Table 3. HNSCC long range PCR of EGFR intron 1.

Sample	vIII mRNA	EGFR amp	Pre mRNA	Full EGFR	Unique breakpoints	Location a
704 RNA	- b	+ c	+ d	Yes	0	0
061 RNA	-	+	-	Yes	0	0
035 RNA	+	+	-	Yes	0	0
836 RNA	+	+	+	Yes	1	4790760
021 RNA	+	-	-	Yes	0	0
681 RNA	-	-	-	Yes	0	0
120810 RNA	-	-	-	Yes	0	0
704 DNA	-	+	NA	NA	1	4676431
061 DNA	-	+	NA	NA	1	4676431
035 DNA	+	+	NA	NA	1	4676431
836 DNA	+	+	NA	NA	1	4676431
021 DNA	+	-	NA	NA	0	0
681 DNA	-	-	NA	NA	4	4784580, 4676431, 4790760, 4724521
120810 DNA	-	-	NA	NA	4	4784752, 4676431, 4790760, 4724521

^a The NCBI reference sequence for EGFR GRCh37.p10 was used with NT_033968.6 for DNA and NM_005228.3 for mRNA

^b mRNA with EGFRvIII transcript is denoted as “+”, wtEGFR only transcript is denoted as “-“

^c Tumor samples with EGFR gene amplification are denoted by “+”

^d Tumor samples with Exon 1 to 8 joining at the pre mRNA level are denoted as “+”.