Copy number variations in the genome of the Qatari population

BMC Genomics

Table 2 Functional Annotation of CNV Regions in the Qatari Genetic Subpopulations^a

		Total number	Nongenic	Genic	miRNA	Genic affecting Mendelian disease genes	# Mendelian genes affected	Overlap DGV	Novel	Novel genic	Promoter site	Transcription factor binding site
Q1 –	0 – homozygous deletions	341	228	113	2	8	8	322	19	7	20	127
	1 – heterozygous deletions	3,316	2,151	1,165	19	76	83	3,091	225	97	248	1,321
	3 – duplication	2,161	1,121	1,040	196	182	223	2,045	116	48	509	980
	4 – amplification	463	290	173	12	18	18	445	18	5	54	145
Sub-total Q1		6,281	3,790	2,491	229	284	332	5,903	378	157	831	2,573
Q2 –	0 – homozygous deletions	293	183	110	1	11	11	287	6	1	14	109
	1 – heterozygous deletions	2,470	1,598	872	15	65	70	2,350	120	53	172	879
	3 – duplication	1,760	913	847	156	124	157	1,694	66	28	409	748
	4 – amplification	434	268	166	11	17	17	422	12	5	52	143
Sub-total Q2		4,957	2,962	1,995	183	217	255	4,753	204	87	647	1,879
Q3 –	0 – homozygous deletions	267	174	93	0	18	8	262	5	2	16	101
	1 – heterozygous deletions	2,858	1,902	956	13	61	65	2,726	132	45	176	1,046
	3 – duplication	1,835	977	858	148	122	141	1,754	81	29	407	772
	4 – amplification	462	284	178	19	23	24	443	19	9	61	146
Sub-total Q3		5,422	3,337	2,085	180	224	238	5,185	237	85	660	2,065
Total		16,660	10,089	6,571	592	725	825	15,841	819	329	2,138	6,517

^aCNVRs were annotated as described in Methods. Distribution of CNVs is summarized by CN class within each subpopulation and by functional class including: Total number = all CNVRs detected; nongenic = CNVRs that do not overlap coding regions; genic = CNVRs that overlap genes; miRNA = CNVRs that overlap microRNAs; Mendelian disease genes = CNVRs that include at least 1 known Mendelian disease gene; DGV = CNVRs that overlap a known CNV from the database of genomic variants; novel = CNVRs that do not overlap known CNVs and are unique to Qataris; novel genic = the subset of novel CNVRs that overlap at least 1 gene; promoter site = CNVRs that overlap promoter elements; transcription factor site = CNVRs that overlap at least 1 transcription factor site. Total for each subpopulation is a sum of deletions and duplications in each subpopulation

ISSN: 1471-2164