Methods for genotyping single nucleotide polymorphisms

Jumping on the Train of Personalized Medicine: A Primer for Non-Geneticist Clinicians: Part 2. Fundamental Concepts in Genetic Epidemiology

With the decrease in sequencing costs, personalized genome sequencing will eventually become common in medical practice. We therefore write this series of three reviews to help non-geneticist clinicians to jump into the fast-moving field of personalized medicine. In the first article of this series, we reviewed the fundamental concepts in molecular genetics. In this second article, we cover the key concepts and methods in genetic epidemiology including the classification of genetic disorders, study designs and their implementation, genetic marker selection, genotyping and sequencing technologies, gene identification strategies, data analyses and data interpretation. This review will help the reader critically appraise a genetic association study. In the next article, we will discuss the clinical applications of genetic epidemiology in the personalized medicine area.

Genetic diversity of Bacillus anthracis in Europe: genotyping methods in forensic and epidemiologic investigations

Bacillus anthracis, the etiological agent of anthrax, a zoonosis relatively common throughout the world, can be used as an agent of bioterrorism. In naturally occurring outbreaks and in criminal release of this pathogen, a fast and accurate diagnosis is crucial to an effective response. Microbiological forensics and epidemiologic investigations increasingly rely on molecular markers, such as polymorphisms in DNA sequence, to obtain reliable information regarding the identification or source of a suspicious strain. Over the past decade, significant research efforts have been undertaken to develop genotyping methods with increased power to differentiate B. anthracis strains. A growing number of DNA signatures have been identified and used to survey B. anthracis diversity in nature, leading to rapid advances in our understanding of the global population of this pathogen. This article provides an overview of the different phylogenetic subgroups distributed across the world, with a particular focus on Europe. Updated information on the anthrax situation in Europe is reported. A brief description of some of the work in progress in the work package 5.1 of the AniBioThreat project is also presented, including (1) the development of a robust typing tool based on a suspension array technology and multiplexed single nucleotide polymorphisms scoring and (2) the typing of a collection of DNA from European isolates exchanged between the partners of the project. The know-how acquired will contribute to improving the EU's ability to react rapidly when the identity and real origin of a strain need to be established.

Exquisite allele discrimination by toehold hairpin primers

The ability to detect and monitor single nucleotide polymorphisms (SNPs) in biological samples is an enabling research and clinical tool. We have developed a surprising, inexpensive primer design method that provides exquisite discrimination between SNPs. The field of DNA computation is largely reliant on using so-called toeholds to initiate strand displacement reactions, leading to the execution of kinetically trapped circuits. We have now similarly found that the short toehold sequence to a target of interest can initiate both strand displacement within the hairpin and extension of the primer by a polymerase, both of which will further stabilize the primer:template complex. However, if the short toehold does not bind, neither of these events can readily occur and thus amplification should not occur. Toehold hairpin primers were used to detect drug resistance alleles in two genes, rpoB and katG, in the Mycobacterium tuberculosis genome, and ten alleles in the Escherichia coli genome. During real-time PCR, the primers discriminate between mismatched templates with Cq delays that are frequently so large that the presence or absence of mismatches is essentially a ‘yes/no’ answer.

A real-time characterization method to rapidly optimize molecular beacon signal for sensitive nucleic acids analysis

This research demonstrates an integrated microfluidic titration assay to characterize the cation concentrations in working buffer to rapidly optimize the signal-to-noise ratio (SNR) of molecular beacons (MBs). The "Microfluidic Droplet Array Titration Assay" (MiDATA) integrated the functions of sample dilution, sample loading, sample mixing, fluorescence analysis, and re-confirmation functions all together in a one-step process. It allows experimentalists to arbitrarily change sample concentration and acquire SNR measurements instantaneously. MiDATA greatly reduces sample dilution time, number of samples needed, sample consumption, and the total titration time. The maximum SNR of molecular beacons is achieved by optimizing the concentrations of the monovalent and divalent cation (i.e., Mg(2+) and K(+)) of the working buffer. MiDATA platform is able to reduce the total consumed reagents to less than 50 μL, and decrease the assay time to less than 30 min. The SNR of the designated MB is increased from 20 to 126 (i.e., enhanced the signal 630 %) using the optimal concentration of MgCl2 and KCl determined by MiDATA. This novel microfluidics-based titration method is not only useful for SNR optimization of molecular beacons but it also can be a general method for a wide range of fluorescence resonance energy transfer (FRET)-based molecular probes.

