Whole genome sequence analysis of BT-474 using complete Genomics’ standard and long fragment read technologies

GigaScience

Table 5 NA12878 simulation of LOH event in BT-474

	Variants in NA12878	Variants based on LOH simulation by length	Variants based on LOH simulation by number of variations
Hom SNPs	1,306,544	1,768,557	1,729,016
Het SNPs	2,081,141	1,619,128	1,658,669
Ratio	1.59	0.92	0.96

The percentage of the BT-474 genome found to be in regions of LOH was used to simulate what would happen to the heterozygous and homozygous variants in the genome of NA12878 if that same amount of LOH was to occur. The simulation demonstrated that the LOH variants, and the increase in homozygous variants as a result, caused a shift in the Het/Hom SNP ratio from 1.59 to 0.92–0.96, similar to the average ratio of the three libraries of 0.98 seen in BT-474. An explanation of the fields are as follows: hom SNPs, total number of homozygous variants; het SNPs, total number of heterozygous variants; variants in NA12878, number of variants of each category in the genome of NA12878; variants based on LOH simulation by length, the change in the number of variants based on applying the percentage of LOH as calculated from the total length of the LOH region in BT-474; variants based on LOH simulation by number of variations, the change in the number of variants based on applying the percent of LOH as calculated from the total number of variants in the LOH region in BT-474

ISSN: 2047-217X