SlideShare a Scribd company logo
Dx29: genetic rare disease
diagnosis support with AI
Pablo Botas
Head of Science, Foundation29
O R G A N I Z A T I O N
P L A T I N U M S P O N S O R S
Thank you!
C O L L A B O R A T O R S
pablo.botas@foundation29.org
Rare genetic diseases are very challenging to diagnose, with the
average child waiting for diagnosis for 5 years. Next generation genetic
sequencing data may hold the key to diagnosis, however analysis can
become a paramount task with multiple factors affecting conclusions.
Dx29, an AI-assisted platform facilitates this task, allowing the
physician to drive the analysis. Dx29 is a free platform developed by
Foudation29, in close collaboration with academic groups
Pablo Botas
Head of Science at Foundation29
https://globalgenes.org/rare-facts/
1 in 10
People
affected by
Rare Disease
3 of 10
Children with a Rare
Disease won’t live to
see their 5th birthday
8 in 10
Have a genetic
origin
4.8 Years
For patients to
receive a diagnosis
95%
of Rare Diseases
lack approved
treatment
10000
Rare Diseases
Rare disease facts
4
5
Lack of diagnosis is lack of data
• Lack of diagnosis is about lack of signal
• Doctors can’t let you know where you are
• Your journey starts by collecting information
6
Diagnosis navigator
7
Diagnosis is about finding a route
• Navigation requires a map and data coordinates
• Inaccurate navigation has very high costs!!
8
Required coordinates:
1. Symptoms
2. Genetic Variants
Icons by different authors from www.flaticon.com
Symptom-based path-finding (diagnosis)
 Rare diseases have complex phenotypes
 Differential diagnosis based on subtle
details
 Rare diseases: inexperience
 Disease evolution is gradual
 Symptom identification is hard
 Short time per patient, independently
of complexity
9
10
Licensed under CC BY-SA-NC
Icons by different authors from www.flaticon.com
Genotype-based path-finding (diagnosis)
 Genetic testing is a black box
 Mutation analysis is often manual
 Symptom identification is hard!
 EMR is not a good communication tool
 Difficult consideration of new symptoms
11
: AI as the GPS powering the navigation
12
New patient
to study
The navigator
DNA data
Symptom extraction
using NLP
1
Variant
prioritization
supported by the
phenotype
2
Candidate
symptoms based
on the mutations
3
Candidate
conditions for
assessment
4 13
1. Symptom identification
 Dx29 uses NCR1,2, developed by the
Centre for Computational Medicine at
SickKids, Toronto
 Deep NN to classify concepts into Human
Phenotype Ontology (HPO)3 terms
EMR, electronic medical records; NN, neural network; NLP, natural language processing
1. Github. 2019. Available from: https://github.com/ccmbioinfo/NeuralCR (Accessed 11 June 2019);
2. Arbabi A, et al. 2019; 7(2):e12596. doi: 10.2196/12596.
3. Köhler S, et al. Nucleic Acids Res 2018;47:D1018–D1027 14
How to compute on concepts?
Rank mutation
pathogenicity based
on public databases:
Exomiser1,2
1. Robinson PN, et al. Genome Res 2014;24:340–34; 2. Github. 2019. Available from: https://github.com/exomiser/Exomiser
(Accessed 11 June 2019); 3. Zhou X, et al. Nat Commun 2014;5:4212; 4. Wang Genomics Lab. 2019. Available from: http://phenolyzer.wglab.org/ (Accessed 11
June 2019); 5. Yang H, et al. Nat Methods 2015;12:841–843
2. Variant analysis
1. Robinson PN, et al. Genome Res 2014;24:340–34; 2. Github. 2019. Available from: https://github.com/exomiser/Exomiser
(Accessed 11 June 2019); 3. Zhou X, et al. Nat Commun 2014;5:4212; 4. Wang Genomics Lab. 2019. Available from: http://phenolyzer.wglab.org/ (Accessed 11
June 2019); 5. Yang H, et al. Nat Methods 2015;12:841–843
What if no genetic
data is available?
Build list of candidate genes
based on disease networks3 :
Phenolyzer4,5
2. Variant analysis
3. Engage with patient: What is missing?
18
4. Results analysis
19
• Open platform to deploy and run diagnosis models
• Data available to academia to develop and test new approaches
• Open-source code and philosophy
• Data donor concept implementation
• Diagnosis of complex cases based on clustering using ML
Overall platform summary
20
• Very useful in areas with
no access to genetic testing
• Cloud-based, no installation
required
• Available (beta) at dx29.ai
• A single variant prioritisation
algorithm
doesn’t work for all conditions
• NLP is an ongoing challenge
• Phenotype quality in
public databases is poor
• Seamless UX is required for a
complex process
• Patients need their own
navigator
• Very good feedback from
physicians
• Exploring symptoms is useful and
innovative
• High performance: academia
This is great, but what about the data used … ?
22
The need for high quality data
Think
about
it!!
24
How are
diseases
named?
• PSR means the object is a pulsar.
• The J reveals that a coordinate system known as J2000 is used.
• 1302 and 6350 are coordinates like the latitude and longitude.
PSR J1302-6350
Dravet Syndrome
Lennox-Gastaut Syndrome
Allan–Herndon–Dudley Syndrome
SCN1A
MECP2
CDKL5
STXBP1
26
Rett Syndrome
West
Dravet
LGSSCN1A
?
A real case:
27
28
SCN1A
Dravet Syndrome
Febrile Seizures
Temporal Lobe Epilepsy
Myoclonic Astatic Epilepsy
Lennox-Gastaut Syndrome
Migrating Partial Epilepsy of Infancy (MMPSI)
Autism
http://epilepsygenetics.net/the-epilepsiome/scn1a-this-is-what-you-need-to-know/
29
30
3 2581703423 4457570
Let’s do a better job!!
https://deepai.org/publication/embedding-complexity-in-the-data-representation-instead-of-in-the-model-a-case-study-using-heterogeneous-medical-data
How to compute on concepts?
Dx29: assisting genetic disease diagnosis with physician-focused AI pipelines
Data locker of patient-owned data, for
the development of new algorithms.
Patients with complex conditions
(multiple genes, big genomic
changes) need an approach based on
mixed learning
: navigator for patients
35
36
Final notes
1. Key technologies: NGS + AI
2. NGS+AI makes healthcare personalized, accurate and affordable
3. NGS+AI require development of standards and platforms
4. Seamless UX is vital for technology adoption
5. Transformation of healthcare into information-centered process
6. Rare diseases offer the perfect niche for testing: want to help?
7. Foundation29 is laying the basis for such transformation
Thanks and …
See you soon!
Thanks also to the sponsors.
Without whom this would not have been posible.
O R G A N I Z A T I O N
P L A T I N U M S P O N S O R S
C O L L A B O R A T O R S

