High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta

Table 1 SNPs and corresponding genes statistically significant when tested for ASE by Sequenom Assay.

Gene	SNP_ID	fdr.p.values	Difference	SR ratio	Mode of ASE
DLK1	rs1802710	3.62E-23	88.6	0.89	Imprinting
PEG3	rs1860565	2.74E-22	98.1	1.00	Imprinting
IGF2	rs680	2.32E-16	94.6	1.04	Imprinting
PEG10	rs13073	4.19E-08	98.4	0.84	Imprinting
PHLDA2	rs13390	4.19E-08	98.1	1.13	Imprinting
DISC1	rs821616	0.022009568	15.3	0.91	Random ASE†
RASGRF1	rs11855231	0.022009568	75.7	0.95	Random mono†
C9orf93	rs1539172	0.039790941	30.0	0.78	Preferential†
TF	rs8649	0.04122505	56.9	0.78	Random ASE†
ACSS2	rs4911163	0.04122505	21.9	0.86	Preferential
KIAA0523	rs3744725	0.04122505	36.5	0.96	Random ASE†

The p-value is adjusted for multiple testing (false discovery rate bound). The average difference of expression between the two alleles in the cDNA of heterozygous individuals is greatest for imprinted genes. SR ratio is the ratio of genotyping success rate of cDNA on gDNA. Mode of ASE summarises the pattern of ASE based on the quantitative allelic expression data. †False positive pattern probably due to a low expression level (see text for details).

ISSN: 2730-6844