See also: IRC log
hello, who are you, pault?
<scribe> scribenick: matthias_samwald
simon: see docs.google.com/document/d/12leHdI-GT2dzRgvVIx13wsXAaCLj6eNGvQ-L2B749f4/edit
<pault> pault = Paul Trevithick of PanGenX in Newton MA
simon: we hope that this use case
can be used to drive development of clinical genomics
... feel free to edit the Google-Doc!
... In a month / a few months we can wrap the ideas up in a joint manuscript
Bob: What will this document be used for?
Simon: We started to draft the
document for internal requirements at Marshfield Clinic.
... but we realized that we also need outside input to have use-cases for community in general
... genomics is a large domain. this use-case should only focus on data storage needs.
Bob: For clinical use or also research?
Simon: Clinical genomics is primary target. For medical providers.
Bob: One thing I would ask: is the typical process of QC etc. in the scope of this document?
Simon: That is in scope.
Bob: Review, annotation,
interpretation etc. should also be in there.
... at Mayo, the results are interpreted by clinical geneticists that write a textual interpretation. That text is then used by the practicing clinicians.
... the EMR would be between the clinical geneticist and the clinician.
... But what goes into EMR? They were not designed for (next gen) genetic data.
... At Mayo, a large panel test is only interpreted in the context in which it was ordered.
... So interpretation is usually quite limited. You could also infer other information from the raw data.
... Are you re-using the data?
(error: last comment was from simon)
Bob: This is work in progress, we are setting up an Oracle database for genetic data (and re-interpretation as needed). Lab reports will still go into established EMR.
Simon: We are planning similar setup at Marshfield.
Bob: This will be a common theme for the next few years, EMR systems are not designed for large genetic data.
Simon: CLIA conformant?
Bob: Pipeline for everything that
ends up in EMR is CLIA-conformant.
... PGRN-Seq chip is not yet CLIA conformant, but we will adopt it inside a CLIA environment.
Simon: How do genetic counselers want the genetic data?
Bob: I believe they get results from analysis pipeline within CLIA environment. They can look at QC metrics and raw data if they wish. They can also check if variants are novel or have already been documented (internally or in external databases). Report from clin geneticist is returned to clinician via EMR
Simon: Very similar to radiology workflow.
Simon: Are you using VCF files or are you using more than that?
Bob: VCF is used on the research
side in bioinformatics pipelines. Not used clinically (as of
... Clinical systems are quite self-contained, they pipe data from one site to the next efficiently.
... We are discussing using VCF clinically, it is not unlikely that this will happen.
... Clinical systems currently use HL7 messages. Result set and size of data are currently still quite small.
... Some of them are quite customized and were built together with vendors of machines.
... But basically they are standard HL7 V2 messages.
... Part of the problem we had with genetic results is that they are so text-based and unstructured.
... They were designed as extensions of clinical tests that were set up before genomics era (similar to Cholesterol measurements etc.)
Bob: We are using TRC Product from Oracle.
Bob: They have several products
that can work together under this platform.
... Mayo Clinic is a member of some of the respective Oracle groups. We are pushing the system past the design specs.
... Will also work on Molecular Decision Support with them.
Matthias: Decision support capabilities in Oracle?
Bob: At the moment very little/almost none, but they are interested in adding this.
Simon: What is the volume of data you expect to put into the Oracle system?
Bob: We are planning on thousands
of Genomes within the next year.
... We expect the system to scale well.
... Not sure regarding SemWeb component in Oracle
Simon: Another topic: retrieval
Bob: Before retrieval, there are
other things to consider
... a patient might have different, contradicting results for a single SNP
... this could be part of continual QC effort (e.g., scanning data and flagging such contradictions)
... We are using TRC system as foundation for our molecular CDSS
... So retrieval is needed to get data to EMR, to CDS engines
... With the cost of sequencing coming down, it might become cheaper to simply re-sequence patients.
... But of course then you have to handle partly duplicated, triplicated results.
Oliver: How do you handle patient
consent, access restrictions?
... We are thinking about regular clinical practice, same as doing a cholesterol test.
Michel: We made some progress on
... I met with Rich, we had a discussion on curating information from drug labels
... Plan to use DOMEO
... Rich produced HTML pages from product labels to use with DOMEO
... Will share once infrastructure is set up
<michel> matthias_samwald: invited to write an editorial for pharmacogenomics journal
<michel> matthias_samwald: submitted to the reasoner evaluation workshop on cds ontology
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