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Effective in-silico sequence-
based prediction of FMDV
vaccine matching
EuFMD Open Session
Borgo Egnazia, 30-10-2018
Yasaman Kalantar-Motamedi,
Sophie Mahendran,
Luca Ferretti, Paolo Ribeca
(Computer)
Mana Mahapatra
Satya Parida
(Data production)
Given a serum, focuses on measuring the ratio between
the neutralising power against the vaccine (homologous)
and the virus being tested (heterologous).
Approach already explored in the past (Reeve et al.) on
smaller datasets.
However more and more serological data available,
coupled with full-capsid (or full-genome) information.
Approach routinely pursued by WRLFMD for quite some
time now.
New attempt based on machine learning approaches.
VNT data
Data intrinsically noisy, with large biological variations.
Trying to separate signal from noise
(garbage in, garbage out!).
Intuitively:
• If two sequences which are similar generate a different
heterologous titre, problem!
Can be corrected, but needs many sequences
• If a measurement gives a surprising value for the
homologous titre, problem!
The goal is being able to filter out bad data.
De-noising
Noisy
Bad
Good
The model is prone to over-fitting!
You can get an almost perfect correlation
with no predictive power.
Subtle problems due to the fact that sampling
is not uniform nor random in sequence variant space
(no freedom to choose samples).
Sample size corrections needed when doing validation.
We think we have found a good definition.
Validation
Better!
Does it really work?
Predicted titres Predicted R1
All GenBank data
The model works in a similar way for other serotypes
(tested A).
Our model allows integration of biochemical features.
We can read out what are the important ones.
We can predict epitopes out of the model
(easy to reproduce most previously published ones—
but that only possible if enough variation in the input).
There is much more data available!
We are integrating it.
Outlook
Acknowledgements
The Pirbright campus is being redeveloped
Yasaman Kalantar-Motamedi
Luca Ferretti
Sophie Mahendran
Mana Mahapatra
Satya Parida

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Effective in-silico sequence based prediction of FMDV vaccine matching (P. Ribeca)

  • 1. Effective in-silico sequence- based prediction of FMDV vaccine matching EuFMD Open Session Borgo Egnazia, 30-10-2018 Yasaman Kalantar-Motamedi, Sophie Mahendran, Luca Ferretti, Paolo Ribeca (Computer) Mana Mahapatra Satya Parida (Data production)
  • 2. Given a serum, focuses on measuring the ratio between the neutralising power against the vaccine (homologous) and the virus being tested (heterologous). Approach already explored in the past (Reeve et al.) on smaller datasets. However more and more serological data available, coupled with full-capsid (or full-genome) information. Approach routinely pursued by WRLFMD for quite some time now. New attempt based on machine learning approaches. VNT data
  • 3. Data intrinsically noisy, with large biological variations. Trying to separate signal from noise (garbage in, garbage out!). Intuitively: • If two sequences which are similar generate a different heterologous titre, problem! Can be corrected, but needs many sequences • If a measurement gives a surprising value for the homologous titre, problem! The goal is being able to filter out bad data. De-noising
  • 5. The model is prone to over-fitting! You can get an almost perfect correlation with no predictive power. Subtle problems due to the fact that sampling is not uniform nor random in sequence variant space (no freedom to choose samples). Sample size corrections needed when doing validation. We think we have found a good definition. Validation
  • 7. Does it really work? Predicted titres Predicted R1 All GenBank data
  • 8. The model works in a similar way for other serotypes (tested A). Our model allows integration of biochemical features. We can read out what are the important ones. We can predict epitopes out of the model (easy to reproduce most previously published ones— but that only possible if enough variation in the input). There is much more data available! We are integrating it. Outlook
  • 9. Acknowledgements The Pirbright campus is being redeveloped Yasaman Kalantar-Motamedi Luca Ferretti Sophie Mahendran Mana Mahapatra Satya Parida