Development Of Single Nucleotide Polymorphisms Research Articles

Génétique des schizophrénies : mise en perspective des schizophrénies à début précoce et autres pathologies du développement

Schizophrenia (SCZ) is a severe brain disorder characterized by hallucinations, delusions, flat and/or inappropriate affect and cognitive impairment. The lifetime risk is about 0.5% with heritability of 65–85%. The prevalence of early-onset schizophrenia (defined here as before 15 years of age) has not been well studied, but is likely to be 5–10% of all cases. The rarity of early-onset SCZ has made it difficult to study. We focus on genetic studies of adults with schizophrenia, highlighting results for early-onset schizophrenia where available. Prior to the past 5years, studies failed to find replicable association or linkage between SCZ and specific genes when appropriate statistical corrections for multiple testing were used. Many false positive results were probably reported using the candidate gene approach. Recently, the development of single nucleotide polymorphism (SNP) “chips” has permitted large genome-wide association study (GWAS) analyses that suggest that across all age groups, a proportion of genetic risk can be attributed to a large number of common SNP, each with a very small effect on risk (odds ratios of 1.1 or less). The greatest known genetic effect is conferred by the 1.5–3 Mb 22q.11.2 deletions, which occurs in ∼ 1/4000–1/6000 births with SCZ developing in 20–30% of carriers. Large SNP and aCGH microarray studies have now identified associations between SCZ and other rare, large copy number variations (CNV, insertions and deletions) with high odds ratios (5–10), including deletions of 1q21, 2p16.3 (neurexin-1 gene), 3q29 and 15q13.3, and duplications of 16p11.2. Some of these CNV are also associated with autism or other developmental disorders as well as epilepsy or intellectual deficiency, suggesting some overlap in the mechanisms that contribute to risks of these disorders. Based on preliminary data from larger-scale analyses in progress, approximately 1–2% of cases carry a CNV that has been clearly associated with SCZ (ORs 4–12). Whole exome and genome sequencing studies of large adult samples will be the next steps to identify rarer SCZ-associated mutations, including point mutations and smaller as well as rarer CNV. Genetic findings are beginning to contribute to an understanding of biological mechanisms of SCZ risk and may lead to new approaches to treatment.

Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provides insights into worldwide population structure

The optimal management of the commercially important, but mostly over-exploited, pelagic tunas, albacore (Thunnus alalunga Bonn., 1788) and Atlantic bluefin tuna (BFT; Thunnus thynnus L., 1758), requires a better understanding of population structure than has been provided by previous molecular methods. Despite numerous studies of both species, their population structures remain controversial. This study reports the development of single nucleotide polymorphisms (SNPs) in albacore and BFT and the application of these SNPs to survey genetic variability across the geographic ranges of these tunas. A total of 616 SNPs were discovered in 35 albacore tuna by comparing sequences of 54 nuclear DNA fragments. A panel of 53 SNPs yielded FST values ranging from 0.0 to 0.050 between samples after genotyping 460 albacore collected throughout the distribution of this species. No significant heterogeneity was detected within oceans, but between-ocean comparisons (Atlantic, Pacific and Indian oceans along with Mediterranean Sea) were significant. Additionally, a 17-SNP panel was developed in Atlantic BFT by cross-species amplification in 107 fish. This limited number of SNPs discriminated between samples from the two major spawning areas of Atlantic BFT (FST =0.116). The SNP markers developed in this study can be used to genotype large numbers of fish without the need for standardizing alleles among laboratories.

