RESUMO

BACKGROUND: In this article, we delineate a loosely selected cohort comprising patients with a history of early-onset breast cancer and/or a familial occurrence of cancer. The aim of this study was to gain insights into the presence of breast cancer-related gene variants in a population from a micro-region in southern Brazil, specifically the Metropolitan Region of Curitiba. This area exhibits a highly genetically mixed population, mirroring the general characteristics of the Brazilian people. METHODS: Comprehensive next-generation sequencing (NGS) multigene panel testing was conducted on 12 patients from the region, utilizing three different library preparation methods. RESULTS: Two pathogenic variants and one candidate pathogenic variant were identified: BRCA2 c.8878C>T, p.Gln2960Ter; CHEK2 c.1100del, p.Thr367Metfs15, and BRCA2 c.3482dup, p.Asp1161Glufs3. CONCLUSION: BRCA2 c.3482dup, a novel candidate pathogenic variant, previously unpublished, is reported. The prevalence of pathogenic variants in this small cohort is similar to that described in the literature. All different library preparation methods were equally proficient in enabling the detection of these variants.

Assuntos

Proteína BRCA2 , Neoplasias da Mama , Quinase do Ponto de Checagem 2 , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Proteína BRCA2/genética , Feminino , Neoplasias da Mama/genética , Neoplasias da Mama/patologia , Quinase do Ponto de Checagem 2/genética , Brasil , Pessoa de Meia-Idade , Adulto , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Testes Genéticos/métodos , Testes Genéticos/normas , Predisposição Genética para Doença

RESUMO

The novel HLA-DPB1*14:01:15 allele differs from DPB1*14:01:01:01 by change of C > T in exon 3.

Assuntos

Alelos , Sequência de Bases , Éxons , Cadeias beta de HLA-DP , Teste de Histocompatibilidade , Doadores de Tecidos , Humanos , Cadeias beta de HLA-DP/genética , Brasil , Análise de Sequência de DNA/métodos , Medula Óssea , Alinhamento de Sequência , Códon , Transplante de Medula Óssea

RESUMO

Cardiovascular diseases (CVDs) are the leading cause of death worldwide across diverse ethnic groups. Among these, atrial fibrillation (AF) stands as one of the most prevalent types of arrhythmias and the primary cause of stroke. Risk factors associated with AF include alcohol consumption, aging, high blood pressure, hypertension, inflammation, and genetic factors. A family history of CVD could indicate an increased risk. Consequently, genetic, and genomic testing should be performed to identify the molecular etiology of CVDs and assess at-risk patients. It is important to note that CVDs are the results of the complex interplay of genes and environmental factors, including ethnicity. In this case, the proband's clinic story includes a history of smoking abuse for 10 years (10 cigarettes per day), obesity, hypertension, and an associated familial history. These risk factors, along with genetic variants, could trigger the early onset of AF. In recent years, genetic and genomic studies have significantly advanced our understanding of CVD etiology, given that next-generation sequencing (NGS) allows for the identification of genetic variants that could contribute to these pathologies. Furthermore, NGS facilitates early diagnosis, personalized pharmacological approaches, and identification of novel biomarkers. Thus, NGS is a valuable tool in CVD management. However, such studies are limited in Ecuador, a low- and middle-income country. Several challenges contribute to this gap, encompassing economic, infrastructural, and educational obstacles. Notably, the cost of genetic and genomic studies may also pose a barrier, restricting access to a portion of the population. In this case report, we present a 56-year-old Ecuadorian woman, who has been diagnosed with AF; however, after performing NGS no disease-associated variants were found, despite having strong clinical signs and symptoms. In summary, this case report contributes valuable insights into the complex interplay between genetic and lifestyle factors in the development and management of AF. The case report aims to underscore the potential impact of genetic variants on disease risk, even when classified as variants of uncertain significance, and the importance of an integral approach to patient care that includes genetic screening, lifestyle interventions, and tailored pharmacological treatment.

RESUMO

HLA-DQB1*02:211 allele differs from DQB1*02:02:01:02 by change of C → A in exon 2.

