UPDG: Utilities package for data analysis of Pooled DNA GWAS

<p>Abstract</p> <p>Background</p> <p>Despite being a well-established strategy for cost reduction in disease gene mapping, pooled DNA association study is much less popular than the individual DNA approach. This situation is especially true for pooled DNA genomewide association study (GWAS), for which very few computer resources have been developed for its data analysis. This motivates the development of UPDG (Utilities package for data analysis of Pooled DNA GWAS).</p> <p>Results</p> <p>UPDG represents a generalized framework for data analysis of pooled DNA GWAS with the integration of Unix/Linux shell operations, Perl programs and R scripts. With the input of raw intensity data from GWAS, UPDG performs the following tasks in a stepwise manner: raw data manipulation, correction for allelic preferential amplification, normalization, nested analysis of variance for genetic association testing, and summarization of analysis results. Detailed instructions, procedures and commands are provided in the comprehensive user manual describing the whole process from preliminary preparation of software installation to final outcome acquisition. An example dataset (input files and sample output files) is also included in the package so that users can easily familiarize themselves with the data file formats, working procedures and expected output. Therefore, UPDG is especially useful for users with some computer knowledge, but without a sophisticated programming background.</p> <p>Conclusions</p> <p>UPDG provides a free, simple and platform-independent one-stop service to scientists working on pooled DNA GWAS data analysis, but with less advanced programming knowledge. It is our vision and mission to reduce the hindrance for performing data analysis of pooled DNA GWAS through our contribution of UPDG. More importantly, we hope to promote the popularity of pooled DNA GWAS, which is a very useful research strategy.</p

Age dependence of ocular biometric measurements under cycloplegia with tropicamide and cyclopentolate

Background: Cyclopentolate continues to be the cycloplegic of choice for refracting young children, although many studies of ocular biometry promote the use of tropicamide. Methods: To clarify the role of drug type in biometric measurements, cycloplegia was induced in two disparate age groups using cyclopentolate and tropicamide on two separate occasions. Refraction, phakometry and A-scan ultrasonography measurements were made on two groups of Tibetan children resident in Nepal. Results: Cyclopentolate produced significantly more cycloplegia in the younger group, which was supported by phakometry measurements. However, in clinical terms, the difference between the measurements was not significant. Conclusion: We conclude that although cyclopentolate is more effective than tropicamide in relaxing accommodation in young children, the use of a local anaesthetic prior to instillation of tropicamide produces refractive data virtually equivalent to that of cyclopentolate, regardless of the age group measured. However, biometric measurements may be susceptible to greater error when near fixation targets are used during phakometry procedures. © 1998 Optometrists Association Australia

Investigating the relationship between <it>UMODL1</it> gene polymorphisms and high myopia: a case–control study in Chinese

<p>Abstract</p> <p>Background</p> <p>The <it>UMODL1</it> gene was found to be associated with high myopia in Japanese. This study aimed to investigate this gene for association with high myopia in Chinese.</p> <p>Methods</p> <p>Two groups of unrelated Han Chinese from Hong Kong were recruited using the same criteria: Sample Set 1 comprising 356 controls (spherical equivalent, SE, within ±1 diopter or D) and 356 cases (SE ≤ −8D), and Sample Set 2 comprising 394 controls and 526 cases. Fifty-nine tag single nucleotide polymorphisms (SNPs) were selected and genotyped for Sample Set 1. Four SNPs were followed up with Sample Set 2. Both single-marker and haplotype analyses were performed with cases defined by different SE thresholds. Secondary phenotypes were also analyzed for association with genotypes.</p> <p>Results</p> <p>Data filtering left 57 SNPs for analysis. Single-marker analysis did not reveal any significant differences between cases and controls in the initial study. However, haplotype GCT for markers rs220168-rs220170-rs11911271 showed marginal significance (empirical <it>P</it> = 0.076; SE ≤ −12D for cases), but could not be replicated in the follow-up study. In contrast, non-synonymous SNP rs3819142 was associated with high myopia (SE ≤ −10D) in the follow-up study, but could not be confirmed using Sample Set 1. The SNP rs2839471, positive in the original Japanese study, gave negative results in all our analyses. Exploratory analysis of secondary phenotypes indicated that allele C of rs220120 was associated with anterior chamber depth (adjusted <it>P</it> = 0.0460).</p> <p>Conclusions</p> <p>Common <it>UMODL1</it> polymorphisms were unlikely to be important in the genetic susceptibility to high myopia in Han Chinese.</p