Optimal Step Length EM Algorithm (OSLEM) for the estimation of haplotype frequency and its application in lipoprotein lipase genotyping

Table 3 OSLEM-reconstructed haplotypes:

Haplotype (LPL exons)*		Frequencies within subgroups
	3 4 5 6 8 9 10	All	Cases	Controls
0:	0 0 000 000 00 00 00	0.4582	0.4933	0.4459
1:	0 0 000 0v 0 00 00 00	0.1191	0.1224	0.1000
2:	0 0 vvv v 0v 0v vv v 0	0.0767	0.0474	0.1077
3:	0 v 000 000 vv v 0 0v	0.0389	0.0361	0.0363
4:	0 0 000 000 vv v 0 0v	0.0320	0.0324	0.0271
5:	0 0 000 000 0v v 0 0v	0.0363	0.0279	0.0443
6:	0 0 vvv v 0v vv v 0 0v	0.0239	0.0250	0.0223
7:	0 0 000 000 0v vv v 0	0.0240	0.0200	0.0248
8:	v 0 000 v 00 00 00 00	0.0200	0.0186	0.0152
9:	0 0 vvv v 0v 00 00 00	0.0211	0.0172	0.0225
Totals:		0.8502	0.8403	0.8461

On 14 Single Nucleotide Polymorphisms of the lipoprotein lipase gene in 163 atherogenic cases and 157 non-atherogenic controls. Geneva, Switzerland, 1999–2000. * SNPs are divided into subgroups according to their locations on exons, for example the first SNP is located on exon3, the second on exon 4, the third, fourth, and fifth are on exon 5, and so on. In the haplotype sequences, v means minor variation and 0 means major variation.

ISSN: 1471-2105