Cross-comparison of the genome sequences from human, chimpanzee, Neanderthal and a Denisovan hominin identifies novel potentially compensated mutations

Zhang, Guojie; Pei, Zhang; Ball, Edward V; Mort, Matthew; Kehrer-Sawatzki, Hildegard; Cooper, David N

doi:10.1186/1479-7364-5-5-453

Human Genomics

Table S3 PCMs covered by the Denisovan sequence but not the Neanderthal sequence

From: Cross-comparison of the genome sequences from human, chimpanzee, Neanderthal and a Denisovan hominin identifies novel potentially compensated mutations

Acc	Chr	Location	Strand	Tag	Disease	Gene	Mutation	AA seq	Type
CM062419	chr1	19483828	-	DP	Leukaemia, risk, association with	AKR7A3	C > T:CT	Asp-Asn	Denisovan
CM098300	chr1	24074507	-	DFP	Eating disorders, association with	CNR2	T > C:CC	Gln-Arg	Ancestral
CM066774	chr1	110267989	+	DP	Periodontitis, association with?	CSF1	T > C:CC	Leu-Pro	Ancestral
CM094244	chr1	111656412	+	FP	Increased enzyme activity, association with?	CHIA	A > G:GA	Asn-Asp	Derived
CM094243	chr1	111656461	+	DFP	Asthma, protection against, association with?	CHIA	G > T:TG	Arg-Met	Derived
CM084968	chr1	150552554	-	DP	Psoriasis, increased risk, association with	FLG	G > A:AG	Pro-Ser	Derived
CM067657	chr1	156591049	+	DP	Guillain-Barré syndrome, reduced risk, association with	CD1E	A > G:GG	Gln-Arg	Ancestral
CM033904	chr1	169444714	+	FP	Flavin-containing monooxygenase 2 (FMO2) gene variant	FMO2	T > C:CC	Term-Gln	Ancestral
CM043273	chr1	195670491	+	DM	Retinitis pigmentosa	CRB1	G > A:AG	Gly-Ser	Derived
CM024366	chr1	224093029	+	DFP	Preeclampsia, association with	EPHX1	A > G:GA	His-Arg	Derived
CM994344	chr10	115795046	+	FP	Gain of function, association with	ADRB1	G > C:CC	Gly-Arg	Ancestral
CM067436	chr11	7020956	+	DM	Spermatogenic failure	NLRP14	G > A:AG	Ala-Thr	Derived
CM043536	chr11	47326617	-	DM	Cardiomyopathy, hypertrophic?	MYBPC3	T > C:CT	Ser-Gly	Derived
CM035848	chr11	57739196	+	FP	Olfactory receptor deficiency?	OR1S1	G > A:GA	Arg-His	Denisovan
CM087504	chr11	102218830	-	DP	Blood pressure, association with	MMP3	T > C:CC	Lys-Glu	Ancestral
CM041241	chr11	112776038	+	FP	Reduced dopamine D2 receptor (DRD2) receptor density, association with?	ANKK1	G > A:AA	Glu-Lys	Ancestral
CM082943	chr11	118720796	-	DM	Primary angle-closure glaucoma?	MFRP	C > T:TT	Arg-His	Ancestral
CM075018	chr11	130255852	-	DP	Coronary heart disease, association with	SNX19	A > C:CC	Leu-Arg	Ancestral
CM091988	chr12	32913201	-	DM	Arrhythmogenic right ventricular cardiomyopathy	PKP2	A > G:GG	Leu-Pro	Ancestral
CM087618	chr12	56152088	+	DFP	Inflammatory bowel disease, association with	GLI1	G > C:CC	Glu-Gln	Ancestral
CM098354	chr12	120099486	+	FP	Altered function, association with	P2RX7	G > A:AA	Ala-Thr	Ancestral
CM065186	chr13	38162690	+	DP	Colorectal cancer, increased risk, association with	FREM2	T > C:CC	Phe-Ser	Ancestral
CM063919	chr13	45546095	-	FP	Higher thrombin-activatable fibrinolysis inhibitor (TAFI) antigen levels, association with	CPB2	C > T:TT	Ala-Thr	Ancestral
CM044579	chr13	51413355	-	DM	Wilson disease?	ATP7B	A > G:GG	Val-Ala	Ancestral
CM063843	chr14	19994994	+	DFP	Amyotrophic lateral sclerosis, association with	APEX1	T > G:GG	Asp-Glu	Ancestral
