Table 1.

A taxonomy of technical research articles on genomic data privacy featured in this Review

Attack or protection	Use	Data flow	Data level	Setting	How attacks or protections are achieved	Attributes studied other than genotypes/how data are used	Refs
Anonymity
Attack	Secondary	Share	Individual	Health care	Re-ID	Demographics, hospital trail	42
				Research	Re-ID	NA	84
						Pedigree	51
					Re-ID, genotype imputation	Signal profiles	90
					Re-ID, genotype inference	Diseases	45
						Visual traits/3D facial structures	46–48
					Re-ID, non-genotypic attribute inference	Demographics, name	53
						Demographics, surname	54
						Face, traits, demographics	44,49,50
					Genotype imputation	NA	85,86
				Research, DTC	Genotype imputation	Pedigree	64
					Genotype imputation, genotype inference, genotype reconstruction	Pedigree	66
			Summary	Research	Membership inference	GWAS statistics	56–58,60,96,97
					Membership inference, genotype inference	Machine learning model, demographics	61
						GWAS statistics, pedigree	106
					Membership inference, non-genotypic attribute inference	Disease status	62
					Membership inference, re-ID, genotype imputation	GWAS statistics	59
					Membership inference, re-ID, genotype inference, genotype reconstruction	GWAS statistics, visual traits	98
Protection	Secondary	Share	Individual	Research	Generalization	RNA sequences	89
					Generalization, suppression, k-anonymity	NA	88
					Masking/hiding, risk assessment	Demographics	93
			Summary	Research	Suppression, risk assessment	NA	92
					Beacons	Disease	95
						GWAS statistics, pedigree	101
					Beacons, differential privacy	GWAS statistics	99,100
					Beacons, risk assessment	GWAS statistics	102
					Differential privacy	GWAS statistics	103–105,107,108
					Generative adversarial network	Disease	109
					Federated learning	GWAS statistics	149
					Risk assessment	NA	82
Confidentiality
Protection	Primary	Use	Individual	Health care	Homomorphic encryption	Disease susceptibility test	78
					Controlled functional encryption	Relatedness tests	79
					SMC	Disease diagnosis	147
				Research	Homomorphic encryption	GWAS computation	142,143
					Homomorphic encryption, SMC	GWAS computation	141,150
					Homomorphic encryption, TEE	GWAS computation	154
					SMC	GWAS computation	145,146
					TEE	GWAS computation	153,155
					Symmetric encryption, cryptographic hardware	GWAS computation	151
				Research, DTC	Homomorphic encryption	Sequence matching, sequence comparison	180
					SMC	Sequence comparison	148
					Fuzzy encryption	Relative identification	182
				DTC	Private set intersection protocols	Paternity test, genetic compatibility test	181
		Store	Individual	Health care	Honey encryption	NA	76
					Secure file format	NA	77
	Secondary	Share	Individual	Research	Blockchain	NA	158
				Research, DTC	Blockchain	NA	157
				DTC	Blockchain, controlled access, homomorphic encryption, SMC	NA	161
			Summary	Research	Blockchain	Machine learning model	159
					Controlled access	GWAS statistics	81
Solitude
Attack	Secondary	Share	Individual	DTC, forensic	Familial search, genotype imputation, genotype reconstruction	Name, e-mail address	74,75
				Forensic	Familial search, re-ID	Demographics	72
					Familial search, re-ID, genotype imputation	Pedigree	73
			Individual, summary	Research, DTC	Non-genotypic attribute inference, kin genotype reconstruction	Pedigree	63
					Attribute inference, kin genotype reconstruction	Pedigree, disease	65
Protection	Primary	Collect	Individual	Forensic	Controlled access, encryptions	NA	39
	Secondary	Share	Individual	DTC, research	Masking/hiding, risk assessment	Pedigree	196

DTC, direct-to-consumer; GWAS, genome-wide association study; ID, identification; NA, not applicable; SMC, secure multiparty computation; TEE, trusted execution environment.