More Related Content

PDF
The Necessary
PPTX
petros tsipouras
PPTX
2016 ngs health_lecture
PDF
London & Partners MedCity Cell & Gene Therapy Report
PDF
2017 BDSRA Whiting and Katz CLN2
PPT
2017 BDSRA Tammen, Grupen, James and Delerue CLN6 CLN7
PDF
Gene Therapy
PDF
The State of Play in Diagnosis
The Necessary
petros tsipouras
2016 ngs health_lecture
London & Partners MedCity Cell & Gene Therapy Report
2017 BDSRA Whiting and Katz CLN2
2017 BDSRA Tammen, Grupen, James and Delerue CLN6 CLN7
Gene Therapy
The State of Play in Diagnosis

Similar to Dx29: assisting genetic disease diagnosis with physician-focused AI pipelines (20)

PDF
Illuminating the Druggable Genome with Knowledge Engineering and Machine Lear...
PDF
Forum on Personalized Medicine: Challenges for the next decade
PPTX
Data-driven drug discovery for rare diseases - Tales from the trenches (CINF ...
PPTX
Diagnostic Testing for Mitochondrial Disease
PDF
Data sharing and analysis
PDF
Zen and the Art of Data Science Maintenance
PPTX
Data Translator: an Open Science Data Platform for Mechanistic Disease Discovery
PDF
Laura Furlong. Big Data in Biomedicine debate. Barcelona, Nov 11 2014
PPT
Creating custom gene panels for next-generation sequencing: optimization of 5...
PDF
Drug Repositioning Conference Washington DC 20190923
PPTX
Identification of pathological mutations from the single-gene case to exome p...
PPTX
Pediatric Genetics & Genomics
PDF
Amia tb-review-15
PDF
Supporting Genomics in the Practice of Medicine by Heidi Rehm
PPTX
Human Genetics & Big Data [sans Ethics]
PPTX
Advanced genomics v_medical_pitt_kent_osu
PPTX
ReComp and P4@NU: Reproducible Data Science for Health
PPTX
Canada's path forward for rare diseases: Discovery to translation
PPT
Avances en genética. Utilidad de la NGS y la bioinformática.
PDF
Deep learning for biomedicine
Illuminating the Druggable Genome with Knowledge Engineering and Machine Lear...
Forum on Personalized Medicine: Challenges for the next decade
Data-driven drug discovery for rare diseases - Tales from the trenches (CINF ...
Diagnostic Testing for Mitochondrial Disease
Data sharing and analysis
Zen and the Art of Data Science Maintenance
Data Translator: an Open Science Data Platform for Mechanistic Disease Discovery
Laura Furlong. Big Data in Biomedicine debate. Barcelona, Nov 11 2014
Creating custom gene panels for next-generation sequencing: optimization of 5...
Drug Repositioning Conference Washington DC 20190923
Identification of pathological mutations from the single-gene case to exome p...
Pediatric Genetics & Genomics
Amia tb-review-15
Supporting Genomics in the Practice of Medicine by Heidi Rehm
Human Genetics & Big Data [sans Ethics]
Advanced genomics v_medical_pitt_kent_osu
ReComp and P4@NU: Reproducible Data Science for Health
Canada's path forward for rare diseases: Discovery to translation
Avances en genética. Utilidad de la NGS y la bioinformática.
Deep learning for biomedicine
Ad