A multiplex single nucleotide polymorphism genotyping method using ligase-based mismatch discrimination and CE-SSCP

Accuracy, simplicity, and cost-effectiveness are the most important criteria for a genotyping method for SNPs compatible with clinical use. One method developed for SNP genotyping, ligase-based discrimination, is considered the simplest for clinical diagnosis. However, multiplex assays using this method are limited by the detection method. Although CE has been introduced as an alternative to error prone microarray-based detection, the design process and multiplex assay procedure are complicated because of the DNA size-dependent separation principle. In this study, we developed a simple and accurate multiplex genotyping method using reaction condition-optimized ligation and high-resolution CE-based SSCP. With this high-resolution CE-SSCP system, we are able to use similar-sized probes, thereby eliminating the complex probe design step and simplifying the optimization process. We found that this method could accurately discriminate single-base mismatches in SNPs of the tp53 gene, used as targets for multiplex detection.

Metal-organic framework MIL-101 as a low background signal platform for label-free DNA detection

A label-free and sensitive fluorescence method for recognition of sequence-specific DNA using DNA-intercalating dye and metal-organic frameworks (MOFs) is developed. Here, MIL-101 (Cr3F(H2O)2O[(O2C)-C6H4-(CO2)]3·nH2O) is introduced as a quenching platform to decrease the high background fluorescence of SYBR Green I (SG)/probe DNA complex. Mechanism investigations show that MIL-101 can strongly adsorb the SG/probe DNA complex through π-π stacking and electrostatic interactions, and as a consequence, the fluorescence of the SG dye is greatly quenched. While in the presence of target DNA, the as-formed rigid double-stranded (ds) structure of DNA will be far away from the surface of MIL-101; meanwhile, the SG dye can be bound with the dsDNA in the mode of intercalation and minor groove binding, resulting in enhancement of the SG dye fluorescence. The increased signal-to-background ratio has a linear relationship with the concentration of target DNA in the range of 0.1-14 nM. It is confirmed that the detection limit is 73 pM (3σ), which is much lower than that based on the carbon nanotubes and graphene oxide platform. Moreover, one-base-mismatched target DNA can be discriminated effectively. With the introduction of MIL-101, the signal-to-background ratio has been improved ∼8-fold, demonstrating that MIL-101 is an efficient low-background signal platform.

Results of a study of genetic factors predisposing to the development of psoriasis among the population of the Russian Federation

Goal. To assess the incidence of genes predisposing to the development of psoriasis based on selected molecular and genetic study methods among the Russian population. Materials and methods. By using allele specific hybridization methods in the form of real-time PCR and RFLP assay (Restriction Fragment Length Polymorphism), single-nucleotide polymorphisms of fragments of 13 genes associated with predisposition to the development of psoriasis were studied in whole blood samples obtained from 45 psoriatic patients: rs4649203 (gene IL-28RA), rs11209026 (gene IL-23R), rs610604 (gene TNFAIP3), rs514315 (gene SERPINB8), rs9304742 (gene ZNF816A), rs17728338 (gene TNIP1), rs13190932 (gene TRAF3IP2), rs2235617 (gene ZNF313), rs27524 (gene ERAP1), rs702873 (gene REL), rs3213094 (gene IL-12B), rs12720356 (gene TYK2), and rs8016947 (gene NFKBI). Results. A set of data on the genotype structure and incidence in respective loci of 13 genes associated with predisposition to develop psoriasis was obtained for the first time based on a Russian sample of patients. At this stage of the study, we failed to reveal any reliable differences concerning the incidence of individual genotypes between psoriatic patients and healthy people because of the small size of the sample. Gene TYK2 (rs1272035) served as an exclusion. The homozygous T/T genotype was revealed more often (p < 0.01) in psoriatic patients (95.6%) vs. healthy people (77.8%), which makes it possible to consider the carriers of this genotype as people predisposed to the development of psoriasis.

Fluorescent silver nanoclusters as DNA probes

Fluorescent silver nanoclusters (few atoms, quantum sized) have attracted much attention as promising substitutes for conventional fluorophores. Due to their unique environmental sensitivities, new fluorescent probes have been developed based on silver nanoclusters for the sensitive and specific detection of DNA. In this review we present the recent discoveries of activatable and color-switchable properties of DNA-templated silver nanoclusters and discuss the strategies to use these new properties in DNA sensing.

