Mass-spectrometry DNA sequencing

Integration of multi-omics data using adaptive graph learning and attention mechanism for patient classification and biomarker identification

With the rapid development and accumulation of high-throughput sequencing technology and omics data, many studies have conducted a more comprehensive understanding of human diseases from a multi-omics perspective. Meanwhile, graph-based methods have been widely used to process multi-omics data due to its powerful expressive ability. However, most existing graph-based methods utilize fixed graphs to learn sample embedding representations, which often leads to sub-optimal results. Furthermore, treating embedding representations of different omics equally usually cannot obtain more reasonable integrated information. In addition, the complex correlation between omics is not fully taken into account. To this end, we propose an end-to-end interpretable multi-omics integration method, named MOGLAM, for disease classification prediction. Dynamic graph convolutional network with feature selection is first utilized to obtain higher quality omic-specific embedding information by adaptively learning the graph structure and discover important biomarkers. Then, multi-omics attention mechanism is applied to adaptively weight the embedding representations of different omics, thereby obtaining more reasonable integrated information. Finally, we propose omic-integrated representation learning to capture complex common and complementary information between omics while performing multi-omics integration. Experimental results on three datasets show that MOGLAM achieves superior performance than other state-of-the-art multi-omics integration methods. Moreover, MOGLAM can identify important biomarkers from different omics data types in an end-to-end manner.

Mass spectrometry-based assays for assessing replicative bypass and repair of DNA alkylation in cells

Endogenous metabolism and environmental exposure can give rise to DNA alkylation, which can elicit deleterious biological consequences. In the search for reliable and quantitative analytical methods to elucidate the impact of DNA alkylation on the flow of genetic information, mass spectrometry (MS) has attracted increasing attention, owing to its unambiguous determination of molecular mass. The MS-based assays obviate conventional colony-picking methods and Sanger sequencing procedures, and retained the high sensitivity of postlabeling methods. With the help of the CRISPR/Cas9 gene editing method, MS-based assays showed high potential in studying individual functions of repair proteins and translesion synthesis (TLS) polymerases in DNA replication. In this mini-review, we have summarized the development of MS-based competitive and replicative adduct bypass (CRAB) assays and their recent applications in assessing the impact of alkylation on DNA replication. With further development of MS instruments for high resolving power and high throughput, these assays should be generally applicable and efficient in quantitative measurement of the biological consequences and repair of other DNA lesions.

A rapid, accurate, and low-cost method for detecting Mycobacterium tuberculosis and its drug-resistant genes in pulmonary tuberculosis: Applications of MassARRAY DNA mass spectrometry

Introduction

Mycobacterium tuberculosis (MTB) identification and drug resistance diagnosis are very important for treatment of drug-resistant tuberculosis (DR-TB). Therefore, high throughput, accurate and low-cost molecular detection techniques are urgently needed. This study aimed to evaluate the clinical application value of MassARRAY in tuberculosis diagnosis and drug resistance screening.

Methods

The limit of detection (LOD) and clinical application value of MassARRAY were evaluated using reference strains and clinical isolates. MTB in bronchoalveolar lavage fluid (BALF) and sputum samples were detected using MassARRAY, quantitative real-time polymerase chain reaction (qPCR) and MGIT960 liquid culture (culture). Using culture as the standard, the efficacy of MassARRAY and qPCR for the detection of TB was analyzed. Mutation of drug resistance genes in MTB clinical isolates was tested using MassARRAY, high-resolution melting curve (HRM), and Sanger sequencing. Using sequencing as the standard, the efficacy of MassARRAY, and HRM for the detection of each drug resistance site of MTB was analyzed. Simultaneously, the mutation of drug resistance genes by the MassARRAY method was compared with the results of drug susceptibility testing (DST), and the genotype-phenotype relationship was analyzed. The ability of MassARRAY to discriminate mixed infections was detected using mixtures of standard strains (M. tuberculosis H37Rv) and drug-resistant clinical isolates and mixtures of wild-type and mutant plasmids.

Results

In MassARRAY, 20 related gene mutations could be detected by two PCR systems. All genes could be accurately detected when the bacterial load was 10⁴ CFU/mL. When the load of wild-type and drug-resistant MTB mixture was 10⁵ CFU/mL (respectively reached 10⁴ CFU/mL), variants and wild-type genes could be detected simultaneously. The sensitivity of MassARRAY (96.9%) for identification was higher than that of qPCR (87.5%) (p < 0.001). The sensitivity and specificity of MassARRAY for all drug resistance gene mutations were 100.0%, with higher accuracy and consistency than HRM (sensitivity = 89.3% and specificity = 96.9%, p = 0.001). Analyzing the relationship between MassARRAY genotype and DST phenotype, the accuracy of katG_315, rpoB_531, rpsL_43, rpsL_88, and rrs_513 sites was 100.0%, and embB_306 and rpoB_526 were inconsistent with the DST results when the base changes were different.

