Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing

Whole-genome sequencing using sequencing technologies such as Illumina enables the accurate detection of small-scale variants but provides limited information about haplotypes and variants in repetitive regions of the human genome. Single-molecule sequencing (SMS) technologies such as Pacific Biosciences and Oxford Nanopore generate long reads that can potentially address the limitations of short-read sequencing. However, the high error rate of SMS reads makes it challenging to detect small-scale variants in diploid genomes. We introduce a variant calling method, Longshot, which leverages the haplotype information present in SMS reads to accurately detect and phase single-nucleotide variants (SNVs) in diploid genomes. We demonstrate that Longshot achieves very high accuracy for SNV detection using whole-genome Pacific Biosciences data, outperforms existing variant calling methods, and enables variant detection in duplicated regions of the genome that cannot be mapped using short reads.

Single-molecule sequencing (SMS) such as Pacific Biosciences and Oxford Nanopore generate long reads with high error rate. Here, the authors develop Longshot, a computational method that detects and phases single nucleotide variants (SNV) in diploid genomes using SMS data.

Evaluation of the Performance of AmpliSeq and SureSelect Exome Sequencing Libraries for Ion Proton

Library preparation for whole-exome sequencing is a critical step serving the enrichment of the regions of interest. For Ion Proton, there are only two exome library preparation methods available, AmpliSeq and SureSelect. Although of major interest, a comparison of the two methods is hitherto missing in the literature. Here, we systematically evaluate the performance of AmpliSeq and SureSelect and present an improved variant calling pipeline. We used 12 in-house DNA samples with genome-wide and exome microarray data and a commercially available reference DNA (NA12878) for evaluation. Both methods had a high concordance (>97%) with microarray genotypes and, when validating against NA12878, a sensitivity and positive predictive values of >93% and >80%, respectively. Application of our variant calling pipeline decreased the number of false positive variants dramatically by 90% and resulted in positive predictive value of 97%. This improvement is highly relevant in research as well as clinical setting.

Long-read sequencing in deciphering human genetics to a greater depth

Through four decades' development, DNA sequencing has inched into the era of single-molecule sequencing (SMS), or the third-generation sequencing (TGS), as represented by two distinct technical approaches developed independently by Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT). Historically, each generation of sequencing technologies was marked by innovative technological achievements and novel applications. Long reads (LRs) are considered as the most advantageous feature of SMS shared by both PacBio and ONT to distinguish SMS from next-generation sequencing (NGS, or the second-generation sequencing) and Sanger sequencing (the first-generation sequencing). Long reads overcome the limitations of NGS and drastically improves the quality of genome assembly. Besides, ONT also contributes several unique features including ultra-long reads (ULRs) with read length above 300 kb and some close to 1 million bp, direct RNA sequencing and superior portability as made possible by pocket-sized MinION sequencer. Here, we review the history of DNA sequencing technologies and associated applications, with a special focus on the advantages as well as the limitations of ULR sequencing in genome assembly.

Description and complete genome sequence of Bradyrhizobium amphicarpaeae sp. nov., harbouring photosystem and nitrogen-fixation genes

A bacterial strain, designated 39S1MBT, isolated from a root nodule of a soybean plant that had been inoculated with root-zone soil of Amphicarpaea bracteata (hog peanut) growing in Canada, was previously characterized and placed in a novel lineage within the genus Bradyrhizobium. The taxonomic status of strain 39S1MBT was verified by genomic and phenotypic analyses. Phylogenetic analyses of individual and concatenated protein-encoding gene sequences (atpD, glnII, recA, gyrB and rpoB) placed 39S1MBT in a lineage distinct from named species. Data for sequence similarities of concatenated genes relative to type strains of named species supported the phylogenetic data. Average nucleotide identity values of genome sequences (84.5-91.7 %) were well below the threshold value for bacterial species circumscription. Based on these data, Bradyrhizobium ottawaense OO99T and Bradyrhizobium shewense ERR11T are close relatives of 39S1MBT. The complete genome of 39S1MBT consists of a single 7.04 Mbp chromosome without a symbiosis island; G+C content is 64.7 mol%. Present in the genome are key photosystem and nitrogen-fixation genes, but not nodulation and type III secretion system genes. Sequence analysis of the nitrogen fixation gene, nifH, placed 39S1MBT in a novel lineage distinct from named Bradyrhizobium species. Data for phenotypic tests including growth characteristics and carbon source utilization supported the sequence-based analyses. Based on the data presented here, a novel species with the name Bradyrhizobium amphicarpaeae sp. nov. is proposed with 39S1MBT (=LMG 29934T=HAMBI 3680T) as the type strain.

A hybrid metal-dielectric zero mode waveguide for enhanced single molecule detection

We fabricated hybrid metal-dielectric nanoslots and measured their optical response at three different wavelengths. The nanostructure is fabricated on a bilayer film formed by the sequential deposition of silicon and gold on a transparent substrate. The optical characterization is done via fluorescence spectroscopy measurements. We characterized the fluorescence enhancement, as well as the lifetime and the detection volume reduction for each wavelength. We observe that the hybrid metal-dielectric nanoslots behave as enhanced zero mode waveguides in the near-infrared spectral region. Their detection volume is such that they can perform enhanced single-molecule detection at tens of μM. We compared their behavior with that of a golden ZMW, and we demonstrated that the dielectric silicon layer improves both the optical performance and the stability of the device.

