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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

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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