Discussion

MassARRAY can obtain base mutation information and identify heteroresistance infections simultaneously when the mutant proportion was at least 5-25%. It has good application prospects in the diagnosis of DR-TB with high throughput, accurate and low-cost.

Prediction, Discovery, and Characterization of Plant- and Food-Derived Health-Beneficial Bioactive Peptides

Nature may have the answer to many of our questions about human, animal, and environmental health. Natural bioactives, especially when harvested from sustainable plant and food sources, provide a plethora of molecular solutions to nutritionally actionable, chronic conditions. The spectrum of these conditions, such as metabolic, immune, and gastrointestinal disorders, has changed with prolonged human life span, which should be matched with an appropriately extended health span, which would in turn favour more sustainable health care: "adding years to life and adding life to years". To date, bioactive peptides have been undervalued and underexploited as food ingredients and drugs. The future of translational science on bioactive peptides-and natural bioactives in general-is being built on (a) systems-level rather than reductionist strategies for understanding their interdependent, and at times synergistic, functions; and (b) the leverage of artificial intelligence for prediction and discovery, thereby significantly reducing the time from idea and concept to finished solutions for consumers and patients. This new strategy follows the path from benefit definition via design to prediction and, eventually, validation and production.

Engineered Whole-Cell-Based Biosensors: Sensing Environmental Heavy Metal Pollutants in Water-a Review

The frequent exposure and accumulation of heavy metals in organisms cause serious health issues affecting a range of organs such as the brain, liver, and reproductive organs in adults, infants, and children. Several parts of the world have high levels of heavy metals affecting millions of people, costing millions of dollars for improving the potability of water and medical treatment of the affected. Hence, water quality assessment is required to monitor the degree of heavy metal contamination in potable water. In nature, organisms respond to various environmental pollutants such as heavy metals, allowing their survival in a diverse environmental niche. With the advent of recombinant DNA technology, it is now possible to manipulate these natural bioreporters into controlled systems which either turn on or off gene expression or activity of enzymes in the presence of specific heavy metals (compound-specific biosensors) otherwise termed as whole-cell biosensors (WCBs). WCBs provide an upper hand compared to other immunosensors, enzyme-based sensors, and DNA-based sensors since microbes can be relatively easily manipulated, scaled up with relative ease, and can detect only the bioavailable heavy metals. In this review, we summarize the current knowledge of the various mechanisms of toxicity elicited by various heavy metals, thence emphasizing the need to develop heavy metal sensing platforms. Following this, the biosensor-based platforms including WCBs for detecting heavy metals developed thus far have been briefly elaborated upon, emphasizing the challenges and solutions associated with WCBs.

Multiprobe Assay for Clinical SEPT9 Methylation Based on the Carbon Dot-Modified Liquid-Exfoliated Graphene Field Effect Transistor with a Potential to Present a Methylation Panorama

The hypermethylation in the promoter region of the SEPT9 gene is associated with the development of colorectal cancer (CRC). Although its clinical significance for early diagnosis and screening of CRC has been demonstrated, the tedious operations in the conventional DNA methylation (DNAm) detection hinder its wide application. Herein, an electronic method for determining SEPT9 methylation in CRC patients is proposed by using the carbon dot-modified liquid exfoliated graphene field effect transistor (CDs-LEG-FET) as the DNAm sensor, the specifically designed probes to capture the SEPT9 gene and the immunologic recognition to recognize 5-methylcytosine (5mC) positions on the anchored sequences. The identification and nanomorphology of the as-prepared materials and devices are executed first by the characterizations of UV-vis, Raman, atomic force microscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and electronic measurements. Then, the role of CDs in enhancing DNAm sensitivity of CD-LEG-FET is manifested by comparing it with that of CD-free LEG-FET. Third, the captured SEPT9 genes on CD-LEG-FETs by different probes are evaluated, and the optimized temperature for hybridizing the target ssDNA sequences is determined to be 48 °C. Furthermore, the detection sensitivity for the low-quantity of DNA samples is demonstrated to be as low as 2 ng. Finally, the methylation degree of the tumor and corresponding noncancerous tissue DNA samples were examined by the proposed electric method and methylight assay in parallel. The diagnostic value of the electrical assay is confirmed by using the receiver operating characteristic curves; meanwhile, the superiority of the CD-LEG-FET platform is found to present a methylation panorama of the target gene.

