RESUMO

Single-cell Hi-C (scHi-C) is a collection of protocols for studying genomic interactions within individual cells. Although data analysis for scHi-C resembles data analysis for bulk Hi-C, the unique challenges of scHi-C, such as high noise and protocol-specific biases, require specialized data processing strategies. In this tutorial chapter, we focus on using pairtools, a suite of tools optimized for scHi-C data, demonstrating its application on a Drosophila snHi-C dataset. While centered on pairtools for snHi-C data, the principles outlined are applicable across scHi-C variants with minor adjustments. This educational chapter aims to guide researchers in using open-source tools for scHi-C analysis, emphasizing critical steps of contact pair extraction, detection of ligation junctions, filtration, and deduplication.

Assuntos

Genômica , Análise de Célula Única , Software , Fluxo de Trabalho , Análise de Célula Única/métodos , Animais , Genômica/métodos , Drosophila/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Biologia Computacional/métodos

RESUMO

Celiac disease is an autoimmune enteropathy caused by the ingestion of minute amounts of gluten in a subset of genetically predisposed individuals. Its onset occurs at different ages and with variable symptoms. The gut microbiome may contribute to this variability. This review aims to provide an overview of the available research on celiac disease gut microbiome and identify the knowledge gap that could guide future studies. Following the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-analysis extension for Scoping Reviews (PRISMA-ScR), four electronic databases were searched for literature from January 2000 to July 2023 addressing celiac disease gut microbiome characterization using next-generation sequencing (NGS) approaches. From the 489 publications retrieved, 48 publications were selected and analyzed, focusing on sample characterization (patients, controls, and tissues) and methodologies used for NGS microbiome analysis and characterization. The majority of the selected publications regarded children and adults, and four were randomized clinical trials. The number of participants per study greatly varied and was typically low. Feces were the most frequently tested sample matrix, and duodenal samples were analyzed in one-third of the studies. Incomplete and diverse information on the methodological approaches and gut microbiome results was broadly observed. While similar trends regarding the relative abundance of some phyla, such as Pseudomonadota (former Proteobacteria), were detected in some studies, others contradicted those results. The observed high variability of technical approaches and possibly low power and sample sizes may prevent reaching a consensus on celiac disease gut microbiome composition. Standardization of research protocols to allow reproducibility and comparability is required, as interdisciplinary collaborations to further data analysis, interpretation, and, more importantly, health outcome prediction or improvement.

RESUMO

DNA markers serve as essential tools in breeding selection and genetic analysis. However, developing DNA markers can be time-consuming and labor-intensive due to the need to identify polymorphisms between cultivars/lines and to design suitable primers. To address these challenges, we have developed DNAMarkMaker, a tool designed to automate the process of primer design for Amplification Refractory Mutation System (ARMS) and Cleaved Amplified Polymorphic Sequences (CAPS) markers, utilizing resequencing data. One key feature of DNAMarkMaker is its user-friendly graphical user interface (GUI), ensuring its accessibility and ease of use, even for researchers not well-versed in bioinformatics. We confirmed DNAMarkMaker's applicability by developing DNA markers for rice, potato, and turnip-each representing distinct genome structures: homozygous diploid, heterozygous autotetraploid, and heterozygous diploid, respectively. DNAMarkMaker will contribute to the rapid and efficient development of DNA markers, accelerating breeding and genetic analysis in various crops.

