Figure 4

Capture pool used for nucleic acid capture and MiSeq analysis.

(a) The heat map indicates test minus reference signals from the probes (Y-axis) chosen from 4 different analyses. 7 separate captures of target nucleic acids were done using 5 probe pools as indicated. (b) The individual reads obtained from MiSeq are shown for the triple negative breast cancer samples. Whole genome amplified DNA plus cDNA was hybridized to a set of biotinylated conserved and specific viral, bacterial, fungal, parasitic and viroid probes, captured on Streptavidin beads and used for tagmentation library preparation and deep sequencing with paired-end 250-nt reads. The MiSeq was done on libraries generated by capture sequences using viral conserved probes (probe pool VCP), viral specific probes (probe pool VSP), pox virus probes (probe pool Pox), bacterial probes (probe pool B1 and B2), fungal/parasitic and viroid probes (probe pool P1 and P2). The MiSeq reads when aligned with the metagenome of PathoChip (Chip probes) clustered mostly at the probe regions of the represented organisms. The genomic location along with the number of MiSeq reads are shown on the figure and represents the genomic co-ordinates. The alignment track of IGV displays two tracks: (the upper) a coverage track and (the lower) the alignment track. IGV colors paired-end alignments that deviate from expectations (horizontal colored lines) and the mismatched bases are displayed in color (A as green, C as blue, G as yellow and T as red) on the grey aligned sequence bar that represents the read.