Whole exome sequencing of a single osteosarcoma case—integrative analysis with whole transcriptome RNA-seq data

Table 9 The integrative analysis - loss of heterozygosity and RNA expression data observed together

Gene name	Chr number	LOHs				RNA expression
Gene name	Chr number	LOH position	Alleles	LOH	LOH p value	logFC	FDR
MS4A14	Chr11	60165358–60165379	G/C	CopyNeutralLOH	0.025	2.46	3.20E-08
DSC2	Chr18	28666554–28666556	A/C	CopyNeutralLOH	0.025	1.87	3.82E-07
RPS4X	ChrX	71495409–71495414	G/C	CopyNeutralLOH	0.01	−1.44	7.25E-07
RPS23	Chr5	81571874	A/C	CopyNeutralLOH	0.005	−1.43	1.04E06
IL7R	Chr5	35874575	C/T	1AlleleGain	0.025	1.59	6.69E-06
PCNXL2	Chr1	233398713	C/T	CopyNeutralLOH	0.01	1.20	0.00027
HILPDA (C7orf68)	Chr7	128098270	T/G	CopyNeutralLOH	0.0001	−1.12	0.00094
HRNR	Chr1	152188041	C/T	Allele(s)Loss	0.025	−3.09	0.00796
MUC4	Chr3	195515594, 195516630	C/G	CopyNeutralLOH	0.025	−2.22	0.01230

Only the genes with significant mRNA expression changes in the tumour tissue compared to that in the control tissue are presented.

ISSN: 1479-7364