MALDI-TOF mass spectrometric detection of multiplex single base extended primers. A study of 17 y-chromosome single-nucleotide polymorphisms

Separation-free single-base extension assay with fluorescence resonance energy transfer for rapid and convenient determination of DNA methylation status at specific cytosine and guanine dinucleotide sites

A separation-free single-base extension (SBE) assay utilizing fluorescence resonance energy transfer (FRET) was developed for rapid and convenient interrogation of DNA methylation status at specific cytosine and guanine dinucleotide sites. In this assay, the SBE was performed in a tube using an allele-specific oligonucleotide primer (i.e., extension primer) labeled with Cy3 as a FRET donor fluorophore at the 5'-end, a nucleotide terminator (dideoxynucleotide triphosphate) labeled with Cy5 as a FRET acceptor, a PCR amplicon derived from bisulfite-converted genomic DNA, and a DNA polymerase. A single base-extended primer (i.e., SBE product) that was 5'-Cy3- and 3'-Cy5-tagged was formed by incorporation of the Cy5-labeled terminator into the 3'-end of the extension primer, but only if the terminator added was complementary to the target nucleotide. The resulting SBE product brought the Cy3 donor and the Cy5 acceptor into close proximity. Illumination of the Cy3 donor resulted in successful FRET and excitation of the Cy5 acceptor, generating fluorescence emission from the acceptor. The capacity of the developed assay to discriminate as low as 10% methylation from a mixture of methylated and unmethylated DNA was demonstrated at multiple cytosine and guanine dinucleotide sites.

Mass spectrometric detection of trace anions: The evolution of paired-ion electrospray ionization (PIESI)

The negative-ion mode of electrospray ionization mass spectrometry (ESI-MS) is intrinsically less sensitive than the positive-ion mode. The detection and quantitation of anions can be performed in positive-ion mode by forming specific ion-pairs during the electrospray process. The paired-ion electrospray ionization (PIESI) method uses specially synthesized multifunctional cations to form positively charged adducts with the anions to be analyzed. The adducts are detected in the positive-ion mode and at higher m/z ratios to produce excellent signal-to-noise ratios and limits of detection that often are orders of magnitude better than those obtained with native anions in the negative-ion mode. This review briefly summarizes the different analytical approaches to detect and separate anions. It focuses on the recently introduced PIESI method to present the most effective dicationic, tricationic, and tetracationic reagents for the detection of singly and multiply charged anions and some zwitterions. The mechanism by which specific structural molecular architectures can have profound effects on signal intensities is also addressed.

A polymer lab-on-a-chip for genetic analysis using the arrayed primer extension on microarray chips

In this work a polymer lab-on-a-chip (LOC), fabricated through MEMS technology, was employed to execute a genetic protocol for the Single Nucleotide Polymorphisms (SNPs) detection. The LOC was made in Poly (methyl methacrylate) (PMMA) and has two levels: the lower one for the insertion and mixing of the reagents, the upper one for the interfacing with the DNA microarray chip. The hereditary hearing loss was chosen as case of study, since the demand for testing such a particular disorder is high and genetics behind the condition is quite clear. The Arrayed Primer EXtension (APEX) genetic protocol was implemented on the LOC to analyze the SNPs. A low density (for detection of up to 10 mutations) and a high density microarray chips (for detection of 245 mutations in 12 genes), containing the primers for the extension, were employed to carry out the APEX reaction on the LOC. Both the microarray chips provide a signal to noise ratio and efficiency comparable with a detection obtained in a conventional protocol in standard conditions. Moreover, significant reduction of the employed PCR volume (from 30 μL to 10 μL) was obtained using the low density chip.

Coupling an universal primer to SBE combined spectral codification strategy for single nucleotide polymorphism analysis

We previously reported a strategy that combines Förster resonance energy transfer (FRET) based spectral codification with a single base extension (SBE) reaction for single nucleotide sequence discrimination in solution. This strategy is capable of unequivocally detect the allele variants present in solution. To extend the use of this tool to any locus of interest, it would be required the development of an universal approach capable of combining a sequence specific SBE primer to an universal sequence labeled and optimized for spectral codification. Here, we extend this concept to a general strategy by means of a labeled universal oligonucleotide primer (donor), a sequence specific primer that allows for incorporation of the complementary acceptor labeled ddNTP, which allows discrimination the allele variant in the sample via the unambiguous FRET signature of the donor/acceptor pair.