Detection of single-nucleotide variations by monitoring the blinking of fluorescence induced by charge transfer in DNA

Charge transfer dynamics in DNA: Photo-induced charge separation and charge-recombination dynamics in DNA was assessed by monitoring the blinking of fluorescence. Single nucleotide variations, mismatch and one base deletion, were differentiated based on the length of the off-time of the blinking, which corresponds to the lifetime of the charge-separated state.

Reactions of buffers in cyanogen bromide-induced ligations

Rapid, template-directed ligation reactions between a phosphate-terminated oligonucleotide and an unphosphorylated reaction partner may be induced by cyanogen bromide (BrCN). Frequently, however, the reaction is low yielding, and even a large excess of the condensing agent can fail to induce quantitative conversions. In this study, we used BrCN to induce chemical primer extension reactions. Here, we report that buffers containing hydroxyl groups react with short oligodeoxynucleotides in the presence of BrCN. One stable adduct between HEPBS buffer and cytosine was characterized by mass spectrometry and NMR after HPLC purification, indicating that a side reaction occurred at this nucleobase. Further, a first example of a primer extension reaction between an unmodified oligodeoxynucleotide as primer and dGMP is reported. Together, our results shed light on the potency, as well as the drawbacks of BrCN as a highly reactive condensing reagent for the ligation of unmodified nucleic acids.

A MEMS-Based Approach to Single Nucleotide Polymorphism Genotyping

Genotyping of single nucleotide polymorphisms (SNPs) allows diagnosis of human genetic disorders associated with single base mutations. Conventional SNP genotyping methods are capable of providing either accurate or high-throughput detection, but are still labor-, time-, and resource-intensive. Microfluidics has been applied to SNP detection to provide fast, low-cost, and automated alternatives, although these applications are still limited by either accuracy or throughput issues. To address this challenge, we present a MEMS-based SNP genotyping approach that uses solid-phase-based reactions in a single microchamber on a temperature control chip. Polymerase chain reaction (PCR), allele specific single base extension (SBE), and desalting on microbeads are performed in the microchamber, which is coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze the SBE product. Experimental results from genotyping of the SNP on exon 1 of the HBB gene, which causes sickle cell anemia, demonstrate the potential of the device for rapid, accurate, multiplexed and high-throughput detection of SNPs.

Single quantum dot analysis enables multiplexed point mutation detection by gap ligase chain reaction

Gene point mutations present important biomarkers for genetic diseases. However, existing point mutation detection methods suffer from low sensitivity, specificity, and a tedious assay processes. In this report, an assay technology is proposed which combines the outstanding specificity of gap ligase chain reaction (Gap-LCR), the high sensitivity of single-molecule coincidence detection, and the superior optical properties of quantum dots (QDs) for multiplexed detection of point mutations in genomic DNA. Mutant-specific ligation products are generated by Gap-LCR and subsequently captured by QDs to form DNA-QD nanocomplexes that are detected by single-molecule spectroscopy (SMS) through multi-color fluorescence burst coincidence analysis, allowing for multiplexed mutation detection in a separation-free format. The proposed assay is capable of detecting zeptomoles of KRAS codon 12 mutation variants with near 100% specificity. Its high sensitivity allows direct detection of KRAS mutation in crude genomic DNA without PCR pre-amplification.

Assignment of SNP allelic configuration in polyploids using competitive allele-specific PCR: application to citrus triploid progeny

BACKGROUND

Polyploidy is a major component of eukaryote evolution. Estimation of allele copy numbers for molecular markers has long been considered a challenge for polyploid species, while this process is essential for most genetic research. With the increasing availability and whole-genome coverage of single nucleotide polymorphism (SNP) markers, it is essential to implement a versatile SNP genotyping method to assign allelic configuration efficiently in polyploids.

SCOPE

This work evaluates the usefulness of the KASPar method, based on competitive allele-specific PCR, for the assignment of SNP allelic configuration. Citrus was chosen as a model because of its economic importance, the ongoing worldwide polyploidy manipulation projects for cultivar and rootstock breeding, and the increasing availability of SNP markers.