More from Plain Concepts (20)

PPTX
R y Python con Power BI, la ciencia y el análisis de datos, juntos
PDF
Video kills the radio star: e-mail is crap and needed disruption
PPTX
Cómo redefinir tu organización con IA
PDF
¿Qué es real? Cuando la IA intenta engañar al ojo humano
PPTX
Inteligencia artificial para detectar el cáncer de mama
PPTX
¿Está tu compañía preparada para el reto de la Inteligencia Artificial?
PDF
Cognitive Services en acción
PDF
El Hogar Inteligente. De los datos de IoT a los hábitos de una familia a trav...
PDF
What if AI was your daughter?
PPTX
Recomendación Basada en Contenidos con Deep Learning: Qué queríamos hacer, Qu...
PPTX
Revolucionando la experiencia de cliente con Big Data e IA
PPTX
IA Score en InfoJobs
PPTX
Recuperación de información para solicitantes de empleo
PPTX
La nueva revolución Industrial: Inteligencia Artificial & IoT Edge
PDF
DotNet 2019 | Sherry List - Azure Cognitive Services with Native Script
PDF
DotNet 2019 | Quique Fernández - Potenciando VUE con TypeScript, Inversify, V...
PDF
DotNet 2019 | Daniela Solís y Manuel Rodrigo Cabello - IoT, una Raspberry Pi ...
PPTX
El camino a las Cloud Native Apps - Introduction
PPTX
El camino a las Cloud Native Apps - Azure AI
PPTX
El camino a las Cloud Native Apps - Application modernization on Azure with c...
R y Python con Power BI, la ciencia y el análisis de datos, juntos
Video kills the radio star: e-mail is crap and needed disruption
Cómo redefinir tu organización con IA
¿Qué es real? Cuando la IA intenta engañar al ojo humano
Inteligencia artificial para detectar el cáncer de mama
¿Está tu compañía preparada para el reto de la Inteligencia Artificial?
Cognitive Services en acción
El Hogar Inteligente. De los datos de IoT a los hábitos de una familia a trav...
What if AI was your daughter?
Recomendación Basada en Contenidos con Deep Learning: Qué queríamos hacer, Qu...
Revolucionando la experiencia de cliente con Big Data e IA
IA Score en InfoJobs
Recuperación de información para solicitantes de empleo
La nueva revolución Industrial: Inteligencia Artificial & IoT Edge
DotNet 2019 | Sherry List - Azure Cognitive Services with Native Script
DotNet 2019 | Quique Fernández - Potenciando VUE con TypeScript, Inversify, V...
DotNet 2019 | Daniela Solís y Manuel Rodrigo Cabello - IoT, una Raspberry Pi ...
El camino a las Cloud Native Apps - Introduction
El camino a las Cloud Native Apps - Azure AI
El camino a las Cloud Native Apps - Application modernization on Azure with c...
Ad

Recently uploaded (20)

