VariantPlex®

Although we have some germline/inherited disease workflows, the best option is to design a custom panel to suit the need for specific targets.

In most cases, we design for FFPE input and the same assays can be used for germline testing. In some cases we have designed custom panels for germline applications and these designs may not transfer to FFPE material with shorter fragment lengths.

Yes, MRD / LAF can be optimized with the VariantPlex panels as outlined below.

1. 200-250 ng input
2. Use a normal dataset
3. Increase sequencing depth
   • At least 8M reads/sample for VariantPlex AML Focus
   • At least 20M reads/sample for VariantPlex Core Myeloid
   • At least 30M reads/sample for VariantPlex Myeloid
4. Use low allele frequency (LAF) cycling conditions (see below)

LAF Cycling Conditions Low Allele Frequency (LAF) cycling conditions are largely the same regardless if you’re running VariantPlex AML Focus, VariantPlex Core Myeloid, or VariantPlex Myeloid panel. The only difference is in the annealing temperature for the PCR1 LAF step (AML: 65°C; Core Myeloid: 63°C, and Myeloid: 62°C). LAF cycling conditions. Customers should use amended PCR1 and PCR2 cycling conditions (longer 65°C/63°C incubation time and less cycles for PCR1 and PCR2). Please note that PCR1 annealing temperature needs to be 62°C for 15 min for the VariantPlex Myeloid catalog panel. LAF cycling adds approximately 3 hours to the hands-off time of the protocol. However, the LAF protocol adjustments allow for more confident per-base calling compared to standard PCR conditions.

PCR1

Temp	Time	Cycles
95C	3min	1
95C	30sec	10
AML Focus: 65C Core Myeloid: 63C	15min
72C	3min	1
4C	Hold	1

PCR2

Temp	Time	Cycle
95C	3min	1
95C	30sec	15
65C	15min
72C	3min	1
4c	Hold	1