15:04:54 RRSAgent has joined #HCLS 15:04:54 logging to http://www.w3.org/2012/05/10-HCLS-irc 15:05:05 Meeting: W3C HCLS – Clinical Decision Support 15:05:09 Chair: Michel Dumontier 15:06:38 ScribeNick: Michel 15:06:52 mscottm2 has joined #hcls 15:08:03 Agenda: CPIC 15:08:19 CPIC is the clinical pharmacogenomics implementation consortium 15:08:31 bobf: member of CPIC 15:08:42 http://pgrn.org/display/pgrnwebsite/PGRN+Home 15:09:12 ... PGRN - pharmagcogenomics research network - 13th year of funding, well organized and funded 15:09:28 ... relates to PharmGKB and CPIC 15:09:42 ... lead discovery and translation in pharmacogenomics 15:10:49 ... PharmGKB is the associated kb for the PGRN; initially funded as part of PGRN. PGRN now just funds research sites and PharmGKB is spun out and has independent funding 15:11:35 ... 14 research sites focused on specific drugs or diseases 15:11:42 http://pgrn.org/display/pgrnwebsite/Research+Groups+and+Network+Resources 15:12:55 ... CGN - center for genomics medicine - sequencing collab with Riken 15:13:35 s/CGN/CGM 15:14:01 ... DSR - deep sequencing resource 15:14:43 ... PG-POP - EMR-linked biobanks; hypothesis testing 15:15:35 ... PHONT - pharmacogenomics ontology - goal is to help bring standardized representation for data in PGRN 15:15:50 ... bobF is a member of this 15:16:17 ... shifting activities towards facilitating and demonstrating how PGx knowledge can be integrated in EMR in order to identify candidates for PGx studies 15:17:17 https://www.pharmgkb.org/index.jsp 15:17:50 ... PharmGKB initially wanted to capture sequencing data, but competing with others (e.g. NCBI), since becoming independent have shifted focus away from collecting sequencing data, to capture knowledge for clinical action 15:18:32 Yesterday has joined #hcls 15:18:35 http://www.pharmgkb.org/projects.jsp 15:21:37 ... CPIC develops and publishes guidelines 15:21:54 ... PharmGKB hosts the electronic version of the guidelines 15:21:56 https://www.pharmgkb.org/resources/cpic_gene-drug_pairs.jsp 15:23:18 ... CPIC groups prepare guidelines 15:23:40 ... based on genotyping that are approved for clinical settings 15:23:47 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098762/pdf/clpt2010279a.pdf 15:23:59 ... publication announcing the formation of CPIC 15:26:36 ... guidelines have two schemes - genotypes into predicted phenotypes, phenotypes into drug dosing guidelines 15:27:37 ... A - quality of evidence; 15:27:40 Level 1: the evidence includes consistent results from well‑designed, well-conducted studies. 15:27:52 Level 2: the evidence is sufficient to determine the effects, but the strength of the evidence is limited by the number, quality, or consistency of the individual studies, by the inability to generalize to routine practice, or by the indirect nature of the evidence. 15:28:01 Level 3: the evidence is insufficient to assess the effects on health outcomes because of the limited number of studies, insufficient power of the studies, important flaws in their design or in the way they were conducted, gaps in the chain of evidence, or lack of information 15:28:17 ... B - strength of recommendation 15:28:17 A: strong recommendation for the statement B: moderate recommendation for the statement C: optional recommendation for the statement 15:29:02 ... challenges and opportunities: have a nice format for publishing these, there is no consistent representation of this information that is machine readable 15:29:23 ... opportunity for this group to make this machine readable and contribute back through PharmGKB 15:30:12 ... groups are facing a challenge of biology - as more information is gathered (drug-disease-interaction) - landscape is getting more complex; 15:30:35 warfarin dependent on 2 different genes 15:30:38 ... warfarin dosing depends on two genes; antidepressants have many genes involved, and the response is complicated 15:30:50 tricyclics dependent on many more 15:30:53 ... so how to address this situation? 