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1.
Cell ; 182(1): 145-161.e23, 2020 07 09.
Artigo em Inglês | MEDLINE | ID: mdl-32553272

RESUMO

Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV genome, along with 14 new reference assemblies, revealed large-scale intermixing of diverse genotypes, as well as thousands of SVs intersecting genes and cis-regulatory regions. Hundreds of SV-gene pairs exhibit subtle and significant expression changes, which could broadly influence quantitative trait variation. By combining quantitative genetics with genome editing, we show how multiple SVs that changed gene dosage and expression levels modified fruit flavor, size, and production. In the last example, higher order epistasis among four SVs affecting three related transcription factors allowed introduction of an important harvesting trait in modern tomato. Our findings highlight the underexplored role of SVs in genotype-to-phenotype relationships and their widespread importance and utility in crop improvement.


Assuntos
Produtos Agrícolas/genética , Regulação da Expressão Gênica de Plantas , Variação Estrutural do Genoma , Solanum lycopersicum/genética , Alelos , Sistema Enzimático do Citocromo P-450/genética , Ecótipo , Epistasia Genética , Frutas/genética , Duplicação Gênica , Genoma de Planta , Genótipo , Endogamia , Anotação de Sequência Molecular , Fenótipo , Melhoramento Vegetal , Locos de Características Quantitativas/genética
2.
Annu Rev Genomics Hum Genet ; 25(1): 77-104, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38663087

RESUMO

The Human Genome Project was an enormous accomplishment, providing a foundation for countless explorations into the genetics and genomics of the human species. Yet for many years, the human genome reference sequence remained incomplete and lacked representation of human genetic diversity. Recently, two major advances have emerged to address these shortcomings: complete gap-free human genome sequences, such as the one developed by the Telomere-to-Telomere Consortium, and high-quality pangenomes, such as the one developed by the Human Pangenome Reference Consortium. Facilitated by advances in long-read DNA sequencing and genome assembly algorithms, complete human genome sequences resolve regions that have been historically difficult to sequence, including centromeres, telomeres, and segmental duplications. In parallel, pangenomes capture the extensive genetic diversity across populations worldwide. Together, these advances usher in a new era of genomics research, enhancing the accuracy of genomic analysis, paving the path for precision medicine, and contributing to deeper insights into human biology.


Assuntos
Genoma Humano , Projeto Genoma Humano , Humanos , Variação Genética , Genômica/métodos , Análise de Sequência de DNA/métodos , Telômero/genética
3.
Genome Res ; 2024 Sep 09.
Artigo em Inglês | MEDLINE | ID: mdl-39251347

RESUMO

Much of the profound interspecific variation in genome content has been attributed to transposable elements (TEs). To explore the extent of TE variation within species, we developed an optimized open-source algorithm, panEDTA, to de novo annotate TEs in a pangenome context. We then generated a unified TE annotation for a maize pangenome derived from 26 reference-quality genomes, which reveals an excess of 35.1 Mb of TE sequences per genome in tropical maize relative to temperate maize. A small number (n = 216) of TE families, mainly LTR retrotransposons, drive these differences. Evidence from the methylome, transcriptome, LTR age distribution, and LTR insertional polymorphisms reveals that 64.7% of the variability is contributed by LTR families that are young, less methylated, and more expressed in tropical maize, whereas 18.5% is driven by LTR families with removal or loss in temperate maize. Additionally, we find enrichment for Young LTR families adjacent to nucleotide-binding and leucine-rich repeat (NLR) clusters of varying copy number across lines, suggesting TE activity may be associated with disease resistance in maize.

