Mapping 250K/500K SNP assay

chapter 4 | 96-Well Plate Protocol 37
single channel pipette for plate-based samples requires too many
pipetting steps, thus creating too high of a chance for error. To
familiarize yourself with the use of multi-channel pipettes, we
strongly recommend practicing several times before processing actual
samples. You can use water to get a feel for the aspiration and
dispensing of a solution to multiple wells simultaneously.
The post-PCR stages (5 through 8) are best performed by the more
experienced operators in your laboratory. These operators should be
proficient in:
• The use of multi-channel pipettes
• High throughput sample processing
Even if you feel comfortable with the protocol and with multichannel
pipetting, do not attempt to transition to 96 samples immediately.
We recommend a moderately paced ramp-up, wherein the operator
first establishes proficiency with 24 samples. Your field application
specialist (FAS) will provide additional guidance on best practices for
a successful lab scale up.
When you are ready to process full 96-well plates, we recommend that
the same operator should not perform too many stages in a given day.
Small teams of individuals dedicated to different stages of the process
has proven to be a highly effective method of managing this workflow.
For example, the full process can be sub-divided into four teams in
which each team is responsible for the following stages:
• Team 1: pre-PCR (digestion, ligation, PCR set-up)
• Team 2: post PCR (purification, quantitation)
• Team 3: post-PCR (normalization, fragmentation, labeling)
• Team 4: array processing (hybridization, fluidics, scanning)
Again, your FAS can provide additional guidance on how best to
configure the lab personnel for the 96-well plate protocol.
Arrays from different enzyme fractions should not be processed by
the same technician on the same day.