A new full-length circular DNA sequencing method for viral-sized genomes reveals that RNAi transgenic plants provoke a shift in geminivirus populations in the field

We present a new method, CIDER-Seq (Circular DNA Enrichment sequencing) for the unbiased enrichment and long-read sequencing of viral-sized circular DNA molecules. We used CIDER-Seq to produce single-read full-length virus genomes for the first time. CIDER-Seq combines PCR-free virus enrichment with Single Molecule Real Time sequencing and a new sequence de-concatenation algorithm. We apply our technique to produce >1200 full-length, highly accurate geminivirus genomes from RNAi-transgenic and control plants in a field trial in Kenya. Using CIDER-Seq we can demonstrate for the first time that the expression of antiviral double-stranded RNA (dsRNA) in transgenic plants causes a consistent shift in virus populations towards species sharing low homology to the transgene derived dsRNA. Our method and its application in an economically important crop plant opens new possibilities in periodic virus sequence surveillance and accurate profiling of diverse circular DNA elements.

Mitochondrial DNA Variants in Patients with Liver Injury Due to Anti-Tuberculosis Drugs

BACKGROUND

Hepatotoxicity is the most severe adverse effect of anti-tuberculosis therapy. Isoniazid's metabolite hydrazine is a mitochondrial complex II inhibitor. We hypothesized that mitochondrial DNA variants are risk factors for drug-induced liver injury (DILI) due to isoniazid, rifampicin or pyrazinamide.

METHODS

We obtained peripheral blood from tuberculosis (TB) patients before anti-TB therapy. A total of 38 patients developed DILI due to anti-TB drugs. We selected 38 patients with TB but without DILI as controls. Next-generation sequencing detected point mutations in the mitochondrial DNA genome. DILI was defined as ALT ≥5 times the upper limit of normal (ULN), or ALT ≥3 times the ULN with total bilirubin ≥2 times the ULN.

RESULTS

In 38 patients with DILI, the causative drug was isoniazid in eight, rifampicin in 14 and pyrazinamide in 16. Patients with isoniazid-induced liver injury had more variants in complex I's NADH subunit 5 and 1 genes, more nonsynonymous mutations in NADH subunit 5, and a higher ratio of nonsynonymous to total substitutions. Patients with rifampicin- or pyrazinamide-induced liver injury had no association with mitochondrial DNA variants.

CONCLUSIONS

Variants in complex I's subunit 1 and 5 genes might affect respiratory chain function and predispose isoniazid-induced liver injury when exposed to hydrazine, a metabolite of isoniazid and a complex II inhibitor.

Next-generation sequencing for the clinical management of hepatitis C virus infections: does one test fits all purposes?

While the prospect of viral cure is higher than ever for individuals infected with the hepatitis C virus (HCV) due to ground-breaking progress in antiviral treatment, success rates are still negatively influenced by HCV's high genetic variability. This genetic diversity is represented in the circulation of various genotypes and subtypes, mixed infections, recombinant forms and the presence of numerous drug resistant variants among infected individuals. Common misclassifications by commercial genotyping assays in combination with the limitations of currently used targeted population sequencing approaches have encouraged researchers to exploit alternative methods for the clinical management of HCV infections. Next-generation sequencing (NGS), a revolutionary and powerful tool with a variety of applications in clinical virology, can characterize viral diversity and depict viral dynamics in an ultra-wide and ultra-deep manner. The level of detail it provides makes it the method of choice for the diagnosis and clinical assessment of HCV infections. The sequence library provided by NGS is of a higher magnitude and sensitivity than data generated by conventional methods. Therefore, these technologies are helpful to guide clinical practice and at the same time highly valuable for epidemiological studies. The decreasing costs of NGS to determine genotypes, mixed infections, recombinant strains and drug resistant variants will soon make it feasible to employ NGS in clinical laboratories, to assist in the daily care of patients with HCV.

Die Rolle seltener Varianten bei häufigen Krankheiten

Häufige Krankheiten, die sog. Volkskrankheiten, sind in der Regel multifaktoriell verursacht, d. h. zu ihrer Entwicklung tragen sowohl genetische Faktoren als auch nicht-genetische Umgebungseinflüsse bei. Die geschätzte Gesamterblichkeit (‑heritabilität) reicht von moderat bis vergleichsweise hoch. Die genetische Architektur ist komplex und kann das gesamte allelische Spektrum, von häufigen Varianten mit niedriger Penetranz bis hin zu seltenen Varianten mit höherer Penetranz, sowie alle möglichen Kombinationen umfassen. Während häufige Varianten seit mehreren Jahren mit großem Erfolg durch genomweite Assoziationsstudien (GWAS) identifiziert werden, war bisher die Identifizierung seltener Varianten, insbesondere aufgrund der großen Zahl beitragender Gene, nur begrenzt erfolgreich. Dies ändert sich derzeit dank der Anwendung von Hochdurchsatz-Sequenziertechnologien („next-generation sequencing“, NGS) und der daraus resultierenden zunehmenden Verfügbarkeit von exom- und genomweiten Sequenzdaten großer Kollektive. In diesem Artikel geben wir einen Überblick über die Bedeutung seltener Varianten bei häufigen Erkrankungen sowie den aktuellen Stand in Bezug auf deren Identifizierung mittels NGS. Wir betrachten insbesondere die folgenden Fragen: Bei welchen häufigen Krankheiten ist ein Beitrag seltener Varianten zu erwarten, wie können diese Varianten identifiziert werden, und welches Potenzial bieten seltene Varianten für das Verständnis biologischer Prozesse bzw. für die Translation in die klinische Praxis?

Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome

We sequenced the genome of the Yoruban reference individual NA19240 on the long-read sequencing platform Oxford Nanopore PromethION for evaluation and benchmarking of recently published aligners and germline structural variant calling tools, as well as a comparison with the performance of structural variant calling from short-read sequencing data. The structural variant caller Sniffles after NGMLR or minimap2 alignment provides the most accurate results, but additional confidence or sensitivity can be obtained by a combination of multiple variant callers. Sensitive and fast results can be obtained by minimap2 for alignment and a combination of Sniffles and SVIM for variant identification. We describe a scalable workflow for identification, annotation, and characterization of tens of thousands of structural variants from long-read genome sequencing of an individual or population. By discussing the results of this well-characterized reference individual, we provide an approximation of what can be expected in future long-read sequencing studies aiming for structural variant identification.

Molecular genetic testing methodologies in hematopoietic diseases: current and future methods

INTRODUCTION

Rapid technological advancements in clinical molecular genetics have increased our diagnostic and prognostic capabilities in health care. Understanding these assays, as well as how they may change over time, is critical for pathologists, clinicians, and translational researchers alike.

METHODS

This review provides a practical summary and basic reference for current molecular genetic technologies, as well as new testing methodologies that are in use, gaining momentum, or anticipated to contribute more broadly in the future.

RESULTS

Here, we discuss DNA and RNA based methodologies including classic assays such as the polymerase chain reaction (PCR), Sanger sequencing, and microarrays, to more cutting-edge next-generation sequencing (NGS) based assays and emerging molecular technologies such as cell-free DNA (cfDNA) or circulating tumor DNA (ctDNA), and NGS-based detection of infectious disease organisms.

CONCLUSION

This review serves as a basic foundation for knowledge in current and emerging clinical molecular genetic technologies.

Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats

Generating a complete, de novo genome assembly for prokaryotes is often considered a solved problem. However, we here show that Pseudomonas koreensis P19E3 harbors multiple, near identical repeat pairs up to 70 kilobase pairs in length, which contained several genes that may confer fitness advantages to the strain. Its complex genome, which also included a variable shufflon region, could not be de novo assembled with long reads produced by Pacific Biosciences’ technology, but required very long reads from Oxford Nanopore Technologies. Importantly, a repeat analysis, whose results we release for over 9600 prokaryotes, indicated that very complex bacterial genomes represent a general phenomenon beyond Pseudomonas. Roughly 10% of 9331 complete bacterial and a handful of 293 complete archaeal genomes represented this ‘dark matter’ for de novo genome assembly of prokaryotes. Several of these ‘dark matter’ genome assemblies contained repeats far beyond the resolution of the sequencing technology employed and likely contain errors, other genomes were closed employing labor-intense steps like cosmid libraries, primer walking or optical mapping. Using very long sequencing reads in combination with assembly algorithms capable of resolving long, near identical repeats will bring most prokaryotic genomes within reach of fast and complete de novo genome assembly.

PaSS: a sequencing simulator for PacBio sequencing

BACKGROUND

Third-generation sequencing platforms, such as PacBio sequencing, have been developed rapidly in recent years. PacBio sequencing generates much longer reads than the second-generation sequencing (or the next generation sequencing, NGS) technologies and it has unique sequencing error patterns. An effective read simulator is essential to evaluate and promote the development of new bioinformatics tools for PacBio sequencing data analysis.

RESULTS

We developed a new PacBio Sequencing Simulator (PaSS). It can learn sequence patterns from PacBio sequencing data currently available. In addition to the distribution of read lengths and error rates, we included a context-specific sequencing error model. Compared to existing PacBio sequencing simulators such as PBSIM, LongISLND and NPBSS, PaSS performed better in many aspects. Assembly tests also suggest that reads simulated by PaSS are the most similar to experimental sequencing data.

CONCLUSION

PaSS is an effective sequence simulator for PacBio sequencing. It will facilitate the evaluation and development of new analysis tools for the third-generation sequencing data.

MammaPrint and BluePrint Molecular Diagnostics Using Targeted RNA Next-Generation Sequencing Technology

Next-generation DNA sequencing is rapidly becoming an indispensable tool for genome-directed cancer diagnostics, but next-generation RNA sequencing (RNA-seq) is currently not standardly used in clinical diagnostics for expression assessment. However, multigene RNA diagnostic assays are used increasingly in the routine diagnosis of early-stage breast cancer. Two of the most widely used tests are currently available only as a central laboratory service, which limits their clinical use. We evaluated the use of RNA-seq as a decentralized method to perform such tests. The MammaPrint and BluePrint RNA-seq tests were found to be equivalent to the clinically validated microarray tests. The RNA-seq tests were highly reproducible when performed in different locations and were stable over time. The MammaPrint RNA-seq test was clinically validated. Our data demonstrate that RNA-seq can be used as a decentralized platform, yielding results substantially equivalent to results derived from the predicate diagnostic device.

CRISPR/Cas: An intriguing genomic editing tool with prospects in treating neurodegenerative diseases

The CRISPR/Cas genome editing tool has led to a revolution in biological research. Its ability to target multiple genomic loci simultaneously allows its application in gene function and genomic manipulation studies. Its involvement in the sequence specific gene editing in different backgrounds has changed the scenario of treating genetic diseases. By unravelling the mysteries behind complex neuronal circuits, it not only paved way in understanding the pathogenesis of the disease but helped in the development of large animal models of different neuronal diseases; thereby opened the gateways of successfully treating different neuronal diseases. This review explored the possibility of using of CRISPR/Cas in engineering DNA at the embryonic stage, as well as during the functioning of different cell types in the brain, to delineate implications related to the use of this super-specialized genome editing tool to overcome various neurodegenerative diseases that arise as a result of genetic mutations.