4.
Genome Res ; 34(7): 1089-1105, 2024 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-38951027

RESUMO

Knowledge of locations and activities of cis-regulatory elements (CREs) is needed to decipher basic mechanisms of gene regulation and to understand the impact of genetic variants on complex traits. Previous studies identified candidate CREs (cCREs) using epigenetic features in one species, making comparisons difficult between species. In contrast, we conducted an interspecies study defining epigenetic states and identifying cCREs in blood cell types to generate regulatory maps that are comparable between species, using integrative modeling of eight epigenetic features jointly in human and mouse in our Validated Systematic Integration (VISION) Project. The resulting catalogs of cCREs are useful resources for further studies of gene regulation in blood cells, indicated by high overlap with known functional elements and strong enrichment for human genetic variants associated with blood cell phenotypes. The contribution of each epigenetic state in cCREs to gene regulation, inferred from a multivariate regression, was used to estimate epigenetic state regulatory potential (esRP) scores for each cCRE in each cell type, which were used to categorize dynamic changes in cCREs. Groups of cCREs displaying similar patterns of regulatory activity in human and mouse cell types, obtained by joint clustering on esRP scores, harbor distinctive transcription factor binding motifs that are similar between species. An interspecies comparison of cCREs revealed both conserved and species-specific patterns of epigenetic evolution. Finally, we show that comparisons of the epigenetic landscape between species can reveal elements with similar roles in regulation, even in the absence of genomic sequence alignment.


Assuntos
Epigênese Genética , Epigenoma , Especificidade da Espécie , Animais , Camundongos , Humanos , Células Sanguíneas/metabolismo , Sequências Reguladoras de Ácido Nucleico , Regulação da Expressão Gênica , Epigenômica/métodos
5.
Nat Methods ; 20(3): 408-417, 2023 03.
Artigo em Inglês | MEDLINE | ID: mdl-36658279

RESUMO

The availability of long reads is revolutionizing studies of structural variants (SVs). However, because SVs vary across individuals and are discovered through imprecise read technologies and methods, they can be difficult to compare. Addressing this, we present Jasmine and Iris ( https://github.com/mkirsche/Jasmine/ ), for fast and accurate SV refinement, comparison and population analysis. Using an SV proximity graph, Jasmine outperforms six widely used comparison methods, including reducing the rate of Mendelian discordance in trio datasets by more than fivefold, and reveals a set of high-confidence de novo SVs confirmed by multiple technologies. We also present a unified callset of 122,813 SVs and 82,379 indels from 31 samples of diverse ancestry sequenced with long reads. We genotype these variants in 1,317 samples from the 1000 Genomes Project and the Genotype-Tissue Expression project with DNA and RNA-sequencing data and assess their widespread impact on gene expression, including within medically relevant genes.


Assuntos
Jasminum , Humanos , Genoma , Análise de Sequência , Genótipo , Iris , Análise de Sequência de DNA/métodos , Genoma Humano , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Software
6.
Plant Cell ; 35(1): 351-368, 2023 01 02.
Artigo em Inglês | MEDLINE | ID: mdl-36268892

RESUMO

The highly diverse Solanaceae family contains several widely studied models and crop species. Fully exploring, appreciating, and exploiting this diversity requires additional model systems. Particularly promising are orphan fruit crops in the genus Physalis, which occupy a key evolutionary position in the Solanaceae and capture understudied variation in traits such as inflorescence complexity, fruit ripening and metabolites, disease and insect resistance, self-compatibility, and most notable, the striking inflated calyx syndrome (ICS), an evolutionary novelty found across angiosperms where sepals grow exceptionally large to encapsulate fruits in a protective husk. We recently developed transformation and genome editing in Physalis grisea (groundcherry). However, to systematically explore and unlock the potential of this and related Physalis as genetic systems, high-quality genome assemblies are needed. Here, we present chromosome-scale references for P. grisea and its close relative Physalis pruinosa and use these resources to study natural and engineered variations in floral traits. We first rapidly identified a natural structural variant in a bHLH gene that causes petal color variation. Further, and against expectations, we found that CRISPR-Cas9-targeted mutagenesis of 11 MADS-box genes, including purported essential regulators of ICS, had no effect on inflation. In a forward genetics screen, we identified huskless, which lacks ICS due to mutation of an AP2-like gene that causes sepals and petals to merge into a single whorl of mixed identity. These resources and findings elevate Physalis to a new Solanaceae model system and establish a paradigm in the search for factors driving ICS.


