Depth correlation plots prepared from exome capture data revealed that artificial background noise arising from the use of target capture kits might be problematic. (a) Correlations of target base coverage depth between four independent NimbleGen captures with the daughter sample from the YRI trio (YRI-D-NM). Two different lots of NimbleGen exome probe libraries were used for this analysis, and correlation anomalies were only observed when comparing data between the two lots. YRI-D-NM-LN1 was captured with one lot and YRI-D-NM-LN2, YRI-D-NM-LN3, and YRI-D-NM-LN4 were captured with the other. (b) Correlations of target base coverage depth between four independent Agilent captures with the daughter sample from the YRI trio (YRI-D-AG). Only one lot of Agilent exome probe library was used for this analysis, and data between different captures consistently correlated well. AG, Agilent exome; D, YRI daughter; LN, lane; NM, NimbleGen exome; r, correlation coefficient.
Parla et al. Genome Biology 2011 12:R97 doi:10.1186/gb-2011-12-9-r97