Video recording (sorry, I missed the first minute!). I tried inserting it directly into Confluence but it seems to be a bit glitchy.
Also can be found on YouTube (private link) where it should work better: https://youtu.be/1LUottSwY8Y
Agenda
Eng – short update on EiB Module 3 mid density platform
Feedback on DArTTag technology from 3 crops
Bodo Raatz – beans
Damien Platten – rice
Moctar Kante – potato
Action items
Liz - to share questions with everyone for further follow up. Try the EiB site?
For polyploids need more information on the read depth we will see under the standard contract, and what the costs will be for higher read depth
Would be good to have standardized metrics to compare technology
Main positives and negatives
Conversion rate from other technologies low (can be up to 50%) - especially a problem for trait specific markers. Need to submit double the number of sites to get the plex at the number you want.
Calls rate and quality of markers that do convert is high
Need consistency of reporting, sometimes get nucleotides, sometimes +-, needs to be consistent. Have had markers not named consistently. Also not obvious what the calls are compared with the submitted sequence for each allele. Working with DArT to resolve this.
Getting good read depth and calls with 384 panels for potato and but not really sure what the call rate will be for routine genotyping under the contract
Not yet getting vcf format which many users need
Bodo saw some issues with hets being resolved - might help to use posterior probabilities eg updog?
For rice have about 500 markers which is sub-optimal for GS or mapping, but has been working well for fingerprinting and background selection. Need to fill in gaps in another round of design.
Questions
Catherine: do you have the script to convert in vcf? because it really depends of the experiment.
Moira: For the technical control, does 384 samples really translate to 383?
Siva and Liz: Could you please elaborate on upfront costs? You mention EiB will provide support for set-up - how do we access these funds and what would they cover?
Liz: Is there a cost to update the panel every year? Recommend revalidating every time the panel is updated as new assays can cause other assays to fail.
Liz: what is the approx. cost of shipping DNA between Intertek (Sweden or Australia) and DArT that would be added to the invoice?
Moctar - getting good call rate with average 80 reads per sample locus. What would be the costs to achive this? Standard genotyping under contract is around 10 calls?
Liz: will other technologies be considered for medium density platforms under EiB M3?