Role of SNP/haplotype map in gene discovery and drug development: An overview

Association of the Sp1 binding site and -1997 promoter variations in COL1A1 with osteoporosis risk: The application of meta-analysis and bioinformatics approaches offers a new perspective for future research

As a complex disease, osteoporosis is influenced by several genetic markers. Many studies have examined the link between the Sp1 binding site +1245 G > T (rs1800012) and -1997 G > T (rs1107946) variations in the COL1A1 gene with osteoporosis risk. However, the findings of these studies have been contradictory; therefore, we performed a meta-analysis to aggregate additional information and obtain increased statistical power to more efficiently estimate this correlation. A meta-analysis was conducted with studies published between 1991-2020 that were identified by a systematic electronic search of the Scopus and Clarivate Analytics databases. Studies with bone mineral density (BMD) data and complete genotypes of the single-nucleotide variations (SNVs) for the overall and postmenopausal female population were included in this meta-analysis and analyzed using the R metaphor package. A relationship between rs1800012 and significantly decreased BMD values at the lumbar spine and femoral neck was found in individuals carrying the "ss" versus the "SS" genotype in the overall population according to a random effects model (p < 0.0001). Similar results were also found in the postmenopausal female population (p = 0.003 and 0.0002, respectively). Such findings might be an indication of increased osteoporosis risk in both studied groups in individuals with the "ss" genotype. Although no association was identified between the -1997 G > T and low BMD in the overall population, those individuals with the "GT" genotype showed a higher level of BMD than those with "GG" in the subgroup analysis (p = 0.007). To determine which transcription factor (TF) might bind to the -1997 G > T in COL1A1, 45 TFs were identified based on bioinformatics predictions. According to the GSE35958 microarray dataset, 16 of 45 TFs showed differential expression profiles in osteoporotic human mesenchymal stem cells relative to normal samples from elderly donors. By identifying candidate TFs for the -1997 G > T site, our study offers a new perspective for future research.

Molecular mapping of soybean rust resistance in soybean accession PI 561356 and SNP haplotype analysis of the Rpp1 region in diverse germplasm

Soybean rust (SBR), caused by Phakopsora pachyrhizi Sydow, is one of the most economically important and destructive diseases of soybean [Glycine max (L.) Merr.] and the discovery of novel SBR resistance genes is needed because of virulence diversity in the pathogen. The objectives of this research were to map SBR resistance in plant introduction (PI) 561356 and to identify single nucleotide polymorphism (SNP) haplotypes within the region on soybean chromosome 18 where the SBR resistance gene Rpp1 maps. One-hundred F(2:3) lines derived from a cross between PI 561356 and the susceptible experimental line LD02-4485 were genotyped with genetic markers and phenotyped for resistance to P. pachyrhizi isolate ZM01-1. The segregation ratio of reddish brown versus tan lesion type in the population supported that resistance was controlled by a single dominant gene. The gene was mapped to a 1-cM region on soybean chromosome 18 corresponding to the same interval as Rpp1. A haplotype analysis of diverse germplasm across a 213-kb interval that included Rpp1 revealed 21 distinct haplotypes of which 4 were present among 5 SBR resistance sources that have a resistance gene in the Rpp1 region. Four major North American soybean ancestors belong to the same SNP haplotype as PI 561356 and seven belong to the same haplotype as PI 594538A, the Rpp1-b source. There were no North American soybean ancestors belonging to the SNP haplotypes found in PI 200492, the source of Rpp1, or PI 587886 and PI 587880A, additional sources with SBR resistance mapping to the Rpp1 region.