RESUMO

BACKGROUND: Somatic genetic alterations of the estrogen receptor 1 gene (ESR1) are enriched in endocrine therapy-resistant, estrogen receptor-positive (ER+) metastatic breast cancer (mBC). Herein, we investigated and compared the clinical and genomic landscape of ESR1-mutant (ESR1MUT) and ESR1 wild type (ESR1WT) ER+/ human epidermal growth factor receptor 2 (HER2)- mBCs. METHODS: Clinical and genomic data were retrieved from cBioPortal using the publicly-available MSK MetTropism dataset. Metastatic, ER+/HER2- mBC samples were included in the analysis. Only oncogenic and likely oncogenic alterations according to OncoKB were included. Statistical analyses were carried out using alpha level of 0.05, with a false discovery rate threshold of 10% for multiple comparisons using the Benjamini-Hochberg method. RESULTS: Among 679 samples, 136 ESR1MUT among 131 tumors were found (19.2%). The frequency of ESR1MUT was higher in ductal versus lobular mBC (21.2% versus 13.8%, P = 0.052) and enriched in liver metastasis compared with other sites (22.5% versus 12.7%; q = 0.02). Compared with ESR1WT mBC, ESR1MUT tumors showed higher fraction of genome altered (FGA) {[0.28 interquartile range (IQR), 0.15-0.43] versus 0.22 (0.11-0.38); P = 0.04} and tumor mutational burden (TMB) [4.89 (IQR 3.46-6.85) versus 3.92 (2.59-6.05) mut/Mb; P = 0.001]. Tumors harboring p.E380X alterations showed higher TMB compared with those with H11-12 alterations [8.24 (IQR 5.06-15.3) versus 4.89 (IQR 3.46-6.75) mut/Mb; P = 0.01]. Genetic alterations of TP53 were enriched in ESR1WT tumors (36% versus 14%) [odds ratio (OR) 3.17, 95% confidence interval (CI) 1.88-5.64, q = 0.001]. Considering signaling pathways, ESR1MUT tumors showed a lower occurrence of TP53 (OR 0.48, 95% CI 0.30-0.74; q = 0.003) and MAPK (OR 0.29, 95% CI 0.11-0.65; q = 0.009) alterations. TP53 (q < 0.001), CDH1 (q < 0.001), and ERBB2 (q < 0.001) demonstrated mutual exclusivity with ESR1MUT. CONCLUSIONS: ER+/HER2- mBCs carrying ESR1MUT exhibit a divergent genomic background, characterized by a lower prevalence of TP53 and MAPK pathway alterations. Less common ESR1 alterations falling outside the H11-H12 region seem to occur in tumors with higher TMB, deserving further investigation to understand their potential actionability.

RESUMO

Crystal-storing histiocytosis is a rare entity due to tumorous deposits of histiocytes containing crystalline inclusions, which in a majority of cases are made of immunoglobulins associated with lymphoproliferative disorders, although association with non-neoplastic disorders has also been reported. The histiocytes may be so abundant to obscure the underlying lymphoplasmacytic neoplasm. On the other hand, the Gaucher-like histiocytes might lead to a misinterpretation of granulomatous inflammation or storage disease. Herein, this case study reported clinical, pathological and next generation sequencing (NGS) features of a case of kappa chain myeloma with Gaucher-like crystal-storing histiocytosis in the bone marrow (BM). The methodology included BM aspiration and biopsy, immunohistochemistry, electron microscopy and NGS study by TruSight Oncology 500. Morphologically, the BM smear showed dense infiltration of sea blue histiocytes and atypical plasma cells with rhomboid crystals in cytoplasm. The BM biopsy showed excessive plasmacytic aggregates and dense histiocytic infiltrates with wrinkled paper-like or needle shaped cytoplasm. These plasma cells were positive for CD138 and showed lambda chain restriction. Electron microscopy highlighted the long rhomboid crystals with distinct periodicity consistent with crystalline immunoglobulins in the histiocytes. In addition, the NGS study from the BM aspiration specimen revealed PARP1, MSH6, KDR, CCND3 and STK11 mutations, which might be associated with inferior survival of myeloma patients. Accordingly, this case died of pneumonia with septic shock during treatment. Our findings suggest that the presence of rhomboid crystals in bone marrow smears may alert pathologists to look for the possibility of crystal-storing histiocytosis and the prognosis of patients with multiple myeloma may depend on the genetic features of tumor cells rather than the association with crystal-storing histiocytosis.