Assuntos

Alelos , Éxons , Cadeias beta de HLA-DQ , Doadores de Tecidos , Humanos , Cadeias beta de HLA-DQ/genética , Brasil , Teste de Histocompatibilidade , Transplante de Medula Óssea , Sequência de Bases , Análise de Sequência de DNA/métodos , Códon , Medula Óssea

RESUMO

AIMS: This study aimed to describe the bacterial microbiome associated with the carapace of three species of Galapagos giant tortoises (Chelonoidis porteri, Chelonoidis donfaustoi, and Chelonoidis vandenburghi) and determine the potential effect of the whitish lesions caused by the fungus Aphanoascella galapagosensis. METHODS AND RESULTS: We used Oxford Nanopore's MinION to evaluate the external bacterial microbiome associated with the carapaces from the aforementioned species. Taxonomic assignment was carried out by Bugseq and the bacterial communities were compared between carapaces with and without lesions using a NMDS with Bray-Curtis as the dissimilarity index. We found four genera of bacteria that were ubiquitous throughout all individuals, suggesting the presence of shared taxa. The results also displayed a significant difference in the microbiome between carapaces with and without lesions, and for species-carapace interaction, but not among species. CONCLUSIONS: This study establishes a baseline of the bacterial diversity of the carapace within three Galapagos giant tortoise species, showcasing the presence of a distinctive microbial community. Furthermore, our findings suggest a significant influence of the fungus Aphanoascella galapagosensis on the bacterial populations inhabiting the carapace of these reptiles.

Assuntos

Bactérias , Microbiota , Tartarugas , Animais , Tartarugas/microbiologia , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Exoesqueleto/microbiologia , Biodiversidade

RESUMO

Anemia is the most common hematological disorder affecting humans. In Peru, anemia is a pressing issue that present the most significant concern due to its adverse effects, such as delayed growth and psychomotor development, in addition to a deficiency in cognitive development. Anemia is a significant public health issue in Peru, which has one of the highest prevalence rates in infants in the Latin American and Caribbean (LAC) region, affecting approximately 43.6 % of children under three years nationally as of 2017, with rural areas experiencing a higher prevalence of approximately 53.3 %. In 2019, the prevalence was highest in the Sierra (48.8 %) and Selva regions (44.6 %), whereas the coast had a lower rate of 33.9 % in children under 36 months. Although the composition of the gut microbiota is relatively well described in children, there is little information on the identification of the microbiota in iron-deficiency anemia. There is evidence that diseases or health conditions can change the microbiota, or vice versa. This study aimed to identify the microbiota in children with anemia who did not recover after iron treatment. In a previous study, we found that the phylum Actinobacteria was predominant in the microbiota of children with anemia. These data will be useful for understanding the functionality of the most important bacteria found in each group at the genus or species level, especially the metabolic pathways in which they participate and their links with iron metabolism. Microbial composition data were obtained through next-generation 16S rRNA sequencing (NGS) of stool samples from children with anemia in southern Peru. Numerous studies have underscored the importance of early symbiotic development in infant health and its long-term impact on health. From infancy, modulation of the gut microbiota can promote long-term health. According to the National Institute of Health (NIH), iron-deficiency anemia may cause serious complications, such as fatigue, headaches, restless legs syndrome, heart problems, pregnancy complications, and developmental delays in children. The development of the gut microbiota is regulated by a complex interplay between host and environmental factors. The bidirectional link between the gut microbiota and anemia plays an important role in tracking the gut microbiota and will be useful in understanding the composition of the intestinal microbiota and its implications in anemia, which has now become a public health problem. Our previous study investigated the microbial composition in children with iron-deficiency anemia and revealed the presence of several bacterial groups, including Proteobacteria, Actinobacteria, Firmicutes, and Chloroflexi. In addition, these data may be useful for investigating the association between the intestinal microbiota of children with persistent anemia and those who have recovered.