Enzyme-free fluorescence microarray for determination of hepatitis B virus DNA based on silver nanoparticle aggregates-assisted signal amplification

In this study, we designed a fluorescence enhancement strategy based on silver nanoparticle (AgNP) aggregates for the detection of hepatitis B virus DNA sequences. AgNPs were functioned with recognition probes (Cy3-probe) and hybrid probes (Oligomer-A and Oligomer-B). The presence of target DNA mediated the formation of sandwich complexes between the immobilized capture probes and the functionalized AgNPs, which was followed by hybridization-induced formation of AgNP aggregates. The fluorescent intensity could be extremely amplified by both the increasing number of fluorophores and metal enhanced fluorescence (MEF) effect. Under optimal conditions, this method achieved a detection limit of 50 fM which was 1560-fold lower than that of un-enhanced fluorescent assays. It was illustrated that the HBV DNA concentrations ranging from 100 fM to 10 nM had a good log-linear correlation with the corresponding fluorescent intensity (R = 0.991). Moreover, this method had high specificity both for distinguishing single-base mismatches and identifying target DNA under the interference of genomic DNA. This fluorescent microarray had high-throughput analytical potential and could apply to many other disease diagnoses.

Directly Accessible and Transferrable Nanofluidic Systems for Biomolecule Manipulation

Molecular detection and manipulation via nanofluidic systems offers new routes for single-molecule analysis to study epigenetic mechanisms and genetic mutation of disease. For detection of single biological molecule, many types of nanomicrofluidic systems have been utilized. Typically, mechanical tethering, fluidic pressure, chemical interactions, or electrical forces allow controllable attraction, enrichment, confinement, and elongation of target molecules. The currently available methods, however, are unable to offer both molecular manipulation and direct and concurrent assessment of target molecules in the system due to the nature of enclosed channels and associated fluidic components. Here, we introduce a wafer-scale nanofluidic system that incorporates an array of accessible open nanochannels and nano-microtrappers to enrich and elongate target molecules (DNA) via the combination of an electric field and hydrodynamic force. The open nanofluidic system allows easy access, direct observation, and manipulation of molecules in the nanochannels. The presence of a stretched single DNA and the efficacy of the nanofluidic system are studied by fluorescence microscopy and atomic force microscopy. Hybrid integration of the nanodevice fabrication with a material transfer printing technique enables to design a highly flexible and transferrable nanofluidic system after molecular concentration.

Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

BACKGROUND

The human genome contains "dark" gene regions that cannot be adequately assembled or aligned using standard short-read sequencing technologies, preventing researchers from identifying mutations within these gene regions that may be relevant to human disease. Here, we identify regions with few mappable reads that we call dark by depth, and others that have ambiguous alignment, called camouflaged. We assess how well long-read or linked-read technologies resolve these regions.

RESULTS

Based on standard whole-genome Illumina sequencing data, we identify 36,794 dark regions in 6054 gene bodies from pathways important to human health, development, and reproduction. Of these gene bodies, 8.7% are completely dark and 35.2% are ≥ 5% dark. We identify dark regions that are present in protein-coding exons across 748 genes. Linked-read or long-read sequencing technologies from 10x Genomics, PacBio, and Oxford Nanopore Technologies reduce dark protein-coding regions to approximately 50.5%, 35.6%, and 9.6%, respectively. We present an algorithm to resolve most camouflaged regions and apply it to the Alzheimer's Disease Sequencing Project. We rescue a rare ten-nucleotide frameshift deletion in CR1, a top Alzheimer's disease gene, found in disease cases but not in controls.

CONCLUSIONS

While we could not formally assess the association of the CR1 frameshift mutation with Alzheimer's disease due to insufficient sample-size, we believe it merits investigating in a larger cohort. There remain thousands of potentially important genomic regions overlooked by short-read sequencing that are largely resolved by long-read technologies.

Long-Read Sequencing Emerging in Medical Genetics

The wide implementation of next-generation sequencing (NGS) technologies has revolutionized the field of medical genetics. However, the short read lengths of currently used sequencing approaches pose a limitation for the identification of structural variants, sequencing repetitive regions, phasing of alleles and distinguishing highly homologous genomic regions. These limitations may significantly contribute to the diagnostic gap in patients with genetic disorders who have undergone standard NGS, like whole exome or even genome sequencing. Now, the emerging long-read sequencing (LRS) technologies may offer improvements in the characterization of genetic variation and regions that are difficult to assess with the prevailing NGS approaches. LRS has so far mainly been used to investigate genetic disorders with previously known or strongly suspected disease loci. While these targeted approaches already show the potential of LRS, it remains to be seen whether LRS technologies can soon enable true whole genome sequencing routinely. Ultimately, this could allow the de novo assembly of individual whole genomes used as a generic test for genetic disorders. In this article, we summarize the current LRS-based research on human genetic disorders and discuss the potential of these technologies to facilitate the next major advancements in medical genetics.

Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing

Advances in transcriptomics have provided an exceptional opportunity to study functional implications of the genetic variability. Technologies such as RNA-Seq have emerged as state-of-the-art techniques for transcriptome analysis that take advantage of high-throughput next-generation sequencing. However, similar to their predecessors, these approaches continue to impose major challenges on full-length transcript structure identification, primarily due to inherent limitations of read length. With the development of single-molecule sequencing (SMS) from PacBio, a growing number of studies on the transcriptome of different organisms have been reported. SMS has emerged as advantageous for comprehensive genome annotation including identification of novel genes/isoforms, long non-coding RNAs and fusion transcripts. This approach can be used across a broad spectrum of species to better interpret the coding information of the genome, and facilitate the biological function study. We provide an overview of SMS platform and its diverse applications in various biological studies, and our perspective on the challenges associated with the transcriptome studies.

100 Years of evolving gene-disease complexities and scientific debutants

It's been over 100 years since the word `gene' is around and progressively evolving in several scientific directions. Time-to-time technological advancements have heavily revolutionized the field of genomics, especially when it's about, e.g. triple code development, gene number proposition, genetic mapping, data banks, gene-disease maps, catalogs of human genes and genetic disorders, CRISPR/Cas9, big data and next generation sequencing, etc. In this manuscript, we present the progress of genomics from pea plant genetics to the human genome project and highlight the molecular, technical and computational developments. Studying genome and epigenome led to the fundamentals of development and progression of human diseases, which includes chromosomal, monogenic, multifactorial and mitochondrial diseases. World Health Organization has classified, standardized and maintained all human diseases, when many academic and commercial online systems are sharing information about genes and linking to associated diseases. To efficiently fathom the wealth of this biological data, there is a crucial need to generate appropriate gene annotation repositories and resources. Our focus has been how many gene-disease databases are available worldwide and which sources are authentic, timely updated and recommended for research and clinical purposes. In this manuscript, we have discussed and compared 43 such databases and bioinformatics applications, which enable users to connect, explore and, if possible, download gene-disease data.

Mass Spectrometry for Investigating the Effects of Toxic Metals on Nucleic Acid Modifications

The extensive use of toxic metals in industry and agriculture leads to their wide distribution in the environment, which raises critical concerns over their toxic effects on human health. Many toxic metals are reported to be mildly mutagenic or non-mutagenic, indicating that genetic-based mechanisms may not be primarily responsible for toxic metal-induced carcinogenesis. Increasing evidence has demonstrated that exposure to toxic metals can alter epigenetic modifications, which may lead to the dysregulation of gene expression and disease susceptibility. It is now becoming clear that a full understanding of the effects of toxic metals on cellular toxicity and carcinogenesis will need to consider both genetic- and epigenetic-based mechanisms. Uncovering the effects of toxic metals on epigenetic modifications in nucleic acids relies on the detection and quantification of these modifications. Mass spectrometry (MS)-based methods for deciphering epigenetic modifications have substantially advanced over the past decade, and they are now becoming widely used and essential tools for evaluating the effects of toxic metals on nucleic acid modifications. This Review provides an overview of MS-based methods for analysis of nucleic acid modifications. In addition, we also review recent advances in understanding the effects of exposure to toxic metals on nucleic acid modifications.

Resolving Phylogenetic Relationships for Streptococcus mitis and Streptococcus oralis through Core- and Pan-Genome Analyses

Taxonomic and phylogenetic relationships of Streptococcus mitis and Streptococcus oralis have been difficult to establish biochemically and genetically. We used core-genome analyses of S. mitis and S. oralis, as well as the closely related species Streptococcus pneumoniae and Streptococcus parasanguinis, to clarify the phylogenetic relationships between S. mitis and S. oralis, as well as within subclades of S. oralis. All S. mitis (n = 67), S. oralis (n = 89), S. parasanguinis (n = 27), and 27 S. pneumoniae genome assemblies were downloaded from NCBI and reannotated. All genes were delineated into homologous clusters and maximum-likelihood phylogenies built from putatively nonrecombinant core gene sets. Population structure was determined using Bayesian genome clustering, and patristic distance was calculated between populations. Population-specific gene content was assessed using a phylogenetic-based genome-wide association approach. Streptococcus mitis and S. oralis formed distinct clades, but species mixing suggests taxonomic misassignment. Patristic distance between populations suggests that S. oralis subsp. dentisani is a distinct species, whereas S. oralis subsp. tigurinus and subsp. oralis are supported as subspecies, and that S. mitis comprises two subspecies. None of the genes within the pan-genomes of S. mitis and S. oralis could be statistically correlated with either, and the dispensable genomes showed extensive variation among isolates. These are likely important factors contributing to established overlap in biochemical characteristics for these taxa. Based on core-genome analysis, the substructure of S. oralis and S. mitis should be redefined, and species assignments within S. oralis and S. mitis should be made based on whole-genome analysis to be robust to misassignment.

Facile single-molecule pull-down assay for analysis of endogenous proteins

The single-molecule pull-down (SiMPull) assay analyzes molecular complexes in physiological conditions from cell or tissue lysates. Currently the approach requires a lengthy sample preparation process, which has largely prevented the widespread adoption of this technique in bioanalysis. Here, we present a simplified SiMPull assay based upon dichlorodimethylsilane-Tween-20 passivation and F(ab) fragment labeling. Our passivation is a much shorter process than the standard polyethylene glycol passivation used in most single-molecule studies. The use of F(ab) fragments for indirect fluorescent labeling rather than divalent F(ab')₂ or whole IgG antibodies allows for the pre-incubation of the detection antibodies, reducing the sample preparation time for single-molecule immunoprecipitation samples. We examine the applicability of our approach to recombinant proteins and endogenous proteins from mammalian cell lysates.

