An application in bioinformatics : a comparison of affymetrix and compugen human genome microarrays

The human genome microarrays from Compugen® and Affymetrix® were compared in the context of the emerging field of computational biology. The two premier database servers for genomic sequence data, the National Center for Biotechnology Information and the European Bioinformatics Institute, were described in detail. The various databases and data mining tools available through these data servers were also discussed. Microarrays were examined from a historical perspective and their main current applications-expression analysis, mutation analysis, and comparative genomic hybridization-were discussed. The two main types of microarrays, cDNA spotted microarrays and high-density spotted microarrays were analyzed by exploring the human genome microarray from Compugen® and the HGU133 Set from Affymetrix® respectively. Array design issues, sequence collection and analysis, and probe selection processes for the two representative types of arrays were described. The respective chip design of the two types of microarrays was also analyzed. It was found that the human genome microarray from Compugen 0 contains probes that interrogate 1,119,840 bases corresponding to 18,664 genes, while the HG-U133 Set from Affymetrix® contains probes that interrogate only 825,000 bases corresponding to 33,000 genes. Based on this, the efficiency of the 25-mer probes of the HG-U133 Set from Affymetrix® compared to the 60-mer probes of the microarray from Compugen® was questioned

The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species

The Mediterranean fruit fly (medfly), Ceratitis capitata, is a major destructive insect pest due to its broad host range, which includes hundreds of fruits and vegetables. It exhibits a unique ability to invade and adapt to ecological niches throughout tropical and subtropical regions of the world, though medfly infestations have been prevented and controlled by the sterile insect technique (SIT) as part of integrated pest management programs (IPMs). The genetic analysis and manipulation of medfly has been subject to intensive study in an effort to improve SIT efficacy and other aspects of IPM control

Detection of Microdeletions by Non-Invasive Prenatal Testing

Background: Non-invasive prenatal testing (NIPT) is currently offered for the detection of Trisomy 21, 13, 18 and sex chromosome aneuploidy. The test is unique because it reaches nearly diagnostic levels of accuracy, otherwise achieved only by invasive procedures like chorionic villus sampling or amniocentesis, but requires only a sample of maternal blood. The NIPT technology continues to advance and a greater variety of genomic alterations can be detected. This research study describes the detection of two different fetal microdeletions using NIPT, which includes whole genome next-generation sequencing, and targeted region capture and sequencing methods. Methods: Whole genome next-generation sequencing, and targeted region capture and sequencing methods, were used on samples of maternal plasma obtained from pregnancies with confirmed microdeletions. The DNA of these samples was compared to control DNA libraries to identify the fetal microdeletions. Results: We were able to identify statistically significant differences between samples to detect fetal microdeletions on chromosome 12p12.1-p11.22 from maternal plasma samples. Identification of a fetal microdeletion on 5p15.33 from maternal plasma samples was achieved, but highlighted the difficulties in detection, and future challenges for NIPT. Conclusion: Our research has demonstrated the ability to detect microdeletions by whole genome next-generation sequencing and targeted region capture and sequencing methods of NIPT. The findings indicate the ability of NIPT to detect a wide range of genomic alterations, which will impact prenatal care in the future if the technology improves. Development and expansion of NIPT has significant public health implications due to its high levels of accuracy as compared to current screening, and safety for the pregnancy as compared to current diagnostic testing options. NIPT could have major ethical implications, and could impact the role of prenatal genetic counselors and physicians

THE CHRONOBIOLOGICAL HYPOTHESIS AND PSYCHOSOCIAL AND CULTURAL GENOMIC THERAPIES: FROM THE EXAMPLE OF PARKINSON’S DISEASE AND NEURODEGENERATIVE PROCESS

