Genbench External issueshttps://gitlab.sib.swiss/clinbio/genbench/genbench-external/-/issues2023-05-04T14:34:23+02:00https://gitlab.sib.swiss/clinbio/genbench/genbench-external/-/issues/1Information to be provided by IMGZ2023-05-04T14:34:23+02:00Valerie BarbieInformation to be provided by IMGZTHIS LIST IS NOT KEPT UPDATED, PLEASE REFER TO THE ISSUES IN THE GB KNOWLEDGE BOARDS.
Here is below the list of actions on IMGZ's side, that are needed to advance the development.
# Lab interface
- [x] Review the lab interface (from th...THIS LIST IS NOT KEPT UPDATED, PLEASE REFER TO THE ISSUES IN THE GB KNOWLEDGE BOARDS.
Here is below the list of actions on IMGZ's side, that are needed to advance the development.
# Lab interface
- [x] Review the lab interface (from the provided PDF) and adjust it as needed for at least the main labs' activities.
- [x] Review the Lab cards Excel file.
- [x] Review the Excel file with all the results to be entered for sample procedures and primary analyses (WP3/Sample proc and primary analysis results for review) sent on 07.03.2023
# Information to be provided
## Pedigree tree
- [x] Provide an example of paper family tree.
## Communications
- [ ] Provide an example of each type of letter that can be sent outside.
- [ ] Provide the templates for billing letters.
## Samples
- [ ] Define the default sample list for normal patients, children/prenatal and complex cases.
- [x] Provide the specifications of the bar coding system that is used for NIPT.
- [x] Provide the list of storage places / biobanking containers.
- [x] Define the list of reasons for troubleshooting, and the fixes that can be applied. The objective is to use a drop-down menu for troubleshooting reasons, instead of a free text.
- [x] Define who can have to freeze, store and send samples (sample manager only, or labs sometimes?).
- [x] Provide the existing templates for barcoding.
- [x] Review the columns on the Incoming samples page.
## Reports
- [ ] Provide templates of lab reports and final reports.
- [ ] Provide the various disclaimer paragraphs that need to be added to the report.
## Material
- [x] Define the format of the material ID.
- [x] Think again about the material ID, that could be too long whrn imported into other software. Maybe keep the Mxxx, Axxx and Pxxx label as additional identifiers?
## Case categories
- [x] Define the list of case categories ("Beratungsprobleme").
- [ ] Provide the possible case outcomes for each category.
- [ ] Prepare the list of possible tasks for a case.
## Assays
- [x] For each incoming sample card, provide the list of possible Procedure type (columns A and B of the Labs card Excel file).
- [x] For each assay type, list the possible assays.
- [ ] Describe the results of each assay (ie the information that need to be stored), and precise if the results entry will be done manually or by uploading a file.
- [ ] Provide an example of each kind of working sheet that should be prepared by GenBench to start an analysis (for DNA extraction, NGS, others...).
- [ ] For each analysis for which a results file will be uploaded, please provide an exemple. Please note that this information won't be manually editable, in case of mistake the file will have to be reloaded.
- [x] Identify the analyses performed in batch (NGS, DNA extraction, etc...) and the naming convention used for the batches.
- [ ] Define the format to use for cytobands.
- [x] Provide the list of results for DNA extraction.
- [ ] Structure the NGS assays results (currently a Powerpoint).
- [ ] Agree on a common nomenclature for assay information: "kit" is used forMLPA, while exome uses "categories"
- [ ] Provide the default duration for all assays.
- [x] Definitely validate that only MLPA and exome require a working sheet.
**MLPA**
- [x] Provide the template of the working sheet that should be printed by GenBench.
**Exome**
- [x] Define the categories and the corresponding default list of genes.
- [x] Define the working sheet format.
- [x] Provide us with an example of the 2 types of gene lists that can be uploaded into GenBench.
- [ ] Provide the list of capture kits.
- [ ] Agree on where to select and show the capture kit.
- [ ] Define the process for exome re-analysis.
- [ ] Review the list of all QC parameters to be entered in GenBench.
## Procedures
- [x] List all possible materials than can be obtained from each procedure.
- [x] Chemagic DNA extraction curve.
- [ ] Provide the default duration for all procedures.
- [x] Definitely validate that only DNA extraction and NIPT require parsing a file for the results entry.
## Genes / diseases
- [ ] Provide the list of genes that can be analyzed for each disease (extract from HGMD).
- [ ] Define the list of possible values for the "Clinical relevance" of a variant; the currently list is: Incidental finding, Carriership, Causal, Unclear).
## Primary analysis
- [ ] Define the list of possible values for the "Overall result category", which is not linked to variants but to the patient; the currently list is: Normal, Abnormal solved, Abnormal not solved.
- [ ] Validate that no other block of information for the result is needed but those listed in the Primary Analysis requirements.
## Calendar
- [X] Provide the list of possible categories for the free slots:
Children
Children-follow-up
Adults-general
Adults-cancer
Adults-reproduction
Adults-pregnancy
Adults-follow-up
Renal or retinal disease
Renal or retinal diasease-follow-up
- [X] Review the list of possible meeting rooms
IMG-1
IMG-2
IMG-3
Chur
WT
Kispi-1
Kispi-2
# Case creation
- [ ] Define the rules about cases creation together with Erlangen, in particular for external samples