Resources for Genetic Variation Studies

Re-situations of scientific knowledge: a case study of a skirmish over clusters vs clines in human population genomics

We track and analyze the re-situation of scientific knowledge in the field of human population genomics ancestry studies. We understand re-situation as a process of accommodating the direct or indirect transfer of objects of knowledge from one site/situation to (one or many) other sites/situations. Our take on the concept borrows from Mary S. Morgan's work on facts traveling while expanding it to include other objects of knowledge such as models, data, software, findings, and visualizations. We structure a specific case study by tracking the re-situation of these objects between three research projects studying human population diversity reported in three articles in Science, Genome Research and PLoS Genetics between 2002 and 2005. We characterize these three engagements as a unit of analysis, a "skirmish," in order to compare: (a) the divergence of interests in how life-scientists answer similar research questions and (b) to track the challenging transformation of workflows in research laboratories as these scientific objects are re-situated individually or in bundles. Our analysis of the case study shows that an accurate understanding of re-situation requires tracking the whole bundle of objects in a project because they interact in particular key ways. The absence or dismissal of these interactions opens the door to unforeseen trade-offs, misunderstandings and misrepresentations about research design(s) and workflow(s) and what these say about the questions asked and the findings produced.

MVSC: A Multi-variation Simulator of Cancer Genome

BACKGROUND

Many forms of variations exist in the genome, which are the main causes of individual phenotypic differences. The detection of variants, especially those located in the tumor genome, still faces many challenges due to the complexity of the genome structure. Thus, the performance assessment of variation detection tools using next-generation sequencing platforms is urgently needed.

METHOD

We have created a software package called the Multi-Variation Simulator of Cancer genomes (MVSC) to simulate common genomic variants, including single nucleotide polymorphisms, small insertion and deletion polymorphisms, and structural variations (SVs), which are analogous to human somatically acquired variations. Three sets of variations embedded in genomic sequences in different periods were dynamically and sequentially simulated one by one.

RESULTS

In cancer genome simulation, complex SVs are important because this type of variation is characteristic of the tumor genome structure. Overlapping variations of different sizes can also coexist in the same genome regions, adding to the complexity of cancer genome architecture. Our results show that MVSC can efficiently simulate a variety of genomic variants that cannot be simulated by existing software packages.

CONCLUSION

The MVSC-simulated variants can be used to assess the performance of existing tools designed to detect SVs in next-generation sequencing data, and we also find that MVSC is memory and time-efficient compared with similar software packages.

Genetic polymorphisms influence runners' responses to the dietary ingestion of antioxidant supplementation based on pequi oil (Caryocar brasiliense Camb.): a before-after study

Genes have been implicated in the levels of oxidative stress, lipids, CVD risk, immune reactivity, and performance. Pequi oil (Caryocar brasiliense) has shown anti-inflammatory and hypotensive effects, besides reducing exercise-induced DNA, tissue damages, and anisocytosis. Given that diet can interact with the human genome to influence health and disease, and because genetic variability can influence response to diet, we aim to investigate the influence of 12 gene polymorphisms on inflammatory markers, postprandial lipids, arterial pressure, and plasma lipid peroxidation of runners (N = 125), before and after 14 days of 400 mg pequi-oil supplementation, after races under closely comparable conditions. Arterial pressure was checked before races; blood samples were taken immediately after racing to perform leukogram and plateletgram, Tbars assay, lipid, and CRP dosages and genotyping. CAT, GST-M1/T1, CRP-G1059C, and MTHFR-C677T polymorphisms influenced post-pequi-oil responses in leukogram; Hp and MTHFR-C677T, in plateletgram; Hp, ACE, GSTT1, and MTHFR-A1298C, in lipid profile; MTHFR-A1298C, in C-reactive protein (CRP) levels; and Hp and MnSOD, in Tbars assay. Differences between ACE genotypes in leukogram and total cholesterol disappeared after pequi, and the same occurred for Hp and MnSOD in Tbars assay and for MTHFR-A1298C with CRP levels. Because genetic inheritance is one of the factors that drive atherosclerosis-related lipid abnormalities, results can contribute to a greater understanding of the influence of genetic polymorphisms in situations that push up free radicals. Knowledge is also expanded on how antioxidant supplementation affects an individual's genes and how athletic genetic makeup can affect the way a person responds to antioxidant supplements.