New Approaches for Genome Assembly and Scaffolding

Affordable, high-throughput DNA sequencing has accelerated the pace of genome assembly over the past decade. Genome assemblies from high-throughput, short-read sequencing, however, are often not as contiguous as the first generation of genome assemblies. Whereas early genome assembly projects were often aided by clone maps or other mapping data, many current assembly projects forego these scaffolding data and only assemble genomes into smaller segments. Recently, new technologies have been invented that allow chromosome-scale assembly at a lower cost and faster speed than traditional methods. Here, we give an overview of the problem of chromosome-scale assembly and traditional methods for tackling this problem. We then review new technologies for chromosome-scale assembly and recent genome projects that used these technologies to create highly contiguous genome assemblies at low cost.

Advancing Personalized Medicine Through the Application of Whole Exome Sequencing and Big Data Analytics

There is a growing attention toward personalized medicine. This is led by a fundamental shift from the ‘one size fits all’ paradigm for treatment of patients with conditions or predisposition to diseases, to one that embraces novel approaches, such as tailored target therapies, to achieve the best possible outcomes. Driven by these, several national and international genome projects have been initiated to reap the benefits of personalized medicine. Exome and targeted sequencing provide a balance between cost and benefit, in contrast to whole genome sequencing (WGS). Whole exome sequencing (WES) targets approximately 3% of the whole genome, which is the basis for protein-coding genes. Nonetheless, it has the characteristics of big data in large deployment. Herein, the application of WES and its relevance in advancing personalized medicine is reviewed. WES is mapped to Big Data “10 Vs” and the resulting challenges discussed. Application of existing biological databases and bioinformatics tools to address the bottleneck in data processing and analysis are presented, including the need for new generation big data analytics for the multi-omics challenges of personalized medicine. This includes the incorporation of artificial intelligence (AI) in the clinical utility landscape of genomic information, and future consideration to create a new frontier toward advancing the field of personalized medicine.

Genome Sequencing of Cladobotryum protrusum Provides Insights into the Evolution and Pathogenic Mechanisms of the Cobweb Disease Pathogen on Cultivated Mushroom

Cladobotryum protrusum is one of the mycoparasites that cause cobweb disease on cultivated edible mushrooms. However, the molecular mechanisms of evolution and pathogenesis of C. protrusum on mushrooms are largely unknown. Here, we report a high-quality genome sequence of C. protrusum using the single-molecule, real-time sequencing platform of PacBio and perform a comparative analysis with closely related fungi in the family Hypocreaceae. The C. protrusum genome, the first complete genome to be sequenced in the genus Cladobotryum, is 39.09 Mb long, with an N50 of 4.97 Mb, encoding 11,003 proteins. The phylogenomic analysis confirmed its inclusion in Hypocreaceae, with its evolutionary divergence time estimated to be ~170.1 million years ago. The genome encodes a large and diverse set of genes involved in secreted peptidases, carbohydrate-active enzymes, cytochrome P450 enzymes, pathogen⁻host interactions, mycotoxins, and pigments. Moreover, C. protrusum harbors arrays of genes with the potential to produce bioactive secondary metabolites and stress response-related proteins that are significant for adaptation to hostile environments. Knowledge of the genome will foster a better understanding of the biology of C. protrusum and mycoparasitism in general, as well as help with the development of effective disease control strategies to minimize economic losses from cobweb disease in cultivated edible mushrooms.

In silico genome analysis reveals the metabolic versatility and biotechnology potential of a halotorelant phthalic acid esters degrading Gordonia alkanivorans strain YC-RL2

Members of genus Gordonia are known to degrade various xenobitics and produce secondary metabolites. The genome of a halotorelant phthalic acid ester (PAEs) degrading actinobacterium Gordonia alkanivorans strain YC-RL2 was sequenced using Biosciences RS II platform and Single Molecular Real-Time (SMRT) technology. The reads were assembled de novo by hierarchical genome assembly process (HGAP) algorithm version 2. Genes were annotated by NCBI Prokaryotic Genome Annotation Pipeline. The generated genome sequence was 4,979,656 bp with an average G+C content of 67.45%. Calculation of ANI confirmed previous classification that strain YC-RL2 is G. alkanivorans. The sequences were searched against KEGG and COG databases; 3132 CDSs were assigned to COG families and 1808 CDSs were predicted to be involved in 111 pathways. 95 of the KEGG annotated genes were predicted to be involved in the degradation of xenobiotics. A phthalate degradation operon could not be identified in the genome indicating that strain YC-RL2 possesses a novel way of phthalate degradation. A total of 203 and 22 CDSs were annotated as esterase/hydrolase and dioxygenase genes respectively. A total of 53 biosynthetic gene clusters (BGCs) were predicted by antiSMASH (antibiotics & Secondary Metabolite Analysis Shell) bacterial version 4.0. The genome also contained putative genes for heavy metal metabolism. The strain could tolerate 1 mM of Cd2+, Co2+, Cu2+, Ni2+, Zn2+, Mn2+ and Pb2+ ions. These results show that strain YC-RL2 has a great potential to degrade various xenobiotics in different environments and will provide a rich genetic resource for further biotechnological and remediation studies.