A novel amplification strategy for genotyping with liquid chromatography-electrospray ionization mass spectrometry

Among numerous available genotyping techniques, mass spectrometry (MS) based methods play a major role in providing high quality genotype data at reasonable costs for research and diagnostics, e.g. for pharmacogenetic applications. Ion-pair reversed-phase liquid chromatography hyphenated to electrospray ionization time-of-flight MS (ICEMS) is, for example, a powerful instrument that allows a direct characterization of complex mixtures of polymerase chain reaction (PCR) amplified DNA fragments. Current limitations of PCR-ICEMS genotyping are mainly concerned with the multiplex PCR set-up. Assay development often requires time-consuming primer design and intensive optimization of PCR conditions. To overcome this restraint, a robust amplification strategy originally combined with arrayed primer extension genotyping was transferred and adapted to ICEMS genotyping. The modifications involved limitation of the primer length, application of two universal sequences and amplification with an appropriate DNA polymerase. To demonstrate the applicability of the novel amplification strategy for ICEMS, a 23-plex pharmacogenetic genotyping assay was developed. After slight optimization steps, an efficient and quantitatively balanced amplification of all targeted markers was achieved, resulting in a convenient characterization of the multiplexed PCR fragments with ICEMS. Expenditure of time, costs and hands-on work associated with assay design and optimization was dramatically lowered compared to previous multiplex PCR-ICEMS assays. The developed 23-plex assay was applied in a pharmacogenetic study including 284 individuals (genotype call rate 99.0%). A total of 399 SNPs were retyped by Sanger sequencing (concordance rate 99.8%). The PCR-ICEMS assay turned out to be an accurate, reliable, cost-effective and a ready-to-use tool for pharmacogenetic genotyping.

Detection of nucleotides in positive-mode electrospray ionization mass spectrometry using multiply-charged cationic ion-pairing reagents

Nucleotides are a class of molecules that play an essential role in biological systems. A new method has been developed in the detection of nucleotides. These molecules can exist as monomers or constituents of oligomers and polymers. As such, they carry from one to several negative charges. In this study, different cationic ion-pairing reagents were used to complex with each of the 28 nucleotide monomers and nucleotide containing compounds. By using this method, this discrete set of anions was able to be detected in the positive-mode electrospray ionization mass spectrometry, as positively charged complexes. Tandem mass spectrometry experiments were also completed on the ion-pairing reagents that performed the best in the single ion monitoring (SIM) ion mode, and the sensitivity was lowered even further for most of the anions. Limits of detection for compounds such as thymidine diphosphate were improved as much as 100 times compared to the positive SIM mode, and 750 times when compared to the negative mode. A few nucleotides did not show a significant increase in sensitivity when analyzed in the positive ion mode, but in general the new method developed herein resulted in a much greater sensitivity than traditional detection in the negative mode.

Simple, efficient, and cost-effective multiplex genotyping with matrix assisted laser desorption/ionization time-of-flight mass spectrometry of hemoglobin beta gene mutations

A number of common mutations in the hemoglobin beta (HBB) gene cause beta-thalassemia, a monogenic disease with high prevalence in certain ethnic groups. As there are 30 HBB variants that cover more than 99.5% of HBB mutant alleles in the Thai population, an efficient and cost-effective screening method is required. Three panels of multiplex primer extensions, followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry were developed. The first panel simultaneously detected 21 of the most common HBB mutations, while the second panel screened nine additional mutations, plus seven of the first panel for confirmation; the third panel was used to confirm three HBB mutations, yielding a 9-Da mass difference that could not be clearly distinguished by the previous two panels. The protocol was both standardized using 40 samples of known genotypes and subsequently validated in 162 blind samples with 27 different genotypes (including a normal control), comprising heterozygous, compound heterozygous, and homozygous beta-thalassemia. Results were in complete agreement with those from the genotyping results, conducted using three different methods overall. The method developed here permitted the detection of mutations missed using a single genotyping procedure. The procedure should serve as the method of choice for HBB genotyping due to its accuracy, sensitivity, and cost-effectiveness, and can be applied to studies of other gene variants that are potential disease biomarkers.

