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SNPs in cancer research and treatment.
Genetic variation in the human genome is an emerging resource for studying cancer, a complex set of diseases characterised by both environmental and genetic contributions. The number of common germ-line variants is great, on the order of 10-15 million per person, and represents a remarkable opportunity to investigate the aetiology, interindividual differences in treatment response and outcomes of specific cancers. The study of genetic variation can elucidate critical determinants in environmental exposure and cancer, which could have future implications for preventive and early intervention strategies. However, we are in the initial stages of characterising the tools (i.e., the single-nucleotide polymorphism, SNP) to rigorously analyse the genetic contributions to complex diseases, such as cancer. If the promise of the genomic era is to be realised, we must integrate this information into new strategies for implementation in both public health measures and, most importantly, provision of individual cancer-related care.
Nondisease genetic testing: reporting of muscle SNPs shows effects on self-concept and health orientation scales.
The purpose of this study was to assess the impact of genetic self-knowledge (nondisease genotype information) on individual self-concept and Health Orientation Scale (HOS). Adult volunteers (n=257) were recruited from an ongoing genetic association study identifying muscle quantitative trait loci (QTLs). Participants completed psychosocial assessments before and after 12 weeks of resistance training of the nondominant arm. At study exit, a genetic counselor informed participants of genetic test results on three to four genes that have an association with muscle-related traits, and counseled subjects on the potential significance of these findings. The second psychosocial assessment was performed immediately following this counseling session. The Tennessee Self-Concept Scale v.2 (TSCS:2) and the HOS showed female subjects to have a significantly greater positive change between first and second assessments, relative to male subjects. Most self-concept subscales improved significantly, when 'neutral' genotypes (no anticipated beneficial or deleterious impact) were reported, compared to positive genotypes. TSCS:2 subscales showing improvement included: total (P=0.013); physical (P=0.004); satisfaction (P=0.019); and behavioral (P=0.047). HOS subscales showing improvement included health image concern (P=0.006); and health expectations (P=0.047). In conclusion, these results suggest that genetic self-knowledge affects self-concept, consistent with the 'attribution' theory. Individuals who received neutral genetic information attributed positive changes from the exercise program to their own abilities, while those who received positive information were more likely to attribute positive changes to their genetics. This study is limited by the ability to determine the direction of the impact of nondisease genetic information presented to participants.
Validity of tagging SNPs across populations for association studies.
Recent advances in high throughput genotyping technologies will allow large-scale association studies to disentangle the genetic basis of human common diseases. Currently, a large-scale genotyping effort is being carried out by the HapMap project and the outcome of this project is expected to help researchers in their efforts to understand how genetic variation influences susceptibility to disease. However, there is some controversy on whether this huge public effort will be of value for those populations not studied in the HapMap project. Here, we present simulation results based on the empirical distribution of linkage disequilibrium (LD) on a large chromosomal region (10 Mb) on human chromosome 20(1,2) for two European and two Asian populations. These results show that statistical power to detect associations does not depend on the population were SNP tagging was performed.
Methods for the selection of tagging SNPs: a comparison of tagging efficiency and performance.
There is great interest in the use of tagging single nucleotide polymorphisms (tSNPs) to facilitate association studies of complex diseases. This is based on the premise that a minimum set of tSNPs may be sufficient to capture most of the variation in certain regions of the human genome. Several methods have been described to select tSNPs, based on either haplotype-block structure or independent of the underlying block structure. In this paper, we compare eight methods for choosing tSNPs in 10 representative resequenced candidate genes (a total of 194.2 kb) with different levels of linkage disequilibrium (LD) in a sample of European-Americans. We compared tagging efficiency (TE) and prediction accuracy of tSNPs identified by these methods, as a function of several factors, including LD level, minor allele frequency, and tagging criteria. We also assessed tagging consistency between each method. We found that tSNPs selected based on the methods Haplotype Diversity and Haplotype r2 provided the highest TE, whereas the prediction accuracy was comparable among different methods. Tagging consistency between different methods of tSNPs selection was poor. This work demonstrates that when tSNPs-based association studies are undertaken, the choice of method for selecting tSNPs requires careful consideration.
Novel SNPs in the CD18 gene validate the association with MPO-ANCA+ vasculitis.
Wegener granulomatosis (WG), microscopic polyangiitis (MP), and Churg-Strauss syndrome (CSS) are characterized by the presence of anti-neutrophil cytoplasmic antibodies (ANCA). Anti-myeloperoxidase (MPO)-ANCA are a typical feature of MP and CSS, while anti-proteinase 3 (PRTN3)-ANCA are highly specific for WG. Several reports indicate that ANCA may directly contribute to pathological processes, ie, through an increase of adhesivity between polymorphonuclear (PMN) and endothelial cells (EC). PMN interact and endothelium interact via the adhesion cascade (AC). CD18 is a key molecule of the AC, as CD18 defects abrogate the adhesion of PMN and cause leukocyte adhesion deficiency, an immunodeficient trait. We have screened the entire coding and regulatory regions of the CD18 gene. Ten single nucleotide polymorphisms (SNP) were identified, four of them showing significant associations with MPO-ANCA(+) vasculitis. One of these SNP's was localized in an alternate transcription initiation site. This polymorphism may influence CD18 gene expression, resulting in dose-dependent increase in adhesion and consecutively facilitated degranulation and respiratory burst. In this manner the pro-adherent genotype may predispose to MPO-ANCA(+) vasculitis.
