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Presentations

Friday December 6 2019

Session 1 – Predicting risk: from Mendelian to polygenic traits

Shamil Sunyaev - Predicting polygenic risk
Melissa Cline - CAGI Theme: CAGI cancer challenges

Selected talks / flash talks

Lipika Ray - Evolution of CAGI over four rounds: computational challenges in analyzing next generation sequencing data
Natàlia Padilla Sirera - BRCA1- and BRCA2-specific in silico tools for variant interpretation in the CAGI 5 ENIGMA challenge
Andrew Sharo - StrVCTVRE: A supervised learning method to predict the pathogenicity of structural variants
Kymberleigh Pagel - OpenCRAVAT: an open source collaborative platform for the annotation of human genetic variation
Vikas Pejaver - A performance-based approach to establish standards for missense
Yue Cao - Predicting pathogenicity of missense variants with weakly supervised regression
Justin Delano - The impact of missense human variation on post-translational modifications in proteins variant impact prediction tools

Session 2 – Ethical considerations for CAGI

Selected talk: Zhiqiang Hu - Privacy time bombs in omics data: latent risk manifests over time
Barbara Koenig and Malia Fullerton - The CAGI Ethics Forum

Session 3 – Salon talks

Vikas Pejaver - CAGI salon introduction
Kymberleigh Pagel - CAGI challenge design and assessment
Lipida Ray - Broadening impact and participation in CAGI

Saturday December 7 2019

Session 4 – Broader perspectives on Human Genome Variation

Michael Snyder - Big data and health

Resources and policies

Anne O'Donnell-Luria - gnomAD
Marc Greenblatt - ClinGen Sequence Variant Interpretation

Session 5 – Missense variants: promises and limitations

John Moult - CAGI Theme: Bespoke approaches often enhance performance with biophysical methods excelling in a few cases while evolutionary methods have a more consistent performance
Iddo Friedberg - CAGI Theme: Prediction methods have high statistical significance but accuracy is low. However, for an identifiable subset of predictions, accuracy is very high
Olivier Lichtarge - CAGI Theme: Methods tend to correlate with each other more than with experiment

Session 6 – Complex traits and non-coding variants

Sean Mooney - CAGI Theme: Predicting complex traits from exomes is fraught, although there have been improvements in the ability to match genomes to profile
Steve Mount - CAGI Theme: There have been improvements in splicing prediction although this is not yet at the state of missense
Predrag Radivojac - Overcoming (many) challenges in evaluating variant interpretation: a machine learning perspective

Session 7 – Assessment of the annotate all missense CAGI challenge

Nilah Ioannidis - Annotate all missense challenge assessment

Meta-predictor panel – potential, prevarication, and policy
Panelists: Rachel Karchin, Nilah Ioannidis, Sean Mooney
Moderator: Steven Brenner

Sunday December 8 2019

Session 8 – AI and diagnostic variants

Serafim Batzoglou - AI methods for genome interpretation
Constantina Bakolitsa - CAGI Theme: CAGI challenges have led to the identification of causal variants overlooked by clinical labs
Selected talk: Erwin Frise - Benchmarking an artificial intelligence method for fast diagnosis of rare genetic disease

Session 9 – Future perspectives

Future of genome interpretation and vision for CAGI panel
Panelists: Rachel Karchin, Olivier Lichtarge, Vikas Pejaver
Moderator: Steven Brenner

Program

A downloadable version of the program, including agenda and abstracts.

Agenda

CAGI Workshop 2019
Assessing the Future of Genome Interpretation
6 – 8 December 2019

Friday, 6 December 2019

12:00-1:00 pm Registration & light refreshments
1:15-3:10 pm Session 1 – Predicting risk: from Mendelian to polygenic traits
1:15-2:00 pm Shamil Sunyaev
Predicting polygenic risk
2:00-2:30 pm Melissa Cline
CAGI Theme: CAGI cancer challenges
2:30-3:10 pm Selected talks / flash talks
Lipika Ray (15 minutes)
Evolution of CAGI over four rounds: computational challenges in analyzing next generation sequencing data
Natàlia Padilla Sirera (5 minutes)
BRCA1- and BRCA2-specific in silico tools for variant interpretation in the CAGI 5 ENIGMA challenge
Andrew Sharo (5 minutes)
StrVCTVRE: A supervised learning method to predict the pathogenicity of structural variants
Kymberleigh Pagel (5 minutes)
OpenCRAVAT: an open source collaborative platform for the annotation of human genetic variation
Vikas Pejaver (5 minutes)
A performance-based approach to establish standards for missense
Yue Cao (1 minute)
Predicting pathogenicity of missense variants with weakly supervised regression
Justin Delano (1 minute)
The impact of missense human variation on post-translational modifications in proteins
variant impact prediction tools
3:10-3:40 pm Break
3:40-5:00 pm Session 2 – Ethical considerations for CAGI
3:40-3:55 pm Selected talk
Zhiqiang Hu
Privacy time bombs in omics data: latent risk manifests over time
3:55-4:35 pm Barbara Koenig and Malia Fullerton
The CAGI Ethics Forum
4:35-5:00 pm Discussion
5:00-5:30 pm Break
5:30-6:30 pm Session 3 – Reports from the CAGI Salon: inspirations for the future
5:30-5:40 pm Steven Brenner
Overview, and charge to participants
5:35-5:45 pm Vikas Pejaver
CAGI Salon introduction
5:45-6:00 pm Kymberleigh Pagel
CAGI challenge design and assessment
6:00-6:15 pm Lipika Ray
Broadening impact and participation in CAGI
6:15-6:30 pm Discussion
6:30-9:00 pm Reception and Poster session