Complete Genome Sequence of Streptomyces olivoreticuli ATCC 31159 Which can Produce Anticancer Bestatin and Show Diverse Secondary Metabolic Potentials

Because of its competitive inhibitor activity against aminopeptidase B, bestatin isolated from the broth of Streptomyces olivoreticuli ATCC 31159 is famous and currently used as an approved therapeutic agent for cancer and bacterial infections. It can be used alone or in combination with other antibiotics or anticancer drugs as adjuvant therapy drug for chemotherapy and radiotherapy. Due to the therapeutic importance of bestatin, mining of its biosynthetic mechanism is imperative. Genome mining, one of the bioinformatics-based approaches for the discovery of novel natural product, has been developed and applied widely. Herein, we reported the complete genome of Streptomyces olivoreticuli ATCC 31159 obtained from American Type Culture Collection (ATCC). It consists of 8,809,793 base pairs with a linear chromosome, GC content of 71.1%, 7520 protein-coding genes, 75 tRNA operons, 21 rRNA operons, 63 sRNAs. In addition, predictive analysis showed that at least 37 putative biosynthetic gene clusters (BGCs) of the secondary metabolites were obtained, 18 new BGCs with low similarity (< 25%) were included. The availability of novel and abundant gene clusters not only will provide clues for cracking the biosynthetic mechanism of bestatin, but also will provide valuable insight for mining the diverse bioactive compounds based on rational strategies.

Enrichment of fetal and maternal long cell-free DNA fragments from maternal plasma following DNA repair

Objective

Cell‐free DNA (cfDNA) fragments in maternal plasma contain DNA damage and may negatively impact the sensitivity of noninvasive prenatal testing (NIPT). However, some of these DNA damages are potentially reparable. We aimed to recover these damaged cfDNA molecules using PreCR DNA repair mix.

Methods

cfDNA was extracted from 20 maternal plasma samples and was repaired and sequenced by the Illumina platform. Size profiles and fetal DNA fraction changes of repaired samples were characterized. Targeted sequencing of chromosome Y sequences was used to enrich fetal cfDNA molecules following repair. Single‐molecule real‐time (SMRT) sequencing platform was employed to characterize long (>250 bp) cfDNA molecules. NIPT of five trisomy 21 samples was performed.

Results

Size profiles of repaired libraries were altered, with significantly increased long (>250 bp) cfDNA molecules. Single nucleotide polymorphism (SNP)‐based analyses showed that both fetal‐ and maternal‐derived cfDNA molecules were enriched by the repair. Fetal DNA fractions in maternal plasma showed a small but consistent (4.8%) increase, which were contributed by a higher increment of long fetal cfDNA molecules. z‐score values were improved in NIPT of all trisomy 21 samples.

Conclusion

Plasma DNA repair recovers and enriches long cfDNA molecules of both fetal and maternal origins in maternal plasma.

What is already known about this topic?

Most of the cell‐free DNA (cfDNA) fragments in maternal plasma have sizes less than 200 bp, with fetal molecules being shorter than maternal ones.

DNA damages exist in cfDNA, particularly single‐strand nicks.

Occasional no call for noninvasive prenatal testing (NIPT) can be caused by insufficient fetal DNA fraction.

What does this study add?

Repair of cfDNA by PreCR repair mix can recover a subset of long (>250 bp) cfDNA molecules.

Both fetal and maternal long cfDNA are enriched by PreCR repair treatment.

Mild but consistent increments in fetal DNA fractions after PreCR repair, which are contributed by higher enrichment of long fetal cfDNA molecules.

PreCR repair treatment improves NIPT of trisomy 21 by elevating z scores resulting in better discrimination of aneuploid from euploid samples.

The Genetic Structures of an Extensively Drug Resistant (XDR) Klebsiella pneumoniae and Its Plasmids

Multi-, extensively-, and pan-drug resistant bacteria are a threat to our health today, because their wide resistance spectra make their infections difficult to cure. In this work, we isolated an extensively drug resistant (XDR) Klebsiella pneumoniae 2-1 strain from the stool sample of a patient diagnosed of colorectal cancer. K. pneumoniae 2-1 was found to be resistant to all the antibiotics tested except for cefepime, tigecycline, and ceftazidime-avibactam. By sequencing the complete genome of K. pneumoniae 2-1, we found it contains a chromosome of 5.23 Mb and two circular plasmids with the size of 246 and 90 kb. The larger plasmid, pKP21HI1 was found to be a new conjugation-defective plasmid belonging to incompatibility group HI1B and a new sequence type. Further comparative genomics analysis and antimicrobial resistance gene analysis showed that although a great deal of changes took place on the chromosome of K. pneumoniae 2-1 in comparison with the reference genome, the extensively drug resistance phenotype of K. pneumoniae 2-1 is primarily due to the two multidrug resistant plasmids it contains. This work explains the genetic and mechanistic basis of the extensive drug resistance of K. pneumoniae 2-1, and found that plasmids play key roles in the strong antibiotic resistance of bacteria.

Enhancing the optical detection of mutants from healthy DNA with diamondoids

A polarized laser pulse can distinguish between healthy and mutated DNA nucleotides hydrogen bonded to small diamond cages.

Complete genome sequence unveiled cellulose degradation enzymes and secondary metabolic potentials in Streptomyces sp. CC0208

Marine Streptomyces sp. CC0208 isolated from the Bohai Bay showed high efficiency of cellulose degradation under optimized fermentation parameters. Also, as one of the bioinformatics-based approaches for the discovery of novel natural product and enzyme effectively, genome mining has been developed and applied widely. Herein, we reported the complete genome sequence of Streptomyces sp. CC0208.Whole-genome sequencing analysis revealed a genome size of 9,325,981 bp with a linear chromosome, GC content of 70.59% and 8487 protein-coding genes. Abundant genes have predicted functions in antibiotic metabolism and enzymes. A 20 enzymes closely associated with cellulose degradation were discovered. A total of 25 biosynthetic gene clusters (BGCs) of secondary metabolites were identified, including diverse classes of natural products. The availability of genome sequence of Streptomyces sp. CC0208 not only will assist in cracking the mechanism of cellulose degradation but also will provide the insights into the significant secondary metabolic potentials for the production of diverse compound classes based on rational strategies.

