HiScanSQ users, could you provide us with your experience?

[Mahmoud]

Hi all,

Our institute is going to get the HiScanSQ machine but we don't have direct contact with core facilities that had the same machine. We need to know from those who worked on it what are their concerns and recommendations

I know that many of you will recommend getting a HiSeq but we cannot afford such step.

Thanks,

Mahmoud

[matth431]

Hi all,

Our institute is going to get the HiScanSQ machine but we don't have direct contact with core facilities that had the same machine. We need to know from those who worked on it what are their concerns and recommendations

I know that many of you will recommend getting a HiSeq but we cannot afford such step.

Thanks,

Mahmoud

Ours gives very good data when operational - most of our downtime has been caused by fluidics issues as (unlike HiSeq) these are an addition to the machine (the SQ module) rather than being an integral part. Make sure to wash routinely and monitor the flow - any blockage issues could be indicative of a failure with the syringes that pump the reagents.

We've also had a number of communication issues between the HiScan and PC but Illumina are getting better at spotting/resolving these as they ship more units. You'll probably also benefit from a newer spec PC as Illumina have switched from using Dell since they launched the HiSeq2500.

Otherwise, we routinely get 18-19Gbp of data per lane loading libraries at 10pM (Qubit quantification works best). Illumina recommend 700-800k/mm2 cluster density but we've had decent data at the 900-1000k level.

If you intend to use the "Scan" part of "HiScan" (i.e. scanning GoldenGate/Infinium beadchips), then I would recommend planning experiments not to overlap between sequencing and scanning - although you CAN pause a sequencing run for an hour or so to scan beadchips, it's a hassle since you have to exit the HCS control software and thus enter a lot of the sequencing run parameters again when resuming sequencing. Fortunately, the beadchips scan well even a week or so after hybridisation.

[Mahmoud]

Thanks,

I have been informed by Illumina agent that the SQ module will be discontinued this year.