Multi-omics integration-a comparison of unsupervised clustering methodologies

With the recent developments in the field of multi-omics integration, the interest in factors such as data preprocessing, choice of the integration method and the number of different omics considered had increased. In this work, the impact of these factors is explored when solving the problem of sample classification, by comparing the performances of five unsupervised algorithms: Multiple Canonical Correlation Analysis, Multiple Co-Inertia Analysis, Multiple Factor Analysis, Joint and Individual Variation Explained and Similarity Network Fusion. These methods were applied to three real data sets taken from literature and several ad hoc simulated scenarios to discuss classification performance in different conditions of noise and signal strength across the data types. The impact of experimental design, feature selection and parameter training has been also evaluated to unravel important conditions that can affect the accuracy of the result.

Automation of mass spectrometric detection of analytes and related workflows: A review

The developments in mass spectrometry (MS) in the past few decades reveal the power and versatility of this technology. MS methods are utilized in routine analyses as well as research activities involving a broad range of analytes (elements and molecules) and countless matrices. However, manual MS analysis is gradually becoming a thing of the past. In this article, the available MS automation strategies are critically evaluated. Automation of analytical workflows culminating with MS detection encompasses involvement of automated operations in any of the steps related to sample handling/treatment before MS detection, sample introduction, MS data acquisition, and MS data processing. Automated MS workflows help to overcome the intrinsic limitations of MS methodology regarding reproducibility, throughput, and the expertise required to operate MS instruments. Such workflows often comprise automated off-line and on-line steps such as sampling, extraction, derivatization, and separation. The most common instrumental tools include autosamplers, multi-axis robots, flow injection systems, and lab-on-a-chip. Prototyping customized automated MS systems is a way to introduce non-standard automated features to MS workflows. The review highlights the enabling role of automated MS procedures in various sectors of academic research and industry. Examples include applications of automated MS workflows in bioscience, environmental studies, and exploration of the outer space.

Clinical Mass Spectrometry in the Bioinformatics Era: A Hitchhiker's Guide

Mass spectrometry (MS) is a sensitive, specific and versatile analytical technique in the clinical laboratory that has recently undergone rapid development. From initial use in metabolic profiling, it has matured into applications including clinical toxicology assays, target hormone and metabolite quantitation, and more recently, rapid microbial identification and antimicrobial resistance detection by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In this mini-review, we first succinctly outline the basics of clinical mass spectrometry. Examples of hard ionization (electron ionization) and soft ionization (electrospray ionization, MALDI) are presented to demonstrate their clinical applications. Next, a conceptual discourse on mass selection and determination is presented: quadrupole mass filter, time-of-flight mass spectrometer and the Orbitrap; and MS/MS (tandem-in-space, tandem-in-time and data acquisition), illustrated with clinical examples. Current applications in (1) bacterial and fungal identification, antimicrobial susceptibility testing and phylogenetic classification, (2) general unknown urine toxicology screening and expanded new-born metabolic screening and (3) clinical metabolic profiling by gas chromatography are outlined. Finally, major limitations of MS-based techniques, including the technical challenges of matrix effect and isobaric interference; and novel challenges in the post-genomic era, such as protein molecular variants, are critically discussed from the perspective of service laboratories. Computer technology and structural biology have played important roles in the maturation of this field. MS-based techniques have the potential to replace current analytical techniques, and existing expertise and instrument will undergo rapid evolution. Significant automation and adaptation to regulatory requirements are underway. Mass spectrometry is unleashing its potentials in clinical laboratories.

Partial replication of two rumination-related candidate gene studies

Two recent papers associated candidate genes with brooding rumination, a possible cognitive endophenotype for depression, in children ages 8-14 years. Stone et al. reported that BDNF val66met polymorphism predicted brooding in adolescence. Woody et al. reported that children carrying at least one copy of a CRHR1 TAT haplotype reported less brooding than their peers in the presence of maternal depression. We attempted to replicate and extend these findings in a sample of twins aged 12-16 years. We analyzed the BDNF val66met (rs6265) polymorphism and two (rs242924 and rs7209436) out of three single nucleotide polymorphisms (SNPs) that Woody et al. used to create a CRHR1 haplotype. We controlled for maternal history of depression and clustering within families. Unlike Stone et al., we found higher brooding among BDNF Met carriers. This main effect was qualified by an interaction with pubertal status, with the effect driven by more physically mature participants. Similar to Woody et al., we found an interaction between CRHR1 SNPs and maternal depression, with the homozygous minor genotype acting as a protective factor against brooding in the presence of maternal depression. Findings provide partial support for the influence of candidate genes in two environmentally sensitive systems on brooding.

