ndna Tim Hughes Avdeling for Medisinsk Oslo Universitets Sykehus (Ullevål)

Transcription

1 ndna Utvikling av nasjonal analyse- og lagringspla3orm for DNA sekvensdata i helsevesenet Tim Hughes Avdeling for Medisinsk Gene@kk Oslo Universitets Sykehus (Ullevål)

2 My goal Present the ndna project and its underlying e- infrastructure (TSD) In the context of the issues of relevance to the proposed forum: data storage and challenges in our field areas of with other research legal and ethical aspects of data access Finally, present some opinions about the proposed forum

3 The data DNA sequence Total length of the 23 human chromosomes (genome) = 3 billion bases Sequencing involves reading of the sequence of bases

4 data: High Throughput Sequencing Similar to low throughput (Sanger) sequencing Orders of magnitude speed- up and cost through massive Billions of short reads in one run Sequencing one human genome can be done in hours instead of years research And more generally biology

5 Where is data generated in Norway? Core facility located at UiO and OUS Funded by: Producing trillions of bases of raw data per year Other labs with private HTS machines Radium Ski Bodø

6 E- infrastructure requirements Storage TBs just for the raw data And more for the downstream analyses high bandwidth between storage and CPU for mapping reads back to the genome for wide array of downstream analyses usually trivially parallelisable Why not use Notur and Norstore? Human data even meta- data that has been de- is considered cannot store data on user system with username/password access data requires: two part encrypted storage (?) control of data (REK) of sniffing through separate physical or virtual machines

7 The setup Sharing data is not straight forward No offsite backup All IT maintenance done ourselves (hardware and soiware) Others have similar problems >>

8 TSD: USIT s Tjeneste Sensi@ve Data Goal: store compute share, large sensi@ve data in a secure way Effec@vely a secure version of exis@ng non- secure services (Notur and Norstore) Ini@ated in 2009 with other users: Radium Hospitalet Psykologisk Ins@tuc (UiO) TSD 1.0: just storage >> complete 2011

9 TSD 2.0 Founding users lacked sharing (e.g. with collaborators) required secure user management Many other users appeared Notur and Norstore became involved and provided funding ndna project was funded by NFR through Verdikt

10 What is the ndna project? Nasjonal analyse- og lagringspla3orm for DNA sekvensdata i helsevesenet diagnos@c and not research Funded by NFR Verdikt program (bruker ini@ert forskning) Bruker: OUS Avdeling for Medisinsk Gene@kk Research partners Informa@kk Ins@@tuc UiO UiO HPC group OUS IT Project end date: summer 2015

11 Why ndna HTS makes rapid from research to searching for causal variant with instead of a pocket light in the not- too- distant- future sequencing will be performed up- front for future reference queriable by expert systems Expert system (Cardiology) Front- end DNA analysis sojware TSD 2.0 (USIT/Norstore/Notur) Expert system (immunology) Sequencing center Requires similar func@onality as research projects, plus: extra security more automa@on more reliability

12 TSD 2.0 progress USIT (UiO) currently requirements from users: OUS Medial as center (ndna) OUS Medical as research center epitwin Addison s disease Many other users (not all working on DNA data e.g. Department of Psychology) System design to start in spring 2012 Big challenge for the ndna project: can TSD 2.0 develop an architecture that will sa@sfy the legal requirements for diagnos@c DNA data?

13 The future for sequence data 168 babies born in Norway every day 55 norwegians diagnosed with cancer every day large needs

14 Opinions about the proposed forum Generally very to the forum We are (together with our partners) in the middle of many of the processes described in the forum proposal: system requirement on- going users of the infrastructure huge group of users understand legal and ethical aspects of research data plenty of this in the ndna project knowledge Norstore s "white paper requirement to USIT Has to be approved by Data@lsynet

15 Thanks for listening