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Genetic and genomic analysis of classic aniridia in Saudi Arabia.

ABSTRACT: PURPOSE: To determine the genetic and genomic alterations underlying classic aniridia in Saudi Arabia, a region with social preference for consanguineous marriage. METHODS: Prospective study of consecutive patients referred to a pediatric ophthalmologist in Saudi Arabia (2005-2009). All patients had paired box gene 6 (PAX6) analysis (sequencing and multiplex ligation-dependent probe amplification analysis if sequencing was normal). If PAX6 analysis was negative, the following were performed: candidate gene sequencing (forkhead box C1 [FOXC1], paired-like homeodomain transcription factor 2 [PITX2], cytochrome P450, family 1, subfamily B [CYP1B1], paired-like homeodomain transcription factor 3 [PITX3], and v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog [MAF]) and molecular karyotyping by array competitive genomic hybridization (250K single nucleotide polymorphism (SNP) arrays). RESULTS: All 12 probands (4 months-25 years of age; four boys and eight girls) had lens opacity and foveal hypoplasia in addition to no grossly visible iris. Four cases were familial. All cases were products of consanguineous unions except for three, one of which was endogamous. Heterozygous PAX6 mutations (including two novel mutations) were detectable in all but two cases, both of which were sporadic. In one of these two cases, the phenotype segregated with homozygosity for a previously-reported pathogenic missense FOXC1 variant (p.P297S) when homozygosity for chromosome 11q24.2 deletion (chr11:125,001,547-125,215,177 [rs114259885; rs112291840]) was also present. In the other, no genetic or genomic abnormalities were found. CONCLUSIONS: The classic aniridia phenotype in Saudi Arabia is typically caused by heterozygous PAX6 mutations, even in the setting of enhanced homozygosity from recent shared parental ancestry. For PAX6-negative cases, interaction between missense variation in an anterior segment developmental gene and copy number variation elsewhere in the genome may be a potential mechanism for the phenotype.

SUBMITTER: Khan AO

PROVIDER: S-EPMC3060157 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Genetic and genomic analysis of classic aniridia in Saudi Arabia.

Khan Arif O AO Aldahmesh Mohammed A MA Alkuraya Fowzan S FS

Molecular vision 20110311

<h4>Purpose</h4>To determine the genetic and genomic alterations underlying classic aniridia in Saudi Arabia, a region with social preference for consanguineous marriage.<h4>Methods</h4>Prospective study of consecutive patients referred to a pediatric ophthalmologist in Saudi Arabia (2005-2009). All patients had paired box gene 6 (PAX6) analysis (sequencing and multiplex ligation-dependent probe amplification analysis if sequencing was normal). If PAX6 analysis was negative, the following were p ...[more]

PMID: 21423868

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Project description:BackgroundThe present study was conducted to discover genetic imbalances such as DNA copy number variations (CNVs) associated with gastric cancer (GC) and to examine their association with different genes involved in the process of gastric carcinogenesis in Saudi population.MethodsFormalin-fixed paraffin-embedded (FFPE) tissues samples from 33 gastric cancer patients and 15 normal gastric samples were collected. Early and late stages GC samples were genotyped and CNVs were assessed by using Illumina HumanOmni1-Quad v.1.0 BeadChip.ResultsCopy number gains were more frequent than losses throughout all GC samples compared to normal tissue samples. The mean number of the altered chromosome per case was 64 for gains and 40 for losses, and the median aberration length was 679115bp for gains and 375889bp for losses. We identified 7 high copy gain, 52 gains, 14 losses, 32 homozygous losses, and 10 copy neutral LOHs (loss of heterozygosities). Copy number gains were frequently detected at 1p36.32, 1q12, 1q22, 2p11.1, 4q23-q25, 5p12-p11, 6p21.33, 9q12-q21.11, 12q11-q12, 14q32.33, 16p13.3, 17p13.1, 17q25.3, 19q13.32, and losses at 1p36.23, 1p36.32, 1p32.1, 1q44, 3q25.2, 6p22.1, 6p21.33, 8p11.22, 10q22.1, 12p11.22, 14q32.12 and 16q24.2. We also identified 2 monosomy at chromosome 14 and 22, 52 partially trisomy and 22 whole chromosome 4 neutral loss of heterozygosities at 13q14.2-q21.33, 5p15.2-p15.1, 5q11.2-q13.2, 5q33.1-q34 and 3p14.2-q13.12. Furthermore, 11 gains and 2 losses at 1p36.32 were detected for 11 different GC samples and this region has not been reported before in other populations. Statistical analysis confirms significant association of H. pylori infection with T4 stage of GC as compare to control and other stages.ConclusionsWe found that high frequency of copy number gains and losses at 1p36.23, 1p32.1, 1p36.32, 3q25.2, 6p21.33 and 16q24.2 may be common events in gastric cancer. While novel CNVs at 1p36.32 harbouring PRDM16, TP73 and TP73-AS1 genes showed 11 gains and 2 losses for 11 different GC cases and this region is not reported yet in Database of Genomic Variants may be specific to Saudi population.

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Genetic and genomic analysis of classic aniridia in Saudi Arabia.

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Genetic and genomic analysis of classic aniridia in Saudi Arabia.

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