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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
  1. 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])