Kun:LabNotes/MONOD/2014-5-9: Difference between revisions

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==MONOD V1N3 selected set==
==MONOD V1N3 selected set==
*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.  
*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 [[Media:131227_MiSeq_probeEfficiency_matrix_12May14.txt|131227_MiSeq]] and [[Media:140414_MiSeq_probeEfficiency_matrix|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: [[Media:MONOD_V1N3_selected_12May14.txt|MONOD_V1N3_selected_12May14.txt]].
*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 [[Media:131227_MiSeq_probeEfficiency_matrix_12May14.txt|131227_MiSeq]] and [[Media:140414_MiSeq_probeEfficiency_matrix.txt|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: [[Media:MONOD_V1N3_selected_12May14.txt|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.
*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.
   ./[[Media:probe2padlockCpgLib12May2014V6.txt|probe2padlockCpgLib12May2014V6.pl]] [[Media:MONOD_V1N3_selected_12May14.txt|MONOD_V1N3_selected_12May14.txt]]
   ./[[Media:probe2padlockCpgLib12May2014V6.txt|probe2padlockCpgLib12May2014V6.pl]] [[Media:MONOD_V1N3_selected_12May14.txt|MONOD_V1N3_selected_12May14.txt]]
*Oligo sequences to order: [[Media:MONOD_V1N3_selected_12May14_oligos_to_order.txt|]MONOD_V1N3_selected_12May14_oligos_to_order.txt]
*Oligo sequences to order: [[Media:MONOD_V1N3_selected_12May14_oligos_to_order.txt|]MONOD_V1N3_selected_12May14_oligos_to_order.txt]

Revision as of 00:28, 13 May 2014

MONOD V1N3 selected set

  • 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: [[Media:MONOD_V1N3_selected_12May14_oligos_to_order.txt|]MONOD_V1N3_selected_12May14_oligos_to_order.txt]