CONCLUSIONS

Fifteen SNP markers were successfully designed that produced clear allele signals that were in agreement with previous genotyping results at the diploid level. The analysis of DNA mixes between two haploid lines (Clementine and pummelo) at 13 different ratios revealed a very high correlation (average = 0·9796; s.d. = 0·0094) between the allele ratio and two parameters [θ angle = tan(-1) (y/x) and y' = y/(x + y)] derived from the two normalized allele signals (x and y) provided by KASPar. Separated cluster analysis and analysis of variance (ANOVA) from mixed DNA simulating triploid and tetraploid hybrids provided 99·71 % correct allelic configuration. Moreover, triploid populations arising from 2n gametes and interploid crosses were easily genotyped and provided useful genetic information. This work demonstrates that the KASPar SNP genotyping technique is an efficient way to assign heterozygous allelic configurations within polyploid populations. This method is accurate, simple and cost-effective. Moreover, it may be useful for quantitative studies, such as relative allele-specific expression analysis and bulk segregant analysis.

Genetic analysis with nanoPCR

Polymerase chain reaction (PCR) has become a standard and important molecular biological technique with numerous applications in genetic analysis, forensics and in vitro diagnostics. Since its invention in the 1980s, there has been dramatic performance improvement arising from long-lasting efforts to optimize amplification conditions in both academic studies and commercial applications. More recently, a range of nanometer-sized materials including metal nanoparticles, semiconductor quantum dots, carbon nanomaterials and polymer nanoparticles, have shown unique effects in tuning amplification processes of PCR. It is proposed that these artificial nanomaterials mimic protein components in the natural DNA replication machinery in vivo. These so-called nanomaterials-assisted PCR (nanoPCR) strategies shed new light on powerful PCR with unprecedented sensitivity, selectivity and extension rate. In this review, we aim to summarize recent progress in this direction and discuss possible mechanisms for such performance improvement and potential applications in genetic analysis (particularly gene typing and haplotyping) and diagnostics.

A multiplex PCR for the simultaneous detection and genotyping of the Echinococcus granulosus complex

Echinococcus granulosus is characterized by high intra-specific variability (genotypes G1–G10) and according to the new molecular phylogeny of the genus Echinococcus, the E. granulosus complex has been divided into E. granulosus sensu stricto (G1–G3), E. equinus (G4), E. ortleppi (G5), and E. canadensis (G6–G10). The molecular characterization of E. granulosus isolates is fundamental to understand the spatio-temporal epidemiology of this complex in many endemic areas with the simultaneous occurrence of different Echinococcus species and genotypes. To simplify the genotyping of the E. granulosus complex we developed a single-tube multiplex PCR (mPCR) allowing three levels of discrimination: (i) Echinococcus genus, (ii) E. granulosus complex in common, and (iii) the specific genotype within the E. granulosus complex. The methodology was established with known DNA samples of the different strains/genotypes, confirmed on 42 already genotyped samples (Spain: 22 and Bulgaria: 20) and then successfully applied on 153 unknown samples (Tunisia: 114, Algeria: 26 and Argentina: 13). The sensitivity threshold of the mPCR was found to be 5 ng Echinoccoccus DNA in a mixture of up to 1 µg of foreign DNA and the specificity was 100% when template DNA from closely related members of the genus Taenia was used. Additionally to DNA samples, the mPCR can be carried out directly on boiled hydatid fluid or on alkaline-lysed frozen or fixed protoscoleces, thus avoiding classical DNA extractions. However, when using Echinococcus eggs obtained from fecal samples of infected dogs, the sensitivity of the mPCR was low (<40%). Thus, except for copro analysis, the mPCR described here has a high potential for a worldwide application in large-scale molecular epidemiological studies on the Echinococcus genus.

The dog tapeworm Echinococcus granulosus (E. granulosus) is a cosmopolitan parasite. The adult worms reside in the small intestine of their definitive hosts (dogs). Infective eggs are shed with the feces into the environment and are orally ingested by intermediate hosts where they develop into the metacestode (larval) stage, causing cystic echinococcosis (CE) in humans and livestock. Ten intraspecific genotypes of E. granulosus (G1 to G10) have been reported from different intermediate host species. Based on the recently established molecular phylogeny, E. granulosus is now considered a complex consisting of four species: E. granulosus sensu stricto (G1/G2/G3), E. equinus (G4), E. ortleppi (G5) and E. canadensis (G6–G10). Simple and highly discriminative molecular epidemiological approaches are needed to explore dynamics, life cycle patterns, and the pathogenicity of the members of this complex. We here introduce a one-step multiplex PCR (mPCR) protocol for the genotyping and discrimination of the different members of the E. granulosus complex, allowing three levels of discrimination: (i) Echinococcus genus, (ii) E. granulosus complex, and (iii) genetic variants within the E. granulosus complex. The relatively complicated task of E. granulosus complex speciation and genotyping is clearly simplified by mPCR, and this technique therefore represents a useful tool for routine practice.

