How to randomize for sample multiplexing and flow cell placement?

[User001]

We’re about to start targeted sequencing for a study with about 1500 samples (500 trios). The samples will be multiplexed at 96x per flow cell lane.

Does anyone have suggestions on how to randomize the samples in regards to sample prep/ flow-cell placement? Would you randomize by individual samples or by families (keeping trios together)? It may not affect results much, but I would like to avoid reviewer comments down the road.

[User001]

We’re about to start targeted sequencing for a study with about 1500 samples (500 trios). The samples will be multiplexed at 96x per flow cell lane.

Does anyone have suggestions on how to randomize the samples in regards to sample prep/ flow-cell placement? Would you randomize by individual samples or by families (keeping trios together)? It may not affect results much, but I would like to avoid reviewer comments down the road.

In case anyone is curious, we decided to keep families on the same 96 well prep-plate and randomize 48 cases and 48 controls to each plate. This should minimize enrichment-effects among families and balence these effects between cases and controls.