RESUMO

Fundamentally precision oncology illustrates the path in which molecular profiling of tumors can illuminate their biological behavior, diversity, and likely outcomes by identifying distinct genetic mutations, protein levels, and other biomarkers that underpin cancer progression. Next-generation sequencing became an indispensable diagnostic tool for diagnosis and treatment guidance in current clinical practice. Nowadays, tissue analysis benefits from further support through methods like comprehensive genomic profiling and liquid biopsies. However, precision medicine in the field of oncology presents specific hurdles, such as the cost-benefit balance and widespread accessibility, particularly in countries with low- and middle-income. A key issue is how to effectively extend next-generation sequencing to all cancer patients, thus empowering treatment decision-making. Concerns also extend to the quality and preservation of tissue samples, as well as the evaluation of health technologies. Moreover, as technology advances, novel next-generation sequencing assessments are being developed, including the study of Fragmentomics. Therefore, our objective was to delineate the primary uses of next-generation sequencing, discussing its' applications, limitations, and prospective paths forward in Oncology.

RESUMO

Monkeypox (Mpox) is a zoonotic disease caused by the monkeypox virus (MPXV). MPXV can be transmitted by close contact with lesions, body fluids, respiratory droplets, and contaminated materials. A new pattern of spread among sexual networks has been recently described. The present work aimed to report the epidemiological and genomic characterization of the 2022 MPXV outbreak in central Argentina. A total of 113 scabs and/or lesion swab specimens were studied. MPXV infection was confirmed in 46.0% of the studied patients, all of whom were men. Varicella-zoster virus infection was the most frequent differential diagnosis. Eight complete viral genomes were obtained by next-generation sequencing. The Argentinian sequences were grouped intermingled with other sequences from the 2022 MPXV outbreak, related to samples from the USA, Europe, and Peru. Taken together, our study provided an initial assessment of the genetic and epidemiological characteristics of the 2022 MPXV outbreak in Córdoba, Argentina.

Assuntos

Surtos de Doenças , Genoma Viral , Monkeypox virus , Mpox , Argentina/epidemiologia , Humanos , Masculino , Mpox/epidemiologia , Mpox/virologia , Monkeypox virus/genética , Feminino , Adulto , Pessoa de Meia-Idade , Sequenciamento Completo do Genoma , Animais , Adulto Jovem , Idoso , Adolescente

RESUMO

Introduction: Infections acquired during healthcare setting stay pose significant public health threats. These infections are known as Healthcare-Associated Infections (HAI), mostly caused by pathogenic bacteria, which exhibit a wide range of antimicrobial resistance. Currently, there is no knowledge about the global cleaning process of hospitals and the bacterial diversity found in ICUs of Brazilian hospitals contributing to HAI. Objective: Characterize the microbiome and common antimicrobial resistance genes present in high-touch Intensive Care Unit (ICU) surfaces, and to identify the potential contamination of the sanitizers/processes used to clean hospital surfaces. Methods: In this national, multicenter, observational, and prospective cohort, bacterial profiles and several antimicrobial resistance genes from 41 hospitals across 16 Brazilian states were evaluated. Using high-throughput 16S rRNA amplicon sequencing and real-time PCR, the bacterial abundance and resistance genes presence were analyzed in both ICU environments and cleaning products. Results: We identified a wide diversity of microbial populations with a recurring presence of HAI-related bacteria among most of the hospitals. The median bacterial positivity rate in surface samples was high (88.24%), varying from 21.62 to 100% in different hospitals. Hospitals with the highest bacterial load in samples were also the ones with highest HAI-related abundances. Streptococcus spp., Corynebacterium spp., Staphylococcus spp., Bacillus spp., Acinetobacter spp., and bacteria from the Flavobacteriaceae family were the microorganisms most found across all hospitals. Despite each hospital particularities in bacterial composition, clustering profiles were found for surfaces and locations in the ICU. Antimicrobial resistance genes mecA, bla KPC-like, bla NDM-like, and bla OXA-23-like were the most frequently detected in surface samples. A wide variety of sanitizers were collected, with 19 different active principles in-use, and 21% of the solutions collected showed viable bacterial growth with antimicrobial resistance genes detected. Conclusion: This study demonstrated a diverse and spread pattern of bacteria and antimicrobial resistance genes covering a large part of the national territory in ICU surface samples and in sanitizers solutions. This data should contribute to the adoption of surveillance programs to improve HAI control strategies and demonstrate that large-scale epidemiology studies must be performed to further understand the implications of bacterial contamination in hospital surfaces and sanitizer solutions.