RESUMO

S-methyl-5'-thioadenosine phosphorylase (MTAP) deficiency is an emerging biomarker in non-small cell lung cancer (NSCLC) and beyond. The MTAP gene is located in the chromosomal region 9p21.3, which shows one of the most common homozygous deletions across all human cancers (9p21 loss). Loss of 9p21 is found in the majority of pleural mesotheliomas, where it serves as an established diagnostic marker. Until recently, fluorescence in situ hybridization (FISH) was the gold standard for the detection of 9p21 losses, but loss of MTAP expression by immunohistochemistry (IHC) gains increasing importance as an easy to apply and cost-effective diagnostic surrogate marker. Besides, MTAP loss, which has been reported in 13% of NSCLC, is becoming an emerging predictive biomarker in two different scenarios in NSCLC and other cancer types: 1) MTAP loss seems to negatively predict the response to immune checkpoint inhibitor (ICI) treatment via silencing of the tumor microenvironment, and 2) MTAP loss serves as a predictive biomarker for novel targeted treatment strategies. MTAP deficiency leads to an impaired function of the protein arginine methyltransferase 5 (PRMT5) due to its partial inhibition by MTAP's accumulating substrate methylthioadenosine (MTA). This process leaves MTAP deficient tumor cells heavily dependent on the remaining function of PRMT5, making it a perfect target for synthetic lethality. Indeed, MTA-cooperative PRMT5-inhibitors are now tested in several clinical trials with promising early results in solid malignancies. With its emergence as a predictive biomarker, the implementation of MTAP IHC into diagnostic routine for NSCLC and other tumors is likely to take place soon. In this review article, we summarize the current literature on the role of MTAP in thoracic tumors and evaluate different testing methods, including IHC, FISH and next generation sequencing.

RESUMO

This article aims to bring clinicians' awareness to the widespread impact of urinary tract infection (UTI) on the lives of women and to the advances that offer hope for future improvements in the diagnosis and management of UTI. Thanks to physiological, anatomical, and lifestyle factor differences, women face heightened vulnerability to UTIs compared to men. In fact, women are four times more likely than men to develop a UTI and around half of these women encounter UTI recurrence, which is a significant source of both physical and psychosocial burdens. Despite the current shortcomings in diagnosis and management, emerging diagnostic technologies promise to identify UTIs more accurately and rapidly, offering women hope for a revolution in UTI management. Meanwhile, clinicians have the opportunity to reduce the psychosocial burden by recognizing the value of patients' lived experiences and ensuring their care plan is in alignment with their patients' goals and expectations for medical care.

RESUMO

Thrombotic hemangioma with organizing/anastomosing features (THOA) is a newly identified variant within the spectrum of hemangiomas that harbor mutations in the guanine nucleotide-binding protein alpha subunit (GNA) genes (like GNAQ or GNA11). While THOA shares similarities with anastomosing hemangioma, it possesses distinct clinical and morphological characteristics that make it a separate entity. All reported cases of THOA have demonstrated benign behavior. However, histologic features such as anastomosing vascular growth, mitotic figures, and endothelial hobnailing may raise concerns for a low-grade malignant vascular neoplasm. We report the case of a 74-year-old female with an unremarkable medical history who presented with a vascular lesion on her upper torso. The lesion persisted after the initial biopsy and was re-excised, displaying similar histologic characteristics. Next-generation sequencing (NGS) revealed a GNAQ mutation (p.Q209H) in both samples. Notably, a TP53 mutation (p.R273H) was detected in the first specimen but was absent in the subsequent excision. The lesion was diagnosed as persistent THOA. This case report discusses the salient features, genetic profile, and prognosis of this uncommon lesion.

