Results of the multipoint linkage analysis using MERLIN.

<p>Note: All linkage regions with a LOD score >1.5 at the peak marker in at least one of the multipoint analyses, nonparametric (NPL), dominant (DOM), or recessive (REC), are presented. The upper and lower bounds of each linkage peak interval presented were selected based on covering all markers with a LOD or HLOD score within one LOD score unit of the peak marker's LOD score. The peak LOD scores are indicated with <b>bold text</b>. Chr, chromosome; SNP, single nucleotide polymorphism; LOD, logarithm of the odds; HLOD, heterogeneity logarithm of the odds.</p

Worldwide distribution of the minor (risk) allele, G, of rs613872 in <i>TCF4.</i>

<p>Data from the Human Genome Diversity Project, available online through the UCSC genome browser at <a href="http://genome.ucsc.edu/" target="_blank">http://genome.ucsc.edu/</a>. Note the higher prevalence of the risk allele in sample populations from Europe, the Middle East, and Southern Asia and the absence of the risk allele in sample populations from Africa, Eastern Asia, and Central and South America.</p

Expression profile of glucosaminyl (N-acetyl) transferase 2 in the developing mouse lens.

<p>The expression of <i>Gcnt2</i> at different developmental time points was normalized to <i>Gapdh</i>. The x-axis and y-axis represent the developmental time point and the normalized expression level of <i>Gcnt2</i> mRNA, respectively. Note: red line: expression of <i>Gcnt2</i>; blue dashed line: linear regression.</p

Characterization of the <i>GCNT2</i> deletion responsible for congenital cataracts in PKCC215.

<p><b>A</b>) Model of chromosome 6 indicating the placement of the primer pairs in the PCR amplification of the <i>GCNT2</i> region. Visualization (on a 1.5% agarose gel) of the amplification products from each primer pair with the DNA of <b>B</b>) an unaffected and <b>C</b>) affected member of PKCC215. Amplification of the genomic DNA of the affected individual was successful (produced specific PCR products) with the primer pairs indicated in green. Amplification of the affected individual’s DNA failed (non-specific or no PCR products) with the primer pairs indicated in red. Note: Asterisk indicates non-specific PCR products.</p

Primer sequences used for the amplification of <i>LIM2</i> coding exons.

<p>Primer sequences used for the amplification of <i>LIM2</i> coding exons.</p

Comparison of genotype frequencies between Duke dataset and dataset used in Baratz et al. (2010), and between male and female in Duke dataset for rs613872.

<p>*<b>N: total sample size.</b></p><p>**<b>Heterozygous frequencies are elevated in all datasets and are highlighted in bold.</b></p

Plot of the top multipoint linkage peak on chromosome 18.

<p>SNP markers are plotted along the x-axis by their deCODE map position, and the LOD/HLOD scores for each marker are plotted along the y-axis. The results of the FASTLINK/HOMOG dominant two-point analysis are indicated with black circles, and the results of the MERLIN dominant multipoint analysis are indicated with a black line. The SNP rs4941043 is the peak marker from the two-point analysis (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0018044#pone-0018044-t003" target="_blank"><b>Table 3</b></a>). The location of the <i>FCD2</i> peak (Sundin <i>et al.</i>, 2006) and the most significantly associated SNP, rs613872, from the FECD GWAS performed by Baratz <i>et al.</i> (2010) are indicated by arrows. The location of the <i>TCF4</i> gene is also indicated for reference. 2PT, two-point results; MPT, multipoint results; cM, centiMorgans; LOD, logarithm of the odds; HLOD, heterogeneity logarithm of the odds.</p

Primer sequences for the confirmation of <i>GCNT2</i> deletion breakpoints in PKCC215.

<p>Primer sequences for the confirmation of <i>GCNT2</i> deletion breakpoints in PKCC215.</p

Slit-lamp photograph of affected individual 9 of PKCC214.

<p>This photograph depicts a nuclear cataract that developed during infancy.</p

Mutations reported in <i>GCNT2</i>.

<p>Mutations reported in <i>GCNT2</i>.</p