Kun:LabNotes/MONOD/2014-5-12
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MONOD V1N3 selected set[edit]
- The probes were selected from MONOD V1 (aka GP1_V4) and V3, based on the efficiency and variability of the capture. It represents a refined probe sets for more efficient and uniform capture of real cancer specimens.
- I calculated the normalized capture efficiencies (unique reads per million mappable unique reads) for all the probes, and the CV across all samples analyzed in 131227_MiSeq and 140414_MiSeq runs. Only probes that have the efficiency between 100-1000, and CV below 0.6 were included. With such criteria, 725 probes in the V1 set and 1764 probes in the V3 set were selected: MONOD_V1N3_selected_12May14.txt.
- Many probes in the MONOD V1 set have CpG sites in the H1/H2 capturing arms. Since these probes were designed for regions that are methylated in cancer samples, I had an idea that perhaps synthesizing the probes for the methylated templates only would enrich for cancer DNA in the mixture. Therefore, I only assemble the probes for the methylated DNA.
./probe2padlockCpgLib12May2014V6.pl MONOD_V1N3_selected_12May14.txt
- Oligo sequences to order: MONOD_V1N3_selected_12May14_oligos_to_order.txt.
- These oligos were combined with Chris' microsatellite probes in a single 12k order: Media:CustomArray_13May14_order.xlsx