RESUMO

Tamaricaceae comprises about 120 species and has a long evolutionary history, Tamarix Linn accounts for approximately 75% of the total species in this family. It is the most widely distributed and diverse genus in the family. They have important ecological significance for transforming deserts and improving climate conditions. However, Tamarix is the most poorly classified genera among flowering plants owing to its large variability and high susceptibility to interspecific hybridization. In this study, the complete chloroplast genomes of three Tamarix species and one draft chloroplast genome were obtained in this study. Combined with eight chloroplast genomes deposited in GenBank, complete chloroplast sequences of 12 Tamarix species were used for further analysis. There are 176 non-SSR-related indels and 681 non-indel-related SSRs in the 12 Tamarix chloroplast genomes. The mononucleotide SSRs are the most prevalent among all types of SSRs. The mVISTA results indicate high sequence similarities across the chloroplast genome, suggesting that the chloroplast genomes are highly conserved, except for sample Tamarix androssowii (ENC850343). The IR regions and the coding regions are more conserved than the single-copy and noncoding regions. The trnF-ndhJ, ndhC-trnM-CAU, ycf1, and trnL-UAG-ndhF regions are the most variable and have higher variability than those of the universal DNA markers. Finally, the first phylogenetic tree of Tamaricaceae was constructed which confirmed the monophyly of Tamarix in Tamaricaceae. The first phylogenetic tree of Tamarix was based on the complete chloroplast genome to date, the changes in branch length and support rate can potentially help us clarify the phylogenetic relationships of Tamarix. All the obtained genetic resources will facilitate future studies in population genetics, species identification, and conservation biology of Tamarix.

RESUMO

Hunner-type interstitial cystitis (HIC) is a chronic inflammatory disease of the urinary bladder with an unknown etiology. We conducted comprehensive immunogenomic profiling of bladder specimens obtained by biopsy and cystectomy from 37 patients with HIC. Next-generation RNA sequencing demonstrated abundant plasma cell infiltration with frequent light chain restriction in HIC-affected bladder tissue. Subsequent analysis of the B-cell receptor repertoire revealed spatial and temporal expansion of B-cell clones. The extent of B-cell clonal expansion was significantly correlated with the gene expression levels of TNFSF13 and TNFSF13B, which encode APRIL and BAFF, respectively. These findings indicate that APRIL and BAFF are the key regulators of clonal B-cell expansion in HIC and might serve as therapeutic targets in this debilitating disease. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

RESUMO

PURPOSE OF REVIEW: A number of molecular characteristics are essential for accurate diagnosis and prognostication in glioma. RECENT FINDINGS: The 2021 WHO classification of brain tumors and recent Food and Drug Administration (FDA) pathology agnostic drug approvals highlight the importance of molecular testing in the management of glioma. For diffuse gliomas, it is important to identify IDH mutations, given the favorable clinical behavior and potential for using FDA approved IDH inhibitors in the near future. MGMT promoter methylation testing is the most established molecular marker for response to temozolomide in IDH wild-type glioblastoma and in turn impacts overall survival. Moreover, identification of certain mutations and molecular markers, such as BRAF V600E, hypermutation or elevated tumor-mutational burden and NTRK fusions allow for the use of FDA approved agents that are tumor-agnostic. Finally, molecular testing opens options for clinical trials that are essential for diseases with limited treatment options like gliomas.

RESUMO

Next-generation sequencing (NGS) coupled with bioinformatic tools has revolutionized the detection of copy number variations (CNVs), which are implicated in the emergence of Mendelian disorders. In this study, we evaluated the diagnostic yield of exome sequencing-based CNV analysis in 449 patients with suspected Mendelian disorders. We aimed to assess the diagnostic yield of this recently utilized method and expand the clinical spectrum of intragenic CNVs. The cohort underwent whole exome sequencing (WES) and clinical exome sequencing (CES). Using GATK-gCNV, we identified 12 pathogenic CNVs that correlated with their clinical findings and resulting in a diagnostic yield of 2.67%. Importantly, the study emphasizes the role of CNVs in the etiology of Mendelian disorders and highlights the value of exome sequencing-based CNV analysis in routine diagnostic processes.

