KORA-gen

Infrastructure to provide phenotypes, genotypes and biosamples for collaborative genetic epidemiological research

Quality measures

Initially 1796 subjects have been selected from KORA F3 whereas 1515 (84.4%) were in the age range of 45 to 69 and 281 (15.6%) in the age range between 24 and 44 in each case at the baseline examination (S3 1994/95). At completion of the genotyping 152 (8.5 %) subjects have been excluded from the dataset due to quality insurance needs resulting in 1644 complete subjects in the final KORA 500K dataset.

Descriptive statistics

The KORA 500K sample is random sample of 1388 subjects from KORA F3 in the age range 55 to 79 years. The sample is enriched by 144 young cases with atopic disease and by additional 112 subjects that are randomly selected in the age range 35 to 54 years (please have a look at the corresponding table 5).

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KORA 500k Project

Study population

KORA is a population-based research platform. In total, four surveys have been conducted. KORA S3 consists of representative samples of 4,856 subjects. In 2003/04, 2,974 participants returned for follow-up (KORA F3). With 1644 of these subjects from the age-range 25-69 years a genome-wide analysis has been performed using Affymetrix 500K oligonucleotide array set consisting of two chips (Sty I and Nsp I) containing a total of 500,568 SNPs. These were hybridized with genomic DNA in accordance with the manufacturer`s standard recommendations. Genotypes have been determined using the software BRLMM version 1.4.0 with standard settings proposed by Affymetrix.

Table 1: Distribution of call rates per chip
	Nsp	Sty
Mean	98,28%	98,19%
Median	98,53%	98,46%
Minimum	93,06%	93,46%
Maximum	99,74%	99,76%
5%-Quantil	96,36%	96,12%
95%Quantil	99,46%	99,43%

Table 2: Distribution of call rates per SNP (N=500,568)
Min.	1st Qu.	Median	Mean	3rd Qu.	Max.
48.72%	97.87%	99.33%	98.26%	99.88%	100%

Table 3: Observed genotype distributions, numbers of polymorph and monomorph SNPs:
	Absolute number	Relative number
A/A (monomorph)	17,531	3.5 %
A/A - A/B	65,699	13.4 %
A/A - B/B	42	0.0086 %
A/A - A/B - B/B	406,760	83.0 %
Table 3: Observed genotypes (without chromosome X) with A/A major genotype, A/B heterozygote genotype, B/B minor genotype.

With respect to the minor allele frequency (MAF) of the polymorph SNPs we observe a median MAF of 19.3%. XXX (YYY%) of the SNPs have a MAF of 1 % and below.

Table 4: Distribution of minor allele frequencies (without chromosome X and monomorph SNPs)
Min.	1st Qu.	Median	Mean	3rd Qu.	Max.
0.0%	7.4%	19.3%	20.9%	33.6%	50%

Table 5: Distribution of age and gender in KORA 500K
Age		Sex
S3	F3	Male		Female		RowTotal
		Count	Frequency	Count	Frequency	Count	Frequency
25-29 years	35-39 years	18	0.022	30	0.036	48	0.029
30-34 years	40-44 years	46	0.057	30	0.036	76	0.046
35-39 years	45-49 years	29	0.036	43	0.052	72	0.044
40-44 years	50-54 years	23	0.028	37	0.045	60	0.036
45-49 years	55-59 years	138	0.17	155	0.19	293	0.18
50-54 years	60-64 years	176	0.22	166	0.2	342	0.21
55-59 years	65-69 years	163	0.2	170	0.2	333	0.2
60-64 years	70-74 years	110	0.14	111	0.13	221	0.13
65-69 years	75-79 years	110	0.14	89	0.11	199	0.12
Column Total		813	0.49	831	0.51	1644	1