Determination of cis/trans phase of variations in the MC1R gene with allele-specific PCR and single base extension

The MC1R gene encodes a protein with key regulatory functions in the melanin synthesis. A multiplex PCR and a multiplex single base extension protocol were established for genotyping six exonic MC1R variations highly penetrant for red hair (R), four exonic MC1R variations weakly penetrant for red hair (r), two frameshift variations highly penetrant for red hair (R) and three variations in the promoter region. We genotyped 600 individuals from Denmark using either CE or MALDI-TOF MS as the detection platform. A total of 62 individuals were genotyped R/R and among the 62 individuals, 57 had red hair and five had blond hair colour. Two different R alleles may be located in cis (RR/-) position or trans (R/R) position, and the phenotype associated with RR/- and R/R may be different. Two allele-specific PCRs were established with primers targeting the -G445A variation in the MC1R promoter and the allele-specific PCR products were used in the multiplex single base extension assay. In all 62 individuals, the MC1R variants were situated in trans position. Another 18 individuals with red hair colour were either genotyped R/- or R/r, suggesting that other genes influence hair colour.

Screening serum biomarkers of fatty liver disease using proteomic technology

AIM: To analyze the serum proteomic pattern of the fatty liver disease (FLD) patients, to build a diagnostic model and to evaluate its clinic significance using magnetic bead and MALDI-TOF-MS.

METHODS: WCX magnetic bead and MALDI-TOF-MS were used to detect the serum proteomic patterns of 95 modest FLD patients, 76 mild FLD patients and 99 healthy persons (HP). Biomarker Wizard software was used to analyze protein peaks for significant difference. The model was then built by Biomarker Patterns Software and was further evaluated in blind test for reliability.

RESULTS: A diagnostic pattern for modest FLD from HP using m/z 7626.2, 24147.7, 6118.2 was established with 90.2% sensitivity and 93.9% specificity. A sensitivity of 90.9% and a specificity of 92.0% in blind test were obtained. One diagnostic pattern using m/z 7626.2, 3286.0, 2760.7, 2543.1, 2746.1 was established to differentiate mild from modest FLD; the other diagnostic pattern using m/z 7626.2, 11721.0, 24141.7, 8529.1, 9042.7 was established to differentiate mild FLD from HP.

CONCLUSION: Proteomic technology can significantly identify novel significant biomarkers in the serum. The diagnostic pattern consisting of three differential protein peaks can discriminate the modest FLD from HP. The diagnostic pattern consisting of five specific differential protein peaks can differentiate mild from modest FLD as well as mild FLD from HP.

Microbead device for isolating biotinylated oligonucleotides for use in mass spectrometric analysis

We describe a prototypical device for isolating biotinylated oligonucleotides for use in mass spectrometric analysis. It consists of monomeric avidin-coated microbeads trapped in a pipette tip and has been used for genotyping single nucleotide polymorphisms (SNPs) with the previously developed solid phase capture-single base extension (SPC-SBE) method. The device reduces processing time for genotyping by SPC-SBE and allows direct spotting of sample for rapid analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). In addition, it allows simultaneous processing of multiple samples and can be reused after regeneration of beads with no carryover effects. These results indicate that the microbead device is a low-cost tool that enhances sample cleanup prior to MS for SNP genotyping.

High-throughput mutational screening for beta-thalassemia by single-nucleotide extension

In this work a high-throughput method based on the single-nucleotide extension (SNE) reaction and multicolour detection in a DNA sequencer was developed to screen for eight mutations in the human beta-globin gene: IVSI.110, cd39, IVSI.1, IVSI.6, IVSII.745, HbC, HbS and cd6. The method has been validated on a large number of samples for the two most common mutations causing beta-thalassemia in the Mediterranean area (IVSI.110 and cd39). The development of a high-throughput, fast and reliable method to assay beta-thalassemia mutations represents a significant improvement in molecular diagnosis of this disease. The multicolour detection and the use of multiple injections further enhances the throughput of mutational screening by the DNA sequencer and facilitates automated genotyping for routine molecular diagnostics.

