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 4 Gene deletion 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 probability	RD _observed	RD _expected
YRI	NA18523	BCL2L15	BCL2-like 15	1	114225268	114231520	1.000	533	1158
YRI	NA18523	HIPK1	homeodomain interacting protein kinase 1	1	114298778	114317657	1.000	2539	5272
TSI	NA20533	GLOD4	glyoxalase domain containing 4	17	610163	632245	1.000	1322	2295
TSI	NA20533	C1QBP	complement component 1, q subcomponent binding protein	17	5277059	5282317	1.000	793	1416
TSI	NA20533	C17orf91	chromosome 17 open reading frame 91	17	1562414	1563890	1.000	369	574
YRI	NA18523	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	1	115052679	115060304	1.000	702	1462
YRI	NA18523	TRI3	tripartite motif-containing 33	1	114741793	114808533	1.000	2610	5225
TSI	NA20533	TRPV3	transient receptor potential cation channel, subfamily V, member 3	17	3363961	3404894	1.000	3365	5275
TSI	NA20774	PTMAP1	prothymosin, alpha pseudogene 1 (gene sequence 26)	6	30725671	30728671	1.000	132	260
TSI	NA20796	SNRNP27	small nuclear ribonucleoprotein 27 kDa (U4/U6.U5)	2	69974621	69977184	0.998	105	194
TSI	NA20807	HIST1H2BC	histone cluster 1, H2bc	6	26231731	26232111	0.998	42	90
TSI	NA20772	ULBP1	UL16 binding protein 1	6	150331436	150332954	0.997	104	205
TSI	NA20807	CYP2A13	cytochrome P450, family 2, subfamily A, polypeptide 13	19	46291375	46293686	0.996	126	204
YRI	NA18508	PTMAP1	prothymosin, alpha pseudogene 1 (gene sequence 26)	6	30725671	30728671	0.992	145	230
CEU	NA07000	PSG8	pregnancy specific beta-1-glycoprotein 8	19	47950287	47960273	0.990	29	70
CEU	NA11893	PSG8	pregnancy specific beta-1-glycoprotein 8	19	47950287	47960273	0.985	43	86
TSI	NA20771	PTMAP1	prothymosin, alpha pseudogene 1 (gene sequence 26)	6	30725671	30728671	0.980	533	862
TSI	NA20773	CCK	cholecystokinin	3	42274594	42280126	0.971	282	474
CEU	NA07000	HMGN4	high mobility group nucleosomal binding domain 4	6	26653414	26653686	0.966	68	132
CEU	NA12749	HMGN4	high mobility group nucleosomal binding domain 4	6	26653414	26653686	0.966	156	286
TSI	NA20772	AIF1	allograft inflammatory factor 1	6	31692086	31692262	0.964	51	124
CEU	NA12348	DUSP10	dual specificity phosphatase 10	1	219942377	219946216	0.962	155	242
YRI	NA18508	ULBP1	UL16 binding protein 1	6	150331436	150332954	0.941	40	79
YRI	NA18523	PPM1J	protein phosphatase, Mg2+/Mn2+ dependent, 1 J	1	113056116	113057756	0.891	560	924
TSI	NA20807	POU5F1	POU class 5 homeobox 1	6	31240884	31241803	0.891	124	193
TSI	NA20772	SERPINA11	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11	14	93978696	93984864	0.889	786	1243
CEU	NA07000	KRT18P19	keratin 18 pseudogene 19	12	51630379	51632393	0.887	85	174
CEU	NA12348	ULBP1	UL16 binding protein 1	6	150331436	150332954	0.879	49	88
YRI	NA18523	RHOC	ras homolog gene family, member C	1	113054308	113055529	0.867	557	955
CEU	NA12348	STBD1	starch binding domain 1	4	77446947	77450177	0.839	246	395
CEU	NA07000	POU5F1	POU class 5 homeobox 1	6	31240884	31241803	0.823	106	169
CEU	NA12749	SNRNP27	small nuclear ribonucleoprotein 27 kDa (U4/U6.U5)	2	69974621	69977184	0.775	142	216
TSI	NA20752	POU5F1	POU class 5 homeobox 1	6	31240884	31241803	0.723	76	142
TSI	NA20807	HIST1H2BO	histone cluster 1, H2bo	6	27969220	27969600	0.723	48	88
TSI	NA20589	POU5F1	POU class 5 homeobox 1	6	31240884	31241803	0.697	61	117
TSI	NA20786	NPSR1	neuropeptide S receptor 1	7	34884213	34884321	0.678	51	88

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ISSN: 1471-2105

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