Sequence determinants of human microsatellite variability

BMC Genomics

Table 5 Spearman's rank correlations of heterozygosity with microsatellite sequence properties and measures of variation across individuals

	1 STR region			2 STR regions			3 STR regions
	Di	Tri	Tetra	Di	Tri	Tetra	Tetra
Number of loci	30	133	325	10	15	97	12
Sequence properties
G/C content of flanking sequence	0.247	0.037	-0.034	0.237	0.291	0.142	0.035
Number of nucleotides separating STR regions	-	-	-	0.140	0.568	0.032	0.252
Measures of variation across individuals
Number of distinct alleles	0.424	0.431	0.517	0.628	0.497	0.596	0.644
Variance in number of repeats	0.325	0.502	0.800	0.636	0.750	0.779	0.846
Range of number of repeats	0.151	0.326	0.492	0.646	0.304	0.672	0.681
Mean PCR fragment size	0.040	0.007	-0.016	-0152	0.571	0.126	0.308
Mean number of repeats	0.564	0.239	0.134	0.455	0.018	0.388	0.503
Maximum number of repeats	0.465	0.228	0.384	0.669	0.235	0.562	0.706
Minimum number of repeats	0.335	-0.036	-0.044	0.049	-0.079	-0.036	0.385

Spearman's rank correlation coefficients (ρ) are shown for comparisons of microsatellite heterozygosity with continuous microsatellite sequence properties and with measures of variation across individuals in the HGDP-CEPH data set. Microsatellites were classified by the number of separate STR regions embedded in their sequence and by their repeat unit size. Hyphens indicate comparisons that were not evaluated. For three STR regions, no comparisons were performed for di-nucleotide and tri-nucleotide loci because of small sample size (3 and 2, respectively). Correlations with P < 0.05 are highlighted in bold.

ISSN: 1471-2164