SNPlexing the human Y-chromosome: a single-assay system for major haplogroup screening

SNPs are one of the main sources of DNA variation among humans. Their unique properties make them useful polymorphic markers for a wide range of fields, such as medicine, forensics, and population genetics. Although several high-throughput techniques have been (and are being) developed for the vast typing of SNPs in the medical context, population genetic studies involve the typing of few and select SNPs for targeted research. This results in SNPs having to be typed in multiple reactions, consuming large amounts of time and of DNA. In order to improve the current situation in the area of human Y-chromosome diversity studies, we decided to employ a system based on a multiplex oligo ligation assay/PCR (OLA/PCR) followed by CE to create a Y multiplex capable of distinguishing, in a single reaction, all the major haplogroups and as many subhaplogroups on the Y-chromosome phylogeny as possible. Our efforts resulted in the creation of a robust and accurate 35plex (35 SNPs in a single reaction) that when tested on 165 human DNA samples from different geographic areas, proved capable of assigning samples to their corresponding haplogroup.

Multiplex genotyping of cytochrome p450 single-nucleotide polymorphisms by use of MALDI-TOF mass spectrometry

BACKGROUND

Polymorphisms in cytochrome P450 (CYP450) genes contribute to interindividual differences in the metabolism of xenobiotic chemicals, including the vast majority of drugs, and may lead to toxicity and adverse drug reactions. Studies on these polymorphisms in research and diagnostic settings typically involve large-scale genotyping and hence require high-throughput assays.

METHODS

We used the previously developed solid-phase capture-single-base extension (SPC-SBE) approach for concurrent analysis of 40 single-nucleotide polymorphisms (SNPs) of CYP2C9 and 50 SNPs of CYP2A13, both genes belonging to the CYP450 family. Desired SNP-containing regions for each gene were amplified in a single-step multiplex PCR. We designed a library of primers to anneal immediately upstream of the selected SNPs and extended it with biotinylated terminators using PCR products as templates. Biotinylated extension products were isolated by affinity purification and analyzed with MALDI-TOF mass spectrometry to determine SNP genotypes.

RESULTS

We analyzed 11 samples for CYP2C9 and 14 samples for CYP2A13 with unambiguous detection of SNPs in all samples. Many samples showed a high occurrence of heterozygotes for both genes, with as many as 10 of 50 SNPs appearing as heterozygotes in 1 sample genotyped for CYP2A13.

CONCLUSIONS

The SPC-SBE method provides an efficient means for genotyping SNPs from the CYP450 family. This approach is suitable for automation and can be extended to other genotyping applications.

Typing of multiple single-nucleotide polymorphisms using ribonuclease cleavage of DNA/RNA chimeric single-base extension primers and detection by MALDI-TOF mass spectrometry

A novel single-base extension (SBE) assay using cleavable and noncleavable SBE primers in the same reaction mix is described. The cleavable SBE primers consisted of deoxyribonucleotides and one ribonucleotide (hereafter denoted chimeric primers), whereas the noncleavable SBE primers consisted of only deoxyribonucleotides (hereafter denoted standard primers). Biotin-labeled ddNTPs were used in the SBE reaction, and the SBE products were purified using the monomeric avidin triethylamine purification protocol, ensuring that only primers extended with a biotin-ddNTP in the 3'-end were isolated. A ribonuclease mix was developed to specifically cleave the chimeric primers, irrespective of the base of the ribonucleotide, whereas standard primers without a ribonucleotide were unaffected by the ribonuclease treatment. The SBE products were analyzed in linear mode using a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer. The cleaved SBE products were detected in the 2000-5500 m/z range, and the noncleaved SBE products were detected in the 5500-10 000 m/z range. The method was validated by typing 17 Y chromosome single-nucleotide polymorphisms in 100 males with a 17-plex SBE package containing 9 chimeric primers and 8 standard primers.