15:31:10 ... current approach is not feasible in terms of scalability 15:31:42 ... another challenge has to do with outcome data. Little data that genotype-based therapy is effective 15:32:04 http://pgrn.org/display/pgrnwebsite/Network-wide+Projects 15:32:33 ... out of scope for CPIC, but in scope for translational pharmacogenetics project (TPP) 15:32:56 ... funded to implement these guidelines internally, and develop and collect metrics to compare across sites 15:33:51 ... the last 2 challenges/opportunities have to do with biological knowledge. Sequencing uncovering large numbers of variants 15:33:59 ... all could impact previously published guidelines 15:34:25 ... CPIC will have to revise guidelines; expanding the number of alleles that have a defined effect; (star alleles) 15:36:01 ... another challenge - predicting the phenotype (functional effect) based on genotype; normally based on lab studies - errors in this and lack of precision 15:36:08 predicting the functional diplotype based on phenotype 15:36:54 ... with multiple genes involved in a pathway - things get messy quickly - a kind of systems biology approach is required 15:37:48 Regrets from Joanne - she wasn't able to schedule around this meeting and has Mark Musen visiting. 15:38:46 michel: had a discussion at AMIAA about exponential guidelines to capture all of a patient's gene combos 15:39:02 ... for making this machine-understanable: 15:39:32 ... .. need to look at sophisticated approaches for retrieving phenotype data 15:39:48 ... .. matthias has been looking at SPARQL Simple Rules 15:39:59 ... .. also looking at OpenCDS 15:40:22 ... where do we start the discussion about what's the best machine-readable format? 15:41:59 BobF: PharmGKB isn't interested in "bit flipping" 15:42:20 ... anything we do would need to be compatible with or translatable to existing commercial EHR systems 15:42:45 ... if we can make CDS rules expressable in existing systems would be well-recieved 15:43:16 ... revolution would be viewed as academic 15:43:42 michel: at Mayo, what CDS is available to physicians? 15:43:56 ... could rules be used there? 15:44:09 BobF: discussing this with Mayo now 15:44:20 ... looking at systems like OpenCDS 15:44:39 ... looking at these options now 15:45:24 michel: while we'll persue a SemWeb approach, we need to work with a partner who will apply them to an existing in-house system 15:47:15 ericP: does existing EMR systems capture the PGx information that a PGx CDS needs 15:48:11 bobf: there are no commercial EHRs that i'm aware of that directly supports genetic information 15:48:17 ... degree of information varies 15:48:34 genotype information captured under misc in existing systems 15:48:50 ... you could put base pairs, alleles, genotype 15:49:30 ... rules can be tied to a drug 15:49:39 ... so that an event pops up to the physician 15:50:11 ... prespective / postpective - 15:51:37 ericp: not only not just capturing the information, but also not doing the assessment of effectiveness 15:52:58 rich: how population specific are these guidelines? in the elderly you might suggest a lower dose, but these person has 5 other issues; 15:53:21 bobf: CPIC is specific on genotype-guided therapy 15:53:24 /me asks richard - what is an SSRI? 15:53:49 selective serotonin reuptake inhibitor - popular antidepressant class 15:53:52 tx 15:53:54 -> http://en.wikipedia.org/wiki/Selective_serotonin_reuptake_inhibitor SSRIs 15:54:14 you guys are fast 15:54:22 bobf: going beyond genotype-based guidelines really needs CDS 15:56:46 drugs from different locales (countries) will have different potency so must be taken into consideration. 15:59:20 zakim, who is here? 15:59:20 On the phone I see no one 15:59:21 On IRC I see Yesterday, mscottm2, RRSAgent, egombocz, BobF, boycer, achille_zappa, loriy, MacTed, michel, Zakim, ericP 15:59:58 Bob knows me. 16:00:20 I am from Duke 16:01:32 I wasn't sure what my interest will be on this call so didn't want to properly register. 16:01:40 This is my first call. 16:02:05 Thanks for the welcome! 16:04:59 thanks, very informative 16:07:32 Scott: Isn't it an uphill battle with pharmacogenomic info not on the radar for the clinic? 16:07:42 http://lists.w3.org/Archives/Public/public-semweb-lifesci/2012May/0017.html 16:08:48 BobF: There are dozens of clinics that are far ahead with this although most solutions are still ad hoc 16:09:31 SW_HCLS()11:00AM has ended 16:09:32 Attendees were 16:09:42 rrsagent, draft minutes 16:09:42 I have made the request to generate http://www.w3.org/2012/05/10-HCLS-minutes.html michel 16:09:46 rrsagent, make log world-visible 16:11:49 RRSAgent, draft 'em harder 16:11:49 I'm logging. I don't understand 'draft 'em harder', ericP. Try /msg RRSAgent help 16:12:47 RRSAgent, bye 16:12:47 I see no action items