Copy Number Variation detection from 1000 Genomes project exon capture sequencing data

Wu, Jiantao; Grzeda, Krzysztof R; Stewart, Chip; Grubert, Fabian; Urban, Alexander E; Snyder, Michael P; Marth, Gabor T

doi:10.1186/1471-2105-13-305

BMC Bioinformatics

Table 3 Gene duplication calls in the SC dataset

From: Copy Number Variation detection from 1000 Genomes project exon capture sequencing data

Population	Sample	Gene name	Gene function	Chr	Start [bp]	End [bp]	Posterior probablity	RD _observed	RD _expected
CEU	NA12348	CD300LB	CD300 molecule-like family member b	17	70030472	70039195	1.000	638	420
TSI	NA20533	CLDN10	claudin 10	13	95003009	95028269	1.000	2108	1582
CHB	NA18526	SNRNP27	small nuclear ribonucleoprotein 27 kDa (U4/U6.U5)	2	69974621	69977184	1.000	530	383
CHB	NA18532	CES1	carboxylesterase 1 (monocyte/macrophage serine esterase 1)	16	54401930	54424468	1.000	501	337
TSI	NA20752	NOM1	nucleolar protein with MIF4G domain 1	7	156435193	156455158	1.000	1335	966
TSI	NA20796	AHNAK	AHNAK nucleoprotein	11	62040792	62059238	1.000	7330	5169
TSI	NA20796	ZNF264	zinc finger protein 264	19	62408577	62416161	0.999	1276	888
TSI	NA20801	GPR128	G protein-coupled receptor 128	3	101811391	101896535	0.998	14747	8265
TSI	NA20772	STX16	syntaxin 16	20	56660469	56684753	0.998	2101	1605
TSI	NA20769	MRPS6	mitochondrial ribosomal protein S6	21	34419511	34436770	0.998	1585	1203
TSI	NA20774	ELAVL4	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	1	50383216	50439437	0.998	782	567
TSI	NA20804	CYP2A13	cytochrome P450, family 2, subfamily A, polypeptide 13	19	46291375	46293686	0.997	1289	984
TSI	NA20774	CREB5	cAMP responsive element binding protein 5	7	28494318	28825421	0.996	1435	954
TSI	NA20796	ZNF32	zinc finger protein 32	10	43459504	43461587	0.996	911	646
TSI	NA20520	C6orf145	chromosome 6 open reading frame 145	6	3668852	3683381	0.995	2015	1601
CEU	NA12348	GDNF	glial cell derived neurotrophic factor	5	37851510	37870647	0.994	306	217
CHB	NA18561	PSMB4	proteasome (prosome, macropain) subunit, beta type, 4	1	149638688	149640730	0.986	3461	2216
CEU	NA12546	DAZAP2	DAZ associated protein 2	12	49920394	49922509	0.985	2265	1651
TSI	NA20752	AATF	apoptosis antagonizing transcription factor	17	32380539	32488077	0.976	1157	843
CEU	NA12749	PAQR5	progestin and adipoQ receptor family member V	15	67439474	67483215	0.976	1684	1239
TSI	NA20769	BCL2L11	BCL2-like 11 (apoptosis facilitator)	2	111597794	111638279	0.965	1813	1435
TSI	NA20804	PILRA	paired immunoglobin-like type 2 receptor alpha	7	99809603	99835466	0.909	962	752
TSI	NA20589	C8orf85	chromosome 8 open reading frame 85	8	118019664	118024121	0.903	147	91
TSI	NA20752	CCKAR	cholecystokinin A receptor	4	26092358	26100987	0.902	712	532
JPT	NA18973	HBG2	hemoglobin, gamma G	11	5278820	5523329	0.901	4151	3094
TSI	NA20774	HIPK1	homeodomain	1	114298778	114317657	0.900	2374	1626
TSI	NA20774	ODC1	ornithine decarboxylase 1	2	10498301	10502609	0.897	1489	935
TSI	NA20796	STBD1	starch binding domain 1	4	77446947	77450177	0.885	978	664
TSI	NA20589	CRIPAK	cysteine-rich PAK1 inhibitor	4	1378300	1379640	0.877	76	38
YRI	NA19189	PSMB4	proteasome (prosome, macropain) subunit, beta type, 4	1	149638688	149640730	0.853	2622	2090
TSI	NA20774	STX16	syntaxin 16	20	56660469	56684753	0.811	949	704
JPT	NA18980	CES1	carboxylesterase 1 (monocyte/macrophage serine esterase 1)	16	54401930	54424468	0.788	1679	1036
TSI	NA20774	PAQR5	progestin and adipoQ receptor family member V	15	67439474	67483215	0.788	1048	676
CHB	NA18561	CRNN	cornulin	1	150648694	150651333	0.778	4845	3172
TSI	NA20774	DKK4	dickkopf homolog 4 (Xenopus laevis)	8	42350775	42353720	0.760	493	362
TSI	NA20589	NOM1	nucleolar protein with MIF4G domain 1	7	156435193	156455158	0.740	1052	801
TSI	NA20769	RNF122	ring finger protein 122	8	33525813	33535831	0.734	2574	2004
TSI	NA20796	ZNF521	zinc finger protein 521	18	20896674	21184908	0.721	3536	2738
TSI	NA20769	VLDLR	very low density lipoprotein receptor	9	2625453	2631499	0.676	2092	1624

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ISSN: 1471-2105

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