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Gene mapping in an anophthalmic pedigree of a consanguineous Pakistani family opened new horizons for research

S Saleha
S Saleha
, 
M Ajmal
M Ajmal
, 
S Zafar
S Zafar
 and 
A Hameed
A Hameed
   | Aug 02, 2016
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Article Category: Original Article
Published Online: Aug 02, 2016
Page range: 77 - 84
DOI: https://doi.org/10.1515/bjmg-2016-0010
Keywords
© 2016 Walter de Gruyter GmbH, Berlin/Boston
This article is distributed under the terms of the Creative Commons Attribution Non-Commercial License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Map of Pakistan showing the provincial subdivisons; detailed map of Khyber Pakhtunkhwa with the Kohat region highlighted.
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.
Photograph of the eye of an anophthalmic patient of a Pakistani family.

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.
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.
Gel electropherograms for STR markers D3S1262, D3S2436 and D3S1580, demonstrating homozygosity for the affected members (2MOP003 and 2MOP006) in the studied family.

Primer sets used for amplification of the single exon of the SOX2 gene.

PrimersSequences (5’>3’)PCR Fragment Size (bp)
Sox2_1aFSox2_1aRCCT CTC TCT TTT TTT CCC CTCT CCG ACA AAA GTT TCC431
Sox2_1bFSox2_1bRGCG GCA ACC AGA AAA ACAGCA GCG TGT ACT TAT CCT T291
Sox2 1cFSox2_1cRGCT CAT GAA GAA GGA TAA GTGCT GGT CAT GGA GTT GTA283
Sox2 1dFSox2_1dRCAT GAA CGG CTG GAG CAAAGT GCT GGG ACA TGT GAA407
Sox2_1eFSox2_1eRTTA CCT CTT CCT CCC ACT CCTC CAT GCT GTT TCT TAC T286

Primer sets used for amplification of the promoter sequence of the SOX2 gene.

PrimersSequences (5’>3’)PCR Fragment Size (bp)
5’ F25’ R3AGT CCC GGC CGG GCC GAGGGT AGC CCA GCT GGT CCT G602
3’ F3’ RGGC GTG AAC CAG CGC ATG GGGA GCG TAC CGG GTT TTC TC612
5’UTR F5’UTR RCGC TGA TTG GTC GCT AGA ACTT CAG CTC CGT CTC CAT CAT518
3’UTR.1F3’UTR.1RGGG GTG CAA AAG AGG AGA GTAGAA AAA TAT TGG CAA ATT CTC GC490
3’UTR.2F3’UTR.2RAAC ATG GCA ATC AAA ATG TCCATT CTC GGC AGA CTG ATT CAA514
3’UTR.3F3’UTR.3RCCC CCT TTA TTT TCC GTA GTTATC ATC CAG CCG TTT CTT TTT353

List of short tandem repeat markers used for genotyping in clinical anophthalmia.

ChromosomeGeneSTR MarkersDistance (cM)Amplified Length (bp)
14q32–D14S617GATA168F06GATA136B0191.092.697.0141-173212-232133-157
14q24.3CHX10D14S588D14S53D14S60671.082.785.9117-141151-155254-286
18q21.3RAXD18S858ATA7D07D18S6454.964.760.1193-208126-147188-208
14q21-22OTX2GATA168F06GATA136B0192.697.0212-232133-157
3q26.3-q27SOX2D3S1565D3S2427D3S1262D3S2436D3S1580D3S1311190.3192.1205.2208.5208.7213.1239-245203-245100-132164-180139-155128-160
eISSN:
1311-0160
Language:
English
Publication timeframe:
2 times per year
Journal Subjects:
Medicine, Basic Medical Science, other
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