Assuntos

Variações do Número de Cópias de DNA , Sequenciamento do Exoma , Doenças Genéticas Inatas , Humanos , Masculino , Feminino , Doenças Genéticas Inatas/genética , Doenças Genéticas Inatas/diagnóstico , Criança , Adulto , Pré-Escolar , Adolescente , Sequenciamento de Nucleotídeos em Larga Escala , Exoma/genética , Lactente , Pessoa de Meia-Idade , Adulto Jovem

RESUMO

BACKGROUND: Accurate identification of the etiology of lower respiratory tract infections (LRTI) is crucial, particularly for immunocompromised patients with more complex etiologies. The advent of next-generation sequencing (NGS) has enhanced the effectiveness of pathogen detection. However, assessments of the clinical diagnostic value of targeted NGS (tNGS) in immunocompromised patients with LRTI are limited. METHODS: To evaluate the diagnostic value of tNGS in immunocompromised patients with LRTI, a total of 88 patients, of whom 54 were immunocompromised, were enrolled. These patients underwent tNGS testing of bronchoalveolar lavage fluid (BALF). Results from both metagenomic next-generation sequencing (mNGS) and conventional microbiological tests (CMT) were also available for all participants. The performance of tNGS was assessed by comparing its findings against mNGS, CMT, and the clinical composite diagnosis. RESULTS: In the cohort of 88 patients, tNGS showed comparable diagnostic value to mNGS and was significantly superior to CMT. Compared to CMT and composite reference standard, tNGS showed sensitivity of 94.55% and 90.48%, respectively. In immunocompromised patients, despite a more diverse pathogen variety, tNGS maintained similar sensitivity to mNGS and outperformed CMT. tNGS positively influenced etiologic diagnosis and antibiotic decision-making in 72.72% of cases, leading to a change in antibiotic regimen in 17.05% of cases. We also compared the detection of microbial nucleic acids by tNGS with mNGS and found that tNGS could identify 87.99% of the microbial nucleic acids identified by mNGS. CONCLUSION: In summary, our study demonstrated that tNGS offers promising clinical diagnostic accuracy in immunocompromised patients, as evidenced by its favorable comparison with CMT, the composite reference standard, and mNGS.

Assuntos

Líquido da Lavagem Broncoalveolar , Sequenciamento de Nucleotídeos em Larga Escala , Hospedeiro Imunocomprometido , Metagenômica , Infecções Respiratórias , Humanos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Masculino , Feminino , Metagenômica/métodos , Infecções Respiratórias/diagnóstico , Infecções Respiratórias/microbiologia , Pessoa de Meia-Idade , Líquido da Lavagem Broncoalveolar/microbiologia , Idoso , Adulto , Sensibilidade e Especificidade , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/classificação , Adulto Jovem

RESUMO

[This corrects the article DOI: 10.3389/fcimb.2024.1436509.].

RESUMO

While significant strides have been made in understanding pharmacogenetics (PGx) and gene-drug interactions, there remains limited characterization of population-level PGx variation. This study aims to comprehensively profile global star alleles (haplotype patterns) and phenotype frequencies in 58 pharmacogenes associated with drug absorption, distribution, metabolism, and excretion. PyPGx, a star-allele calling tool, was employed to identify star alleles within high-coverage whole genome sequencing (WGS) data from the 1000 Genomes Project (N = 2504; 26 global populations). This process involved detecting structural variants (SVs), such as gene deletions, duplications, hybrids, as well as single nucleotide variants and insertion-deletion variants. The majority of our PyPGx calls for star alleles and phenotype frequencies aligned with the Pharmacogenomics Knowledge Base, although notable population-specific frequencies differed at least twofold. Validation efforts confirmed known SVs while uncovering several novel SVs currently undefined as star alleles. Additionally, we identified 210 small nucleotide variants associated with severe functional consequences that are not defined as star alleles. The study serves as a valuable resource, providing updated population-level star allele and phenotype frequencies while incorporating SVs. It also highlights the burgeoning potential of cost-effective WGS for PGx genotyping, offering invaluable insights to improve tailored drug therapies across diverse populations.

Assuntos

Alelos , Farmacogenética , Sequenciamento Completo do Genoma , Humanos , Sequenciamento Completo do Genoma/métodos , Farmacogenética/métodos , Frequência do Gene , Polimorfismo de Nucleotídeo Único , Genoma Humano , Fenótipo , Haplótipos , Variação Estrutural do Genoma , Testes Farmacogenômicos/métodos , Projeto Genoma Humano

RESUMO

Three novel HLA-A intronic variants, HLA-A*03:01:01:121, HLA-A*29:02:01:41 and HLA-A*30:02:01:24, detected by next-generation sequencing.