Recent research on Parkinson’s Disease (PD) revealed some common etiopathogenic mechanisms underlying a large range of chronic diseases, and more specifically the deregulation of chronobiological rhythms that may start in the very beginning of such pathological development. Contrary to the bottom-up tradition, the post-genomic biology provides now a much favorable zeitgeist to integrate holistic interventions in both biomedical research and mainstream medical practice. Such integrative efforts may not only improve our understanding of system-level dynamics about health and disease, but also opens larger possibilities for new clinical options that bring positive pathological evolutions while globally increasing quality of life of patients, caregivers, and their families. To facilitate the transition, we renew the invitation to join our international open source research project in widely testing the Creative Psychosocial Genomic Healing Experience (CPGHE), an evidence-based construction of a holistic and naturalist intervention with its standardized version specially designed to offer easy adaption for scientific investigation towards an evidence-based integration of holistic intervention possibilities

Genetic Loci Contributing to Spontaneous Autoimmune Diabetes

Background and Aims: Spontaneous type 1 diabetes (T1D) in the BioBreeding (BB) rat mimics human T1D as the rats experience weight loss, polydipsia, polyuria, ketoacidosis, onset during puberty and insulin-dependency within a day after diagnosis. Because the DP rat develops T1D spontaneously, it is a prime laboratory animal for dissecting the genetics of T1D susceptibility without the need for external manipulation. The BB rat is comprised of two separate substrains; the diabetes prone (BBDP) and the diabetes resistant (BBDR). Failure to express the Gimap5 protein is associated with lymphopenia (lyp) and linked to T1D in the BBDP rat. In an intercross between F1(BBDP x F344) rats we identified a rat with a recombination event on rat chromosome (RNO) 4, allowing us to fix 34Mb of F344 between D4Rat253 and D4Rhw6 in the congenic DR.lyp rat line with two Mb of BBDP DNA, encompassing the Gimap5 mutation, introgressed on the DR genetic background. The aim of this thesis was to characterize the F344 DNA introgression, test the hypothesis that the introgression would result in 1) no effect on T1D development or 2) protection from T1D, generate congenic sublines and positionally clone and characterize the resulting candidate genes on rat RNO4. Material and Methods: The F344 fragment in the DRF.f/f rat line was fixed onto the DR.lyp background in a total of nine backcross and seven intercross matings. To generate DRF.f/f congenic sublines, DRF.f/f rats were crossed to inbred BBDR or DR.lyp/lyp rats and the offspring genotyped, phenotyped for lymphopenia and monitored for T1D. Positional candidate genes were then subjected to coding sequence analysis, cDNA sequencing and/or quantitative real-time (qRT) PCR expression analysis. Results: DRF.f/f rats, homozygous for the F344 allele, were lymphopenic but did not develop T1D while all (100%) DR.lyp/lyp rats developed T1D by 83 days of age. Generation of congenic sublines revealed that reduction of the DRF.f/f F344 DNA fragment by 26 Mb (42.52 Mb-68.51 Mb) retained complete T1D protection. Further dissection revealed that a 2 Mb interval of F344 DNA (67.41-70.17 Mb) (Iddm38) resulted in 47% protection while retaining <1 Mb of F344 DNA at the distal end (Iddm39) resulted in 28% protection, both of which significantly delayed onset. Comparative analysis of T1D frequency in the DRF.f/f congenic sublines refined the Iddm38 and Iddm39 intervals to approximately 670 Kb between SNP SS105325016 and D4Rat26 and 340 Kb proximal to Gimap5, respectively. Coding sequence analysis revealed TCR Vβ 8E, 12 and 13 as candidate genes in Iddm38 and Znf467 and Atp6v0e2 in Iddm39. Quantitative RT-PCR analysis of whole organ as well as in FACS sorted thymocytes and peripheral T-cells stained with CD4 and CD8 monoclonal antibodies showed a reduction in expression of four out of five Gimap genes located within the Iddm39 interval, in addition to Gimap5, in DR.lyp/lyp spleen and mesenteric lymph nodes (MLN) when compared to DR.+/+. Conclusions: Our data demonstrates that introgression of a 34 Mb region of the F344 genome, proximal to the mutated Gimap5 gene, renders the congenic DR.lyp/lyp rat T1D resistant despite being lymphopenic. Generation of congenic sublines revealed that spontaneous T1D in the BB rat is controlled, in part, by at least two genetic loci, Iddm38 and Iddm39, in addition to the Gimap5 mutation on RNO4. Coding sequence analysis revealed TCR Vβ 8E, 12 and 13 as candidate genes in Iddm38 and Znf467 and Atp6v0e2 as candidate genes in Iddm39. Quantitative RT-PCR expression analysis suggests that the lack of the Gimap5 protein in the DR.lyp/lyp congenic rat impairs expression of the entire Gimap gene family and regulates T-cell homeostasis in the peripheral lymphoid organs. The molecular identification and characterization of the genetic factors protecting from T1D in the DRF.f/f congenic rat line should prove critical to disclose the mechanisms by which T1D develops in the BB rat