Calcinated gold nanoparticle arrays for on-chip, multiplexed and matrix-free mass spectrometric analysis of peptides and small molecules

A patterned gold nanoparticle microarray, functionalized with a nanoscale silicate coating, has been developed for on-chip, high-throughput mass spectrometric analyses of biomolecules with minimal sample preparation and reagent costs. Fabrication was realized by the combination of layer-by-layer functionalization of the nanoparticles with suitable polyelectrolytes, followed by fluidic patterning of the glass microarray support and calcination for permanent fixation of the nano-coating. Performance of the microarray was evaluated for surface-assisted laser-desorption/ionization mass spectrometry (SALDI-MS), where the nano-silicate coating was found to enhance SALDI efficiency, resulting in comparable performance to some common organic matrices for small and medium sized molecules. Performance contributing factors of this material have been discussed; heat confinement and interband transition/plasmonic resonance may play important roles. Taking the accessibility of fabrication, performance, and reusability of this substrate together, the material developed here provides a new tool for multiplexed and chip-based mass spectrometric analysis.

Measuring specificity in multi-substrate/product systems as a tool to investigate selectivity in vivo

Multiple substrate enzymes present a particular challenge when it comes to understanding their activity in a complex system. Although a single target may be easy to model, it does not always present an accurate representation of what that enzyme will do in the presence of multiple substrates simultaneously. Therefore, there is a need to find better ways to both study these enzymes in complicated systems, as well as accurately describe the interactions through kinetic parameters. This review looks at different methods for studying multiple substrate enzymes, as well as explores options on how to most accurately describe an enzyme's activity within these multi-substrate systems. Identifying and defining this enzymatic activity should help clear the way to using in vitro systems to accurately predicting the behavior of multi-substrate enzymes in vivo. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.

Mass spectrometric investigation of the role of the linking polypeptide chain in DNA polymerase I

DNA polymerase I offers great promise for a wide range of biotechnological applications due to its capability to add labeled nucleotides into double-stranded large DNA molecules by using both polymerase and nuclease domains. Accordingly, it is crucially important to thoroughly characterize this enzyme for further developments. Although the enzyme has been thus far characterized using mainly traditional analytical instruments, here we utilized an advanced and convenient means of mass spectrometry to elucidate enzymatic functions and mechanisms by measuring DNA oligomers generated by polymerase and nuclease reactions. Our analysis revealed several novel enzymatic features, including the observation that polymerase readily dissociates from the DNA molecules containing a wide single-stranded section. From this finding, we reasoned a serious situation of DNA break because polymerase domains cannot efficiently repair the wide single-stranded section, which is susceptible to DNA breaks. Furthermore, we deduced a plausible explanation for a paradoxical question as to why two domains of polymerase and 5'-nuclease are linked by a small and flexible polypeptide in polymerase I. The polypeptide link seems to prevent a 5'-nuclease from causing DNA breaks by locating a polymerase domain closely for immediate repair reaction. Here we present experimental evidence to prove our hypothesis via a set of mass spectrometric analyses as well as single DNA molecule observation and bacterial cell growth assay. Consequently, mass spectrometric analysis for DNA polymerase I provides a meaningful biological insight that a polypeptide link can be a molecular leash to control an aggressive domain in order to prevent unmanageable damages.

Mass spectrometry-based cDNA profiling as a potential tool for human body fluid identification

Several mRNA markers have been exhaustively evaluated for the identification of human venous blood, saliva, and semen in forensic genetics. As new candidate human body fluid specific markers are discovered, evaluated, and reported in the scientific literature, there is an increasing trend toward determining the ideal markers for cDNA profiling of body fluids of forensic interest. However, it has not been determined which molecular genetics-based technique(s) should be utilized to assess the performance of these markers. In recent years, only a few confirmatory, mRNA/cDNA-based methods have been evaluated for applications in body fluid identification. The most frequently described methods tested to date include quantitative polymerase chain reaction (qPCR) and capillary electrophoresis (CE). However these methods, in particular qPCR, often favor narrow multiplex PCR due to the availability of a limited number of fluorescent dyes/tags. In an attempt to address this technological constraint, this study explored matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) for human body fluid identification via cDNA profiling of venous blood, saliva, and semen. Using cDNA samples at 20pg input phosphoglycerate kinase 1 (PGK1) amounts, body fluid specific markers for the candidate genes were amplified in their corresponding body fluid (i.e., venous blood, saliva, or semen) and absent in the remaining two (100% specificity). The results of this study provide an initial indication that MALDI-TOF MS is a potential fluorescent dye-free alternative method for body fluid identification in forensic casework. However, the inherent issues of low amounts of mRNA, and the damage caused to mRNA by environmental exposures, extraction processes, and storage conditions are important factors that significantly hinder the implementation of cDNA profiling into forensic casework.