Assuntos

Alelos , Antígenos HLA-A , Sequenciamento de Nucleotídeos em Larga Escala , Íntrons , Humanos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Antígenos HLA-A/genética , Teste de Histocompatibilidade/métodos , Antígeno HLA-A3/genética , Análise de Sequência de DNA/métodos

RESUMO

Background: When individuals infected with human immunodeficiency virus (HIV) experience pulmonary infections, they often exhibit severe symptoms and face a grim prognosis. Consequently, early, rapid, and accurate pathogen diagnosis is vital for informing effective treatment strategies. This study aimed to use metagenomic next-generation sequencing (mNGS) and targeted mNGS (tNGS) to elucidate the characteristics of pulmonary infections in HIV and non-HIV individuals. Methods: This study enrolled 90 patients with pulmonary infection at the Department of Infectious Diseases of The First Hospital of Jilin University from June 2022 to May 2023, and they were divided into HIV (n=46) and non-HIV (n=44) infection groups. Their bronchoalveolar lavage fluid (BALF) was collected for mNGS analysis to evaluate the differences in pulmonary infection pathogens, and tNGS detection was performed on BALF samples from 15 HIV-infected patients. Results: A total of 37 pathogens were identified in this study, including 21 bacteria, 5 fungi, 5 viruses, 5 mycobacteria, and 1 mycoplasma. The sensitivity of mNGS was 78.9% (71/90), which is significantly higher than that of conventional methods (CTM) (39/90, P=1.5E-8). The combination of mNGS with CTM can greatly enhance the sensitivity of pathogen detection. The prevalence of Pneumocystis jirovecii (82.6% vs. 9.1%), cytomegalovirus (CMV) (58.7% vs. 0%), and Epstein-Barr virus (EBV) (17.4% vs. 2.3%) was significantly higher in the HIV infection group than in the non-HIV infection group (P<0.05). Although no statistically significant difference was observed, the detection rate of Mycobacteria was higher in HIV-infected patients (17.4%) than in the non-HIV group (6.8%). Furthermore, the tNGS results of BALF from 15 HIV-infected patients were not entirely consistent with the mNGS results., and the concordance rate of tNGS for the detection of main pathogens reached 86.7% (13/15). Conclusion: Next-generation sequencing (NGS) can accurately detect pathogens in the BALF of patients with pulmonary infection. The sensitivity of tNGS is comparable to that of mNGS. Therefore, this technique should be promoted in the clinic for better patient outcomes.

Assuntos

Líquido da Lavagem Broncoalveolar , Infecções por HIV , Sequenciamento de Nucleotídeos em Larga Escala , Metagenômica , Humanos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Infecções por HIV/complicações , Infecções por HIV/virologia , Masculino , Feminino , Metagenômica/métodos , Líquido da Lavagem Broncoalveolar/microbiologia , Líquido da Lavagem Broncoalveolar/virologia , Pessoa de Meia-Idade , Adulto , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/classificação , Idoso , Sensibilidade e Especificidade , Vírus/genética , Vírus/isolamento & purificação , Vírus/classificação , Metagenoma , Infecções Respiratórias/virologia , Infecções Respiratórias/microbiologia , Infecções Respiratórias/diagnóstico

RESUMO

This case reports a middle-aged male patient who was HIV-negative and initially misdiagnosed as pulmonary tuberculosis but was eventually diagnosed with disseminated Talaromyces marneffei (T. marneffei) infection by next-generation sequencing. The patient presented with respiratory symptoms, recurrent bone pain, and subcutaneous masses as the main symptoms. After one year of antifungal treatment, the symptoms improved obviously, but the symptoms recurred after two weeks of drug withdrawal, and the symptoms were relieved after re-administration of antifungal drugs again. This report highlights the need for the rapid evaluation of fungal infections with metagenomic next-generation sequencing (mNGS) in patients with an inadequate diagnostic basis for tuberculosis infection or a poor response to antituberculosis drugs. In addition, long-term follow-up is needed to observe disease recurrence in patients with disseminated T. marneffei infection.

