Skip to main content

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