Map of Pakistan showing the provincial subdivisons; detailed map of Khyber Pakhtunkhwa with the Kohat region highlighted.
Photograph of the eye of an anophthalmic patient of a Pakistani family.
Table 1
List of short tandem repeat markers used for genotyping in clinical anophthalmia.
| Chromosome | Gene | STR Markers | Distance (cM) | Amplified Length (bp) |
|---|---|---|---|---|
| 14q32 | – | D14S617 GATA168F06 GATA136B01 | 91.0 92.6 97.0 | 141-173 212-232 133-157 |
| 14q24.3 | CHX10 | D14S588 D14S53 D14S606 | 71.0 82.7 85.9 | 117-141 151-155 254-286 |
| 18q21.3 | RAX | D18S858 ATA7D07 D18S64 | 54.9 64.7 60.1 | 193-208 126-147 188-208 |
| 14q21-22 | OTX2 | GATA168F06 GATA136B01 | 92.6 97.0 | 212-232 133-157 |
| 3q26.3-q27 | SOX2 | D3S1565 D3S2427 D3S1262 D3S2436 D3S1580 D3S1311 | 190.3 192.1 205.2 208.5 208.7 213.1 | 239-245 203-245 100-132 164-180 139-155 128-160 |
cM: centimorgan; bp: base pair.
Table 2
Primer sets used for amplification of the single exon of the SOX2 gene.
| Primers | Sequences (5’>3’) | PCR Fragment Size (bp) |
|---|---|---|
| Sox2_1aF Sox2_1aR | CCT CTC TCT TTT TTT CCC C TCT CCG ACA AAA GTT TCC | 431 |
| Sox2_1bF Sox2_1bR | GCG GCA ACC AGA AAA ACA GCA GCG TGT ACT TAT CCT T | 291 |
| Sox2 1cF Sox2_1cR | GCT CAT GAA GAA GGA TAA GT GCT GGT CAT GGA GTT GTA | 283 |
| Sox2 1dF Sox2_1dR | CAT GAA CGG CTG GAG CAA AGT GCT GGG ACA TGT GAA | 407 |
| Sox2_1eF Sox2_1eR | TTA CCT CTT CCT CCC ACT C CTC CAT GCT GTT TCT TAC T | 286 |
PCR: polymerase chain reaction; bp: base pair; F: forward; R: reverse.
Table 3
Primer sets used for amplification of the promoter sequence of the SOX2 gene.
| Primers | Sequences (5’>3’) | PCR Fragment Size (bp) |
|---|---|---|
| 5’ F2 5’ R3 | AGT CCC GGC CGG GCC GAG GGT AGC CCA GCT GGT CCT G | 602 |
| 3’ F 3’ R | GGC GTG AAC CAG CGC ATG G GGA GCG TAC CGG GTT TTC TC | 612 |
| 5’UTR F 5’UTR R | CGC TGA TTG GTC GCT AGA A CTT CAG CTC CGT CTC CAT CAT | 518 |
| 3’UTR.1F 3’UTR.1R | GGG GTG CAA AAG AGG AGA GTA GAA AAA TAT TGG CAA ATT CTC GC | 490 |
| 3’UTR.2F 3’UTR.2R | AAC ATG GCA ATC AAA ATG TCC ATT CTC GGC AGA CTG ATT CAA | 514 |
| 3’UTR.3F 3’UTR.3R | CCC CCT TTA TTT TCC GTA GTT ATC ATC CAG CCG TTT CTT TTT | 353 |
PCR: polymerase chain reaction; bp: base pair; F: forward; R: reverse; 5’UTR: 5’ untranslated region; 3’UTR: 3’ untrans-lated region.
Pedigree of a consanguineous Pakistani family with STR genotyping data mapped to a locus on chromosome 3q26.3-q27. Both parents are carriers of the defective (boxed) chromosome. The affected individuals (filled square and circles) are homozygotes for the defective chromosome.
Gel electropherograms for STR markers D3S1262, D3S2436 and D3S1580, demonstrating homozygosity for the affected members (2MOP003 and 2MOP006) in the studied family.