The clinical implementation of copy number detection in the age of next-generation sequencing

INTRODUCTION

The role of copy number variants (CNVs) in disease is now well established. In parallel NGS technologies, such as long-read technologies, there is continual development and data analysis methods continue to be refined. Clinical exome sequencing data is now a reality for many diagnostic laboratories in both congenital genetics and oncology. This provides the ability to detect and report both SNVs and structural variants, including CNVs, using a single assay for a wide range of patient cohorts. Areas covered: Currently, whole-genome sequencing is mainly restricted to research applications and clinical utility studies. Furthermore, detecting the full-size spectrum of CNVs as well as somatic events remains difficult for both exome and whole-genome sequencing. As a result, the full extent of genomic variants in an individual's genome is still largely unknown. Recently, new sequencing technologies have been introduced which maintain the long-range genomic context, aiding the detection of CNVs and structural variants. Expert commentary: The development of long-read sequencing promises to resolve many CNV and SV detection issues but is yet to become established. The current challenge for clinical CNV detection is how to fully exploit all the data which is generated by high throughput sequencing technologies.

Improved nucleic acid extraction protocols for Ganoderma boninense, G. miniatocinctum and G. tornatum

The first and most crucial step of all molecular techniques is to isolate high quality and intact nucleic acids. However, DNA and RNA isolation from fungal samples are usually difficult due to the cell walls that are relatively unsusceptible to lysis and often resistant to traditional extraction procedures. Although there are many extraction protocols for Ganoderma species, different extraction protocols have been applied to different species to obtain high yields of good quality nucleic acids, especially for genome and transcriptome sequencing. Ganoderma species, mainly G. boninense causes the basal stem rot disease, a devastating disease that plagues the oil palm industry. Here, we describe modified DNA extraction protocols for G. boninense, G. miniatocinctum and G. tornatum, and an RNA extraction protocol for G. boninense. The modified salting out DNA extraction protocol is suitable for G. boninense and G. miniatocinctum while the modified high salt and low pH protocol is suitable for G. tornatum. The modified DNA and RNA extraction protocols were able to produce high quality genomic DNA and total RNA of ~ 140 to 160 µg/g and ~ 80 µg/g of mycelia respectively, for Single Molecule Real Time (PacBio Sequel^® System) and Illumina sequencing. These protocols will benefit those studying the oil palm pathogens at nucleotide level.

Miniaturized flow cell with pneumatically-actuated vertical nanoconfinement for single-molecule imaging and manipulation

Convex Lens-induced Confinement (CLiC) is a single-molecule imaging technique that uses a deformable glass flow cell to gently trap, manipulate, and visualize single molecules within micro- and nano-structures, to enable a wide range of applications. Here, we miniaturize the CLiC flow cell, from 25 × 25 to 3 × 3 mm 2 and introduce pneumatic control of the confinement. Miniaturization of the flow cell improves fabrication throughput by almost two orders of magnitude and, advantageous for pharmaceutical and diagnostic applications where samples are precious, significantly lowers the internal volume from microliters to nanoliters. Pneumatic control of the device reduces the confinement gradient and improves mechanical stability while maintaining low autofluorescence and refractive index-matching with oil-immersion objectives. To demonstrate our "mini CLiC" system, we confine and image DNA in sub-50 nm nanogrooves, with high DNA extension consistent with the Odijk confinement regime.

Long reads: their purpose and place

In recent years long-read technologies have moved from being a niche and specialist field to a point of relative maturity likely to feature frequently in the genomic landscape. Analogous to next generation sequencing, the cost of sequencing using long-read technologies has materially dropped whilst the instrument throughput continues to increase. Together these changes present the prospect of sequencing large numbers of individuals with the aim of fully characterizing genomes at high resolution. In this article, we will endeavour to present an introduction to long-read technologies showing: what long reads are; how they are distinct from short reads; why long reads are useful and how they are being used. We will highlight the recent developments in this field, and the applications and potential of these technologies in medical research, and clinical diagnostics and therapeutics.

Detecting AGG Interruptions in Females With a FMR1 Premutation by Long-Read Single-Molecule Sequencing: A 1 Year Clinical Experience

The fragile X syndrome arises from the FMR1 CGG expansion of a premutation (55–200 repeats) to a full mutation allele (>200 repeats) and is the most frequent cause of inherited X-linked intellectual disability. The risk for a premutation to expand to a full mutation allele depends on the repeat length and AGG triplets interrupting this repeat. In genetic counseling it is important to have information on both these parameters to provide an accurate risk estimate to women carrying a premutation allele and weighing up having children. For example, in case of a small risk a woman might opt for a natural pregnancy followed up by prenatal diagnosis while she might choose for preimplantation genetic diagnosis (PGD) if the risk is high. Unfortunately, the detection of AGG interruptions was previously hampered by technical difficulties complicating their use in diagnostics. Therefore we recently developed, validated and implemented a new methodology which uses long-read single-molecule sequencing to identify AGG interruptions in females with a FMR1 premutation. Here we report on the assets of AGG interruption detection by sequencing and the impact of implementing the assay on genetic counseling.