Table 3. Sanger sequencing of PCR amplicons for the α -3.7kb deletion in 25 homozygous α -3.7kb and 5 normal individuals in Kilifi, Kenya.
| Released_key | 648184022 | 836466359 | 891210787 | 539560608 | 391787794 | 604702281 | 818082173 | 251883490 | 640859222 | 130037624 | 787645827 | 167368322 | 114762936 | 115163414 | 116814170 | 116828578 | 123017600 | 129122739 | 130028961 | 130546094 | 131709234 | 134168958 | 134421137 | 134501405 | 137928280 | 520269712 | 434039943 | 424597966 | 429643240 | 754351794 | 429586481 | 117865639 | 297748035 | 138218129 | 520269712 | 434039943 | 424597966 | 429643240 | 754351794 | 429586481 | 117865639 | 297748035 | 138218129 | ||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chip_id | 5583612155_R01C01 | 5583612121_R04C01 | 5583612103_R04C01 | 5583612084_R03C01 | 5583612106_R04C01 | 5583612069_R01C01 | 5588392045_R04C01 | 5583612069_R03C01 | 5583612132_R02C01 | 5588392041_R02C01 | 5588392009_R02C01 | 5767745121_R02C01 | 5626627008_R01C01 | 5751823150_R01C01 | 5636411175_R03C01 | 5636622086_R02C01 | 5626627093_R01C01 | 5636622089_R03C01 | 5636411079_R02C01 | 5636411197_R03C01 | 5636622060_R04C01 | 5751823150_R01C01 | 5636411175_R03C01 | 5636622086_R02C01 | 5626627093_R01C01 | 5636622089_R03C01 | 5636411079_R02C01 | 5636411197_R03C01 | 5636622060_R04C01 | ||||||||||||||||||||||||||||||||
| Sequencing primers | note | Base-gene
assignment |
Base
ID No. |
HBA2 | HBA1 | Base
ID No |
Reference
allele |
||||||||||||||||||||||||||||||||||||||||||||||||||||||
| A2/3.7-F | HBA 5' SEQ | HBA 3' SEQ | 3.7-R | A2-R | position | base | rs number | relative to
ATG |
position | base | rs number | relative to
ATG |
HBA2 | HBA1 | |||||||||||||||||||||||||||||||||||||||||||||||
| primer
(A2/3.7-F) |
221882-901 | CCCCTCGCCAAGTCCACCCC | NA | NA | NA | NA | NA | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | A | B | C | D | E | F | G | H | I | A | B | C | D | E | F | G | H | I | |||||||||||
| T2/C1 | 1 | 221996 | T | rs1043385709 | -916 | 225802 | C | NA | -916 | 1 | T | C | T | T | T | T | - | T | T | T | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | T | T | T | T | T | T | T | T | T | - | C | C | - | C | C | - | C | C | ||||||
| AC2/--1 | 2 | 222003-004 | AC | rs1388103544 | -908 | 225808-809 | del | rs1297040092 | -908 | 2 | AC | -- | AC | AC | AC | AC | - | - | AC | AC | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | AC | AC | AC | AC | AC | AC | AC | AC | AC | - | -- | -- | - | -- | -- | - | -- | -- | ||||||
| G2/A1 | 3 | 222239 | G | rs143196637 | -673 | 226043 | A | rs3760045 | -673 | 3 | G | A | G | G | G | G | G | G | G | G | G | G | G | G | - | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | - | G | A | - | A | G | A | A | G | ||||||
| CT2/TC1 | 4 | 222416 | CT | rs2858943 | -496 | 226219 | TC | rs878891332 | -496 | 4 | C | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | - | T | T | - | T | T | T | T | T | ||||||
| CT2/TC1 | 5 | 222417 | C T | rs4021962 | -495 | 226220 | T C | NA | -495 | 5 | T | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | - | C | C | - | C | C | C | C | C | ||||||
| G2/C1 | 6 | 222846 | G | NA | -43 | 226679 | C | NA | -43 | 6 | G | C | C | C | - | - | C | - | - | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | - | C | C | - | C | C | C | C | C | ||||||
| Ensembl
Gene start |
222864 | NA | NA | -37 | 226673 | C | NA | -37 | |||||||||||||||||||||||||||||||||||||||||||||||||||||
| Met start
(ATG) |
222912-914 | ATG | NA | 1 | 226716 | ATG | NA | 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||
| primer (HBA
5' SEQ) |
222930-950 | GACAAGACCAACGTCAAGGCC | NA | 18-38 | 226734-754 | GACAAGACCAACGTCAAGGCC | NA | 18-38 | |||||||||||||||||||||||||||||||||||||||||||||||||||||
| primer (HBA
3' SEQ) |
223310-332 | GGACCCGGTCAACTTCAAGGTGA | NA | 399-401 | 227114-136 | GGACCCGGTCAACTTCAAGGTGA | NA | 399-401 | |||||||||||||||||||||||||||||||||||||||||||||||||||||
