Primer: SNP-associated studies and what they can teach us

Effects of RHD gene polymorphisms on distinguishing weak D or DEL from RhD- in blood donation in a Chinese population

BACKGROUND

Weak D or DEL red blood cell units may be mistyped as RhD- by current serology assays, which can lead to incompatible transfusion to RhD- recipients and further cause anti-D immunization. Molecular RHD blood group typing is a very effective method for overcoming current technical limits. The purpose of this study was to identify RHD single-nucleotide polymorphisms (SNPs) and compare the genotype prevalence among confirmed RhD- individuals in a Chinese population as well as explore effective biomarkers for current weak D or DEL detection before blood transfusion.

METHODS

In the present study, 125 weak D (1, 2, 3, and 4.1) or DEL and 185 RhD- blood samples from donors detected by current standard serology were collected. Genotyping system was used to analyze the SNPs of RHD in each sample.

RESULTS

Seven SNPs (rs592372, rs11485789, rs6669352, rs3118454, rs1053359, rs590787, and rs3927482) were detected in the RHD region. Rs3118454, rs1053359, rs590787, and rs3927482 showed significant differences between the weak D (1, 2, 3 and 4.1) or DEL and RhD- groups. Further combined analysis of the allelic distribution of these four SNPs revealed their higher frequencies in the RhD- group.

CONCLUSION

The SNPs rs3118454, rs1053359, rs590787, and rs3927482 in RHD showed a significantly higher frequency among an RhD- Chinese population and are potential biomarkers.

Candidate single nucleotide polymorphism markers for arsenic responsiveness of protein targets

Arsenic is a toxic metalloid that causes skin cancer and binds to cysteine residues—a property that could be used to infer arsenic responsiveness of a target protein. Non-synonymous Single Nucleotide Polymorphisms (nsSNPs) result in amino acid substitutions and may alter arsenic binding with cysteine residues. Thus, the objective of this investigation was to identify and analyze nsSNPs that lead to substitutions to or from cysteine residues as an indication of increased or decreased arsenic responsiveness. We hypothesize that integration of data on molecular impacts of nsSNPs and arsenic-gene relationships will identify nsSNPs that could serve as arsenic responsiveness markers. We have analyzed functional and structural impacts data for 5,811 nsSNPs linked to 1,224 arsenic-annotated genes. In addition to the identified candidate nsSNPs for increased or reduced arsenic responsiveness, we observed i) a nsSNP that results in the breakage of a disulfide bond, as candidate marker for reduced arsenic responsiveness of KLK7, a secreted serine protease participate in normal shedding of the skin; and ii) 6 pairs of vicinal cysteines in KLK7 protein that could be binding sites for arsenic. In summary, our analysis identified non-synonymous SNPs that could be used to evaluate responsiveness of a protein target to arsenic. In particular, an epidermal expressed serine protease with crucial function in normal skin physiology was prioritized on the basis of abundance of vicinal cysteines for further research on arsenic-induced keratinocyte carcinogenesis.

Large flanking sequence effects in single nucleotide mismatch detection using fluorescent nucleoside C(f)

The first systematic study of flanking sequence effects on mismatch detection by a fluorescent nucleotide is described, using fluoroside C(f). Although a high degree of variance was observed in fluorescence intensity of mismatched duplexes between different flanking sequences, C(f) was able to distinguish a mismatch from the fully base-paired duplex in 13 out of 16 sequences, and even identify each mismatch in 10 of those flanking sequences. For the flanking sequences where fluoroside C(f) did not unambiguously determine its base-pairing partner, the experimental conditions were varied in an attempt to facilitate mismatch identification. No beneficial effect on the relative fluorescence intensities was achieved by changing the temperature, adding organic co-solvents or potassium iodide. In contrast, mercuric ions selectively quenched the fluorescence intensity of the C(f).T mismatch, effectively resolving the overlap of all emission spectra and thereby facilitating identification of all base-pairing partners in any flanking sequence by C(f). This is the first time mercuric ions have been used to selectively quench the fluorescence of a single mismatch. A noticeable characteristic of C(f) is that, unlike most fluorosides, the fluorescence intensity of C(f) was not quenched to a discernable degree by a flanking G-C pair.

Evidence of uneven selective pressure on different subsets of the conserved human genome; implications for the significance of intronic and intergenic DNA

Background

Human genetic variation produces the wide range of phenotypic differences that make us individual. However, little is known about the distribution of variation in the most conserved functional regions of the human genome. We examined whether different subsets of the conserved human genome have been subjected to similar levels of selective constraint within the human population. We used set theory and high performance computing to carry out an analysis of the density of Single Nucleotide Polymorphisms (SNPs) within the evolutionary conserved human genome, at three different selective stringencies, intersected with exonic, intronic and intergenic coordinates.

Results

We demonstrate that SNP density across the genome is significantly reduced in conserved human sequences. Unexpectedly, we further demonstrate that, despite being conserved to the same degree, SNP density differs significantly between conserved subsets. Thus, both the conserved exonic and intronic genomes contain a significantly reduced density of SNPs compared to the conserved intergenic component. Furthermore the intronic and exonic subsets contain almost identical densities of SNPs indicating that they have been constrained to the same degree.

Conclusion

Our findings suggest the presence of a selective linkage between the exonic and intronic subsets and ascribes increased significance to the role of introns in human health. In addition, the identification of increased plasticity within the conserved intergenic subset suggests an important role for this subset in the adaptation and diversification of the human population.

The TaqMan method for SNP genotyping

Single nucleotide polymorphisms (SNPs) are common DNA sequence variations that occur at single bases within the genome. SNPs have been instrumental in elucidating the genetic basis of common, complex diseases using genome-wide association studies, candidate gene case-control association studies, and genome-wide linkage analyses. A key to these studies is genotyping of SNPs. Various methods for SNP genotyping have been developed. For a particular genotyping project, the choice of method is dependent on the number of SNPs (n) and the number of DNA samples (m) to be genotyped. For a genome-wide or large-scale project with very high n and small m, the Affymetrix SNP GeneChip and Illumina GoldenGate BeadChips assays are the ideal methods. For a project involving a small number of SNPs (small n) and a large population (high m), the TaqMan assay is the preferred technology as it has high throughput and is highly accurate, precise, time-efficient, and cost-effective. Here, we describe the detailed procedures for TaqMan SNP genotyping assay, including preparation of high-quality DNA samples, the operating protocol, clarification of technical issues, and discussion of several cautionary notes.

Evolutionary pattern of protein architecture in mammal and fruit fly genomes

Mutations, which can alter amino acid constitution, contribute greatly to protein evolution. However, little is reported of their pattern during protein structural evolution. We investigated the distribution of non-synonymous single nucleotide polymorphisms (nsSNPs) and insertions/deletions (indels) along mammal and fruit fly proteins. We found the nsSNPs (and d(N)) and indels increased in protein boundary regions, and this pattern is inversely correlated with the distribution of protein domain density. Additionally, synonymous substitutions (and d(S)) are reduced in 5' and 3' regions, indicating more variable protein boundaries, compared with central interior. All evidence suggests that the inner part of coding sequences (CDSs) is comparatively conserved, whereas the 5' and 3' regions, with higher evolution rates, are more variable. We assumed that due to greater frequencies of nsSNPs and indels in adaptive regions of CDSs it could be easier to ultimately alter, gain, or lose amino acids, thus becoming the front line of protein evolution.