Structural variation of the malaria-associated human glycophorin A-B-E region

Louzada, Sandra; Algady, Walid; Weyell, Eleanor; Zuccherato, Luciana W.; Brajer, Paulina; Almalki, Faisal; Scliar, Marilia O.; Naslavsky, Michel S.; Yamamoto, Guilherme L.; Duarte, Yeda A. O.; Passos-Bueno, Maria Rita; Zatz, Mayana; Yang, Fengtang; Hollox, Edward J.

doi:10.1186/s12864-020-06849-8

BMC Genomics

Table 1 Glycophorin structural variants identified in this study

From: Structural variation of the malaria-associated human glycophorin A-B-E region

Variant	Proximal breakpoint hg19	Distal breakpoint hg19	Variant size (kb)	Resolution of breakpoint (kb)	Index sample	Genes involved	Breakpoint identification method	In ref. [11]
DEL1	chr4:144835143–144,835,279	chr4:144945375–144,945,517	110	0.143	NA19223	GYPB	PCR-Sanger	Yes
DEL2	chr4:144912872–144,913,001	chr4:145016127–145,016,256	103	0.130	NA19144	GYPB	PCR-Sanger	Yes
DEL4	chr4:144750739–144,760,739	chr4:144950739–144,960,739	200	10	HG01986	GYPB,GYPE	1000G Seq	Yes
DEL6	chr4:144780045–144,780,137	chr4:145004120–145,004,212	224	0.093	HG04039	GYPE and GYPB	PCR-Sanger	Yes
DEL7	chr4:144780111–144,780,497	chr4:144900945–144,901,334	121	0.390	HG02716	GYPE	PCR-Sanger	Yes
DEL13	chr4:144925739–144,935,739	chr4:145035739–145,045,739	110	10	NA20867	GYPA/B fusion gene	1000G Seq	Yes
DEL15	chr4:144800739 144,802,739	chr4:144920739–144,922,739	119	2	HGDP01172	GYPB/E fusion gene	SD	No
DEL16	chr4:144752739–144,754,739	chr4:144952739–144,954,739	200	2	BR1296010301	GYPE and GYPB	SD	No
DEL17	chr4:144882739–144,987,739	chr4:144984739--144,987,739	103	3	BR1183605501	GYPB	SD	No
DEL18	chr4:144755739–144,757,739	chr4:144875739–144,878,739	123	2	BR1099223302	GYPE	SD	No
DUP2	chr4: 145039739–145,041,739	chr4: 144919739–144,921,739	120	2	NA18593	GYPB/A fusion gene	PCR-Sanger	Yes
DUP3	chr4:145004465–145,004,526	chr4:144780388–144,780,449	224	0.062	NA19360	GYPB, GYPE	PCR-Sanger	Yes
DUP4	Multiple	Multiple	n/a	n/a	HG02554	GYPB/A fusion gene, GYPE	Ref. [11]	Yes
DUP5	Multiple, including chr4:145113700	Multiple, including chr4:144936865	n/a	0.001	HG02585	GYPB, GYPE	PCR-Sanger	Yes
DUP7	chr4:144895000–144,905,000	chr4:144775000–144,785,000	120	10	HG02679	GYPE	1000G Seq	Yes
DUP8	chr4:14504573 9–145,048,739	chr4:144808739–144,810,739	240	3	I1_S_Irula1, HG03837	GYPB, GYPE/A fusion gene	SD	Yes
DUP14	chr4:144853613–144,853,688	chr4:144723019–144,723,094	131	0.076	NA18646	GYPE	PCR-Sanger	Yes
DUP22	chr4:144926739–144,929,739	chr4:144881739–144,884,739	45	3	BR210800138, HG02181	GYPB (partial)	SD	Yes
DUP26	chr4:145065739–145,075,739	chr4:144830739–144,840,739	155	10	HG03729	GYPA	1000G Seq	Yes
DUP27	chr4: 145039739–145,041,739	chr4: 144919739–144,921,739	120	2	NA12249	GYPB/A fusion gene	PCR-Sanger	Yes
DUP29	chr4:144939393–144,939,452	chr4:144825584–144,825,643	114	0.060	HG03686	GYPE and GYPB	PCR-Sanger	No
DUP30	chr4:144989739–144,991,739	chr4:144885739–144,887,739	102	2	HGDP00543	GYPB	SD	No
DUP33	chr4:144959739–144,962,739	chr4:144849739–144,851,739	111	3	BR54409051	GYPB	SD	No
DUP34	chr4:145002739–145,004,739	chr4:144900739–144,902,739	102	2	BR1086675791	GYPB	SD	No
DUP35	chr4:144878739–144,880,739	chr4:144758739–14,476,073,939	120	2	BR981404021	GYPE	SD	No

Notes: SD = sequence depth analysis of high coverage genomic sequencing. DUP19 (NA19223), DUP25 (HG02031), DUP28 (NA19084) no clear 5 kb window pattern, DEL4 and DEL16, and DUP2 and DUP27 share overlapping breakpoint regions and may be the same variants. DUP23 (HG02491) and DUP24 (hg03837), identified by reference [11], share population and breakpoint regions with DUP8 and are classified as DUP8. The column titled “in ref. [11]” indicates whether the variant was previously observed by Leffler et al. (reference [11])

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com