Assuntos

Infecção Hospitalar , Farmacorresistência Bacteriana , Unidades de Terapia Intensiva , RNA Ribossômico 16S , Brasil , Humanos , RNA Ribossômico 16S/genética , Infecção Hospitalar/microbiologia , Estudos Prospectivos , Farmacorresistência Bacteriana/genética , Bactérias/genética , Bactérias/efeitos dos fármacos , Bactérias/isolamento & purificação , Bactérias/classificação , Hospitais , Reação em Cadeia da Polimerase em Tempo Real , Antibacterianos/farmacologia

RESUMO

The novel HLA-A*33:01:21 allele, first described in a potential bone marrow donor from Brazil.

Assuntos

Alelos , Éxons , Antígenos HLA-A , Humanos , Sequência de Bases , Transplante de Medula Óssea , Brasil , Teste de Histocompatibilidade , Antígenos HLA-A/genética , Análise de Sequência de DNA/métodos , Doadores de Tecidos

RESUMO

Objective: This systematic review aimed to investigate the changes in the composition of the subgingival microbiota among subjects with normo-weight, overweight and obesity, in conditions of periodontal health and disease. Materials and Methods: The protocol for this study was designed following PRISMA guidelines. Records were identified using different search engines (PubMed/MedLine, Scopus and Web of Science). Observational studies, in human subjects diagnosed with obesity (BMI >30kg/m2) and periodontal disease (gingivitis and periodontitis), on the analysis of subgingival microbiota were selected. Eight articles were included. Results: The subgingival microbiota of 1,229 subjects (n=894 exposure group and n=335 control group) was analyzed. Periodontal pathogens were the most common bacteria detected in subjects with obesity and periodontitis (Porphyromonas gingivalis, Tannerella forsythia, Campylobacter gracilis, Eubacterium nodatum, Fusobacterium nucleatum spp. vincentii, Parvimonas micra, Prevotella intermedia, Campylobacter rectus, and Aggregatibacter actinomycetemcomitans), as along with some accessory pathogens such as: Streptococcus gordonii, and Veillonella parvula that favor the virulence of late colonizers. Conclusions: Although there are evident alterations in the composition of the subgingival microbiota in subjects with obesity and periodontitis, it is still a challenge to identify a specific pattern of microbiota in these subjects. If associations between subgingival plaque microorganisms and obesity are confirmed, microbiome analysis could be a useful tool to improve preventive measures and the management of people with obesity.

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Objetivo: Esta revisión sistemática tuvo como objetivo investigar los cambios en la composición de la microbiota subgingival entre sujetos con normopeso, sobrepeso y obesidad, en condiciones de salud y enfermedad periodontal. Materiales y métodos: El protocolo de este estudio se diseñó siguiendo las directrices PRISMA. Los registros se identificaron utilizando diferentes motores de búsqueda (PubMed/MedLine, Scopus y Web of Science). Se seleccionaron estudios observacionales en sujetos humanos diagnosticados con obesidad (IMC >30kg/m2) y enfermedad periodontal (gingivitis y periodontitis), sobre el análisis de la microbiota subgingival. Se incluyeron ocho artículos. Resultados: Se analizó la microbiota subgingival de 1229 sujetos (n = 894 grupo de exposición y n = 335 grupo de control). Los patógenos periodontales fueron las bacterias más comunes detectadas en los sujetos con obesidad y periodontitis (Porphyromonas gingivalis, Tannerella forsythia, Campylobacter gracilis, Eubacterium nodatum, Fusobacterium nucleatum spp. vincentii, Parvimonas micra, Prevotella intermedia, Campylobacter rectus y Aggregatibacter actinomycetemcomitans), junto con algunos patógenos accesorios, como Streptococcus gordonii y Veillonella parvula, que favorecen la virulencia de los colonizadores tardíos. Conclusiones: Aunque existen alteraciones evidentes en la composición de la microbiota subgingival en sujetos con obesidad y periodontitis, sigue siendo un reto identificar un patrón específico de microbiota en ellos. Si se confirman las asociaciones entre los microorganismos de la placa subgingival y la obesidad, el análisis del microbioma podría ser una herramienta útil para mejorar las medidas preventivas y el manejo de las personas con obesidad.