Multiplex protein detection with DNA readout via mass spectrometry

Multiplex protein quantification has been constrained by issues of assay specificity, sensitivity and throughput. This research presents a novel approach that overcomes these limitations using antibody-oligonucleotide conjugates for immuno-polymerase chain reaction (immuno-PCR) or proximity ligation, coupled with competitive PCR and MALDI-TOF mass spectrometry. Employing these combinations of technologies, we demonstrate multiplex detection and quantification of up to eight proteins, spanning wide dynamic ranges from femtomolar concentrations, using only microliter sample volumes.

Enhanced in-source fragmentation in MALDI-TOF-MS of oligonucleotides using 1,5-diaminonapthalene

The capability to rapidly and confidently determine or confirm the sequences of short oligonucleotides, including native and chemically-modified DNA and RNA, is important for a number of fields. While matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) has been used previously to sequence short oligonucleotides, the typically low fragmentation efficiency of in-source or post-source decay processes necessitates the accumulation of a large number of spectra, thus limiting the throughput of these methods. Here we introduce a novel matrix, 1,5-diaminonapthalene (DAN), for facile in-source decay (ISD) of DNA and RNA molecular anions, which allows for rapid sequence confirmation. d-, w-, and y-series ions are prominent in the spectra, complementary to the (a-B)- and w- ions that are typically produced by MALDI post-source decay (PSD). Results are shown for several model DNA and RNA oligonucleotides, including combinations of DAN-induced fragmentation with true tandem TOF MS (MS/MS) for pseudo-MS(3) and "activated-ion PSD."

Whole cancer genome sequencing by next-generation methods

Traditional approaches to sequence analysis are widely used to guide therapy for patients with lung and colorectal cancer and for patients with melanoma, sarcomas (eg, gastrointestinal stromal tumor), and subtypes of leukemia and lymphoma. The next-generation sequencing (NGS) approach holds a number of potential advantages over traditional methods, including the ability to fully sequence large numbers of genes (hundreds to thousands) in a single test and simultaneously detect deletions, insertions, copy number alterations, translocations, and exome-wide base substitutions (including known "hot-spot mutations") in all known cancer-related genes. Adoption of clinical NGS testing will place significant demands on laboratory infrastructure and will require extensive computational expertise and a deep knowledge of cancer medicine and biology to generate truly useful "clinically actionable" reports. It is anticipated that continuing advances in NGS technology will lower the overall cost, speed the turnaround time, increase the breadth of genome sequencing, detect epigenetic markers and other important genomic parameters, and become applicable to smaller and smaller specimens, including circulating tumor cells and circulating free DNA in plasma.

Comprehensive next-generation cancer genome sequencing in the era of targeted therapy and personalized oncology

DNA sequence analysis has become a significant laboratory test in oncology, permitting treatment to become increasingly personalized for both solid tumors and hematologic malignancies. Traditional approaches to sequence analysis, including Sanger sequencing, pyrosequencing and allele-specific PCR, are now widely used to guide therapy for patients diagnosed with lung and colorectal cancer as well as for melanoma, sarcomas (e.g., gastrointestinal stromal tumors) and subtypes of leukemia and lymphoma. Traditional sequence analysis has been limited in bandwidth and throughput and as a result, has been focused exclusively on testing the most common aberrations in key genes or fully sequencing single genes. The massively parallel or next-generation sequencing (NGS) approach to DNA analysis holds a number of potential advantages over the traditional methods, including the ability to fully sequence large numbers of genes (hundreds to thousands) in a single test. Furthermore, NGS can simultaneously detect deletions, insertions, copy number alterations, translocations and exome-wide base substitutions (including known hot-spot mutations) in all known cancer-related genes. However, significant challenges, particularly with respect to demands on expertise and infrastructure, will have to be overcome to translate NGS to the bedside of the cancer patient. Extensive computational expertise is required to bring NGS into clinical context, and a deep knowledge of cancer medicine and cancer biology will be required to generate truly useful, so-called 'clinically actionable' reports for clinicians. While NGS is on the cusp of being launched as a clinical test, it may be expected that the near future will continue to bring major advances in the technology that will lower the overall cost, speed up the turnaround time, increase the breadth of genome sequencing, and detect epigenetic markers and other important genomic parameters, while becoming applicable to smaller and smaller specimens, including circulating tumor cells and circulating free DNA in plasma.

