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Table 3 SNP classifications and recommendations using 622 passing samples derived from blood or cell line

From: Smokescreen: a targeted genotyping array for addiction research

SNPolisher ConversionType Previously validated markers Previously failed-validation markers De novo markers Total SNPs Recommendation to keep for analysis
PolyHighResolution 441120 (68.26 %) 17595 (2.72 %) 7547 (1.17 %) 466262 (72.15 %) yes
NoMinorHom 62639 (9.69 %) 6360 (0.98 %) 6173 (0.96 %) 75172 (11.63 %) yes
MonoHighResolution 12095 (1.87 %) 7061 (1.09 %) 28614 (4.43 %) 47770 (7.39 %) yes if previously validated or de novo
Other 6031 (0.93 %) 14515 (2.24 %) 27537 (4.26 %) 48083 (7.44 %) no
CallRateBelowThreshold 3078 (0.48 %) 2856 (0.42 %) 1080 (0.17 %) 7014 (1.09 %) no
OTV 370 (0.06 %) 535 (0.08 %) 860 (0.13 %) 1765 (0.27 %) yes if off-target variant genotyped
Hemizygous 180 (0.03 %) 1 (<0.01 %) 0 (0.00 %) 181 (0.03 %) yes if visually inspected
TOTAL 525513 (81.32 %) 48923 (7.57 %) 71811 (11.11 %) 646247  
  1. Previously validated’ or ‘Previously failed-validation’ are markers tested by the manufacturer. ‘De novo’ are markers on the array but not validated by the manufacturer. ‘PolyHighResolution’ and ‘NoMinorHom’ are markers with good cluster resolution. ‘MonoHighResolution’ indicates that fewer than two examples of the minor allele was present. ‘CallRateBelowThreshold’ indicated that the SNP call rate is below the threshold while other properties are above the threshold. ‘Other’ are markers where one or more cluster properties falls below its threshold