Profiling 627 mitochondrial nucleotides via the analysis of a 23-plex polymerase chain reaction by liquid chromatography-electrospray ionization time-of-flight mass spectrometry

We present a rapid and informative mitochondrial DNA profiling system, which has high forensic impact. The assay is based on the analysis of a 23-plex PCR by ion-pair reversed-phase high-performance liquid chromatography online hyphenated to electrospray ionization time-of-flight mass spectrometry (ICEMS). In a single 25-min run, an overall number of 627 nucleotide positions were screened. The vast majority of observed sequence variations were explainable by alterations of the allelic states of the 23 target SNPs, which were selected on their ability to increase forensic discrimination within West Eurasian populations. Within an Austrian population sample comprising 90 unrelated men, 14 different, nontarget SNP-related sequence variations--13 base substitutions and 1 deletion--were detected by ICEMS and confirmed by sequencing. All amplified sequences were located outside of the routinely sequenced hypervariable segments (HVS-I and HVS-II) of the noncoding control region. Accordingly, the genetic information obtained by the 23-plex PCR-ICEMS assay could be combined with HVS-I/HVS-II sequencing results to one highly discriminating mtDNA profile, which covered approximately 7.5% of the total mtDNA genome. With the 23-plex PCR-ICEMS assay, DNA mixtures were detected and the allelic ratios were accurately quantified. The observed robustness and sensitivity underlined the practical applicability of the assay in forensic science, which was proven by typing eight representative casework samples.

Standardized peptidome profiling of human urine by magnetic bead separation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

BACKGROUND

Peptidome profiling of human urine is a promising tool to identify novel disease-associated biomarkers; however, a wide range of preanalytical variables influence the results of peptidome analysis. Our aim was to develop a standardized protocol for reproducible urine peptidome profiling by means of magnetic bead (MB) separation followed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS).

METHODS

MBs with defined surface functionalities (hydrophobic interaction, cation exchange, and metal ion affinity) were used for peptide fractionation of urine. Mass accuracy and imprecision were calculated for 9 characteristic mass signals (M(r), 1000-10,000). Exogenous variables (instrument performance, urine sampling/storage conditions, freezing conditions, and freeze-thaw cycles) and endogenous variables (pH, urine salt and protein concentrations, and blood and bacteria interferences) were investigated with urine samples from 10 male and 10 female volunteers.

RESULTS

We detected 427 different mass signals in the urine of healthy donors. Within- and between-day imprecision in relative signal intensities ranged from 1% to 14% and from 4% to 16%, respectively. Weak cation-exchange and metal ion affinity MB preparations required adjustment of the urinary pH to 7. Storage time, storage temperature, the number of freeze-thaw cycles, and bacterial and blood contamination significantly influenced urine peptide patterns. Individual urine peptide patterns differed significantly within and between days. This imprecision was diminished by normalization to a urinary protein content of 3.5 microg.

CONCLUSION

This reliable pretreatment protocol allows standardization of preanalytical modalities and facilitates reproducible peptidome profiling of human urine by means of MB separation in combination with MALDI-TOF MS.

Liquid chromatography-electrospray ionization mass spectrometry for simultaneous detection of mtDNA length and nucleotide polymorphisms

We demonstrate the applicability of ion-pair reversed-phase high-performance liquid chromatography-electrospray ionization time-of-flight mass spectrometry (ICEMS) for the simultaneous characterization of length and nucleotide polymorphisms. Two sections within the first (HVS-I) and second (HVS-II) hypervariable segments of the mitochondrial (mt)DNA control region were selected as targets, both containing poly-cytosine (C) tracts, which display length heteroplasmy at a substantial frequency in the population. The two mtDNA sections were simultaneously amplified and analyzed by ICEMS in 90 maternally unrelated mother-offspring pairs from Austria. The findings were confirmed by direct sequencing of the polymerase chain reaction products. For the detailed characterization of present-length heteroplasmic variants, the results retrieved through ICEMS were more informative compared with those derived from direct sequencing. Hence, ICEMS represents an interesting option for successful application in forensic science.