Rapid universal identification of bacterial pathogens from clinical cultures by using a novel sloppy molecular beacon melting temperature signature technique

A real-time PCR assay with the ability to rapidly identify all pathogenic bacteria would have widespread medical utility. Current real-time PCR technologies cannot accomplish this task due to severe limitations in multiplexing ability. To this end, we developed a new assay system which supports very high degrees of multiplexing. We developed a new class of mismatch-tolerant "sloppy" molecular beacons, modified them to provide an extended hybridization range, and developed a multiprobe, multimelting temperature (T(m)) signature approach to bacterial species identification. Sloppy molecular beacons were exceptionally versatile, and they were able to generate specific T(m) values for DNA sequences that differed by as little as one nucleotide to as many as 23 polymorphisms. Combining the T(m) values generated by several probe-target hybrids resulted in T(m) signatures that served as highly accurate sequence identifiers. Using this method, PCR assays with as few as six sloppy molecular beacons targeting bacterial 16S rRNA gene segments could reproducibly classify 119 different sequence types of pathogenic and commensal bacteria, representing 64 genera, into 111 T(m) signature types. Blinded studies using the assay to identify the bacteria present in 270 patient-derived clinical cultures including 106 patient blood cultures showed a 95 to 97% concordance with conventional methods. Importantly, no bacteria were misidentified; rather, the few species that could not be identified were classified as "indeterminate," resulting in an assay specificity of 100%. This approach enables highly multiplexed target detection using a simple PCR format that can transform infectious disease diagnostics and improve patient outcomes.

Sequence confirmation of chemically modified RNAs using exonuclease digestion and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

A broadly applicable, robust, and rapid method for complete sequence confirmation of highly modified oligonucleotides containing a mixture of 2'-deoxy, 2'-fluoro, 2'-o-methyl, abasic and ribonucleotides is presented. The passenger (sense) and guide (antisense) strands from synthetic short interfering RNA duplexes (siRNA) were digested individually using both 5'- and 3'-exonucleases and the resulting ladders were analyzed using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Conditions for enzymatic digestion and MALDI-TOF mass analysis were investigated and optimized, and the digestion pattern and sequence coverage of each strand was discussed. Complete sequence confirmation for the antisense strands of four synthetic RNA duplexes was obtained, whereas a three-base sequence gap in the 5'-end was observed for all four sense strands. A general strategy is proposed for routine sequence confirmation of highly modified oligonucleotides, and the potential for complete automation of the method is also discussed.

Use of genome-wide high-throughput technologies in biomarker development

In recent years, the usage of high-throughput technologies in the fields of genomics, transcriptomics, proteomics and metabolomics for biomarker discovery has expanded enormously. Biomarkers can be applied for many purposes, including diagnosis, prognosis, staging and selecting appropriate patient therapy. In addition, biomarkers can provide information on disease mechanism or progression. Biomarker development for clinical application encompasses phases for their discovery and characterization, assay development and, finally, implementation using automated platforms employed in clinical laboratories. However, translation from bench to bedside outside a research-oriented environment has proven to be more difficult. This is reflected by only few new biomarkers being integrated into clinical application in the last years. This article reviews currently used high-throughput technologies for the identification of biomarkers, as well as present approaches to increase the percentage of biomarkers that pass the barriers for clinical application.

Quantitative Single-letter Sequencing: a method for simultaneously monitoring numerous known allelic variants in single DNA samples

Background

Pathogens such as fungi, bacteria and especially viruses, are highly variable even within an individual host, intensifying the difficulty of distinguishing and accurately quantifying numerous allelic variants co-existing in a single nucleic acid sample. The majority of currently available techniques are based on real-time PCR or primer extension and often require multiplexing adjustments that impose a practical limitation of the number of alleles that can be monitored simultaneously at a single locus.

Results

Here, we describe a novel method that allows the simultaneous quantification of numerous allelic variants in a single reaction tube and without multiplexing. Quantitative Single-letter Sequencing (QSS) begins with a single PCR amplification step using a pair of primers flanking the polymorphic region of interest. Next, PCR products are submitted to single-letter sequencing with a fluorescently-labelled primer located upstream of the polymorphic region. The resulting monochromatic electropherogram shows numerous specific diagnostic peaks, attributable to specific variants, signifying their presence/absence in the DNA sample. Moreover, peak fluorescence can be quantified and used to estimate the frequency of the corresponding variant in the DNA population.

Using engineered allelic markers in the genome of Cauliflower mosaic virus, we reliably monitored six different viral genotypes in DNA extracted from infected plants. Evaluation of the intrinsic variance of this method, as applied to both artificial plasmid DNA mixes and viral genome populations, demonstrates that QSS is a robust and reliable method of detection and quantification for variants with a relative frequency of between 0.05 and 1.

Conclusion

This simple method is easily transferable to many other biological systems and questions, including those involving high throughput analysis, and can be performed in any laboratory since it does not require specialized equipment.

Overview of DNA sequencing strategies

Efficient and cost-effective DNA sequencing technologies have been, and may continue to be, critical to the progress of molecular biology. This overview of DNA sequencing strategies provides a high-level review of six distinct approaches to DNA sequencing: (a) dideoxy sequencing; (b) cyclic array sequencing; (c) sequencing-by-hybridization; (d) microelectrophoresis; (e) mass spectrometry; and (f) nanopore sequencing. The primary focus is on dideoxy sequencing, which has been the dominant technology since 1977, and on cyclic array strategies, for which several competitive implementations have been developed since 2005. Because the field of DNA sequencing is changing rapidly, this unit represents a snapshot of this particular moment.

