Table 3.

Genomic deletions and breakpoints identified by the assay

Patient ID	Gene	Genomic event	Breakpoint identified by NGS system					Breakpoint identified by amplification of the deletion junction
			Chromosome	Starta	Enda	Size (bp)	Average ratiob	Chromosome	Start	End	Size (bp)
F16	FLCN	Deletion exons 1–3	17	17134237	17141880	7644	0.377	17	17134286	17141828	7543
F17	FLCN	Deletion exons 14	17	17115904	17117646	1743	0.534	17	17115898	17117706	1809
F18	FLCN	Deletion exons 9–14	17	untargeted regionc	17123085	---	0.513	17	17115206	17123002	7747
F19	FLCN	Deletion exons 9–14	17	untargeted regionc	17123085	---	0.516	17	17115206	17123002	7747

^aBreakpoints are defined by the external boundaries of 20 bp-intervals. Breakpoints are flanked by Alu repeats

^bAverage of normalized depth ratio of each 20 bp-interval

^cThe breakpoint is within the 3′ flank of the FLCN gene, which was not included in the panel