Superoxide dismutase, catalase, glutathione peroxidase and gluthatione S-transferases M1 and T1 gene polymorphisms in three Brazilian population groups

Antioxidants such as superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX1) reduce the oxidation rates in the organism. Gluthatione S-transferases (GSTs) play a vital role in phase 2 of biotransformation of many substances. Variation in the expression of these enzymes suggests individual differences for the degree of antioxidant protection and geographical differences in the distribution of these variants. We described the distribution frequency of CAT (21A/T), SOD2 (Ala9Val), GPX1 (Pro198Leu), GSTM1 and GSTT1 polymorphisms in three Brazilian population groups: Kayabi Amerindians (n = 60), Kalunga Afro-descendants (n = 72), and an urban mixed population from Federal District (n = 162). Frequencies of the variants observed in Kalunga (18% to 58%) and Federal District (33% to 63%) were similar to those observed in Euro and Afro-descendants, while in Kayabi (3% to 68%), depending on the marker, frequencies were similar to the ones found in different ethnic groups. Except for SOD2 in all population groups studied here, and for GPX1 in Kalunga, the genotypic distributions were in accordance with Hardy-Weinberg Equilibrium. These data can clarify the contribution of different ethnicities in the formation of mixed populations, such as that of Brazil. Moreover, outcomes will be valuable resources for future functional studies and for genetic studies in specific populations. If these studies are designed to comprehensively explore the role of these genetic polymorphisms in the etiology of human diseases they may help to prevent inconsistent genotype-phenotype associations in pharmacogenetic studies.

The effect of hydrogen peroxide-induced oxidative stress on leukocytes depends on age and physical training in healthy human subjects carrying the same genotypes of antioxidant enzymes' gene polymorphisms

OBJECTIVES

Reactive oxygen species account for the background levels of oxidatively damaged DNA in normal tissues. Physical exercise increases oxygen consumption and can cause oxidative stress. This stress can also involve deficient antioxidant defenses, which can be influenced by certain genetic polymorphisms. Because regular exercise is a known inducer of antioxidant enzymes, the objective of this study was to compare, by comet assay, differences in the DNA damage between apparently healthy individuals and trained aerobic sportsmen carrying the same single nucleotide polymorphisms of manganese superoxide dismutase (Val9Ala), catalase (-21A/T), glutathione peroxidase 1 (Pro198Leu), before and after exposing leukocytes from peripheral blood to hydrogen peroxide (H₂O₂).

METHODS

Athletes were compared with nonathletes after a situation that promotes reactive oxygen species increase (a race). Blood samples were submitted to genotyping and comet assay, and the athletes and nonathletes were paired according to their gender, age, and MnSOD, CAT, and GPx-1 genotypes.

RESULTS

For nonathletes, there was a positive correlation between H₂O₂ concentrations and DNA damage levels. For athletes, these correlations showed differences between sexes, indicating that running may impose higher oxidative stress on the DNA of women than of men. Significant differences appeared for nonathletes in the comparisons between younger and older age groups after treatment with H₂O₂ at 250 μM.

CONCLUSIONS

This suggests that, for individuals carrying the same genotypes of antioxidant enzymes' genes, the effect of H₂O₂-induced oxidative stress depends mainly on age and physical training. It also suggests that aerobic physical training can reduce oxidative damages to DNA, preventing related diseases in older people.

