For linkage analysis, polymorphic microsatellite markers (Human
MapPairs Set, ver. 8; Research Genetics, Inchinnan,
Scotland, UK) were amplified by polymerase chain reaction (PCR). Three
sets of markers were analyzed: those corresponding to the known loci of
eye-specific transcription factor genes,
16 a further 40
reported to define loci closest to the greatest number of expressed
sequence tags,
17 and a set of 387 anonymous markers at 10-
to 20-centimorgan (cM) intervals throughout the genome. PCR reactions
were each performed in a 10-μl volume containing 1.5 mM
MgCl
2, 0.4 mM of each primer, 200 μM dNTPs, 16
mM
(NH
4)
2SO
4,
67 mM Tris-HCl (pH 8.8), 0.01% Tween-20, and 1 U
Taq DNA
polymerase (Bio-Line, London, UK). Amplification was performed with an
initial denaturation for 3 minutes at 95°C, followed by 30 cycles of
denaturation at 95°C for 1 minute, annealing at 55°C for 1 minute,
extension at 72°C for 1 minute, and a final extension at 72°C for 7
minutes. The PCR products were separated on 8% to 10% nondenaturing
polyacrylamide gels (Protogel; National Diagnostics, Edinburgh,
Scotland, UK). The gels were stained with ethidium bromide and
photographed under UV illumination.
On the first indication of linkage to chromosome 10q, the family was
genotyped for more markers across the region. Alleles were assigned to
individuals, and haplotypes of all family members were constructed
(Fig. 1) . The genotypic data were used to calculate the two-point lod
scores, using the Cyrillic (http://www.cyrillicsoftware.com) and
MLINK (ftp://linkage.rockefeller.edu/software/linkage/)
software programs.
18 Allele frequencies were calculated
from the normal, ethnically matched population. The phenotype was
analyzed as an autosomal recessive trait with complete penetrance at a
frequency of 0.0001 for the disease gene.