Mobile element scanning (ME-Scan) by targeted high-throughput sequencing

BMC Genomics

Table 3 Comparison of ME-Scan results to 1,708 presumably fixed AluYb8/9 insertions in the human reference genome

Individual	Index	Number of ME-Scan negative loci	False Negative rate (%)	Genotypes checked by PCR¹	Checked and Present by PCR²
Replication
A	ACCAT	147	8.61	18	4
A	TATTC	145	8.49	18	4
Pooling
A	ACCAT	400	23.4	18	4
B	TATTC	420	24.6	18	2
C	GGTTA	400	23.4	17	5
D	CGCTA	164	9.60	17	2
D	TTGAT	134	7.85	17	2
Combined	All	100³	5.85	123	23

¹ The number of genotypes compared differs from sample to sample due to occasional uncertain genotype calls (missing data) in the PCR and gel genotyping assays.
² These genotypes represent actual false negative ME-Scan results (absent according to ME-Scan, present by PCR.)
³ For 100 of the 1,708 loci, ME-Scan did not observe the insertion-present allele in any of the samples tested ("Combined").

ISSN: 1471-2164