Electrochemical measurements of DNA melting on surfaces

Thermal denaturation, or melting, measurements are a classic technique for analysis of thermodynamics of nucleic base driven associations in solution, as well as of interactions between nucleic acids and small molecule ligands such as drugs or carcinogens. Performed on surface-immobilized DNA films, this well-established technique can help understand how energetics of surface hybridization relate to those in solution, as well as provide high-throughput platforms for screening of small molecule ligands. Here we describe methods for measuring DNA melting transitions at solid/liquid interfaces with focus on the role of immobilization chemistry, including a common "immobilization-through-self-assembly" approach that is effective at moderate temperatures, and a thermo-stable approach based on polymer-supported DNA monolayers that can be used at elevated temperatures. We also discuss conditions necessary for reversible measurements, as signified by superimposition of the association (cooling) and dissociation (heating) transitions of immobilized DNA strands.

Advances in understanding relationship between miRNA single nucleotide polymorphisms and colorectal cancer

The occurrence and development of colorectal cancer (CRC) are a multifactorial, multi-step evolutionary process. Gene polymorphisms are often involved in tumor development and prognosis. Recent studies have found that certain microRNA (miRNA) single nucleotide polymorphisms were associated with genetic susceptibility to and prognosis of CRC. Understanding the relationship between miRNA single nucleotide polymorphisms and CRC can provide new clues to the detection, prevention, and prognostic evaluation of CRC.

SNP identification and allelic-specific PCR markers development for TaGW2, a gene linked to wheat kernel weight

TaGW2, an orthologous gene of rice OsGW2, has been associated with kernel width and weight of bread wheat (Triticum aestivum). Difference in TaGW2 coding sequence was not found among different wheat varieties in previous researches. In this study, we found eight exons and seven introns in TaGW2 with a full-length cDNA sequence of 1,275 bp, which contains a conserved function domain and seven splice sites that shared homology with rice OsGW2. A single T-base insertion in the eighth exon of TaGW2 on chromosome 6A was detected in a large-kernel wheat variety, Lankaodali. This insertion mutation reduces the coding protein sequence from normal 424 amino acids (~47.2 kDa) to 328 amino acids (~37.1 kDa) by truncating 96 amino acids. The result was validated by identifying histidine-tagged TaGW2 proteins encoded by both alleles of the mutant and the wild types in SDS-PAGE. Allele-specific PCR markers were developed based on the single nucleotide polymorphism (SNP) site. The SNP markers were genotyped for an F(2) segregation population from the cross of Lankaodali × Chinese Spring. Seed traits of F(2:3) families were evaluated in three different environments. The association analysis indicated that F(2:3) families with the mutated TaGW2 allele significantly increased kernel width (KW) and thousand-kernel weight (TKW), and slightly improved kernel length (KL). Using the SNP markers, another two varieties harbored the mutated TaGW2 allele were successfully identified from 22 additional wheat varieties, and they both have large KW and TKW. Cloning and sequencing of the gene further confirmed the functions of the mutated allele of TaGW2 in the two large kernel varieties. The results suggested that TaGW2 may negatively regulate kernel size variation, which shares the same function as OsGW2 in rice. The successful development of SNP markers provides a useful tool for improving kernel yield in wheat.

An improved allele-specific PCR primer design method for SNP marker analysis and its application

BACKGROUND

Although Single Nucleotide Polymorphism (SNP) marker is an invaluable tool for positional cloning, association study and evolutionary analysis, low SNP detection efficiency by Allele-Specific PCR (AS-PCR) still restricts its application as molecular marker like other markers such as Simple Sequence Repeat (SSR). To overcome this problem, primers with a single nucleotide artificial mismatch introduced within the three bases closest to the 3'end (SNP site) have been used in AS-PCR. However, for one SNP site, nine possible mismatches can be generated among the three bases and how to select the right one to increase primer specificity is still a challenge.

