Identification of recurrent and novel mutations in TULP1 in Pakistani families with early-onset retinitis pigmentosa

Contains fulltext : 108208.pdf (publisher's version ) (Open Access)PURPOSE: To identify the genetic defects underlying retinitis pigmentosa (RP) in Pakistani families. METHODS: Genome-wide high-density single-nucleotide-polymorphism microarray analysis was performed using the DNA of nine affected individuals from two large families with multiple consanguineous marriages. Data were analyzed to identify homozygous regions that are shared by affected sibs in each family. Sanger sequencing was performed for genes previously implicated in autosomal recessive RP and allied retinal dystrophies that resided in the identified homozygous regions. Probands from both families underwent fundus examination and electroretinogram measurements. RESULTS: The tubby-like protein 1 gene (TULP1) was present in the largest homozygous region in both families. Sequence analysis identified a previously reported mutation (c.1138A>G; p.Thr380Ala) in one family and a novel pathogenic variant (c.1445G>A; p.Arg482Gln) in the other family. Both variants were found to be present in a homozygous state in all affected individuals, were heterozygous present in the unaffected parents, and heterozygous present or absent in normal individuals. Affected individuals of both families showed an early-onset form of RP. CONCLUSIONS: Homozygosity mapping, combined with candidate-gene analysis, successfully identified genetic defects in TULP1 in two large Pakistani families with early-onset retinitis pigmentosa

Role of ACE and PAI-1 Polymorphisms in the Development and Progression of Diabetic Retinopathy.

In the present study we determined the association of angiotensin converting enzyme (ACE) and plasminogen activator inhibitor-1 (PAI-1) gene polymorphisms with diabetic retinopathy (DR) and its sub-clinical classes in Pakistani type 2 diabetic patients. A total of 353 diabetic subjects including 160 DR and 193 diabetic non retinopathy (DNR) as well as 198 healthy controls were genotyped by allele specific polymerase chain reaction (PCR) for ACE Insertion/Deletion (ID) polymorphism, rs4646994 in intron 16 and PAI-1 4G/5G (deletion/insertion) polymorphism, rs1799768 in promoter region of the gene. To statistically assess the genotype-phenotype association, multivariate logistic regression analysis was applied to the genotype data of DR, DNR and control individuals as well as the subtypes of DR. The ACE genotype ID was found to be significantly associated with DR (p = 0.009, odds ratio (OR) 1.870 [95% confidence interval (CI) = 1.04-3.36]) and its sub-clinical class non-proliferative DR (NPDR) (p = 0.006, OR 2.250 [95% CI = 1.098-4.620]), while PAI polymorphism did not show any association with DR in the current cohort. In conclusion in Pakistani population the ACE ID polymorphism was observed to be significantly associated with DR and NPDR, but not with the severe form of the disease i.e. proliferative DR (PDR)

Logistic regression analysis for rs4646994 and rs1799768 in <i>ACE</i> and <i>PAI</i> genes in Pakistani type 2 diabetic cohort.

<p>Logistic regression analysis for rs4646994 and rs1799768 in <i>ACE</i> and <i>PAI</i> genes in Pakistani type 2 diabetic cohort.</p

Demographic data of the patients genotyped for <i>ACE</i> and <i>PAI</i> polymorphisms in the present study.

<p>Demographic data of the patients genotyped for <i>ACE</i> and <i>PAI</i> polymorphisms in the present study.</p

Pedigree structure and segregation analysis of disease causing variants in the IRD cohort.

<p>Arrows point to the probands.</p

Frequent variants pre-screened in 28 LCA families.

<p>^#In original description [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119806#pone.0119806.ref064" target="_blank">64</a>] this variant erroneously was indicated as c.3101T>C.</p><p>^$In lymphoblast cells, 50% of the resulting mRNA contains a cryptic exon resulting in a predicted stop mutation and 50% of the mRNA is normal [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119806#pone.0119806.ref028" target="_blank">28</a>].</p><p>Frequent variants pre-screened in 28 LCA families.</p

Results of targeted Sanger sequencing and genetic analyses of 13 IRD families.

<p>Hz, Homozygous; Mb, Megabases; SS, Sanger sequencing entire gene; TSS, targeted Sanger sequencing; DNA, Deoxyribonucleic acid.</p><p>Results of targeted Sanger sequencing and genetic analyses of 13 IRD families.</p