SNP assay to detect the 'Hyuuga' red-brown lesion resistance gene for Asian soybean rust

Asian soybean rust (ASR), caused by Phakopsora pachyrhizi Syd., has the potential to become a serious threat to soybean, Glycine max L. Merr., production in the USA. A novel rust resistance gene, Rpp?(Hyuuga), from the Japanese soybean cultivar Hyuuga has been identified and mapped to soybean chromosome 6 (Gm06). Our objectives were to fine-map the Rpp?(Hyuuga) gene and develop a high-throughput single nucleotide polymorphism (SNP) assay to detect this ASR resistance gene. The integration of recombination events from two different soybean populations and the ASR reaction data indicates that the Rpp?(Hyuuga) locus is located in a region of approximately 371 kb between STS70887 and STS70923 on chromosome Gm06. A set of 32 ancestral genotypes which is predicted to contain 95% of the alleles present in current elite North American breeding populations and the sources of the previously reported ASR resistance genes (Rpp1, Rpp2, Rpp3, Rpp4, Rpp5, and rpp5) were genotyped with five SNP markers. We developed a SimpleProbe assay based on melting curve analysis for SNP06-44058 which is tighly linked to the Rpp?(Hyuuga) gene. This SNP assay can differentiate plants/lines that are homozygous/homogeneous or heterozygous/heterogeneous for the resistant and susceptible alleles at the Rpp?(Hyuuga) locus.

Genetic diversity and medicinal drug response in eye care

BACKGROUND

Individual variation in drug response and adverse drug reactions are a serious problem in medicine. This inter-individual variation in drug response could be due to multiple factors such as disease determinants, environmental and genetic factors. Much has been published in the literature in recent years about the potential of pharmacogenetic testing and individualized medicine. The development of personalized medicine is truly an exciting area of research.

METHODS

This pharmacogenetic concept in ophthalmology has existed for more than a century. Although substantial studies that link genetic variants to inter-individual difference in drug response have been reported in several diseases such as cancer and heart diseases, such studies are progressing slowly in the eye field. In this short article, an attempt has been made to summarize these results.

RESULTS

Recently, there have been some small-scale studies that seem to associate the drug response to the genotype of patients in two major eye disorders, namely age-related macular degeneration (ARMD) and glaucoma.

CONCLUSION

These studies are still in their infancy, and do not suggest that a pharmacogenetic basis of drug development is a credible concept and can become reality in the future. This is because most drug responses involve a large number of genes that have several polymorphisms and it is unlikely that any one single gene dictates the drug response. Therefore, a polygenic approach, whole genome single nucleotide polymorphism (SNP) analysis and a molecular understanding of disease itself may provide a better insight in the future about genetic predisposing factors for adverse drug reactions.

SNPs: impact on gene function and phenotype

Single nucleotide polymorphism (SNP) is the simplest form of DNA variation among individuals. These simple changes can be of transition or transversion type and they occur throughout the genome at a frequency of about one in 1,000 bp. They may be responsible for the diversity among individuals, genome evolution, the most common familial traits such as curly hair, interindividual differences in drug response, and complex and common diseases such as diabetes, obesity, hypertension, and psychiatric disorders. SNPs may change the encoded amino acids (nonsynonymous) or can be silent (synonymous) or simply occur in the noncoding regions. They may influence promoter activity (gene expression), messenger RNA (mRNA) conformation (stability), and subcellular localization of mRNAs and/or proteins and hence may produce disease. Therefore, identification of numerous variations in genes and analysis of their effects may lead to a better understanding of their impact on gene function and health of an individual. This improved knowledge may provide a starting point for the development of new, useful SNP markers for medical testing and a safer individualized medication to treat the most common devastating disorders. This will revolutionize the medical field in the future. To illustrate the effect of SNPs on gene function and phenotype, this minireview focuses on evidences revealing the impact of SNPs on the development and progression of three human eye disorders (Norrie disease, familial exudative vitreoretinopathy, and retinopathy of prematurity) that have overlapping clinical manifestations.

SNPs in disease gene mapping, medicinal drug development and evolution

Single nucleotide polymorphism (SNP) technologies can be used to identify disease-causing genes in humans and to understand the inter-individual variation in drug response. These areas of research have major medical benefits. By establishing an association between the genetic make-up of an individual and drug response it may be possible to develop a genome-based diet and medicines that are more effective and safer for each individual. Additionally, SNPs can be used to understand the molecular mechanisms of sequence evolution. It has been found that throughout the given gene, the rate, type and site of nucleotide substitutions as well as the selection pressure on codons is not uniform. The residues that evolve under strong selective pressures are found to be significantly associated with human disease. Deleterious mutations that affect biological function of proteins are effectively being rejected by natural selection from the gene pool. If substituted nucleotides are fixed during evolution then they may have selection advantages, they may be neutral, or they may be deleterious and cause pathology. Therefore, it is possible that disease-associated SNPs (or pathology) and evolution can be related to one another.

