Can I use PE 250 bp sequencing chemistry to improve FLT3-ITD detection?

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Sequencing with paired-end (PE) 250 bp chemistry instead of PE 150 bp chemistry to detect FLT3-ITD variants depends on the length and exact position (insertion site) of the internal tandem duplication (ITD).

In the AML and MYE panels, two of the five FLT3 amplicons do not overlap across Read1 and Read2 when sequenced with PE 150 bp chemistry. PE 250 bp chemistry may improve the ability to detect the variant if the ITD insertion site is at the end of the read and may reach into the gap between both reads.

However, take caution because error rates toward the late cycles are higher compared to early cycles.

In addition, the data processing time increases compared to datasets that were generated with PE 150 bp sequencing chemistry. 

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