CM073244	chr14	20010446	+	DP	Faster cognitive decline in Alzheimer's disease, association with	NP	G > A:AG	Gly-Ser	Derived
CM068495	chr15	49316404	-	DP	Increased cortical bone mass density, association with	CYP19A1	T > C:CC	Val-Val	Ancestral
CM045806	chr15	83248435	+	FP	Reduced affinity for gemcitabine, association with	SLC28A1	G > A:AG	Val-Ile	Derived
CM102885	chr16	10908349	+	DP	Multiple sclerosis, increased risk, association with	CIITA	G > C:CC	Gly-Ala	Ancestral
CM093131	chr16	55950234	+	DP	Helicobacter pylori-related gastric carcinoma, association with	CCL22	A > C:CC	Asp-Ala	Ancestral
CM067679	chr17	7858004	+	DP	Lung cancer, susceptibility to, association with	GUCY2D	T > A:AA	Leu-His	Ancestral
CM073339	chr17	24310977	-	DM	Febrile seizures?	SEZ6	T > C:CC	Thr-Ala	Ancestral
CM057951	chr17	37960432	+	DP	Endometriosis, association with	HSD17B1	A > G:AG	Ser-Gly	Denisovan
CM994214	chr17	39808591	-	DP	Reduced post-stroke mortality, association with	ITGA2B	A > C:GC	Ile-Ser	Unsure
CM091892	chr17	42363569	+	DP	Hypertension, association with	GOSR2	G > A:AG	Arg-Lys	Derived
CM091876	chr17	73642170	+	DP	Epidermodysplasia verruciformis, susceptibility in HIV, association with	TMC8	A > T:TA	Asn-Ile	Derived
CM000831	chr19	3546794	-	DP	Bronchial asthma, association with	TBXA2R	A > G:GG	Tyr-Tyr	Ancestral
CM030470	chr19	18041451	-	DP	Tuberculosis, susceptibility to, association with	IL12RB1	A > G:GG	Met-Thr	Ancestral
CM044082	chr19	18407678	-	DP	Spina bifida, reduced risk, association with	isyna1	T > C:CC	Leu-Leu	Ancestral
CM057586	chr19	40534926	+	DP	Increased beta-cell function, association with	FFAR1	G > A:AA	Arg-His	Ancestral
CM057545	chr19	50560149	-	DP	Lung adenocarcinoma, increased risk, association with	ERCC2	G > T:GT	Arg-Arg	Denisovan
CM044227	chr19	60088712	+	DP	Aggressive periodontitis, reduced risk, assoc with	FCAR	A > G:GG	Arg-Arg	Ancestral
CM003809	chr2	38155681	-	DP	Breast or lung cancer, association with	CYP1B1	C > A:AA	Ala-Ser	Ancestral
CM101950	chr2	98363138	+	DM	Progressive cone dystrophy?	CNGA3	C > T:TC	Pro-Leu	Derived
CM092797	chr2	169550992	-	FP	Alternate splicing, association with	ABCB11	T > C:CT	Gly-Gly	Derived
CM066575	chr2	218738088	-	DP	AIDS progression, protection, association with	IL8RA	A > C:CC	Met-Arg	Ancestral
CM057769	chr2	234266408	+	FP	Altered enzyme activity, association with	UGT1A6	T > G:GG	Ser-Ala	Ancestral
CM910018	chr2	241466189	+	DP	Hyperoxaluria, association with	AGXT	A > G:GG	Ile-Met	Ancestral
CM053304	chr20	54257212	+	DP	Obesity, association with	MC3R	C > A:AA	Thr-Lys	Ancestral
CM970391	chr22	18331207	+	DFP	Schizoaffective disorder, association with	COMT	C > G:GG	Leu-Leu	Ancestral
CM961335	chr22	30817700	+	DM	Glucose/galactose malabsorption	SLC5A1	G > A:AA	Ala-Thr	Ancestral
CM930187	chr22	40853887	-	DP	Parkinson's disease, association with	CYP2D6	G > A:GA	Arg-Cys	Denisovan
CM099899	chr22	41888870	+	FP	Increased pregnenolone levels, association with	TSPO	A > G:GG	Thr-Ala	Ancestral
CM025430	chr4	2975841	+	FP	Activity, association with	GRK4	C > T:TT	Ala-Val	Ancestral
CM013959	chr4	23424760	-	DP	Diabetes, type 2, association with	PPARGC1A	C > T:TC	Gly-Ser	Derived
