Table 3.

EBV LMP-1 patterns in 23 subjects with whole genome sequence extracted from BLGSP, including 14 with samples in EMBLEM who were also genotyped in this study using the Sanger method.

Case ID	WGS depth		EBV type	LMP-1 Pattern from WGS		LMP-1 pattern from Sanger
	Tumor	Normal		Tumor	Normal	Normal
Nine Paired BLGSP samples of tumor and buccal (normal) samples*
BLGSP-71-06-00012	1525.09	10.20	1	F	F	–
BLGSP-71-06-00020	549.83	569.85	1	D	D	–
BLGSP-71-06-00072	773.10	724.81	2	AI	AI	–
BLGSP-71-06-00076	1129.61	144.91	1	AIII	AIII	–
BLGSP-71-06-00143	1275.68	240.18	1	D	D	–
BLGSP-71-06-00146	655.55	27.22	1	ABIII	ABIII	–
BLGSP-71-06-00251	1708.80	3848.28	1/2	AIII	AVI	–
BLGSP-71-06-00255	2972.55	358.95	1	AIII	AIII	–
BLGSP-71-06-00277	3965.62	15.03	1	F	n/a	–
14 paired BLGSP samples of tumor and blood (normal) samples and Sanger data from LMP-1 gene targeted PCR sequencing in the EMBLEM study
BLGSP-71-08-00033	1492.4	1.1	2	D	n/a	D
BLGSP-71-08-00036	645.5	1.0	2	D	n/a	D
BLGSP-71-08-00038	1055.9	1.6	1	D	n/a	AB7
BLGSP-71-08-00041	1766.1	1.3	1	D	n/a	A3
BLGSP-71-08-00050#	1424.7	4.3	n/a	ABII	n/a	ABII
BLGSP-71-08-00191#	3.6	1.8	n/a	NA	n/a	n/a
BLGSP-71-08-00194	2705.2	15.2	1	AIII	AIII	n/a
BLGSP-71-08-00197	3053.0	32.6	1	I	I	K
BLGSP-71-08-00199	2914.7	3.6	1	I	n/a	n/a
BLGSP-71-08-00200	1526.9	2.9	1	D	n/a	D
BLGSP-71-08-00204	2818.9	2.5	1	ABII	n/a	AB7
BLGSP-71-08-00205	1116.6	3.4	1	D	n/a	n/a
BLGSP-71-08-00206	3558.9	2.9	1	I	n/a	I
BLGSP-71-08-00210	1776.2	3.1	1	D	n/a	K

*The last three digits of the samples used to annotate the phylogenetic tree in Figure 3 B .

#These samples could not be classified for EBV type due to insufficient sequence coverage in EBNA-2.

n/a, Not applicable because sequence data was insufficient to genotype samples for EBV LMP-1 patterns.