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Genomic Data in the CDM


(Clair Blacketer) #1

After lots of interest at the OHDSI symposium I would like to formally initiate a working group to discuss the addition of genomic data to the CDM. There has been some discussion on the forums here and Kyu-pyo Kim and @Yurang_Park presented a wonderful poster at the symposium detailing the extension they created specifically for this purpose. In this group I would like to leverage as much of their work as we can while making sure our proposal meets the needs of as many collaborators as possible. Please leave a comment if you would like to join and I will send out a doodle poll in a few days to find the best time for us to meet.


CDM Genomics WG Meeting
Genetic Data?
How to store maternal or paternal relatives?
(Robert Miller) #2

I would like to join the effort.

(Karthik) #3

I would like to join.

(Melanie Philofsky) #4

Sign me up!

(Jerome Dixon) #5

I would like to join

(Hamed Abedtash) #6

I’d like to join.

(Yu Rang Park) #7

Thank you very much for your positive response.
Of course I’d like to join.
We hope that the extended version of the CDM genome will be available for further research through contributions from community members.
Please feel free to send us any personal comments or improvements on the poster.

(ShinSeojeong) #8

Hi, I’m seojeong at Ajou University in Korea and would like to join!
We also have been making CDM extension version for storing Genetic data especially Next Generation Sequencing (NGS) results. Our Genetic CDM was built based on the ISO / TS20429, a global reporting standard of NGS analysis result.
We presented this project at Oncology working group face-to-face meeting at OHDSI symposium in Washington last week. So it seems to be nice if we work building Genetic CDM together with oncology subgroup. We hope contribute this effort!

(Seng Chan You) #9

I’d like to join, too!

(최윤이) #10

I would like to join.

(Kyu Pyo Kim) #11

Hello everyone. I am quite happy that a lot of people shared these needs. Yu Rang and I shall upload our poster tables on to GitHub by next week. I due believe that these efforts can allow realization of precision medicine.

(Gregory Klebanov) #12

sign me up as well, please

(Wendy Rubinstein) #13

Sign me up too.

(Sunah Song) #14

I would like to join!

(Seng Chan You) #15

As NGS in cancer patients was started to be covered by Korean national insurance system from this year, many Korean hospitals in OHDSI network are just beginning to collect genomic data in caner patients.

18,000+ cases of Foundation Medicine (FMI) single nucleotide variants now available in the NCI Genomic Data Commons (GDC). (enter link description here) If clinical and genomic information of such open databases can be converted into CDM, it will be combined with real world CDM data to create strong evidences.

I think oncology working group can cooperate with genomic data group for this ambitious goal, since it has been hard to convert clinical information in open genomic database into OMOP-CDM until now.
@rimma @clairblacketer

(Andrew Williams) #16

I would like to join also.

(Abhishek Venkataramanan) #17

I would like to join as well

(Michel Van Speybroeck) #18

I’m interested to join as well

(Jinlei Liu) #19

Please sign me up too!

(Qi Yang) #20

Sign me up please!