Assuntos
Physalis , Solanaceae , Solanaceae/genética , Physalis/genética , Physalis/metabolismo , Evolução Biológica , Mutação , Edição de Genes
7.
Bioinformatics ; 40(8)2024 08 02.
Artigo em Inglês | MEDLINE | ID: mdl-39110522

RESUMO

MOTIVATION: A common method for analyzing genomic repeats is to produce a sequence similarity matrix visualized via a dot plot. Innovative approaches such as StainedGlass have improved upon this classic visualization by rendering dot plots as a heatmap of sequence identity, enabling researchers to better visualize multi-megabase tandem repeat arrays within centromeres and other heterochromatic regions of the genome. However, computing the similarity estimates for heatmaps requires high computational overhead and can suffer from decreasing accuracy. RESULTS: In this work, we introduce ModDotPlot, an interactive and alignment-free dot plot viewer. By approximating average nucleotide identity via a k-mer-based containment index, ModDotPlot produces accurate plots orders of magnitude faster than StainedGlass. We accomplish this through the use of a hierarchical modimizer scheme that can visualize the full 128 Mb genome of Arabidopsis thaliana in under 5 min on a laptop. ModDotPlot is bundled with a graphical user interface supporting real-time interactive navigation of entire chromosomes. AVAILABILITY AND IMPLEMENTATION: ModDotPlot is available at https://github.com/marbl/ModDotPlot.


Assuntos
Arabidopsis , Software , Sequências de Repetição em Tandem , Arabidopsis/genética , Sequências de Repetição em Tandem/genética , Genoma de Planta , Interface Usuário-Computador , Genômica/métodos
8.
Nature ; 570(7759): 117-121, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31068692

RESUMO

Aneuploidy, which refers to unbalanced chromosome numbers, represents a class of genetic variation that is associated with cancer, birth defects and eukaryotic micro-organisms1-4. Whereas it is known that each aneuploid chromosome stoichiometry can give rise to a distinct pattern of gene expression and phenotypic profile4,5, it remains a fundamental question as to whether there are common cellular defects that are associated with aneuploidy. Here we show the existence in budding yeast of a common aneuploidy gene-expression signature that is suggestive of hypo-osmotic stress, using a strategy that enables the observation of common transcriptome changes of aneuploidy by averaging out karyotype-specific dosage effects in aneuploid yeast-cell populations with random and diverse chromosome stoichiometry. Consistently, aneuploid yeast exhibited increased plasma-membrane stress that led to impaired endocytosis, and this defect was also observed in aneuploid human cells. Thermodynamic modelling showed that hypo-osmotic-like stress is a general outcome of the proteome imbalance that is caused by aneuploidy, and also predicted a relationship between ploidy and cell size that was observed in yeast and aneuploid cancer cells. A genome-wide screen uncovered a general dependency of aneuploid cells on a pathway of ubiquitin-mediated endocytic recycling of nutrient transporters. Loss of this pathway, coupled with the endocytic defect inherent to aneuploidy, leads to a marked alteration of intracellular nutrient homeostasis.


Assuntos
Aneuploidia , Pressão Osmótica , Proteoma/genética , Proteoma/metabolismo , Saccharomyces cerevisiae/citologia , Saccharomyces cerevisiae/genética , Estresse Fisiológico , Membrana Celular/metabolismo , Membrana Celular/patologia , Proteínas de Ligação a DNA/metabolismo , Endocitose , Complexos Endossomais de Distribuição Requeridos para Transporte/metabolismo , Homeostase , Humanos , Cariótipo , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Termodinâmica , Fatores de Transcrição/metabolismo , Transcriptoma/genética , Ubiquitina/metabolismo , Complexos Ubiquitina-Proteína Ligase/metabolismo
9.
Proc Natl Acad Sci U S A ; 119(34): e2120665119, 2022 Aug 23.
Artigo em Inglês | MEDLINE | ID: mdl-35984901

RESUMO

Despite a long and rich history of scientific investigation, fluid turbulence remains one of the most challenging problems in science and engineering. One of the key outstanding questions concerns the role of coherent structures that describe frequently observed patterns embedded in turbulence. It has been suggested, but not proved, that coherent structures correspond to unstable, recurrent solutions of the governing equation of fluid dynamics. Here, we present experimental and numerical evidence that three-dimensional turbulent flow tracks, episodically but repeatedly, the spatial and temporal structure of multiple such solutions. Our results provide compelling evidence that coherent structures, grounded in the governing equations, can be harnessed to predict how turbulent flows evolve.

