Buffy coat specimens remain viable as a DNA source for highly multiplexed genome-wide genetic tests after long term storage

Table 4 ACCORD Illumina Omni1-Quad Statistical Genotype QC Analysis Results

Step	Samples Remaining	SNPs Remaining	Dropped (% of Remaining)
Post-Laboratory QC	32	1,140,419 (inc CNV probes)
Remove CNV probes (not analyzed)		1,048,713	91,706
Drop SNPs with 100% missing data	32	1,015,235	33,478 (3.3%)
Drop samples with > 1% missing data	32	1,015,235	0 (0%)
Total	32	1,015,235
QC Statistic	N	Value	Comments
Mean per sample Genotype Missing Rate (range; sem)	32	0.20% (0.07-0.62%; 0.024%)	For all SNPs
		0.21% (0.07-0.64%; 0.025%)	SNPs with < 100% missing genotypes
Median per sample Genotype Missing Rate	32	0.16%
Mean per SNP Genotype Missing Rate (range; sem)	1,015,235	0.21% (0-37.5%; 0.0012%)	32 Samples
Median per SNP Genotype Missing Rate	1,015,235	0%	32 Samples

The upper part of the table shows the samples and SNPs that were dropped at each step of the Statistical Genotype QC analysis and the total number remaining. The lower part of the table summarizes values of the key QC statistics in the samples and SNPs remaining after the QC steps.

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