SNPs and polygenic disorders: a less gloomy view.
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Association of anger-related traits with SNPs in the TPH gene.
Since both aggression-related traits and serotonergic activity are partially heritable and correlate inversely, variations in genes of the serotonergic system might then, to some extent, account for variations in aggression-related behavior. Tryptophan hydroxylase (TPH) is the rate limiting biosynthetic enzyme in the serotonin pathway and regulates levels of serotonin. Recently, a genetic variation in TPH has been associated with aggression and anger-related traits in volunteers. We investigated a sample of community-based healthy volunteers (n = 154) and suicide attempters (n = 86), a clinical population with a high risk for elevated impulsive aggression and related traits. The subjects were genotyped for a A218C and a A779C single nucleotide polymorphism (SNP) located in the TPH gene. All subjects were administered standard psychiatric interviews as well as self-report questionnaires for aggression, irritability and anger-related traits. For anger-related traits, a multivariate effect of the tryptophan hydroxylase genotype and an interaction effect for genotype and diagnosis was observed in healthy volunteers and suicide attempters after controlling for age and educational level. U-carriers in both groups showed higher scores for State Anger, Trait Anger and Angry Temperament. These findings support the hypothesis that the A218C and the A779C SNP in the TPH gene may be associated with anger-related traits in German samples.
Site-selective RNA scission at two sites for precise genotyping of SNPs by mass spectrometry.
Short RNA fragments containing single nucleotide polymorphism (SNP) sites have been selectively clipped out of substrate RNA by using complementary DNA having two acridine residues and Lu(III), and the genotype of the substrate is accurately and easily determined by mass analysis of these fragments.
Microchip capillary gel electrophoresis with electrochemical detection for the analysis of known SNPs.
A novel microchip-based single nucleotide polymorphism (SNP) screening system has been developed. The system utilizes capillary gel electrophoresis (CGE) with electrochemical detection in a chip-based format to accomplish rapid scoring of a mock SNP site. The accuracy of the thermostable polymerase and the advantages of coupling this technique to microfluidics are demonstrated. An electrochemically labeled chain terminator is used in the single base extension (SBE) reaction, in which the terminator is incorporated only when its Watson-Crick complementary base is present at the mock SNP site. The resulting electrochemically active extension product is subsequently separated from any excess terminator by CGE and detected by sinusoidal voltammetry. Although no attempts at optimization have been made, the analysis is performed in less than 4 min. The technique presented could lead to a fast, simple, and cost effective SNP scoring system.
Electrochemical SNPs detection using an abasic site-containing DNA on a gold electrode.
An abasic site-containing DNA combined with lumiflavin allows amperometric determination of single nucleotide polymorphism through hydrogen bond-mediated nucleobase recognition in water by using abasic sites as a molecular recognition field.
Single nucleotide polymorphisms (SNPs) within Bov-A2 SINE in the second intron of bovine and buffalo k-casein (CSN3) gene.
The genetic polymorphism of an entire Bov-A2 element located in the second intron of the buffalo and bovine k-casein (CSN3) gene was investigated by amplification and sequencing of PCR products. Single nucleotide polymorphisms were detected. A PCR-RFLP method was developed to detect an A or G mutation at position 605 of bovine Bov-A2 element which creates a BfaI polymorphic site. The frequencies of the B allele, with the BfaI site, were for 0.275, 0.775, 0.750, 0.975, respectively, for Italian Holstein Friesian, Grey Alpine, Friuli Red Pied and Reggio bovine breeds. The mutation rate (substitutions and deletions/insertions per nucleotide site per year) was 2.5 x 10(-9) for Bov-A2 sequences in the second intron of CSN3. The comparison with other Bov-A2 elements suggests that this retroelement might be an important source of single nucleotide polymorphism for analysis of Bovidae genomes.
Mapping of equine potassium chloride co-transporter (SLC12A4) and amino acid transporter (SLC7A10) and preliminary studies on associations between SNPs from SLC12A4, SLC7A10 and SLC7A9 and osmotic fragility of erythrocytes.
Consensus DNA sequences from human, mouse and/or rat were used to design oligonucleotide primers for equine homologues of exons 16, 17 and 20-23 of potassium chloride co-transporter (SLC12A4) and exons 10, 11 and 3, 4, respectively, for two amino acid transporters (SLC7A10 and SLC7A9). DNA sequences of the PCR products showed high sequence identity to these regions. Equine BAC clones were obtained for SLC12A4 and SLC7A10 and mapped to equine chromosomes ECA3p13 and ECA10p15, respectively, by fluorescence in situ hybridization (FISH). Several single nucleotide polymorphisms (SNP) were found. Substitutions of A/G were found within exon 17 of SLC12A4, within intron 11 of SLC7A10 and within intron 3 of SLC7A9. The SNP associated with SLC7A10 and SLC7A9 were sufficiently polymorphic to investigate associations with erythrocyte fragility among a group of 20 thoroughbred horses. A non-parametric rank-sum test showed a weak association between erythrocyte fragility and the SNP associated with SLC7A10 (P < 0.05).
Eleven single nucleotide polymorphisms (SNPs) at a hypervariable locus on pig chromosome 6.
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Seven SNPs in the porcine INSL3 gene encoding Leydig cell insulin like hormone.
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SNPs in the porcine INHA gene and linkage mapping to SSC15.
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Linkage mapping of SNPs in the porcine relaxin gene.
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