10.
Genome Res ; 31(5): 910-918, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33811084

RESUMO

An increasingly important scenario in population genetics is when a large cohort has been genotyped using a low-resolution approach (e.g., microarrays, exome capture, short-read WGS), from which a few individuals are resequenced using a more comprehensive approach, especially long-read sequencing. The subset of individuals selected should ensure that the captured genetic diversity is fully representative and includes variants across all subpopulations. For example, human variation has historically focused on individuals with European ancestry, but this represents a small fraction of the overall diversity. Addressing this, SVCollector identifies the optimal subset of individuals for resequencing by analyzing population-level VCF files from low-resolution genotyping studies. It then computes a ranked list of samples that maximizes the total number of variants present within a subset of a given size. To solve this optimization problem, SVCollector implements a fast, greedy heuristic and an exact algorithm using integer linear programming. We apply SVCollector on simulated data, 2504 human genomes from the 1000 Genomes Project, and 3024 genomes from the 3000 Rice Genomes Project and show the rankings it computes are more representative than alternative naive strategies. When selecting an optimal subset of 100 samples in these cohorts, SVCollector identifies individuals from every subpopulation, whereas naive methods yield an unbalanced selection. Finally, we show the number of variants present in cohorts selected using this approach follows a power-law distribution that is naturally related to the population genetic concept of the allele frequency spectrum, allowing us to estimate the diversity present with increasing numbers of samples.


Assuntos
Genoma Humano , Polimorfismo de Nucleotídeo Único , Exoma/genética , Frequência do Gene , Genética Populacional , Humanos , Análise de Sequência de DNA/métodos
11.
Genome Res ; 31(7): 1203-1215, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-33947700

RESUMO

In contrast to the western honey bee, Apis mellifera, other honey bee species have been largely neglected despite their importance and diversity. The genetic basis of the evolutionary diversification of honey bees remains largely unknown. Here, we provide a genome-wide comparison of three honey bee species, each representing one of the three subgenera of honey bees, namely the dwarf (Apis florea), giant (A. dorsata), and cavity-nesting (A. mellifera) honey bees with bumblebees as an outgroup. Our analyses resolve the phylogeny of honey bees with the dwarf honey bees diverging first. We find that evolution of increased eusocial complexity in Apis proceeds via increases in the complexity of gene regulation, which is in agreement with previous studies. However, this process seems to be related to pathways other than transcriptional control. Positive selection patterns across Apis reveal a trade-off between maintaining genome stability and generating genetic diversity, with a rapidly evolving piRNA pathway leading to genomes depleted of transposable elements, and a rapidly evolving DNA repair pathway associated with high recombination rates in all Apis species. Diversification within Apis is accompanied by positive selection in several genes whose putative functions present candidate mechanisms for lineage-specific adaptations, such as migration, immunity, and nesting behavior.

12.
Nat Rev Genet ; 19(6): 329-346, 2018 06.
Artigo em Inglês | MEDLINE | ID: mdl-29599501

RESUMO

Several new genomics technologies have become available that offer long-read sequencing or long-range mapping with higher throughput and higher resolution analysis than ever before. These long-range technologies are rapidly advancing the field with improved reference genomes, more comprehensive variant identification and more complete views of transcriptomes and epigenomes. However, they also require new bioinformatics approaches to take full advantage of their unique characteristics while overcoming their complex errors and modalities. Here, we discuss several of the most important applications of the new technologies, focusing on both the currently available bioinformatics tools and opportunities for future research.


Assuntos
Mapeamento Cromossômico/métodos , Biologia Computacional/métodos , Perfilação da Expressão Gênica/métodos , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Transcriptoma , Animais , Humanos
13.
BMC Bioinformatics ; 24(1): 263, 2023 Jun 23.
Artigo em Inglês | MEDLINE | ID: mdl-37353753

RESUMO

BACKGROUND: Protein-protein interactions play a crucial role in almost all cellular processes. Identifying interacting proteins reveals insight into living organisms and yields novel drug targets for disease treatment. Here, we present a publicly available, automated pipeline to predict genome-wide protein-protein interactions and produce high-quality multimeric structural models. RESULTS: Application of our method to the Human and Yeast genomes yield protein-protein interaction networks similar in quality to common experimental methods. We identified and modeled Human proteins likely to interact with the papain-like protease of SARS-CoV2's non-structural protein 3. We also produced models of SARS-CoV2's spike protein (S) interacting with myelin-oligodendrocyte glycoprotein receptor and dipeptidyl peptidase-4. CONCLUSIONS: The presented method is capable of confidently identifying interactions while providing high-quality multimeric structural models for experimental validation. The interactome modeling pipeline is available at usegalaxy.org and usegalaxy.eu.