RESUMO

Purpose: Lung cancer is the leading cause of cancer-related deaths worldwide. However, with the optimization of screening strategies and advances in treatment, mortality has been decreasing in recent years. In this study, we describe non-small cell lung cancer patients diagnosed between 2021 and 2022 at a high-complexity hospital in Latin America, as well as the immunohistochemistry techniques used to screen for ROS1 rearrangements, in the context of the recent approval of crizotinib for the treatment of ROS1 rearrangements in non-small cell lung cancer in Colombia. Methods: A descriptive cross-sectional study was conducted. Sociodemographic, clinical, and molecular pathology information from non-small cell lung cancer individuals who underwent immunohistochemistry to detect ROS1 rearrangements between 2021 and 2022 at Fundación Valle del Lili (Cali, Colombia) was recorded. The clinical outcomes of confirmed ROS1 rearrangements in non-small cell lung cancer patients were reported. Results: One hundred and thirty-six patients with non-small cell lung cancer were included. The median age at diagnosis was 69.8 years (interquartile range 61.9-77.7). At diagnosis, 69.8% (n = 95) were at stage IV. ROS1 immunohistochemistry was performed using the monoclonal D4D6 antibody clone in 54.4% (n = 74) of the cases, while 45.6% (n = 62) were done with the monoclonal SP384 antibody clone. Two patients were confirmed to have ROS1 rearrangements in non-small cell lung cancer using next-generation sequencing and received crizotinib. On follow-up at months 5.3 and 7.0, one patient had a partial response, and the other had oligo-progression, respectively. Conclusion: Screening for ROS1 rearrangements in non-small cell lung cancer is imperative, as multiple prospective studies have shown improved clinical outcomes with tyrosine kinase inhibitors. Given the recent approval of crizotinib in Colombia, public health policies must be oriented toward early detection of driver mutations and prompt treatment. Additionally, future approvals of newly tested tyrosine kinase inhibitors should be anticipated.

RESUMO

The novel HLA-C*01:273 allele, first described in a potential bone marrow donor from Brazil.

Assuntos

Alelos , Éxons , Antígenos HLA-C , Humanos , Antígenos HLA-C/genética , Brasil , Teste de Histocompatibilidade , Sequência de Bases , Doadores de Tecidos , Análise de Sequência de DNA/métodos , Alinhamento de Sequência , Códon

RESUMO

The brown dog tick, Rhipicephalus linnaei (Audouin, 1826), is distributed across the American continent and is formerly known as the "tropical lineage". It belongs to the Rhipicephalus sanguineus (Latreille, 1806) species complex, referred to as R. sanguineus (sensu lato). Mitochondrial genome sequences are frequently used for the identification and represent reference material for field studies. In the present study, the entire mitochondrial genomes of R. linnaei (∼15 kb) collected from dogs in Mexico were sequenced and compared with available mitogenomes of R. sanguineus (s.l.). The mitochondrial genome is ∼90% identical to the reference genome of R. sanguineus (sensu stricto, former "temperate lineage") and > 99% identical to R. linnaei mitogenome derived from the neotype. Two additional mitogenomes were obtained and described as R. linnaei and R. turanicus from dogs in Saudi Arabia. The present study delivers a molecular reference for R. linnaei from America and complements R. linnaei mitogenomes from Africa, Asia and Australia. We propose to consider the complete mitogenome, as the reference for American R. linnaei, even when partial mitochondrial cox1, 12S rRNA or 16S rRNA genes are characterised.

RESUMO

The genomic characteristics of Peruvian patients with gastric adenocarcinoma from diverse socioeconomic backgrounds were examined in consideration of the possibility that patients from different socioeconomic backgrounds may be exposed to different risk factors. We conducted a prospective pilot study in two Peruvian cities (Lima and Ica). This study enrolled 15 patients from low socioeconomic status (LSES) and 15 patients from medium/high socioeconomic status (MHSES). The genomic profiling of gastric adenocarcinoma samples was done through the FoundationOne CDx platform. We compared the genomic characteristics and the need for targeted therapy and immunotherapy between LSES and MHSES. The genes with higher rates of alterations were TP53 (73.3% vs. 50.0%, P = 0.2635); CDH1 (26.7% vs. 28.6%, P = 1); CDKN2A (20.0% vs. 28.6%, P = 1); KRAS (33.3% vs. 7.1%, P = 0.1686); ARID1A (20.0% vs. 14.3%, P = 1); MLL2 (13.3% vs. 21.4%, P = 1) and SOX9 (33.3% vs. 0.0%, P = 0.0421) in LSES versus HMSES, respectively. There was no significant difference in tumor mutational burden (P = 0.377) or microsatellite status (P = 1). The LSES group had a higher need for targeted therapy or immunotherapy according to gene involvement and alterations. A significant genomic difference exists among patients with gastric adenocarcinoma of different socioeconomic status, which may result in a different need for targeted therapy and immunotherapy.

