Table 2. Study design.

Enrichment approach		I2HCP	TSCP	WES
Library design	Kit, supplier	Custom SureSelect, Agilent	TruSight Cancer, Illumina	All Exon v5, Agilent
	Target region	400 Kb	255 Kb	50,400 Kb
	Target genes	122	94	≈21,500
	Target SNPs	47 identification, 43 risk	284 risk	All coding SNPs
Technical details	Input DNA	3 μg DNA	50 ng DNA	3 μg DNA
	Bait length	120-mer RNA	80-mer DNA	120-mer RNA
	Fragmentation	Covaris DNA shearing	Nextera tagmentation	Covaris DNA shearing
	Capture	In solution hybridization	In solution hybridization	In solution hybridization
	Prepared at	CNAG	ICO	CNAG
	Library prep. time	4–5 days	3 days	4–5 days
Run	Platform	Hiseq 2000, Illumina	Hiseq 2000, Illumina	Hiseq 2000, Illumina
	Kit	TruSeq SBS v3: 200 cycle	TruSeq SBS v3: 200 cycle	TruSeq SBS v3: 200 cycle
	Throughput	24 patients/lane, 1.5 Gb/patient	24 patients/lane, 1.5 Gb/patient	2.6 patients/lane, 13.6 Gb/patient
	Run time	11 day	11 day	11 day
Computing per sample	CPU time	50 h	44 h	93 h
	Storage	2.2 GB	1.7 GB	20.5 GB
Other sequencing options. HiSeq2500 rapid run	Kit	HiSeq rapid SBS kit v2, 200 cycle, 60 Gb	HiSeq rapid SBS kit v2, 200 cycle, 60 Gb	HiSeq rapid SBS kit v2, 200 cycle, 60 Gb
	Throughput	40 patients/flow cell	40 patients/flow cell	4.3 patients/flow cell
	Run time	27 h	27 h	27 h
Other sequencing options. MiSeq	Kit	MiSeq Reagent kit v3: 600 cycle, 15 Gb	MiSeq Reagent kit v3: 600 cycle, 15 Gb	Not feasible with MiSeq
	Throughput	10 patients/flow cell	10 patients/flow cell
	Run time	39 h	39 h