RESULTS

In this study, different from the previous reports which used a limited quantity of primers randomly (several or dozen pairs), we systematically investigated the effects of mismatch base pairs, mismatch sites and SNP types on primer specificity with 2071 primer pairs, which were designed based on SNPs from Brassica oleracea 01-88 and 02-12. According to the statistical results, we (1) found that the primers designed with SNP (A/T), in which the mismatch (CA) in the 3rd nucleotide from the 3' end, had the highest allele-specificity (81.9%). This information could be used when designing primers from a large quantity of SNP sites; (2) performed the primer design principle which forms the one and only best primer for every SNP type. This is never reported in previous studies. Additionally, we further identified its availability in rapeseed (Brassica napus L.) and sesame (Sesamum indicum). High polymorphism percent (75%) of the designed primers indicated it is a general method and can be applied in other species.

CONCLUSION

The method provided in this study can generate primers more effectively for every SNP site compared to other AS-PCR primer design methods. The high allele-specific efficiency of the SNP primer allows the feasibility for low- to moderate- throughput SNP analyses and is much suitable for gene mapping, map-based cloning, and marker-assisted selection in crops.

A fluorescence light-up Ag nanocluster probe that discriminates single-nucleotide variants by emission color

Rapid and precise screening of small genetic variations, such as single-nucleotide polymorphisms (SNPs), among an individual's genome is still an unmet challenge at point-of-care settings. One crucial step toward this goal is the development of discrimination probes that require no enzymatic reaction and are easy to use. Here we report a new type of fluorescent molecular probe, termed a chameleon NanoCluster Beacon (cNCB), that lights up into different colors upon binding SNP targets. NanoCluster Beacons (NCBs) are collections of a small number of Ag atoms templated on single-stranded DNA that fluoresce strongly when placed in proximity to particular DNA sequences, termed enhancers. Here we show the fluorescence emission color of a NCB can change substantially (a shift of 60-70 nm in the emission maximum) depending upon the alignment between the silver nanocluster and the DNA enhancer sequence. Chameleon NCBs exploit this color shift to directly detect SNPs, based on the fact that different SNPs produce a different alignment between the Ag nanocluster and the enhancer. This SNP detection method has been validated on all single-nucleotide substitution scenarios in three synthetic DNA targets, in six disease-related SNP targets, and in two clinical samples taken from patients with ovarian serous borderline tumors. Samples with single-nucleotide variations can be easily identified by the naked eye under UV excitation, making this method a reliable and low-cost assay with a simple readout format.

Reliable and rapid characterization of functional FCN2 gene variants reveals diverse geographical patterns

BACKGROUND

Ficolin-2 coded by FCN2 gene is a soluble serum protein and an innate immune recognition element of the complement system. FCN2 gene polymorphisms reveal distinct geographical patterns and are documented to alter serum ficolin levels and modulate disease susceptibility.

METHODS

We employed a real-time PCR based on Fluorescence Resonance Energy Transfer (FRET) method to genotype four functional SNPs including -986 G > A (#rs3124952), -602 G > A (#rs3124953), -4A > G (#rs17514136) and +6424 G > T (#rs7851696) in the ficolin-2 (FCN2) gene. We characterized the FCN2 variants in individuals representing Brazilian (n = 176), Nigerian (n = 180), Vietnamese (n = 172) and European Caucasian ethnicity (n = 165).

RESULTS

We observed that the genotype distribution of three functional SNP variants (-986 G > A, -602 G > A and -4A > G) differ significantly between the populations investigated (p < 0.0001). The SNP variants were highly linked to each other and revealed significant population patterns. Also the distribution of haplotypes revealed distinct geographical patterns (p < 0.0001).

CONCLUSIONS

The observed distribution of the FCN2 functional SNP variants may likely contribute to altered serum ficolin levels and this may depend on the different disease settings in world populations. To conclude, the use of FRET based real-time PCR especially for FCN2 gene will benefit a larger scientific community who extensively depend on rapid, reliable method for FCN2 genotyping.

A room-temperature adenosine-based molecular beacon for highly sensitive detection of nucleic acids

This study developed a simple, sensitive, and selective molecular beacon for detecting nucleic acids at room temperature based on coralyne induced conformational change of a MB through A(2)-coralyne-A(2) coordination.

