Genome-wide linkage analysis of a Parkinsonian-pyramidal syndrome pedigree by 500 K SNP arrays.

Robust SNP genotyping technologies and data analysis programs have encouraged researchers in recent years to use SNPs for linkage studies. Platforms used to date have been 10 K chip arrays, but the possible value of interrogating SNPs at higher densities has been considered. Here, we present a genome-wide linkage analysis by means of a 500 K SNP platform. The analysis was done on a large pedigree affected with Parkinsonian-pyramidal syndrome (PPS), and the results showed linkage to chromosome 22. Sequencing of candidate genes revealed a disease-associated homozygous variation (R378G) in FBXO7. FBXO7 codes for a member of the F-box family of proteins, all of which may have a role in the ubiquitin-proteosome protein-degradation pathway. This pathway has been implicated in various neurodegenerative diseases, and identification of FBXO7 as the causative gene of PPS is expected to shed new light on its role. The performance of the array was assessed and systematic analysis of effects of SNP density reduction was performed with the real experimental data. Our results suggest that linkage in our pedigree may have been missed had we used chips containing less than 100,000 SNPs across the genome.

PRKN, DJ-1, and PINK1 screening identifies novel splice site mutation in PRKN and two novel DJ-1 mutations.

We present results of mutation screening of PRKN gene in 93 Iranian Parkinson's disease (PD) patients with average age at onset (AAO) of 42.2 years. The gene was screened by direct sequencing and by a semi-quantitative PCR protocol for detection of sequence rearrangements. Heterozygous rearrangements were tested by reverse transcription-polymerase chain reaction (RT-PCR). Nine different PRKN mutations were found. One of these, IVS9+1G>A, affects splicing and is novel. Two mutated PRKN alleles were observed in each of 6 patients whose average AAO was 25.7 years. Only 1 patient carried a single mutated allele and his AAO was 41 years. Among patients with AAO of <30 years, 31.3% had two mutated alleles, while only 2.6% with AAO of >30 years carried a PRKN mutation. Analysis of PRKN by RT-PCR led to identification of a novel exon expressed in leukocytes of control and PD individuals. The alternatively spliced transcript if translated would code a protein without a RING Finger 2 domain. Its functional relevance remains to be shown. DJ-I and PINK1 were also screened. Two novel DJ-1 mutations, c.91-2A>G affecting splicing and c.319G>C causing Ala107Pro, were observed among patients with AAO of <31 years, suggesting that PD in a high fraction (>12%) of this group of Iranian patients may be due to mutations in DJ-1. Mutations in PINK1 were not observed. Our results complement previous findings on LRRK2 mutations among Iranian PD patients.

Four mutations (three novel, one founder) in TACSTD2 among Iranian GDLD patients.

PURPOSE: To perform a mutation screening of TACSTD2 in 13 Iranian Gelatinous Drop-like Corneal Dystrophy (GDLD) pedigrees. To assess genotype-phenotype correlations. To determine intragenic SNP haplotypes associated with the mutations, so as to gain information on their origin. METHODS: The coding region of TACSTD2 was sequenced in the probands of 13 unrelated Iranian GDLD pedigrees. Variations were assessed in other available affected and unaffected family members and in unrelated normal control subjects by restriction fragment length polymorphism (RFLP). The variations were classified as being associated with disease if they segregated with the disease phenotype in the families, were not observed in 100 control individuals, disrupted protein expression, or affected conserved positions in the coded protein. Three intragenic single-nucleotide polymorphisms (SNPs) were used to define haplotypes associated with putative disease-causing mutations. RESULTS: The probands were each homozygous for one of four putative disease-causing variations observed in TACSTD2: C66X, F114C, L186P, and E227K. Three of these are novel. E227K was found in 10 of the Iranian patients. There were some phenotypic differences among different patients carrying this mutation-for example, with respect to age at onset. Genotyping of intragenic SNPs identified four haplotypes. C66X, F114C, and L186P were each associated with a haplotype common among control chromosomes, whereas all E227K alleles were associated with a haplotype not found among the control chromosomes. CONCLUSIONS: Although mutations in TACSTD2 among Iranian patients with GDLD were heterogeneous, E227K was found to be a common mutation. It is suggested that E227K may be a founder mutation in this population. Based on positions of known mutations in TACSTD2, significance of the thyroglobulin domain of the TACSTD2 protein in the pathogenesis of GDLD is suggested.

Variation in plasma leptin levels in young Iranian children with cystic fibrosis.

INTRODUCTION: Poor weight gain is one of the most important mortality hazards in cystic fibrosis (CF) patients. The mechanisms that may hinder body weight regulation are not completely understood. Leptin and its role in fat mass could be related to control of weight gain in CF patients. As the previous data are conflicting, we aimed to investigate serum leptin level in Iranian CF children compared to a control group. MATERIAL AND METHODS: Forty-three CF patients aged from 3 to 120 months and 43 age-matched controls were enrolled. Patients were recruited from the outpatient clinic of the Children's Medical Center Hospital. Controls were visited in the general outpatient clinic for an annual check-up. Both groups were divided into three subgroups based on age: 3 to 12 months, 13 to 48 months, and 49 to 120 months. Body mass index (BMI) was calculated for all the participants. Serum leptin levels were measured applying a solid phase enzyme-linked immunosorbent assay (ELISA). RESULTS: Leptin levels and BMI values were significantly different between patients and controls (p = 0.02, p < 0.001, respectively) but only patients aged 13-48 months had significantly higher levels of leptin than age-matched controls (p = 0.016). Overall male patients' mean leptin level was significantly higher than in female patients (p = 0.032) and male controls (p < 0.001). CONCLUSIONS: Leptin level in our patients was significantly higher than controls. It seems that leptin levels during infancy are higher than in adult patients. Further studies are required on specific genotypes, gender and age to reveal the probable correlation with BMI and leptin levels in CF patients from different ethnic groups.

Identification of four novel potentially Parkinson's disease associated LRRK2 variations among Iranian patients.

The results of mutation screening of 24 exons of LRRK2 in 60 Iranian Parkinson's Disease patients are presented. The Iranian cohort represents a novel population and was notably young (average age at onset of disease: 36.0 years). Fifty sequence variations were found, seventeen of which are novel. Variations considered possibly associated with disease were screened in available family members, 145 additional patients and 220 control individuals. It was surmised that four novel sequence variations (IVS49+178A>G, p.R1725Q, p.Q1823K, and p.D2175H) may be associated with PD status, albeit they may be very rare non-disease associated variations. The four variations were all observed in the heterozygous state in early onset cases. If one or more of the variations do indeed contribute to disease status, their penetrance is expected to be low.

Applying a neural network to predict the thermodynamic parameters for an expanded nearest-neighbor model.

Predicting the secondary and tertiary structure of RNAs largely depends on our capabilities in estimating the thermodynamics of RNA duplexes. In this work, an expanded nearest-neighbor model, designated INN-48, is established. The thermodynamic parameters of this model are predicted using both multiple linear regression analysis and neural network analysis. It is suggested that due to the increase in the number of parameters and the insufficiency of the existing data, neural network analysis results in more reliable predictions. Furthermore, it is suggested that INN-48 can be used to estimate the thermodynamics of RNA duplex formation for longer sequences, whereas INN-HB, the previous model on which INN-48 is based, can be used for short sequences.