(trust)
2. Labor/healthcare discrimination top concerns
3. Differences in correlation with income and education
E. De Cristofaro. “Users' Attitudes, Perception, and Concerns in the
Era of Whole Genome Sequencing.” (USEC 2014)
19
20. The rise of a new research community
Studying privacy issues
Exploring techniques to protect privacy
20
21. Differential Privacy
Computing number/location of SNPs associated to disease
Significance/correlation between a SNP and a disease
A. Johnson and V. Shmatikov. “Privacy-Preserving Data Exploration in
Genome-Wide Association Studies.” Proceedings of KDD, 2013
21
Privacy in Genome Wide Association Studies (GWAS)
22. Privacy-Preserving Genomic Tests
Individuals retain control of their sequenced
genome
Allow doctors/labs to run genetics tests, but:
1. Genome never disclosed, only test output is
2. Pharmas can keep test specifics confidential
… two main approaches …
22
23. (i)DNA
sample
(i) Clinical and
Environmental
data
(ii) Encrypted SNPs
(iii)Disease
Risk
Computation
CERTIFIED
INSTITUTION (CI)
MEDICAL
UNIT (MU)
STORAGE AND
PROCESSING UNIT (SPU)
PATIENT
(P)
1. Using Semi-Trusted Parties
23
24. 1. Using Semi-Trusted Parties
Ayday et al. (WPES’13)
Data is encrypted and stored at a “Storage Process Unit”
Disease susceptibility testing
Ayday et al. (DPM’13)
Encrypting raw genomic data (short reads)
Allowing medical unit to privately retrieve them
Danezis and De Cristofaro (WPES’14)
Regression for disease susceptibility
24
25. doctor
or lab
genome
individual
test specifics
Secure
Function
Evaluation
test result test result
• Private Set Intersection (PSI)
• Authorized PSI
• Private Pattern Matching
• Homomorphic Encryption
• Garbled Circtuis
• […]
Output reveals nothing beyond
test result
• Paternity/Ancestry Testing
• Testing of SNPs/Markers
• Compatibility Testing
• […]
2. Users keep sequenced genomes
25
26. 2. Users keep sequenced genomes
Baldi et al. (CCS’11)
Privacy-preserving version of a few genetic tests, based
on private set operations
Paternity test, Personalized Medicine, Compatibility Tests
(First work to consider fully sequenced genomes)
De Cristofaro et al. (WPES’12), extends the above
Framework and prototype deployment on Android
Adds Ancestry/Genealogy Testing
26
27. Private Set Intersection (PSI)
Server Client
S ={s1, ,sw} C ={c1, ,cv}
Private
Set Intersection
SÇC
27
30. Open Problems
Where do we store genomes?
Encryption can’t guarantee security past 30-50 yrs
Reliability and availability issues?
Cryptography
Efficiency overhead
Data representation assumptions
How much understanding required from users?
30
31. We all leave biological cells behind…
Hair, saliva, etc., can be collected and sequenced?
Compare this “attack” to re-identifying millions
of DNA donors or hacking into 23andme…
The former: expensive, prone to mistakes, only works
against a handful of targeted victims
The latter: very “scalable”
Why do we even care
about genome privacy?
31
32. Epilogue
Whole Genome Sequencing
A revolution in healthcare
Raises worrisome privacy/ethical concerns
The Genomic Privacy research community
Understanding the privacy issues
Privacy-preserving testing on whole genomes
Possible using efficient crypto protocols & cross-discipline
collaboration
A number of open research issues…
32
33. For more info:
http://genomeprivacy.org
Also:
E. Ayday, E. De Cristofaro, J.P. Hubaux, G. Tsudik.
“Whole Genome Sequencing: Revolutionary
Medicine or Privacy Nightmare?”
IEEE Computer Magazine
34. Thank you!
Special thanks to
E. Ayday, P. Baldi, R. Baronio, G. Danezis, S. Faber,
P. Gasti, J-P. Hubaux, B. Malin, G. Tsudik.