Enantiomeric separation and determination of absolute stereochemistry of asymmetric molecules in drug discovery—Building chiral technology toolboxes

The application of Chiral Technology, or the (extensive) use of techniques or tools for the determination of absolute stereochemistry and the enantiomeric or chiral separation of racemic small molecule potential lead compounds, has been critical to successfully discovering and developing chiral drugs in the pharmaceutical industry. This has been due to the rapid increase over the past 10-15 years in potential drug candidates containing one or more asymmetric centers. Based on the experiences of one pharmaceutical company, a summary of the establishment of a Chiral Technology toolbox, including the implementation of known tools as well as the design, development, and implementation of new Chiral Technology tools, is provided.

Pharmacogenetics and the concept of individualized medicine

Adverse drug reaction in patients causes more than 2 million hospitalizations including 100,000 deaths per year in the United States. This adverse drug reaction could be due to multiple factors such as disease determinants, environmental and genetic factors. In order to improve the efficacy and safety and to understand the disposition and clinical consequences of drugs, two rapidly developing fields--pharmacogenetics (focus is on single genes) and pharmacogenomics (focus is on many genes)--have undertaken studies on the genetic personalization of drug response. This is because many drug responses appear to be genetically determined and the relationship between genotype and drug response may have a very valuable diagnostic value. Identification and characterization of a large number of genetic polymorphisms (biomarkers) in drug metabolizing enzymes and drug transporters in an ethnically diverse group of individuals may provide substantial knowledge about the mechanisms of inter-individual differences in drug response. However, progress in understanding complex diseases, its negative psychosocial consequences, violation of privacy or discrimination, associated cost and availability and its complexity (extensive geographic variations in genes) may become potential barriers in incorporating this pharmacogenetic data in risk assessment and treatment decisions. In addition, it requires increased enthusiasm and education in the clinical community and an understanding of pharmacogenetics itself by the lay public. Although individualized medications remain as a challenge for the future, the pharmacogenetic approach in drug development should be still continued. If it becomes a reality, it delivers benefits to improve public health and allow genetically subgroup diseases thereby avoiding adverse drug reactions (by knowing in advance who should be treated with what drug and how).

Genetic diversity and new therapeutic concepts

The differences in medicinal drug responses among individuals had been known for quite some time. Some patients exhibit a life-threatening adverse reaction while others fail to show an expected therapeutic effect. Intermediate responses between the above two extreme cases are also known. In fact, it has been recently reported that approximately 100,000 deaths and more than 2 million hospitalizations annually in the United States are due to properly prescribed medications. This interindividual variability could be due in part to genetically determined characteristics of target genes or drug metabolizing enzymes. This has now been substantiated by a variety of studies. We know that "one size fits all" is not correct. Therefore, the application of pharmacogenetic concepts to clinical practice is an excellent goal in the postgenomic era. The successful completion of the human genome project provided necessary molecular tools, such as high-throughput SNP genotyping, HapMap, and microarray, that can be applied to develop proper therapeutic options for individuals. Recently, there have been considerable scientific, corporate, and policy interest in pharmacotherapy. However, identification of causal variations in a target gene is only a starting point, and the progress in this rapidly developing field is slower than expected. One major drawback could be due to the multigene determinant of drug response that requires a genome-wide screening. Additionally, application of pharmacogenetic knowledge into clinical practice requires a high level of accuracy, precision (risk/benefit ratio), and strict regulations. This is because the pharmacogenetic approach raises several ethical, moral, and legal questions. It is also necessary that both health professionals and the general public must be urgently educated. Despite these limitations, translation of pharmacogenomic data into clinical practice would certainly provide better opportunities to increase the safety and efficacy of medicine in the future.