Assuntos
COVID-19 , Mapeamento de Interação de Proteínas , Humanos , RNA Viral/metabolismo , SARS-CoV-2 , Saccharomyces cerevisiae/metabolismo
14.
N Engl J Med ; 382(6): 525-533, 2020 02 06.
Artigo em Inglês | MEDLINE | ID: mdl-32023372

RESUMO

BACKGROUND: We previously reported the results of a trial of prenatal vitamin D supplementation to prevent asthma and recurrent wheeze in young children, which suggested that supplementation provided a protective effect at the age of 3 years. We followed the children through the age of 6 years to determine the course of asthma and recurrent wheeze. METHODS: In this follow-up study, investigators and participants remained unaware of the treatment assignments through the children's sixth birthday. We aimed to determine whether, when maternal levels of 25-hydroxyvitamin D were taken into account, children born to mothers who had received 4400 IU of vitamin D3 per day during pregnancy (vitamin D group) would have a lower incidence of asthma and recurrent wheeze at the age of 6 years than would those born to mothers who had received 400 IU of vitamin D3 per day (control group). Time-to-event methods were used to compare the treatment groups with respect to time to the onset of asthma or recurrent wheeze. Multivariate methods were used to compare longitudinal measures of lung function between the treatment groups. RESULTS: There was no effect of maternal vitamin D supplementation on asthma and recurrent wheeze in either an intention-to-treat analysis or an analysis with stratification according to the maternal 25-hydroxyvitamin D level during pregnancy. There was no effect of prenatal vitamin D supplementation on most of the prespecified secondary outcomes. We found no effects of prenatal supplementation on spirometric indexes. Although there was a very small effect on airway resistance as measured by impulse oscillometry, this finding was of uncertain significance. CONCLUSIONS: Vitamin D supplementation during the prenatal period alone did not influence the 6-year incidence of asthma and recurrent wheeze among children who were at risk for asthma. (Funded by the National Heart, Lung, and Blood Institute; VDAART ClinicalTrials.gov number, NCT00920621.).


Assuntos
Resistência das Vias Respiratórias/efeitos dos fármacos , Asma/prevenção & controle , Suplementos Nutricionais , Cuidado Pré-Natal , Vitamina D/administração & dosagem , Vitaminas/administração & dosagem , Asma/epidemiologia , Criança , Feminino , Seguimentos , Humanos , Incidência , Análise de Intenção de Tratamento , Pulmão/efeitos dos fármacos , Pulmão/embriologia , Gravidez , Sons Respiratórios/efeitos dos fármacos , Espirometria , Vitamina D/análogos & derivados , Vitamina D/sangue
15.
Genome Res ; 30(9): 1258-1273, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32887686

RESUMO

Improved identification of structural variants (SVs) in cancer can lead to more targeted and effective treatment options as well as advance our basic understanding of the disease and its progression. We performed whole-genome sequencing of the SKBR3 breast cancer cell line and patient-derived tumor and normal organoids from two breast cancer patients using Illumina/10x Genomics, Pacific Biosciences (PacBio), and Oxford Nanopore Technologies (ONT) sequencing. We then inferred SVs and large-scale allele-specific copy number variants (CNVs) using an ensemble of methods. Our findings show that long-read sequencing allows for substantially more accurate and sensitive SV detection, with between 90% and 95% of variants supported by each long-read technology also supported by the other. We also report high accuracy for long reads even at relatively low coverage (25×-30×). Furthermore, we integrated SV and CNV data into a unifying karyotype-graph structure to present a more accurate representation of the mutated cancer genomes. We find hundreds of variants within known cancer-related genes detectable only through long-read sequencing. These findings highlight the need for long-read sequencing of cancer genomes for the precise analysis of their genetic instability.