Evaluation of gene polymorphisms in exercise-induced oxidative stress and damage

Many potentially significant genetic variants related to oxidative stress have been identified and performance in endurance sports is a multi-factorial phenotype. Thus, it was decided to investigate the influences of the haptoglobin (Hp), MnSOD (Val9Ala), CAT (21A/T), GPX1 (Pro198Leu), ACE, glutathione S-transferases M1 (GSTM1) and T1 (GSTT1) genes' polymorphisms on the oxidative stress and damage suffered by human athletes (runners). Blood samples taken immediately after a race were submitted to genotyping, comet and TBARS assays, biochemical analyses of creatine kinase (CK), aspartate aminotransferase (AST) and alanine aminotransferase (ALT). MnSOD significantly influenced results of CK and a possible association between Hp1F-1S and Hp1S-2 genotypes with a superior TBARS values was found. Higher or lower TBARS and CK values or DNA damage also depended on the interaction between Hp and ACE or GST genotypes, indicating that MnSOD and Hp polymorphisms can be determining factors in performance, at least for runners.

Genomic Approaches to the Host Response to Pathogens

The need to better understand host–pathogen interactions has risen with the expansion in genomics and related technologies. This chapter focuses on two aspects of the host response to pathogens where major advances are being made using genomic approaches. The availability of complete genomic sequences of an expanding number of pathogens, the human and mouse genome sequences, and the advent of genome-wide genotyping and gene expression profiling has opened up new avenues of investigation in the field. The genotype of the pathogen plays a major role in the response of the host to infection with more virulent pathogenic strains possessing the capability to interfere with the host immune response. In addition, different individuals in a population can have very different responses to a genetically identical pathogen. Part of the differential response is governed by the underlying genetic differences between individuals. The advent of genome-wide genotyping using single nucleotide polymorphisms or microsatellite markers is leading to major advances in molecular epidemiology. The future impact of genomic approaches on the development of diagnostics and therapeutics is discussed for infectious diseases. This includes defining the basis of genetic susceptibility to infection and system-wide molecular response to a pathogen.

High throughput ‘omics’ approaches to assess the effects of phytochemicals in human health studies

Human health is affected by many factors. Diet and inherited genes play an important role. Food constituents, including secondary metabolites of fruits and vegetables, may interact directly with DNA via methylation and changes in expression profiles (mRNA, proteins) which results in metabolite content changes. Many studies have shown that food constituents may affect human health and the exact knowledge of genotypes and food constituent interactions with both genes and proteins may delay or prevent the onset of diseases. Many high throughput methods have been employed to get some insight into the whole process and several examples of successful research, namely in the field of genomics and transcriptomics, exist. Studies on epigenetics and RNome significance have been launched. Proteomics and metabolomics need to encompass large numbers of experiments and linked data. Due to the nature of the proteins, as well as due to the properties of various metabolites, experimental approaches require the use of comprehensive high throughput methods and a sufficiency of analysed tissue or body fluids. In this contribution, we describe the basic tools currently used in nutrigenomics studies and indicate the general requirements for future technology methodological routings.

Genetic variation in human disease and a new role for copy number variants

While complex diseases, such as inflammatory bowel disease, do not follow distinctive Mendelian inheritance patterns, there is now considerable evidence from twin and pedigree studies to show that there are significant genetic influences in the development of many such diseases. In times past, this type of information was considered to be interesting, and was used mainly to alert other members of the families that they may also be at increased risk of developing the disease. However, with the ability to evaluate the genetic basis of common disease, this information will have important consequences for the diagnosis, prevention and treatment of the disorder. The genetic basis for common disease is likely to be more complicated than we had previously anticipated, since we now recognise epigenetic causes of disease, and other subtle gene regulatory mechanisms. Copy number variants have been highlighted in this review, as being a phenomenon that we have known about for a long time, but that has not previously been clearly associated with human disease. As complex disease is related to changes in gene expression, any variation in the human genome that alters gene expression is now a candidate for being involved in the disease process.