Regional scale distribution of imidazolinone herbicide-resistant alleles in red rice ( Oryza sativa L.) determined through SNP markers

Red rice is the main weed in rice paddy fields. Imidazolinone herbicides in resistant rice cultivars currently provide a unique opportunity to control red rice in large-scale rice fields. However, the continuous use of this technology has resulted in imidazolinone-resistant red rice biotypes. This study aimed to identify the mechanism of herbicide resistance and the frequency and spatial distribution of the known imidazolinone herbicide-resistant alleles in red rice. The nucleotide sequence of the ALS gene indicated that the G 654E, S 653D and A 122T mutations are present in the imidazolinone herbicide-resistant rice cultivars IRGA 422 CL, SATOR CL and PUITÁ INTA CL, respectively. This information and the nucleotide sequence surrounding these mutations were used for the development of single nucleotide polymorphism (SNP) molecular markers to identify the possible mutations that confer herbicide resistance in red rice. This analysis was carried out in a total of 481 plants from 38 populations collected as individuals that escaped control with the herbicides imazethapyr and imazapic in rice paddy fields in Southern Brazil. The G 654E mutation was the most frequent, being found in 100% and 90.9% of the populations in the 2006/2007 and 20007/2008 seasons, respectively. In addition, the S 653D and A 122T mutations were also present either alone or as double or triple mutations in some plants. Target site insensitivity is the predominant mechanism of resistance in red rice resistant to imidazolinone herbicides in Southern Brazil. The high frequency of the S 653D mutation, the same mutation responsible for the resistance in the rice cultivar largely used in Southern Brazil, indicates that gene flow is occurring from the rice cultivar to red rice. Management practices related to increasing crop sanitation and decreasing of herbicide selection pressure through crop rotation should be enforced to prevent the evolution of herbicide resistance in red rice.

SNPs At the origins of the databases of an innovative biotechnology tool

The discovery that DNA sequence variations can influence the response of an individual to a drug or can predict the outcome of a disease has added a new dimension to evidence-based medicine. It is clear that the goals, risks, and benefits of drug therapy can be better assessed if the underlying genome of the patient is known. The relevance of identifying patients at increased risk of adverse drug reactions, the application of genomic technologies to drug development and the clarification of the mechanisms of drug action on cells will be important targets in the therapeutic approach to medicine in the 21st century. In this review, we summarize the development of single nucleotide polymorphisms (SNPs) and give computational biological data for SNPs databases.

Cadherins as Targets for Genetic Diseases

The 6-billion human population provides a vast reservoir of mutations, which, in addition to the opportunity of detecting very subtle defects, including specific cognitive dysfunctions as well as late appearing disorders, offers a unique background in which to investigate the roles of cell-cell adhesion proteins. Here we focus on inherited human disorders involving members of the cadherin superfamily. Most of the advances concern monogenic disorders. Yet, with the development of single nucleotide polymorphism (SNP) association studies, cadherin genes are emerging as susceptibility genes in multifactorial disorders. Various skin and heart disorders revealed the critical role played by desmosomal cadherins in epidermis, hairs, and myocardium, which experience high mechanical stress. Of particular interest in that respect is the study of Usher syndrome type 1 (USH1), a hereditary syndromic form of deafness. Studies of USH1 brought to light the crucial role of transient fibrous links formed by cadherin 23 and protocadherin 15 in the cohesion of the developing hair bundle, the mechanoreceptive structure of the auditory sensory cells, as well as the involvement of these cadherins in the formation of the tip-link, a key component of the mechano-electrical transduction machinery. Finally, in line with the well-established role of cadherins in synaptic formation, maintenance, strength, and plasticity, a growing number of cadherin family members, especially protocadherins, have been found to be involved in neuropsychiatric disorders.

Development of single nucleotide polymorphism (SNP) markers for use in commercial maize (Zea mays L.) germplasm