CM033593	chr4	100479812	-	DP	Alcoholism, increased risk, association with?	ADH1C	T > C:CC	Ile-Val	Ancestral
CM064956	chr4	109893565	-	DP	Colorectal cancer, increased risk, association with	AGXT2L1	A > G:GG	Ser-Pro	Ancestral
CM030066	chr4	149576925	-	FP	Reduced expression, association with	NR3C2	T > C:TC	Ile-Val	Denisovan
CM080365	chr4	155711209	+	DP	Increased clot stiffness, association with	FGB	G > A:AA	Arg-Lys	Ancestral
CM057405	chr4	156355126	+	DP	Severe obesity, in men, association with	NPY2R	C > T:TT	Ile-Ile	Ancestral
CM067358	chr5	22114341	-	DP	Lung cancer, susceptibility to, association with	CDH12	C > T:TT	Val-Met	Ancestral
CM094788	chr5	121441107	-	DFP	Breast cancer, increased risk, in African American women, association with	LOX	C > T:TT	Arg-Gln	Ancestral
CM013815	chr5	147461148	+	DP	Atopy, maternally inherited, association with	SPINK5	G > A:GA	Glu-Lys	Denisovan
CM083577	chr6	24611569	+	DFP	Impaired cognitive function, association with	ALDH5A1	C > T:TT	His-Tyr	Ancestral
CM086146	chr6	25921129	-	DP	Uric acid concentration, association with	SLC17A1	G > A:AA	Thr-Ile	Ancestral
CM052232	chr6	80683094	-	DP	Age-related maculopathy, association with	ELOVL4	T > C:CT	Met-Val	Derived
CM073245	chr7	34784638	+	DP	Panic disorder, in males, association with	NPSR1	A > T:TT	Asn-Ile	Ancestral
CM084696	chr7	87017537	-	DFP	Parkinson's disease, association with	ABCB1	A > G:GG	Gly-Gly	Ancestral
CM091200	chr7	129737976	+	DP	Prostate cancer, aggressive early-onset, association with	CPA4	G > T:TT	Gly-Cys	Ancestral
CM952203	chr7	142350235	-	FP	Kell blood group variation	KEL	A > G:GA	Leu-Pro	Derived
CM073993	chr7	150188598	+	FP	Reduced activity, association with	ABP1	C > G:GG	His-Asp	Ancestral
CM973386	chr8	18124281	+	FP	Increased activity, association with	NAT1	G > A:AG	Val-Ile	Derived
CM099895	chr8	24412708	+	DP	Schizophrenia, association with	ADAM7	A > C:CC	Asn-His	Ancestral
CM064954	chr8	26683945	-	DP	Hypertension, association with?	ADRA1A	A > G:GG	Cys-Arg	Ancestral
CM033767	chr8	27414422	+	DFP	Coronary heart disease, in Caucasians, association with	EPHX2	A > G:GA	Lys-Arg	Derived
CM034886	chr8	91059655	-	DP	Lung cancer, association with?	NBN	C > G:GG	Glu-Gln	Ancestral
CM045665	chr8	120033233	-	DP	Osteoporotic fractures, association with	TNFRSF11B	G > C:CG	Asn-Lys	Derived
CM093465	chr9	2181309	+	DFP	Schizophrenia, association with	SMARCA2	C > G:GC	Asp-Glu	Derived
CM073190	chrX	43475980	+	DP	Bipolar disorder, association with?	MAOA	T > G:TG	Arg-Arg	Denisovan
CR072321	chr1	11841858	-	DFP	Diabetes, type, 2, reduced risk, association with	NPPB	A > G:GG		Ancestral
CR080762	chr1	15645754	+	DM	Pancreatitis, chronic?	CTRC	T > C:CC		Ancestral
CR080761	chr1	15645757	+	DM	Pancreatitis, chronic?	CTRC	A > G:GG		Ancestral
CR016187	chr1	87101113	-	FP	Increased selenocysteine insertion sequence (SECIS) efficiency, association with	sep15	C > T:TT		Ancestral
CR092707	chr1	201194130	-	DFP	Lower insulin resistance, association with	ADIPOR1	C > T:TT		Ancestral
CR034628	chr10	26545502	+	DP	Obesity, association with?	GAD2	G > A:GA		Denisovan
CR061340	chr11	35397552	-	DFP	Progressing stroke, increased risk, association with	SLC1A2	T > G:GG		Ancestral