High-resolution melting analysis for SNP genotyping and mapping in tetraploid alfalfa (Medicago sativa L.)

Single nucleotide polymorphisms (SNPs) represent the most abundant type of genetic polymorphism in plant genomes. SNP markers are valuable tools for genetic analysis of complex traits of agronomic importance, linkage and association mapping, genome-wide selection, map-based cloning, and marker-assisted selection. Current challenges for SNP genotyping in polyploid outcrossing species include multiple alleles per loci and lack of high-throughput methods suitable for variant detection. In this study, we report on a high-resolution melting (HRM) analysis system for SNP genotyping and mapping in outcrossing tetraploid genotypes. The sensitivity and utility of this technology is demonstrated by identification of the parental genotypes and segregating progeny in six alfalfa populations based on unique melting curve profiles due to differences in allelic composition at one or multiple loci. HRM using a 384-well format is a fast, consistent, and efficient approach for SNP discovery and genotyping, useful in polyploid species with uncharacterized genomes. Possible applications of this method include variation discovery, analysis of candidate genes, genotyping for comparative and association mapping, and integration of genome-wide selection in breeding programs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9566-x) contains supplementary material, which is available to authorized users.

Gold nanoparticles for high-throughput genotyping of long-range haplotypes

Completion of the Human Genome Project and the HapMap Project has led to increasing demands for mapping complex traits in humans to understand the aetiology of diseases. Identifying variations in the DNA sequence, which affect how we develop disease and respond to pathogens and drugs, is important for this purpose, but it is difficult to identify these variations in large sample sets. Here we show that through a combination of capillary sequencing and polymerase chain reaction assisted by gold nanoparticles, it is possible to identify several DNA variations that are associated with age-related macular degeneration and psoriasis on significant regions of human genomic DNA. Our method is accurate and promising for large-scale and high-throughput genetic analysis of susceptibility towards disease and drug resistance.

Use of high-resolution melting and melting temperature-shift assays for specific detection and identification of Bacillus anthracis based on single nucleotide discrimination

Single nucleotide polymorphisms (SNPs) are important diagnostic markers for the detection and differentiation of Bacillus anthracis. High-Resolution Melting (HRM) and Melting Temperature (Tm)-shift methods are two approaches that enable SNP detection without the need for expensive labeled probes. We evaluated the potential diagnostic capability of those methods to discriminate B. anthracis from the other members of the B. cereus group. Two assays targeting B. anthracis-specific SNPs in the plcR and gyrA genes were designed for each method and used to genotype a panel of 155 Bacilli strains. All B. anthracis isolates (n=65) were correctly and unambiguously identified. Assays also proved to be appropriate for the direct genotyping of biological samples. They could reliably detect B. anthracis in contaminated organs containing as little as 10(3)CFU/ml, corresponding to a few genome equivalents per reaction. The HRM and Tm-shift applications described here represent valuable tools for specific identification of B. anthracis at reduced cost.

Detection of mutations by flow cytometric melting point analysis of PCR products

Exploring the possibilities offered by flow cytometric microbead analyses for the detection of genetic alterations, an assay based on the dependence of the melting point of double-stranded DNA molecules on their length has been developed, making use of PCR products carrying biotin and fluorescent moiety on their two ends. The samples of different length PCR products immobilized on streptavidine coated microbeads are heat-treated in the presence of formamide at temperatures between the melting point of the longer and that of the shorter PCR product, when the mean fluorescence intensity of the beads carrying the shorter molecules decreases as a result of denaturation, as opposed to the sample containing the longer product. The efficacy and sensitivity of the method is demonstrated in the case of the assessment of the degree of triplet expansion in Huntington's disease. Its utility for the detection of point mutations in heterozygous clinical samples is shown in the case of the BRCA1 gene. The assay is simple and may be offered for the purposes of clinical diagnostics of a number of genetic conditions. These include screening of samples for triplet expansions and SNPs predisposing for particular pathological or pharmacogenomic conditions. In general, the method described herein is offered for the diagnosis of any pathological condition where the length of a genomic or cDNA sequence is expected to be different from that of the normal allele.

Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis

BACKGROUND

Single nucleotide polymorphisms (SNPs) are the most common type of sequence variation among plants and are often functionally important. We describe the use of 454 technology and high resolution melting analysis (HRM) for high throughput SNP discovery in tetraploid alfalfa (Medicago sativa L.), a species with high economic value but limited genomic resources.

