failed Affymetrix’s internal validation process (see Table 3).Table 3SNP classifications and recommendations using 622 passing samples derived from blood or cell lineSNPolisher ConversionTypePreviously validated markersPreviously failed-validation markersDe novo markersTotal SNPsRecommendation to keep for analysisPolyHighResolution441120 (68.26 %)17595 (2.72 %)7547 (1.17 %)466262 (72.15 %)yesNoMinorHom62639 (9.69 %)6360 (0.98 %)6173 (0.96 %)75172 (11.63 %)yesMonoHighResolution12095 (1.87 %)7061 (1.09 %)28614 (4.43 %)47770 (7.39 %)yes if previously validated or de novoOther6031 (0.93 %)14515 (2.24 %)27537 (4.26 %)48083 (7.44 %)noCallRateBelowThreshold3078 (0.48 %)2856 (0.42 %)1080 (0.17 %)7014 (1.09 %)noOTV370 (0.06 %)535 (0.08 %)860 (0.13 %)1765 (0.27 %)yes if off-target variant genotypedHemizygous180 (0.03 %)1 (<0.01 %)0 (0.00 %)181 (0.03 %)yes if visually inspectedTOTAL525513 (81.32 %)48923 (7.57 %)71811 (11.11 %)646247‘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