The development of single nucleotide polymorphism (SNP) markers in maize offers the opportunity to utilize DNA markers in many new areas of population genetics, gene discovery, plant breeding and germplasm identification. However, the steps from sequencing and SNP discovery to SNP marker design and validation are lengthy and expensive. Access to a set of validated SNP markers is a significant advantage to maize researchers who wish to apply SNPs in scientific inquiry. We mined 1,088 loci sequenced across 60 public inbreds that have been used in maize breeding in North America and Europe. We then selected 640 SNPs using generalized marker design criteria that enable utilization with several SNP chemistries. While SNPs were found on average every 43 bases in 1,088 maize gene sequences, SNPs that were amenable to marker design were found on average every 623 bases; representing only 7% of the total SNPs discovered. We also describe the development of a 768 marker multiplex assay for use on the Illumina® BeadArray™ platform. SNP markers were mapped on the IBM2 intermated B73 × Mo17 high resolution genetic map using either the IBM2 segregating population, or segregation in multiple parent-progeny triplets. A high degree of colinearity was found with the genetic nested association map. For each SNP presented we give information on map location, polymorphism rates in different heterotic groups and performance on the Illumina® platform.

Single-reaction for SNP Genotyping on Agarose Gel by Allele-specific PCR in Black Poplar (Populus nigra L.)

The wide development of single nucleotide polymorphism (SNP) markers also in non-model species increases the need for inexpensive methods that do not require sophisticated equipment and time for optimization. This work presents a new method for polymerase chain reaction (PCR) amplification of multiple specific alleles (PAMSA), which allows efficient discrimination of SNP polymorphisms in one reaction tube with standard PCR conditions. This improved PAMSA requires only three unlabeled primers: a common reverse primer and two allele-specific primers having a tail of different length to differentiate the two SNP alleles by the size of amplification products on agarose gel. A destabilizing mismatch within the five bases of the 3′ end is also added to improve the allele specificity. To validate the accuracy of this method, 94 full-sib individuals were genotyped with three SNPs and compared to the genotypes obtained by cleaved amplified polymorphic sequence (CAPS) or derived CAPS. This method is flexible, inexpensive, and well suited for high throughput and automated genotyping.

Single Nucleotide Polymorphisms (SNPs): History, Biotechnological Outlook and Practical Applications

The recent introduction of molecular biology methods to pharmacology, to assess how DNA sequence variations can influence the response of an individual to a drug, has opened new dimensions in the evidence based analysis of goals, risks and benefits of drug therapy. The development of diagnostic test systems to identify patients at increased risk of adverse drug reactions, the application of genomic technologies to drug development, and the clarification of the mechanisms of drug action on cells represent actual challenges for both clinicians and researchers. In this review, we emphasize on the investigative tools of molecular biology-based pharmacology with particular reference to the development of single nucleotide polymorphisms (SNPs) and new developing trends of this technology. Keywords: restriction fragment length polymorphisms, single nucleotide polymorphisms, polymerase chain reaction, genotyping, dna microarray, pharmacogenomics, pharmacogenetics

Single nucleotide polymorphism discovery and linkage mapping of lipoxygenase-2 gene (Lx2) in soybean

Lipoxygenase-2 (Lx 2) in soybean seed is mainly responsible for generation of grassy-beany and bitter flavors. Genetic elimination of this flavor can be accelerated by the development of single nucleotide polymorphism (SNP) markers linked to Lx 2. A frame map based on simple sequence repeat (SSR) markers was constructed first using a recombinant inbred line (RIL) population of Pureunkong × Jinpumkong 2. Sixty-five SSR markers were incorporated into 13 linkage groups (LGs) spanning a total of 737 cM. Among five primer pairs designed from the Lx 2 gene sequence, one produced an amplicon with sequence variations between Pureunkong and Jinpumkong 2. Three SNPs, T/C, G/A and C/A, were identified at 251,367 and 420 bp, respectively, in the intron region of the 804 bp amplified product. Using single base chain extension based on the capture probe sequence in the 5' region of the T/C SNP, the 90 RILs were genotyped for each allele of Lx 2. The allelic segregation for the SNP linked toLx 2 was in accordance with the expected ratio of 1:1 in the RIL population. Based on the results of linkage analysis between Lx 2 and the SSR markers, Lx 2 was found to be positioned on one end of LG F in the frame map, flanked by the SSR markers Satt522 and Sat074. This study demonstrates that SNP markers closely linked to Lx 2can be developed to facilitate marker-assisted selection and fine mapping of the region around this locus.