Assuntos
Neoplasias da Mama/genética , Variação Estrutural do Genoma , Sequenciamento Completo do Genoma/métodos , Linhagem Celular Tumoral , Variações do Número de Cópias de DNA , Metilação de DNA , DNA de Neoplasias , Feminino , Humanos , Nanoporos , Organoides , RNA-Seq
16.
PLoS Pathog ; 17(4): e1009537, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33930099

RESUMO

Klebsiella pneumoniae (Kp) is an important cause of healthcare-associated infections, which increases patient morbidity, mortality, and hospitalization costs. Gut colonization by Kp is consistently associated with subsequent Kp disease, and patients are predominantly infected with their colonizing strain. Our previous comparative genomics study, between disease-causing and asymptomatically colonizing Kp isolates, identified a plasmid-encoded tellurite (TeO3-2)-resistance (ter) operon as strongly associated with infection. However, TeO3-2 is extremely rare and toxic to humans. Thus, we used a multidisciplinary approach to determine the biological link between ter and Kp infection. First, we used a genomic and bioinformatic approach to extensively characterize Kp plasmids encoding the ter locus. These plasmids displayed substantial variation in plasmid incompatibility type and gene content. Moreover, the ter operon was genetically independent of other plasmid-encoded virulence and antibiotic resistance loci, both in our original patient cohort and in a large set (n = 88) of publicly available ter operon-encoding Kp plasmids, indicating that the ter operon is likely playing a direct, but yet undescribed role in Kp disease. Next, we employed multiple mouse models of infection and colonization to show that 1) the ter operon is dispensable during bacteremia, 2) the ter operon enhances fitness in the gut, 3) this phenotype is dependent on the colony of origin of mice, and 4) antibiotic disruption of the gut microbiota eliminates the requirement for ter. Furthermore, using 16S rRNA gene sequencing, we show that the ter operon enhances Kp fitness in the gut in the presence of specific indigenous microbiota, including those predicted to produce short chain fatty acids. Finally, administration of exogenous short-chain fatty acids in our mouse model of colonization was sufficient to reduce fitness of a ter mutant. These findings indicate that the ter operon, strongly associated with human infection, encodes factors that resist stress induced by the indigenous gut microbiota during colonization. This work represents a substantial advancement in our molecular understanding of Kp pathogenesis and gut colonization, directly relevant to Kp disease in healthcare settings.


Assuntos
Microbioma Gastrointestinal/genética , Intestinos/microbiologia , Klebsiella/genética , Plasmídeos/genética , Animais , Bacteriemia/genética , Proteínas de Bactérias/genética , Feminino , Aptidão Genética/fisiologia , Loci Gênicos/fisiologia , Genoma Bacteriano , Interações Hospedeiro-Patógeno/genética , Resistência a Canamicina/genética , Infecções por Klebsiella/microbiologia , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Óperon/genética , Especificidade de Órgãos/genética , Virulência/genética , beta-Lactamases/genética
17.
Curr Allergy Asthma Rep ; 23(3): 189-194, 2023 03.
Artigo em Inglês | MEDLINE | ID: mdl-36749447

RESUMO

PURPOSE OF REVIEW: We review the literature and discuss the logistics of testing pregnant patients for penicillin allergy. RECENT FINDINGS: As in the general population, pregnant patients commonly report a penicillin allergy, but most patients are able to tolerate penicillin. Avoidance of beta-lactams in pregnancy is associated with increased morbidity: longer hospitalizations, more frequent infections, and more complications. Penicillin allergy testing is safe in pregnant patients, and obstetricians are eager for allergists to offer this procedure to their patients. As allergists, we can improve our patients' health outcomes by offering penicillin allergy testing in our practices. The protocols for testing both with and without skin testing in pregnant patients have been studied, and future studies will continue to clarify the safety and efficacy of penicillin allergy delabeling in pregnant patients.


Assuntos
Hipersensibilidade a Drogas , Hipersensibilidade , Gravidez , Feminino , Humanos , beta-Lactamas , Antibacterianos/uso terapêutico , Penicilinas , Hipersensibilidade a Drogas/epidemiologia , Testes Cutâneos/métodos , Hipersensibilidade/tratamento farmacológico
18.
Nucleic Acids Res ; 49(21): e124, 2021 12 02.
Artigo em Inglês | MEDLINE | ID: mdl-34551429

RESUMO

Genome copy number is an important source of genetic variation in health and disease. In cancer, Copy Number Alterations (CNAs) can be inferred from short-read sequencing data, enabling genomics-based precision oncology. Emerging Nanopore sequencing technologies offer the potential for broader clinical utility, for example in smaller hospitals, due to lower instrument cost, higher portability, and ease of use. Nonetheless, Nanopore sequencing devices are limited in the number of retrievable sequencing reads/molecules compared to short-read sequencing platforms, limiting CNA inference accuracy. To address this limitation, we targeted the sequencing of short-length DNA molecules loaded at optimized concentration in an effort to increase sequence read/molecule yield from a single nanopore run. We show that short-molecule nanopore sequencing reproducibly returns high read counts and allows high quality CNA inference. We demonstrate the clinical relevance of this approach by accurately inferring CNAs in acute myeloid leukemia samples. The data shows that, compared to traditional approaches such as chromosome analysis/cytogenetics, short molecule nanopore sequencing returns more sensitive, accurate copy number information in a cost effective and expeditious manner, including for multiplex samples. Our results provide a framework for short-molecule nanopore sequencing with applications in research and medicine, which includes but is not limited to, CNAs.


