Health Data Challenge: Matrix factorization and deconvolution methods to quantify tumor heterogeneity in cancer research

from December 10, 2018 to December 14, 2018

The challenge will be dedicated to the quantification of intra-tumor heterogeneity using appropriate statistical methods on cancer omics data. It will take place from December 10th to 14th, at Aussois.

Invited speakers

Eugene Lurie, from BCM, Houston, USA, will present the EDec package.
Pavlo Lutsik, from DKFZ, Heildeberg, Germany, will present the MeDeCom package.
E. Andres Houseman, independent data scientist, USA, will present the RefFreeEWAS package.

 

Scientific challenge


Successful treatment of cancer is still a challenge and this is partly due to a wide heterogeneity of cancer composition across patient population.

Unfortunately, accounting for such heterogeneity is very difficult. Clinical evaluation of tumor heterogeneity often requires the expertise of anatomical pathologists and radiologists.

This challenge will be dedicated to the quantification of intra-tumor heterogeneity using appropriate statistical methods on cancer omics data.

In particular, it will focus on estimating cell types and proportion in biological samples based on averaged DNA methylation and full patient history.
The goal is to explore various statistical methods for source separation/deconvolution analysis (Non-negative Matrix Factorization, Surrogate Variable Analysis, Principal component Analysis, Latent Factor Models, ...). Participants will be made aware of several pitfalls when analyzing omics data (large datasets, missing data, confounding factors…).

Participants will work in interdisciplinary teams.


model_cancer

Who can attend?


Undergrads, PhD students, postdoc, researchers, professors, clinicians and employees from the private sector are welcome.
We look for interdisciplinary expertise in biology, computer science, statistics, bioinformatics or medical sciences.
We expect that participants are familiar with R programming language (or equivalent) and with basic statistical notions. No prior knowledge in omics data is required.

Participants should bring their personal laptops.

General context


Health data challenge is part of a program dedicated to innovation in education. The aim of this program is to provide (i) analytical frameworks to bridge the gap between large dataset and personalized medicine in disease treatments and (ii) innovative pedagogical methods to train students and health professionals to big data analysis in health science. Integrating a large amount of data from different sources and using this knowledge to better characterize specificities of each individual will provide significant opportunities to improve disease diagnosis and to adapt accordingly patients’ treatment and care.

Program

Monday December 10
•    Arrival of the participants
•    19h30-20h30 Dinner
•   20h30-21h30 Introduction about cancer heterogeneity and presentation of the Data Challenge
Tuesday December 11
•    09:30 to 09:45 : Introduction to statistical methods for signal processing
•    09:45 to 10:00 : Introduction to omics data in biomedical research
•  10:00 to 10:15 : Introduction to 3 R packages for deconvolution of methylation data: RefFreeDec, MeDeCom and Edec
•    10:15 to 10:30 : Break
•    10:30 to 12:30 : Challenge #1
•    12:30 to 14:00 : Lunch
•    14:00 to 16:30 : Challenge #1
•    16:30 to 17:00 : Break
•    17:00 to 18:30 : Challenge #1
•    18:30 to 20:00 : Poster session / Wine & Cheese
•    20:00 to 21:30 : Dinner
Wednesday December 12
•    09:00 to 10:00 : Debriefing on challenge #1
•    10:00 to 10:30 : Break
•    10:30 to 11:30 : Introduction to 3 R packages for deconvolution of methylation data: RefFreeDec, MeDeCom and Edec
•    11:30 to 12:30 : Challenge #2
•    12:30 to 14:00 : Lunch
•    14:00 to 16:30 : Free time in the mountain
•    16:30 to 20:00 : Challenge #2
•    20:00 to 21:30 : Dinner (Grill-stone)
Thursday December 13
•    09:00 to 10:00 : Challenge #2
•    10:00 to 10:30 : Break
•    10:30 to 12:30 : Challenge #2
•    12:30 to 14:00 : Lunch
•    14:00 to 14:15 : Introduction to innovative pedagogy
•    14:15 to 14:30 : Introduction to the digital platform codalab
•    14:30 to 16:00 : Brainstorming #1 : how to evaluate participants ?
•    16:00 to 16:30 : Break
•    16:30 to 18:00 : Brainstorming #2 : how to evaluate the pedagogical methods ?
•    20:00 to 21:30 : Gala Dinner and cocktail party
Friday December 14
•    09:00 to 10:00 : Debriefing on challenge #2
•    10:00 to 10:30 : Break
•   10:30 to 12:00 : Challenge diffusion: how to organize your own health data challenge at home!
•    12:00 to 13:30 : Lunch

Where and when

The challenge will take place during 5 days (December 10-14th, 2018) in Aussois, Vanoise, a charming small village in the Vanoise National Park (French Alps). It will end at 12pm on December 14th. If you want to leave Aussois after December 14th, you should spend the last night in another hotel nearby (e.g. hotel des mottets). The remote setting, along with the challenging program, were chosen to promote and enhance interactions between participants.

How to come

Flight

The closest airport is at Lyon Saint Exupery but you might also arrive in Paris. Then you should take the train from the airport to Modane. Check on the website of the SNCF for timetables and reservation.

Train

The most convenient way to come to Aussois is to arrive by train at the railway station in Modane. Then, a bus shuttle will pick you up to go to the conference center (~15 minutes by bus). Please contact us if you need us to book the shuttle or if you want further information.
You can check timetables on the SNCF website.

Car

There is a freeway to Modane, which is located at 15-20 minutes of the conference center in Aussois.
The tourist office provides additional information...

Registration


Registration fees include attendance to the courses, food, bus from the station, housing, conference banquet, and the social event on Wednesday. The challenge is limited to 50 participants.
Please register here

Rates:

•    Early birds (before September 24th) :  Students* 150 € / Faculty-Postdoc 250 € / Industry 400 €
•    Normal (before October 17th) : Students* 250 € / Faculty-Postdoc 450 € / Industry 600 €
•    A supplement of 50 euros will be charged if you prefer to stay in a single room rather than in a double room
* Housing rates can be offered to students upon motivations.

How to pay:

•    By cash or credit card once you arrive at the conference center
•    By bon de commande

Cancellation fees:

•    If you cancel before November, 10: no fees.
•    If you cancel between November, 10 and December, 3: 79 €
•    If you cancel between December, 4 and December, 6: 159 €
•    If you cancel after December, 7: all registration fees


Published on September 18, 2018

Practical informations