Circulating tumor DNA analysis as a real-time method for monitoring tumor burden in melanoma patients undergoing treatment with immune checkpoint blockade

Table 1 Tumor-specific mutation analysis of 10 melanoma tumor specimens

ID^a	BRAF	cKIT	NRAS	Other	Therapy	Radiographic response	ctDNA level analyzed?
01	WT	WT	WT	Chr5: 1,295,228-9	ipilimumab	Immune-related PR	Y
01	WT	WT	WT	GG > AA (TERT) ^b	ipilimumab	Immune-related PR	Y
03	1799T > A	WT	NT	NT	BMS-936559	PD	Y
05	WT	WT	WT	NT	ipilimumab	PD	N
06	WT	WT	WT	NT	BMS-936559	PD	N
07	WT	WT	WT	NT	ipilimumab	PD	N
08	WT	WT	182A > G	NT	BMS-936559	PD	Y
09	WT	WT	WT	NT	BMS-936559	PD	N
10	WT	WT	181C > A	NT	ipilimumab	PD	Y
11	WT	WT	WT	Chr2: 29,551,215	ipilimumab	CR	N
11	WT	WT	WT	C > T (ALK) ^b	ipilimumab	CR	N
12	WT	WT	NT^c	NT	ipilimumab	PD	N

Archived formalin-fixed, paraffin-embedded tumor specimens were analyzed for common, recurrent somatic sequence mutations in BRAF, cKIT, NRAS and TERT[19] using standardized pyrosequencing, melting curve analysis, or Sanger sequencing techniques, as previously described (Wood et. al., Science. 2007 Nov 16;318(5853):1108-13. and Parsons et. al., Science. 2008 Sep 26;321(5897):1807-12.). No mutation was detected in 5 of 10 patients. Previously reported mutations associated with melanoma (BRAF, NRAS, TERT) were found in 4 patients. For one subject (#11) whose tumor was found to be wild type for each of the above genes, whole exome sequencing analysis of tumor and normal samples was employed to identify tumor-specific (somatic) sequence and copy number alterations. (WT, wild type; NT, not tested; PR, partial response; PD, progressive disease; CR, complete response; ^apatient ID numbers are not sequential as 2 patients who died due to disease progression prior to completing their courses of therapy are not included in Table 1; ^bgenomic position, hg19; ^cNo PCR amplified product was obtained after repeated attempts).