The correctness of large scale analysis of genomic data

Implementing a large genomic project is a demanding task, also from the computer science point of view. Besides collecting many genome samples and sequencing them, there is processing of a huge amount of data at every stage of their production and analysis. Efficient transfer and storage of the data is also an important issue. During the execution of such a project, there is a need to maintain work standards and control quality of the results, which can be difficult if a part of the work is carried out externally. Here, we describe our experience with such data quality analysis on a number of levels - from an obvious check of the quality of the results obtained, to examining consistency of the data at various stages of their processing, to verifying, as far as possible, their compatibility with the data describing the sample.

Genetic alteration preceding any chronic diseases: using Human Genomic Project

Since the human genomic project had been completed in 2003, scarce research studies have been done to evaluate the clinical relevance of this project to public health, specifically in the arena of prevention of chronic diseases. Utilizing the structural equation model, with a random sample from National Lung Screening Data. Using SAS software and Proc CALIS for the analysis to assess whether there is a genetic alteration/expression transpires prior to any chronic disease. And to encourage more research studies in this rookie field that merges both public health and prevention of chronic diseases with the human genome. The results of all three proposed models boost the alternative theory, which indicates there is gene alteration/expression anterior to any chronic disease. Therefore, the results stimulate the use of the human genome project in the area of public health in a way that can curtail many dangerous chronic diseases before they hit.

Development of EST-derived SSR Markers with Long-core Repeat in Olive and Their Use for Paternity Testing

In the present work, a set of eight new hexa-nucleotide simple sequence repeats (SSRs) is reported in olive (Olea europaea L). These SSRs loci were generated on the basis of expressed sequence tag (EST) sequences in the frame of an olive genomic project. The markers showed a high level of polymorphism when tested on a set of cultivars used as genitors in the olive breeding program of Córdoba, Spain. The long-core repeat motif of these markers allows a wider separation among alleles, thus permitting an accurate genotyping. Besides, these markers showed comparable levels of polymorphism to di-nucleotide SSRs, the only ones so far reported in olive. Selected on the basis of their discrimination capacity, four of the eight SSRs were used to test their ability for paternity testing in a total of 81 seedlings coming from 12 crosses. The paternity testing showed that seven crosses matched the alleged paternity and the remaining five were products of illicit pollinations. These results exactly matched with previous paternity testing performed with di-nucleotide SSR markers. These results demonstrate the usefulness of the developed hexa-nucleotide repeated motifs for checking the paternity of breeding progenies and suggest their use on variability studies.

Expression of Ovary-Specific Acidic Protein in Steroidogenic Tissues: A Possible Role in Steroidogenesis

Ovary-specific acidic protein (OSAP) is a novel molecule discovered from a genomic project designed to identify ovary-selective genes in mice. Whereas public databases suggest extraovarian expression of OSAP, its tissue distribution has not yet been well documented. Thus, the expression profile of mouse and human OSAP was determined by quantitative real-time RT-PCR using RNAs isolated from various tissues. The results demonstrate that the human and mouse OSAP expression profiles are similar; OSAP is prominently expressed in steroidogenic tissues with the highest level of expression observed in the adrenal gland. Placenta served as an exception and possessed minimal level of OSAP mRNA. Immunohistochemical studies show that mouse OSAP localizes almost exclusively to the steroid-producing cells of the ovary, adrenal gland, and testis. Consistent with predictions made by several subcellular localization algorithms, dual labeling studies in Y-1 mouse adrenocortical cells indicate OSAP resides in the mitochondria. Because of its abundant expression in steroidogenic cells and mitochondrial localization, a role for OSAP in steroidogenesis was determined. OSAP silencing by specific small interfering RNAs significantly inhibits 8-bromoadenosine-cAMP-induced progesterone production in Y-1 cells. Reduction in OSAP levels results in mitochondrial fragmentation and a decrease in the cellular content of mitochondrial DNA, indicative of decreased mitochondrial abundance. Lastly, 8-bromoadenosine-cAMP does not regulate OSAP protein expression in Y-1 cells as is the case for other steroidogenic components known to be induced by cAMP. Collectively these results suggest that OSAP is involved in steroidogenesis, potentially through its ability to maintain mitochondrial abundance and morphology.