PDF
AI And Its Effect On The Evolving IT Sector In Australia - Elevate
PDF
Blue Purple Modern Animated Computer Science Presentation.pdf.pdf
PDF
Modernizing your data center with Dell and AMD
PDF
CIFDAQ's Market Insight: SEC Turns Pro Crypto
PDF
Advanced methodologies resolving dimensionality complications for autism neur...
PDF
Sensors and Actuators in IoT Systems using pdf
PPTX
Understanding_Digital_Forensics_Presentation.pptx
PDF
Chapter 3 Spatial Domain Image Processing.pdf
PDF
Advanced Soft Computing BINUS July 2025.pdf
PDF
cuic standard and advanced reporting.pdf
PDF
Advanced IT Governance
PPTX
Telecom Fraud Prevention Guide | Hyperlink InfoSystem
PDF
Empathic Computing: Creating Shared Understanding
PPTX
MYSQL Presentation for SQL database connectivity
PPTX
Comunidade Salesforce São Paulo - Desmistificando o Omnistudio (Vlocity)
PPTX
breach-and-attack-simulation-cybersecurity-india-chennai-defenderrabbit-2025....
PPTX
20250228 LYD VKU AI Blended-Learning.pptx
PDF
Per capita expenditure prediction using model stacking based on satellite ima...
PDF
Spectral efficient network and resource selection model in 5G networks
PDF
KodekX | Application Modernization Development
AI And Its Effect On The Evolving IT Sector In Australia - Elevate
Blue Purple Modern Animated Computer Science Presentation.pdf.pdf
Modernizing your data center with Dell and AMD
CIFDAQ's Market Insight: SEC Turns Pro Crypto
Advanced methodologies resolving dimensionality complications for autism neur...
Sensors and Actuators in IoT Systems using pdf
Understanding_Digital_Forensics_Presentation.pptx
Chapter 3 Spatial Domain Image Processing.pdf
Advanced Soft Computing BINUS July 2025.pdf
cuic standard and advanced reporting.pdf
Advanced IT Governance
Telecom Fraud Prevention Guide | Hyperlink InfoSystem
Empathic Computing: Creating Shared Understanding
MYSQL Presentation for SQL database connectivity
Comunidade Salesforce São Paulo - Desmistificando o Omnistudio (Vlocity)
breach-and-attack-simulation-cybersecurity-india-chennai-defenderrabbit-2025....
20250228 LYD VKU AI Blended-Learning.pptx
Per capita expenditure prediction using model stacking based on satellite ima...
Spectral efficient network and resource selection model in 5G networks
KodekX | Application Modernization Development