RESULTS

The alfalfa genotypes selected from M. sativa subsp. sativa var. 'Chilean' and M. sativa subsp. falcata var. 'Wisfal', which differ in water stress sensitivity, were used to prepare cDNA from tissue of clonally-propagated plants grown under either well-watered or water-stressed conditions, and then pooled for 454 sequencing. Based on 125.2 Mb of raw sequence, a total of 54,216 unique sequences were obtained including 24,144 tentative consensus (TCs) sequences and 30,072 singletons, ranging from 100 bp to 6,662 bp in length, with an average length of 541 bp. We identified 40,661 candidate SNPs distributed throughout the genome. A sample of candidate SNPs were evaluated and validated using high resolution melting (HRM) analysis. A total of 3,491 TCs harboring 20,270 candidate SNPs were located on the M. truncatula (MT 3.5.1) chromosomes. Gene Ontology assignments indicate that sequences obtained cover a broad range of GO categories.

CONCLUSIONS

We describe an efficient method to identify thousands of SNPs distributed throughout the alfalfa genome covering a broad range of GO categories. Validated SNPs represent valuable molecular marker resources that can be used to enhance marker density in linkage maps, identify potential factors involved in heterosis and genetic variation, and as tools for association mapping and genomic selection in alfalfa.

Electrochemical detection of DNA mutations on a PNA-modified electrode utilizing a single-stranded DNA specific endonuclease

Utilizing a peptide nucleic acid (PNA)-modified electrode and a single-stranded DNA specific endonuclease, a novel electrochemical method to identify DNA mutations has been developed and represents a totally new strategy for the electrochemical diagnosis of human genetic mutations.

Rapid assessment of the stability of DNA duplexes by impedimetric real-time monitoring of chemically induced denaturation

In this article, we report on the electronic monitoring of DNA denaturation by NaOH using electrochemical impedance spectroscopy in combination with fluorescence imaging as a reference technique. The probe DNA consisting of a 36-mer fragment was covalently immobilized on nanocrystalline-diamond electrodes and hybridized with different types of 29-mer target DNA (complementary, single-nucleotide defects at two different positions, and a non-complementary random sequence). The mathematical separation of the impedimetric signals into the time constant for NaOH exposure and the intrinsic denaturation-time constants gives clear evidence that the denaturation times reflect the intrinsic stability of the DNA duplexes. The intrinsic time constants correlate with calculated DNA-melting temperatures. The impedimetric method requires minimal instrumentation, is label-free and fast with a typical time scale of minutes and is highly reproducible. The sensor electrodes can be used repetitively. These elements suggest that the monitoring of chemically induced denaturation at room temperature is an interesting approach to measure DNA duplex stability as an alternative to thermal denaturation at elevated temperatures, used in DNA-melting experiments and single nucleotide polymorphism (SNP) analysis.

Genotyping by alkaline dehybridization using graphically encoded particles

This work describes a nonenzymatic, isothermal genotyping method based on the kinetic differences exhibited in the dehybridization of perfectly matched (PM) and single-base mismatched (MM) DNA duplexes in an alkaline solution. Multifunctional encoded hydrogel particles incorporating allele-specific oligonucleotide (ASO) probes in two distinct regions were fabricated by using microfluidic-based stop-flow lithography. Each particle contained two distinct ASO probe sequences differing at a single base position, and thus each particle was capable of simultaneously probing two distinct target alleles. Fluorescently labeled target alleles were annealed to both probe regions of a particle, and the rate of duplex dehybridization was monitored by using fluorescence microscopy. Duplex dehybridization was achieved through an alkaline stimulus using either a pH step function or a temporal pH gradient. When a single target probe sequence was used, the rate of mismatch duplex dehybridization could be discriminated from the rate of perfect match duplex dehybridization. In a more demanding application in which two distinct probe sequences were used, we found that the rate profiles provided a means to discriminate probe dehybridizations from both of the two mismatched duplexes as well as to distinguish at high certainty the dehybridization of the two perfectly matched duplexes. These results demonstrate an ability of alkaline dehybridization to correctly discriminate the rank hierarchy of thermodynamic stability among four sets of perfect match and single-base mismatch duplexes. We further demonstrate that these rate profiles are strongly temperature dependent and illustrate how the sensitivity can be compensated beneficially by the use of an actuating gradient pH field.