RESUMO

Introduction: The decreasing Helicobacter pylori eradication rate is primarily attributed to antibiotic resistance, and further exacerbated by uniform drug administration disregarding a host's metabolic capability. Consequently, applying personalized treatment based on antibiotic resistance-associated variants and the host's metabolic phenotype can potentially increase the eradication rate. Method: A custom next-generation sequencing panel for personalized H. pylori eradication treatment (NGS-PHET) was designed which targeted the regions for amoxicillin, clarithromycin, metronidazole, tetracycline, and levofloxacin-resistance in H. pylori and human proton-pump inhibitor (PPI) metabolism. The libraries were constructed following customized methods and sequenced simultaneously. The customized framework criteria, grounded in previously reported antibiotic resistance associated variants and the host's PPI metabolism, was applied to the NGS-PHET results and suggested a personalized treatment for each subject, which was validated through each subject's actual eradication outcome. Results: Both previously reported and novel variants were identified from H. pylori sequencing results. Concurrently, five CYP2C19 homozygous extensive metabolizers and three CYP3A4 intermediate metabolizers were identified. Among the total of 12 subjects, clarithromycin triple therapy was suggested for five subjects, bismuth quadruple therapy was suggested for six subjects, and rifabutin triple therapy was suggested for one subject by following the customized framework criteria. The treatment suggestion for nine of the 12 subjects was consistent with the treatment that each subject achieved eradication with. Discussion: Applying the methodology using the NGS-PHET and customized framework helps to perform eradication treatment quickly and effectively in most patients with antibiotic-resistant H. pylori strains, and is also useful in research to find novel antibiotic-resistance candidates.

Assuntos

Antibacterianos , Infecções por Helicobacter , Helicobacter pylori , Sequenciamento de Nucleotídeos em Larga Escala , Medicina de Precisão , Humanos , Helicobacter pylori/efeitos dos fármacos , Helicobacter pylori/genética , Infecções por Helicobacter/tratamento farmacológico , Infecções por Helicobacter/microbiologia , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Medicina de Precisão/métodos , Inibidores da Bomba de Prótons/uso terapêutico , Claritromicina/farmacologia , Claritromicina/uso terapêutico , Masculino , Farmacorresistência Bacteriana/genética , Pessoa de Meia-Idade , Feminino , Adulto , Quimioterapia Combinada , Metronidazol/farmacologia , Metronidazol/uso terapêutico , Amoxicilina/uso terapêutico , Amoxicilina/farmacologia , Citocromo P-450 CYP2C19/genética , Testes de Sensibilidade Microbiana , Levofloxacino/farmacologia , Levofloxacino/uso terapêutico , Tetraciclina/farmacologia , Tetraciclina/uso terapêutico , Resultado do Tratamento

RESUMO

Cancer neoantigens are tumor-specific non-synonymous mutant peptides that activate the immune system to produce an anti-tumor response. Personalized cancer vaccines based on neoantigens are currently one of the most promising therapeutic approaches for cancer treatment. By utilizing the unique mutations within each patient's tumor, these vaccines aim to elicit a strong and specific immune response against cancer cells. However, the identification of neoantigens remains challenging due to the low accuracy of current prediction tools and the high false-positive rate of candidate neoantigens. Since the concept of "proteogenomics" emerged in 2004, it has evolved rapidly with the increased sequencing depth of next-generation sequencing technologies and the maturation of mass spectrometry-based proteomics technologies to become a more comprehensive approach to neoantigen identification, allowing the discovery of high-confidence candidate neoantigens. In this review, we summarize the reason why cancer neoantigens have become attractive targets for immunotherapy, the mechanism of cancer vaccines and the advances in cancer immunotherapy. Considerations relevant to the application emerging of proteogenomics technologies for neoantigen identification and challenges in this field are described.