Dietary Variation and Evolution of Gene Copy Number among Dog Breeds

Prolonged human interactions and artificial selection have influenced the genotypic and phenotypic diversity among dog breeds. Because humans and dogs occupy diverse habitats, ecological contexts have likely contributed to breed-specific positive selection. Prior to the advent of modern dog-feeding practices, there was likely substantial variation in dietary landscapes among disparate dog breeds. As such, we investigated one type of genetic variant, copy number variation, in three metabolic genes: glucokinase regulatory protein (GCKR), phytanol-CoA 2-hydroxylase (PHYH), and pancreatic α-amylase 2B (AMY2B). These genes code for proteins that are responsible for metabolizing dietary products that originate from distinctly different food types: sugar, meat, and starch, respectively. After surveying copy number variation among dogs with diverse dietary histories, we found no correlation between diet and positive selection in either GCKR or PHYH. Although it has been previously demonstrated that dogs experienced a copy number increase in AMY2B relative to wolves during or after the dog domestication process, we demonstrate that positive selection continued to act on amylase copy number in dog breeds that consumed starch-rich diets in time periods after domestication. Furthermore, we found that introgression with wolves is not responsible for deterioration of positive selection on AMY2B among diverse dog breeds. Together, this supports the hypothesis that the amylase copy number expansion is found universally in dogs

The contribution of sociodemographic and clinical factors to length of stay in hospitalized children

BACKGROUND: There is continued attention towards using patient demographic and clinical characteristics available in health administrative data when case mix adjusting the measurement of length of stay (LOS) for hospitalized children. However, little is known about what proportion of children’s LOS is explained by these characteristics. OBJECTIVES: The objectives of the study were to quantify the amount of variation in LOS within and across hospitals that is explained by demographic and clinical factors of hospitalized pediatric patients. METHODS: A retrospective cohort analysis was completed of 818,848 hospitalizations for any reason occurring from 1/1/2014 to 12/31/2014 in one of 44 freestanding children’s hospitals in the Pediatric Health Information Systems (PHIS) dataset. A generalized linear model was derived to simultaneously regress demographic factors [age, race/ethnicity, payer, rural residence, health professional shortage area (HPSA) residence, income, and distance traveled], and clinical factors (severity of illness, type and number of chronic conditions) on LOS. The percentage of LOS attributable to each characteristic within each hospital was quantified using the covariance test of the hospital random effect. RESULTS: The factors with the greatest impact on LOS were severity of illness and chronic condition type and number, with a median (interquartile range) of 16.8% (IQR 15.0%-19.4%) and 4.0% (IQR 2.9%-4.5%) of LOS, respectively, explained by these characteristics across hospitals. LOS varied significantly (p<0.05) with both severity of illness and chronic condition type and number for all 44 hospitals in the cohort. All patient demographic factors, (age, race/ethnicity, payer, rural residence, HSPA residence, income, and distance traveled) had minimal impact on LOS, with <0.1% of LOS explained by each characteristic. Across hospitals, 78.3% (IQR 75.8-80.2%)] of LOS remained unexplained by the patient characteristics under study. CONCLUSIONS: Patients’ clinical characteristics ascertained from administrative data account for approximately one-fifth of LOS whereas their demographic characteristics account for a negligible amount. Efforts to optimize the efficiency of inpatient care for hospitalized children might benefit from uncovering how much of the vast amount of unexplained LOS is due to modifiable aspects of care quality.2018-06-16T00:00:00