Saturday, 7 December 2019
8:00-8:45am Breakfast
8:45-9:00 am Welcome and Recap from Day 1
9:00-10:45 am Session 4 – Broader perspectives on Human Genome Variation
9:00-9:45 am Michael Snyder
Big data and health
9:45-10:45 am Resources and policies
9:45-10:15 am Anne O’Donnell-Luria
gnomAD
10:15-10:45 am Marc Greenblatt
ClinGen Sequence Variant Interpretation
10:45-11:15 am Break
11:15-1:00 pm Session 5 – Missense variants: promises and limitations
11:15-11:45 am John Moult
CAGI Theme: Bespoke approaches often enhance performance with biophysical methods excelling in a few cases while evolutionary methods have a more consistent performance
11:45-12:15 pm Iddo Friedberg
CAGI Theme: Prediction methods have high statistical significance but accuracy is low. However, for an identifiable subset of predictions, accuracy is very high
12:15-12:45 pm Olivier Lichtarge
CAGI Theme: Methods tend to correlate with each other more than with experiment
12:45-1:00 pm CAGI Theme Discussion
1:00-2:00 pm Lunch
2:00-4:00 pm Session 6 – Complex traits and non-coding variants
2:00-2:30 pm Sean Mooney
CAGI Theme: Predicting complex traits from exomes is fraught, although there have been improvements in the ability to match genomes to profile
2:30-3:00 pm Steve Mount
CAGI Theme: There have been improvements in splicing prediction although this is not yet at the state of missense
3:00-3:15 pm Discussion
3:15-3:45 pm Predrag Radivojac
Overcoming (many) challenges in evaluating variant interpretation: a machine learning perspective
3:45-4:00 pm Discussion
4:00-4:30 pm Break
4:30-5:30 pm Session 7 – Assessment of the annotate all missense CAGI challenge
4:30-5:00 pm Nilah Ioannidis, assessor
5:00-5:30 pm Discussion
5:30-6:30 pm Meta-predictor panel – potential, prevarication, and policy
Panelists: Rachel Karchin, Nilah Ioannidis, Sean Mooney
Moderator: Steven Brenner

Sunday, 8 December 2019
8:00-8:45am Breakfast
8:45-9:00 am Welcome and Recap of Day 2
9:00-10:30 am Session 8 – AI and diagnostic variants
9:00-9:45 am Serafim Batzoglou
AI methods for genome interpretation
9:45-10:15 am Constantina Bakolitsa
CAGI Theme: CAGI challenges have led to the identification of causal variants overlooked by clinical labs
10:15-10:30 am Selected talk
Erwin Frise
Benchmarking an artificial intelligence method for fast diagnosis of rare genetic disease
10:30-11:00 am Break
11:00-12:00 pm Session 9 – Future perspectives
11:00-11:45 am Future of genome interpretation and vision for CAGI panel
Panelists: Rachel Karchin, Olivier Lichtarge, Vikas Pejaver
Moderator: Steven Brenner
11:45-12:00 pm Final remarks

Agenda

==========
Friday, December 6
==========

SESSION 1 = Keynote #1
Shamil Sunyaev
SESSION 2 = Missense variants: promises and limitations
John Moult
Olivier Lichtarge
BREAK
SESSION 3 = Missense variants in cancer
Melissa Cline
Talk from Abstracts
BREAK
SESSION 4
Salon presentation(s)
RECEPTION & POSTER SESSION

==========
Saturday, December 7
==========

SESSION 5 = Keynote #2
Michael Snyder
SESSION 6 = Ethical considerations in genome interpretation
Barbara Koenig
Malia Fullerton
Talk from Abstracts
BREAK
SESSION 7 = Pushing the limits
Marc Greenblatt
Predrag Radivojac
Talks from Abstracts or Discussion
LUNCH
SESSION 8
Talks from Abstracts
BREAK
SESSION 9 = Assessment of the Annotate All Missense CAGI challenge
Nilah Ioannidis
Talks from Abstracts or Discussion
SESSION 10 = Future perspectives in genome interpretation
Panel: Future of Genome Interpretation and Vision for CAGI
Moderator: Steven Brenner

==========
Sunday, December 8
==========

SESSION 11 = Keynote #3
Serafim Batzoglou
SESSION 12 = Clinical genomes and non-coding variants
Sean Mooney
Tina Bakolitsa
BREAK
SESSION 13
Panel: TBA
Moderator: Steven Brenner
CLOSING REMARKS

CAGI Special Issue Human Mutation 2019

The CAGI Special Issue of Human Mutation has now been published:

https://onlinelibrary.wiley.com/toc/10981004/2019/40/9

All 34 articles are available free online without a subscription. We thank all assessors, predictors, and data providers who worked on the contributions and congratulate them on publication. While the print issue is now complete, we continue to accept additional manuscripts that will be added to the CAGI online special collection at Human Mutation.

Please distribute widely and follow our Twitter feed @CAGInews and the https://genomeinterpretation.org web site for updates.