. 2019 Nov 7;17:1348–1359. doi: 10.1016/j.csbj.2019.10.004

Table 4.

Selected example of studies that analysed mutations using targeted DNA sequencing in human samples.

Disease	Tissue Origin	Authors	Journal	Genes	Depth	Platform	Target capture mode	Machine	FFPE/fresh frozen (FF)	Duplicate handling	Variant Calling
Acute Myeloid Leukaemia	Tumour	Ivey et al. 2016	New England Journal of Medicine	51	1280x	Agilent Haloplex^HS	Amplification	HiSeq 2000	Not Reported	Not Reported	VarScan2
	Normal Peripheral blood	Abelson et al. 2018	Nature	111	Not Reported	Roche NimbleGen	Hybrid Capture	HiSeq 2000	FF	MBC	Varscan2
	Normal Peripheral blood	Abelson et al. 2018	Nature	111	Not Reported	Agilent SureSelect	Hybrid Capture	HiSeq 2000	FF	MBC	Shearwater ML Pindel
Breast Cancer	Tumour	Ellis et al. 2012	Nature	Variable	Not Reported	Roche NimbleGen	Hybrid Capture	Not Reported	FFPE	Picard	VarScan2
	Tumour	Ellis et al. 2012	Nature	Variable	Not Reported	Roche NimbleGen	Hybrid Capture	Not Reported	FFPE	Picard	BreakDancer
	Germline	Couch et al. 2015	Journal of Clinical Oncology	122	300x	Illumina TruSeq Amplicon	Amplification	HiSeq™ 2000	Not Reported	Not Reported	GATK Unified Genotyper/SAMtools
FL	Tumour	Okosun et al. 2014	Nature Genetics	28	840x	Fluidigm Access Array™	Amplification	Miseq	FF	Not Reported	VarScan2
	Tumour	Pastore et al. 2015	The Lancet Oncology	74	Not Reported	Agilent SureSelect	Hybrid Capture	HiSeq 2500	FFPE	Picard	MuTect
	Tumour	Pastore et al. 2015	The Lancet Oncology	74	Not Reported	Agilent SureSelect	Hybrid Capture	HiSeq 2500	FFPE	Picard	Indel Locator
	Tumour	Araf et al. 2018	Leukaemia	25	8000x	Agilent Haloplex^HS	Amplification	MiSeq	FFPE	UMI	VarScan2
Pancreas	Tumour	Sausen et al. 2015	Nature Communications	116	754x	Agilent SureSelect	Hybrid Capture	HiSeq 2000/25000 & MiSeq	Both	CASAVA	VariantDx
Skin Cancer	Normal Skin	Martincorena et al. 2015	Science	74	500x	Agilent SureDesign	Hybrid Capture	HiSeq 2000/25000	FF	Picard	Shearwater ML