CR068212	chr11	59612604	+	DFP	Asthma, aspirin-intolerant	MS4A2	T > C:CC		Ancestral
CR063407	chr14	50069895	-	DP	Diabetes, type 2, reduced risk, association with	MAP4K5	G > A:AA		Ancestral
CR077666	chr15	71712835	-	DFP	Schizophrenia, reduced risk, association with?	NPTN	C > A:CA		Denisovan
CR084880	chr17	35697157	+	DFP	Hepatocellular carcinoma, reduced risk, association with	CDC6	A > G:GG		Ancestral
CR087465	chr17	39785770	+	DFP	Frontotemporal dementia, association with	GRN	C > T:TT		Ancestral
CR035036	chr18	647685	+	FP	Transcriptional activity, association with	TYMS	G > C:CC		Ancestral
CR032436	chr18	45342041	+	DP	High-density lipoprotein (HDL) cholesterol levels, association with?	LIPG	A > C:CA		Derived
CR087182	chr19	44589133	+	DFP	Rheumatoid arthritis, shorter duration, association with	ZFP36	A > G:GG		Ancestral
CR035033	chr19	46188301	+	FP	Cytochrome P-450 (CYP) 2B6 expression, association with?	CYP2B6	T > C:CC		Ancestral
CR068525	chr2	69467665	-	DFP	Diabetes, type 2, association with	GFPT1	A > G:GG		Ancestral
CR077669	chr2	85748849	-	FP	Increased promoter activity, association with	SFTPB	T > G:GG		Ancestral
CR093507	chr2	168743982	-	DFP	Hypertension, association with	STK39	A > G:GG		Ancestral
CR093026	chr2	169465787	+	DFP	Increased insulin secretion, association with	G6PC2	G > A:AA		Ancestral
CR073559	chr2	224174588	-	DFP	Hypertension, association with	SCG2	C > T:TT		Ancestral
CR053505	chr20	4653756	+	DP	Creutzfeldt-Jakob disease, association with?	PRND	T > C:CC		Ancestral
CR015272	chr22	40858326	-	FP	Intermediate metaboliser, association with?	CYP2D6	C > G:GG		Ancestral
CR055620	chr4	75938792	-	FP	Promoter activity, association with	BTC	C > G:GG		Ancestral
CR093469	chr6	2945302	+	DFP	Breast cancer, decreased risk, association with	NQO2	A > C:CA		Derived
CR035882	chr6	78230101	-	DFP	Suicidal ideation, in major depression, association with	HTR1B	A > C:CA		Derived
CR025333	chr6	137582213	-	DFP	Malaria, susceptibility, association with	IFNGR1	A > G:GG		Ancestral
CR093919	chr6	153121754	+	DP	Pulmonary arterial hypertension, idiopathic, association with?	VIP	T > C:CC		Ancestral
CR016149	chr7	22732746	+	FP	Altered transcriptional activity, association with	IL6	A > G:GG		Ancestral
CR053504	chr7	91995822	-	FP	Gene expression, association with	PEX1	A > G:GA		Derived
CR041138	chr7	99192235	-	DP	Prostate cancer, low aggressiveness, association with	CYP3A4	G > A:AG		Derived
CR072316	chr7	128376663	+	FP	Shorter transcript, association with	IRF5	G > A:AA		Ancestral
CR962526	chr8	41774321	-	DM	Spherocytosis	ANK1	A > G:GA		Derived
CR098013	chr9	22109195	+	DFP	Coronary artery disease, association with	CDKN2BAS	C > T:CT		Denisovan
CR044772	chr9	99499399	-	DP	Lung adenocarcinoma, risk, association with	XPA	T > C:CC		Ancestral
CR020828	chr9	106730356	-	DP	Reduced risk of coronary artery disease, association with	ABCA1	G > C:CC		Ancestral
CR052068	chr9	136911887	+	FP	Promoter activity, association with	FCN2	A > G:GG		Ancestral
CR042847	chr9	138995962	+	DP	HDL cholesterol, association with?	PTGDS	A > C:CC		Ancestral

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ISSN: 1479-7364

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