Single molecule transcription profiling with AFM

Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations.

High-throughput axial MALDI-TOF MS using a 2-kHz repetition rate laser

A high-throughput axial MALDI-TOF mass spectrometer utilizing a laser with a 2-kHz pulse repetition-rate was constructed and tested. This fast mass spectrometer provided a data acquisition rate 10 times faster than a commercially available (200 Hz) axial mass spectrometer, while maintaining comparable limits of detection (200 amol of Glu fib peptide). Mass resolution, only slightly less than the commercial instrument (10 000 vs 14 000), was sufficient for baseline resolution of isotopic clusters of peptides with m/z <2700. A new method of mass calibration, which combined a limited number of internal and external standards, provided the same 15 ppm mass accuracy over the entire sample plate on either instrument. Implementing the 2-kHz laser required a faster data acquisition system and high-voltage pulse electronics, together with a novel strategy for rapid sample plate movements during acquisition, to achieve a sample analysis rate of up to 2 spots/s (with 800 shots/spot). The overall performance of the fast MALDI-TOF MS instrument was demonstrated by the acquisition, in 12 min, of an LC-MS data set from a plate of 625 fractions collected during LC separation of an 16O/18O differentially labeled proteomic sample of a tryptic digest of an E. coli lysate.

Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research

The beginning of this millennium has seen dramatic advances in genomic research. Milestones such as the complete sequencing of the human genome and of many other species were achieved and complemented by the systematic discovery of variation at the single nucleotide (SNP) and whole segment (copy number polymorphism) level. Currently most genomics research efforts are concentrated on the production of whole genome functional annotations, as well as on mapping the epigenome by identifying the methylation status of CpGs, mainly in CpG islands, in different tissues. These recent advances have a major impact on the way genetic research is conducted and have accelerated the discovery of genetic factors contributing to disease. Technology was the critical driving force behind genomics projects: both the combination of Sanger sequencing with high-throughput capillary electrophoresis and the rapid advances in microarray technologies were keys to success. MALDI-TOF MS–based genome analysis represents a relative newcomer in this field. Can it establish itself as a long-term contributor to genetics research, or is it only suitable for niche areas and for laboratories with a passion for mass spectrometry? In this review, we will highlight the potential of MALDI-TOF MS–based tools for resequencing and for epigenetics research applications, as well as for classical complex genetic studies, allele quantification, and quantitative gene expression analysis. We will also identify the current limitations of this approach and attempt to place it in the context of other genome analysis technologies.

The genetics of depression: a review

Major depressive disorder (MDD) is common and moderately heritable. Recurrence and early age at onset characterize cases with the greatest familial risk. Major depressive disorder and the neuroticism personality trait have overlapping genetic susceptibilities. Most genetic studies of MDD have considered a small set of functional polymorphisms relevant to monoaminergic neurotransmission. Meta-analyses suggest small positive associations between the polymorphism in the serotonin transporter promoter region (5-HTTLPR) and bipolar disorder, suicidal behavior, and depression-related personality traits but not yet to MDD itself. This polymorphism might also influence traits related to stress vulnerability. Newer hypotheses of depression neurobiology suggest closer study of genes related to neurotoxic and neuroprotective (neurotrophic) processes and to overactivation of the hypothalamic-pituitary axis, with mixed evidence regarding association of MDD with polymorphisms in one such gene (brain-derived neurotrophic factor [BDNF]). Several genome-wide linkage studies of MDD and related traits have been reported or are near completion. There is some evidence for convergence of linkage findings across studies, but more data are needed to permit meta-analysis. Future directions will include more intensive, systematic study of linkage candidate regions and of the whole genome for genetic association; gene expression array studies; and larger-scale studies of gene-environment interactions and of depression-related endophenotypes.

Optimizing UV laser focus profiles for improved MALDI performance

Matrix assisted laser desorption/ionization (MALDI) applications, such as proteomics, genomics, clinical profiling and MALDI imaging, have created a growing demand for faster instrumentation. Since the commonly used nitrogen lasers have throughput and life span limitations, diode-pumped solid-state lasers are an alternative. Unfortunately this type of laser shows clear performance limitations in MALDI in terms of sensitivity, resolution and ease of use, for applications such as thin-layer sample preparations, acceptance of various matrices (e.g. DHB for glycopeptides) and MALDI imaging. While it is obvious that the MALDI process has some dependence on the characteristics of the laser used, it is unclear which features are the most critical in determining laser performance for MALDI. In this paper we show, for the first time, that a spatially structured laser beam profile in lieu of a Gaussian profile is of striking importance. This result enabled us to design diode-pumped Nd : YAG lasers that on various critical applications perform as well for MALDI as the nitrogen lasers and in some respects even better. The modulation of the beam profile appears to be a new parameter for optimizing the MALDI process. In addition, the results trigger new questions directing us to a better understanding of the MALDI process.