| T2/G1 | 7 | 223383 | T | rs2362746 | 471 | 227187 | G | rs148228241 | 471 | 7 | T | G | G | G | K | K | G | K | G | G | K | K | K | G | G | G | G | G | K | K | G | G | K | K | G | G | K | T | T | T | T | T | T | T | T | T | - | G | G | - | G | G | G | G | G | ||||||
| ApaI | G2/C1 | 8 | 223447 | G | NA | 535 | 227251 | C | NA | 535 | 8 | G | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | G | G | G | G | G | G | G | G | G | - | C | C | - | C | C | C | C | C | |||||
| (IVS2) | del 2/ins 1 | IVS2 | 223447-448 | del | NA | 534 | 227252-258 | TCGGCCC | NA | 534 | IVS2 | DEL | INS | INS | INS | INS | INS | INS | INS | INS | INS | INS | INS | INS | INS | INS | INS | INS | INS | INS | INS | INS | INS | INS | INS | INS | INS | INS | DEL | DEL | DEL | DEL | DEL | DEL | DEL | DEL | DEL | - | INS | INS | - | INS | INS | INS | INS | INS | |||||
| STOP codon
(TAA) |
223597-599 | TAA | NA | 685 | 227408-410 | TAA | NA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| BalI | 2 NOT-CUT/1 CUT | 9 | 223614 | T AGCCG | rs2362745 | 702 | 227425 | T GGCCA | rs1170850212 | 702 | 9 | A | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | - | A | A | A | A | A | - | A | A | - | G | G | - | G | G | G | G | G | |||||
| BalI | 10 | 223618 | TAGCC G | rs3209623 | 706 | 227429 | TGGCC A | rs376827361 | 706 | 10 | G | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | - | G | G | G | G | G | - | G | G | - | A | A | - | A | A | A | A | A | ||||||
| ApaI | 2 CUT/1 NOT-CUT | 11 | 223646 | GGGCCC | rs4021971 | 734 | 227424 | AGCCCC | rs1463287368 | 734 | 11 | G | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | - | G | G | G | G | G | - | G | G | - | A | A | - | A | A | A | A | A | |||||
| ApaI | 12 | 223648 | GG GCCC | rs4021970 | 736 | 227426 | AG CCCC | rs1190061123 | 736 | 12 | G | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | - | G | G | G | G | G | - | G | G | - | C | C | - | C | C | C | C | C | ||||||
| primer
(A2-R) |
223666-683 | AGACCAGGAAGGGCCGGTG | NA | - | NA | NA | NA | NA | |||||||||||||||||||||||||||||||||||||||||||||||||||||
| RsaI | 2 NOT-CUT/1 CUT | 13 | 223672 | G CCC | rs4021966 | 760 | 227483 | G TAC | NA | 760 | 13 | C | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | - | - | - | - | - | C | - | C | C | - | T | T | - | T | T | T | T | T | |||||
| RsaI | 14 | 223673 | GC CC | rs1487591924 | 761 | 227484 | GT AC | NA | 761 | 14 | C | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | - | - | - | - | - | C | - | C | C | - | A | A | - | A | A | A | A | A | ||||||
| Ensemble
gene end |
223709 | NA | NA | NA | 227521 | NA | NA | NA | |||||||||||||||||||||||||||||||||||||||||||||||||||||
| primer
(3.7-R) |
NA | NA | NA | 844-864 | 227698-718 | CGCTGGACCCTAGAGTGCTTT | NA | 844-864 | |||||||||||||||||||||||||||||||||||||||||||||||||||||
Individuals were identified following PCR typing for the -α 3.7 deletion and selected for Sanger sequencing of the amplicons. From the sequence traces the identity of a set of differentiating bases was recorded (*Base ID No.) as highlighted in Figure 2.
The table rows show features ordered by chromosome position.
Sequencing primers: These columns show the span of the Sanger sequencing typically covered by the named primers.
Note: field intifies specific features across the HBA2 and HBA1 region; primers; gene start, stop; restriction enzyme sites 10 distinguishing the -α 3.7 types I, II and III.
HBA2, HBA1: these columns identify the chromosomal position, sequence, rsIDs and position relative to the ATG site for HBA2 and HBA1 aligned to each other.
Sequenced individuals are shown with their unique IDs (chip_id and released keys that match them to the main datasets).
For individuals, the bases identified are shown and coloured according to the reference sequence (green – HBA1, orange – HBA2).
Bases in purple were found to be identical across all individuals sequenced rather than divergent as in the reference sequences. Dashes are bases that were not possible to identify due to short sequences. The full table of this data can be found in Underlying Data2 Table NN_Sanger_Sequence_summary.