Generalized T2 Test for Genome Association Studies

Recent progress in the development of single-nucleotide polymorphism (SNP) maps within genes and across the genome provides a valuable tool for fine-mapping and has led to the suggestion of genomewide association studies to search for susceptibility loci for complex traits. Test statistics for genome association studies that consider a single marker at a time, ignoring the linkage disequilibrium between markers, are inefficient. In this study, we present a generalized T2 statistic for association studies of complex traits, which can utilize multiple SNP markers simultaneously and considers the effects of multiple disease-susceptibility loci. This generalized T2 statistic is a corollary to that originally developed for multivariate analysis and has a close relationship to discriminant analysis and common measure of genetic distance. We evaluate the power of the generalized T2 statistic and show that power to be greater than or equal to those of the traditional chi2 test of association and a similar haplotype-test statistic. Finally, examples are given to evaluate the performance of the proposed T2 statistic for association studies using simulated and real data.

Molecular Ecology Notes: announcement of sister journal to Molecular Ecology

The Editorial Board of Molecular Ecology has decided to inaugurate a sister journal to be entitled, Molecular Ecology Notes. This new journal is being launched to accommodate the rapid expansion in the numbers of primer, computer, and technical notes submitted to our editorial office, as well as to ensure more rapid dissemination of this time-sensitive material. To accomplish this latter goal, we are planning immediate on-line publication (web address to be announced) of notes accepted in the journal, followed by quarterly distribution of a print version. In addition, primer/locus information reported in Primer Notes will be included in a user-friendly database linked to the Molecular Ecology Notes web site. Please note that subscribers to Molecular Ecology will receive Molecular Ecology Notes free of charge. No additional subscriptions or paperwork are required. This policy will ensure that the dissemination of articles published in Molecular Ecology Notes equals that of the mother journal. We feel that the journal and database will offer several advantages to the molecular ecology community. Foremost among these is speed. Our target is on-line publication in less than one month from manuscript receipt — the current lead-time for accepted papers in Molecular Ecology is closer to four months. Although we have instituted procedures to accelerate publication in Molecular Ecology, early publication of Notes on the web will ensure that primers, computer programs, and technical information are disseminated to the community with minimal delay. Secondly, primer information has become increasingly dispersed across multiple papers, journals, and disciplines, and we expect this problem to worsen with the development of single nucleotide polymorphisms (SNPs) for ecologically important genes. The database associated with the journal should minimize scatter and provide a single source for primer sequences, amplification conditions, polymorphism levels, cross-species amplification, and literature citations. Finally, the launch of Molecular Ecology Notes will allow the mother journal to focus on the ecology, evolution, behaviour, and conservation of organisms rather than on distracting (albeit important) technical details. As a consequence, Molecular Ecology will no longer publish primer, computer, and technical notes following the December, 2000 issue. All primer, computer, and technical notes will thereafter appear in both on-line and print versions of Molecular Ecology Notes.

The Homozygous Complete Hydatidiform Mole: A Unique Resource for Genome Studies

The most frequent type of complete hydatidiform mole is a 46, XX homozygote formed by the fertilization of an empty ovum by a single haploid sperm that later duplicates its chromosomes to give a diploid tumor. The homozygous nature of these complete hydatidiform moles makes them unique resources for human genome studies. They can serve as homozygous controls in the development of single nucleotide polymorphism (SNP) markers and provide a way to obtain long-range haplotypes that are useful in population studies. The use of a homozygous control makes it possible to estimate the allele frequencies of the SNP markers in any population by sequencing pooled DNA samples. In this report, we present evidence of homozygosity of a complete hydatidiform mole using 20 diallelic markers distributed across the genome. Furthermore, its usefulness as a homozygous control in SNP development and as a resource for long-range haplotype determination is demonstrated using 11 newly discovered loci in the BRCA2 region on chromosome 13q12–q13.