Dx29: assisting genetic disease diagnosis with physician-focused AI pipelines

  • 1. Dx29: genetic rare disease diagnosis support with AI Pablo Botas Head of Science, Foundation29
  • 2. O R G A N I Z A T I O N P L A T I N U M S P O N S O R S Thank you! C O L L A B O R A T O R S
  • 3. [email protected] Rare genetic diseases are very challenging to diagnose, with the average child waiting for diagnosis for 5 years. Next generation genetic sequencing data may hold the key to diagnosis, however analysis can become a paramount task with multiple factors affecting conclusions. Dx29, an AI-assisted platform facilitates this task, allowing the physician to drive the analysis. Dx29 is a free platform developed by Foudation29, in close collaboration with academic groups Pablo Botas Head of Science at Foundation29
  • 4. https://globalgenes.org/rare-facts/ 1 in 10 People affected by Rare Disease 3 of 10 Children with a Rare Disease won’t live to see their 5th birthday 8 in 10 Have a genetic origin 4.8 Years For patients to receive a diagnosis 95% of Rare Diseases lack approved treatment 10000 Rare Diseases Rare disease facts 4
  • 5. 5
  • 6. Lack of diagnosis is lack of data • Lack of diagnosis is about lack of signal • Doctors can’t let you know where you are • Your journey starts by collecting information 6
  • 8. Diagnosis is about finding a route • Navigation requires a map and data coordinates • Inaccurate navigation has very high costs!! 8 Required coordinates: 1. Symptoms 2. Genetic Variants
  • 9. Icons by different authors from www.flaticon.com Symptom-based path-finding (diagnosis)  Rare diseases have complex phenotypes  Differential diagnosis based on subtle details  Rare diseases: inexperience  Disease evolution is gradual  Symptom identification is hard  Short time per patient, independently of complexity 9
  • 11. Icons by different authors from www.flaticon.com Genotype-based path-finding (diagnosis)  Genetic testing is a black box  Mutation analysis is often manual  Symptom identification is hard!  EMR is not a good communication tool  Difficult consideration of new symptoms 11
  • 12. : AI as the GPS powering the navigation 12
  • 13. New patient to study The navigator DNA data Symptom extraction using NLP 1 Variant prioritization supported by the phenotype 2 Candidate symptoms based on the mutations 3 Candidate conditions for assessment 4 13
  • 14. 1. Symptom identification  Dx29 uses NCR1,2, developed by the Centre for Computational Medicine at SickKids, Toronto  Deep NN to classify concepts into Human Phenotype Ontology (HPO)3 terms EMR, electronic medical records; NN, neural network; NLP, natural language processing 1. Github. 2019. Available from: https://github.com/ccmbioinfo/NeuralCR (Accessed 11 June 2019); 2. Arbabi A, et al. 2019; 7(2):e12596. doi: 10.2196/12596. 3. Köhler S, et al. Nucleic Acids Res 2018;47:D1018–D1027 14
  • 15. How to compute on concepts?
  • 16. Rank mutation pathogenicity based on public databases: Exomiser1,2 1. Robinson PN, et al. Genome Res 2014;24:340–34; 2. Github. 2019. Available from: https://github.com/exomiser/Exomiser (Accessed 11 June 2019); 3. Zhou X, et al. Nat Commun 2014;5:4212; 4. Wang Genomics Lab. 2019. Available from: http://phenolyzer.wglab.org/ (Accessed 11 June 2019); 5. Yang H, et al. Nat Methods 2015;12:841–843 2. Variant analysis
  • 17. 1. Robinson PN, et al. Genome Res 2014;24:340–34; 2. Github. 2019. Available from: https://github.com/exomiser/Exomiser (Accessed 11 June 2019); 3. Zhou X, et al. Nat Commun 2014;5:4212; 4. Wang Genomics Lab. 2019. Available from: http://phenolyzer.wglab.org/ (Accessed 11 June 2019); 5. Yang H, et al. Nat Methods 2015;12:841–843 What if no genetic data is available? Build list of candidate genes based on disease networks3 : Phenolyzer4,5 2. Variant analysis
  • 18. 3. Engage with patient: What is missing? 18
  • 20. • Open platform to deploy and run diagnosis models • Data available to academia to develop and test new approaches • Open-source code and philosophy • Data donor concept implementation • Diagnosis of complex cases based on clustering using ML Overall platform summary 20
  • 21. • Very useful in areas with no access to genetic testing • Cloud-based, no installation required • Available (beta) at dx29.ai • A single variant prioritisation algorithm doesn’t work for all conditions • NLP is an ongoing challenge • Phenotype quality in public databases is poor • Seamless UX is required for a complex process • Patients need their own navigator • Very good feedback from physicians • Exploring symptoms is useful and innovative • High performance: academia
  • 22. This is great, but what about the data used … ? 22
  • 23. The need for high quality data
  • 25. • PSR means the object is a pulsar. • The J reveals that a coordinate system known as J2000 is used. • 1302 and 6350 are coordinates like the latitude and longitude. PSR J1302-6350
  • 26. Dravet Syndrome Lennox-Gastaut Syndrome Allan–Herndon–Dudley Syndrome SCN1A MECP2 CDKL5 STXBP1 26 Rett Syndrome
  • 28. 28
  • 29. SCN1A Dravet Syndrome Febrile Seizures Temporal Lobe Epilepsy Myoclonic Astatic Epilepsy Lennox-Gastaut Syndrome Migrating Partial Epilepsy of Infancy (MMPSI) Autism http://epilepsygenetics.net/the-epilepsiome/scn1a-this-is-what-you-need-to-know/ 29
  • 30. 30
  • 32. Let’s do a better job!! https://deepai.org/publication/embedding-complexity-in-the-data-representation-instead-of-in-the-model-a-case-study-using-heterogeneous-medical-data
  • 33. How to compute on concepts?
  • 35. Data locker of patient-owned data, for the development of new algorithms. Patients with complex conditions (multiple genes, big genomic changes) need an approach based on mixed learning : navigator for patients 35
  • 36. 36 Final notes 1. Key technologies: NGS + AI 2. NGS+AI makes healthcare personalized, accurate and affordable 3. NGS+AI require development of standards and platforms 4. Seamless UX is vital for technology adoption 5. Transformation of healthcare into information-centered process 6. Rare diseases offer the perfect niche for testing: want to help? 7. Foundation29 is laying the basis for such transformation
  • 37. Thanks and … See you soon! Thanks also to the sponsors. Without whom this would not have been posible. O R G A N I Z A T I O N P L A T I N U M S P O N S O R S C O L L A B O R A T O R S

Editor's Notes

  • #20: Esta es nueva, quizás demasiado nivel de detalle