Assuntos
Variações do Número de Cópias de DNA , DNA/análise , Oncologia/métodos , Sequenciamento por Nanoporos/métodos , Neoplasias/genética , Linhagem Celular Tumoral , Humanos
19.
BMC Bioinformatics ; 23(1): 452, 2022 Oct 31.
Artigo em Inglês | MEDLINE | ID: mdl-36316646

RESUMO

BACKGROUND: In modern sequencing experiments, quickly and accurately identifying the sources of the reads is a crucial need. In metagenomics, where each read comes from one of potentially many members of a community, it can be important to identify the exact species the read is from. In other settings, it is important to distinguish which reads are from the targeted sample and which are from potential contaminants. In both cases, identification of the correct source of a read enables further investigation of relevant reads, while minimizing wasted work. This task is particularly challenging for long reads, which can have a substantial error rate that obscures the origins of each read. RESULTS: Existing tools for the read classification problem are often alignment or index-based, but such methods can have large time and/or space overheads. In this work, we investigate the effectiveness of several sampling and sketching-based approaches for read classification. In these approaches, a chosen sampling or sketching algorithm is used to generate a reduced representation (a "screen") of potential source genomes for a query readset before reads are streamed in and compared against this screen. Using a query read's similarity to the elements of the screen, the methods predict the source of the read. Such an approach requires limited pre-processing, stores and works with only a subset of the input data, and is able to perform classification with a high degree of accuracy. CONCLUSIONS: The sampling and sketching approaches investigated include uniform sampling, methods based on MinHash and its weighted and order variants, a minimizer-based technique, and a novel clustering-based sketching approach. We demonstrate the effectiveness of these techniques both in identifying the source microbial genomes for reads from a metagenomic long read sequencing experiment, and in distinguishing between long reads from organisms of interest and potential contaminant reads. We then compare these approaches to existing alignment, index and sketching-based tools for read classification, and demonstrate how such a method is a viable alternative for determining the source of query reads. Finally, we present a reference implementation of these approaches at https://github.com/arun96/sketching .


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala , Software , Análise de Sequência de DNA/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Metagenômica/métodos , Metagenoma , Algoritmos
20.
Mol Microbiol ; 116(1): 260-276, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-33713372

RESUMO

Candida glabrata is an opportunistic pathogen of humans, responsible for up to 30% of disseminated candidiasis. Adherence of C. glabrata to host cells is mediated by adhesin-like proteins (ALPs), about half of which are encoded in the subtelomeres. We performed a de novo assembly of two C. glabrata strains, BG2 and BG3993, using long single-molecule real-time (SMRT) reads, and constructed high-quality telomere-to-telomere assemblies of all 13 chromosomes to assess differences between C. glabrata strains. We documented variation between strains, and in agreement with earlier studies, found high (~0.5%-1%) frequencies of SNVs across the genome, including within subtelomeric regions. We documented changes in ALP gene structure and complement: there are large length differences in ALP genes in different strains, resulting from copy number variation in tandem repeats. We compared strains to characterize chromosome rearrangement events including within the poorly characterized subtelomeric regions. We show that rearrangements within the subtelomere regions all affect ALP-encoding genes, and 14/16 involve just the most terminal ALP gene. We present evidence that these rearrangements are mediated by break-induced replication. This study highlights the constrained nature of subtelomeric changes impacting ALP gene complement and subtelomere structure.


Assuntos
Candida glabrata/genética , Moléculas de Adesão Celular/genética , Telômero/genética , Candidíase/microbiologia , Adesão Celular/fisiologia , Regulação Fúngica da Expressão Gênica/genética , Genoma Fúngico/genética , Humanos , Polimorfismo de Nucleotídeo Único/genética , Recombinação Genética/genética
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