Introduction of an single nucleodite polymorphism-based "Major Y-chromosome haplogroup typing kit" suitable for predicting the geographical origin of male lineages

The European Consortium "High-throughput analysis of single nucleotide polymorphisms for the forensic identification of persons--SNPforID", has performed a selection of candidate Y-chromosome single nucleotide polymorphisms (SNPs) for making inferences on the geographic origin of an unknown sample. From more than 200 SNPs compiled in the phylogenetic tree published by the Y-Chromosome Consortium, and looking at the population studies previously published, a package of 29 SNPs has been selected for the identification of major population haplogroups. A "Major Y-chromosome haplogroup typing kit" has been developed, which allows the multiplex amplification of all 29 SNPs in a single reaction. Allele genotyping was performed with a single base extension reaction (minisequencing) detected by CE. The validation of the multiplex was performed in a total of 1126 unrelated males distributed among 12 worldwide populations. The approach takes advantage of the specific geographic distribution of the Y-chromosome haplogroups and demonstrates the utility of binary polymorphisms to infer the origin of a male lineage.

Typing of single nucleotide polymorphisms by MALDI mass spectrometry: Principles and diagnostic applications

BACKGROUND

After the completion of the human genome sequencing project human genetics has now shifted its focus to DNA variation. DNA variation analysis is considered to be a key in partly understanding the mechanisms of complex diseases or varying patient responses in drug treatment. One of the major goals in genetics is finding the DNA variants that can act as diagnostic markers for predisposition to specific diseases. Moreover, in microbiology DNA variation has long been known to help discriminate and identify bacterial strains and viruses. Diagnostics based on DNA or RNA detection might be advantageous as an early-stage indication can be provided.

METHODS

Many simple and efficient methods for the analysis of nucleic acids are already available. Consequently, the last few years have seen an increased in the use of large-scale analysis of nucleic acids, in basic DNA variation studies along with diagnostics. Mass spectrometry techniques such as matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) can be of great use for genome variation analysis. In particular high-throughput SNP analysis by MALDI can be performed using fully integrated platforms.

CONCLUSIONS

Mass spectrometry-based procedures have promise for SNPs analysis especially for clinical diagnostics.

Quantification of Relative Gene Dosage by Single-Base Extension and High-Performance Liquid Chromatography: Application to the SMN1/SMN2 Gene

One of the most commonly used techniques for genotyping of single-nucleotide polymorphism (SNP) is detection of single-base extensions (SBEs). We present a new, rapid, simple, and highly reliable method for accurate quantification of SNP variants in a single reaction. Our approach is based on SBE detection coupled with high-performance liquid chromatography (HPLC) quantification. To demonstrate the utility of our approach, we report data to determine the gene dosage for relative amounts of alleles in a homologous gene, allowing detection of mutation causing exon skipping in human SMN genes to determine the ratio between the copy numbers of the SMN1/SMN2 gene. We successfully determined the relative ratio of the SMN1 and SMN2 genes and showed assay characteristics using the SBE reaction coupled with HPLC. This assay approach readily scaled to high parallelization with multiplex SBE reactions in a single sample screened in one analysis. By screening for particular SNP genotypes, this assay can be used to determine the relative gene dosage that correlates highly with the patient's disease state. The next challenge is to apply this novel methodology in a clinical screening and quantification setting for special gene regions within highly homologous genes.

Standardized approach to proteome profiling of human serum based on magnetic bead separation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

BACKGROUND

Magnetic bead purification for the analysis of low-abundance proteins in body fluids facilitates the identification of potential new biomarkers by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The aims of our study were to establish a proteome fractionation technique and to validate a standardized blood sampling, processing, and storage procedure for proteomic pattern analysis.

METHODS

We used magnetic bead separation for proteome profiling of human blood by MALDI-TOF MS (mass range, 1000-10,000 Da) and studied the effects on the quality and reproducibility of the proteome analysis of anticoagulants, blood clotting, time and temperature of sample storage, and the number of freeze-thaw cycles of samples.

RESULTS

The proteome pattern of human serum was characterized by approximately 350 signals in the mass range of 1000-10,000 Da. The proteome profile showed time-dependent dynamic changes before and after centrifugation of the blood samples. Serum mass patterns differed between native samples and samples frozen once. The best reproducibility of proteomic patterns was with a single thawing of frozen serum samples.

CONCLUSION

Application of the standardized preanalytical blood sampling and storage procedure in combination with magnetic bead-based fractionation decreases variability of proteome patterns in human serum assessed by MALDI-TOF MS.