Toward single molecule DNA sequencing: direct identification of ribonucleoside and deoxyribonucleoside 5'-monophosphates by using an engineered protein nanopore equipped with a molecular adapter

Individual nucleic acid molecules might be sequenced by the identification of nucleoside 5'-monophosphates as they are released by processive exonucleases. Here, we show that single molecule detection with a modified protein nanopore can be used to identify ribonucleoside and 2'-deoxyribonucleoside 5'-monophosphates, thereby taking a step along this path. Distinct levels of current block are observed for each of the four members of a set of nucleoside 5'-monophosphates when the molecules bind within a mutant alpha-hemolysin pore, (M113R)(7), equipped with the molecular adapter heptakis-(6-deoxy-6-amino)-beta-cyclodextrin. While our results compare favorably with alternative approaches, further work will be required to improve the accuracy of identification of the nucleic acid bases, to feed each released nucleotide into the pore, and to ensure that every nucleotide is captured by the adapter.

Mass spectrometry of RNA

A complex population of non-coding RNAs is present in higher organisms. These RNAs have a multitude of functions and execute control over gene expression through various, often poorly understood, mechanisms. At present, the identification and analysis of functional regulatory RNAs and disparate ribonucleoprotein complexes remain an experimental challenge for biologists. They require specially designed approaches and techniques in genomics and RNA biochemistry. Developments in technologies based on mass spectrometry could offer sensitive and efficient solutions to analysis of the sequence, structure, modification and composition of RNA.

Toward single molecule DNA sequencing: direct identification of ribonucleoside and deoxyribonucleoside 5'-monophosphates by using an engineered protein nanopore equipped with a molecular adapter

Individual nucleic acid molecules might be sequenced by the identification of nucleoside 5'-monophosphates as they are released by processive exonucleases. Here, we show that single molecule detection with a modified protein nanopore can be used to identify ribonucleoside and 2'-deoxyribonucleoside 5'-monophosphates, thereby taking a step along this path. Distinct levels of current block are observed for each of the four members of a set of nucleoside 5'-monophosphates when the molecules bind within a mutant alpha-hemolysin pore, (M113R)(7), equipped with the molecular adapter heptakis-(6-deoxy-6-amino)-beta-cyclodextrin. While our results compare favorably with alternative approaches, further work will be required to improve the accuracy of identification of the nucleic acid bases, to feed each released nucleotide into the pore, and to ensure that every nucleotide is captured by the adapter.

Liquid chromatography-electrospray ionization-mass spectrometry: the future of DNA adduct detection

Over the past 40 years considerable emphasis has been placed on the development of accurate and sensitive methods for the detection and quantitation of DNA adducts. The formation of DNA adducts resulting from the covalent interaction of genotoxic carcinogens with DNA, derived from exogenous and endogenous sources, either directly or following metabolic activation, can if not repaired lead to mutations in critical genes such as those involved in the regulation of cellular growth and subsequent development of cancer. The major analytical challenge has been to detect levels of DNA adducts at the level of 0.1-1 adducts per 10(8) unmodified DNA bases using only low microgram amounts of DNA, and with high specificity and accuracy, in humans exposed to genotoxic carcinogens derived from occupational, environmental, dietary and life-style sources. In this review we will highlight the merits as well as discuss the progress made by liquid chromatography coupled to electrospray ionization mass spectrometry as a method for DNA adduct detection.

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SNP discovery in associating genetic variation with human disease phenotypes

With the completion of the human genome project, attention is now rapidly shifting towards the study of individual genetic variation. The most abundant source of genetic variation in the human genome is represented by single nucleotide polymorphisms (SNPs), which can account for heritable inter-individual differences in complex phenotypes. Identification of SNPs that contribute to susceptibility to common diseases will provide highly accurate diagnostic information that will facilitate early diagnosis, prevention, and treatment of human diseases. Over the past several years, the advancement of increasingly high-throughput and cost-effective methods to discover and measure SNPs has begun to open the door towards this endeavor. Genetic association studies are considered to be an effective approach towards the detection of SNPs with moderate effects, as in most common diseases with complex phenotypes. This requires careful study design, analysis and interpretation. In this review, we discuss genetic association studies and address the prospect for candidate gene association studies, comparing the strengths and weaknesses of indirect and direct study designs. Our focus is on the continuous need for SNP discovery methods and the use of currently available prescreening methods for large-scale genetic epidemiological research until more advanced sequencing methods currently under development will become available.