Assuntos

Neoplasias Gástricas , Humanos , Neoplasias Gástricas/genética , Masculino , Feminino , Pessoa de Meia-Idade , Idoso , Adenocarcinoma/genética , Estudos Prospectivos , Genômica/métodos , Peru/epidemiologia , Projetos Piloto , Adulto , Fatores Socioeconômicos , Mutação , Classe Social , Disparidades Socioeconômicas em Saúde

RESUMO

Introduction: Lynch syndrome (LS) is an inherited cancer predisposition syndrome characterized by a high risk of colorectal and extracolonic tumors. Germline pathogenic variants (GPV) in the PMS2 gene are associated with <15% of all cases. The PMS2CL pseudogene presents high homology with PMS2, challenging molecular diagnosis by next-generation sequencing (NGS). Due to the high methodological complexity required to distinguish variants between PMS2 and PMS2CL, most laboratories do not clearly report the origin of this molecular finding. Objective: The aim of this study was to confirm the GPVs detected by NGS in regions of high homology segments of the PMS2 gene in a Brazilian sample. Methods: An orthogonal and gold standard long-range PCR (LR-PCR) methodology to separate variants detected in the PMS2 gene from those detected in the pseudogene. Results: A total of 74 samples with a PMS2 GPV detected by NGS in exons with high homology with PMS2CL pseudogene were evaluated. The most common was NM_000535.6:c.2182_2184delinsG, which was previously described as deleterious mutation in a study of African-American patients with LS and has been widely reported by laboratories as a pathogenic variant associated with the LS phenotype. Of all GPVs identified, only 6.8% were confirmed by LR-PCR. Conversely, more than 90% of GPV were not confirmed after LR-PCR, and the diagnosis of LS was ruled out by molecular mechanisms associated with PMS2. Conclusion: In conclusion, the use of LR-PCR was demonstrated to be a reliable approach for accurate molecular analysis of PMS2 variants in segments with high homology with PMS2CL. We highlight that our laboratory is a pioneer in routine diagnostic complementation of the PMS2 gene in Brazil, directly contributing to a more assertive molecular diagnosis and adequate genetic counseling for these patients and their families.

RESUMO

Helminth infections, which affect approximately 1.5 billion individuals worldwide (mainly children), are common in low- and middle-income tropical countries and can lead to various diseases. One crucial factor affecting the occurrence of these diseases is the reduced diversity of the gut microbiome due to antibiotic use. This reduced diversity compromises immune health in hosts and alters host gene expression through epigenetic mechanisms. Helminth infections may produce complex biochemical signatures that could serve as therapeutic targets. Such therapies include next-generation probiotics, live biotherapeutic products, and biochemical drug approaches. Probiotics can bind ferric hydroxide, reducing the iron that is available to opportunistic microorganisms. They also produce short-chain fatty acids associated with immune response modulation, oral tolerance facilitation, and inflammation reduction. In this review, we examine the potential link between these effects and epigenetic changes in immune response-related genes by analyzing methyltransferase-related genes within probiotic strains discussed in the literature. The identified genes were only correlated with methylation in bacterial genes. Various metabolic interactions among hosts, helminth parasites, and intestinal microbiomes can impact the immune system, potentially aiding or hindering worm expulsion through chemical signaling. Implementing a comprehensive strategy using probiotics may reduce the impact of drug-resistant helminth strains.

Assuntos

Países em Desenvolvimento , Microbioma Gastrointestinal , Helmintíase , Probióticos , Probióticos/uso terapêutico , Probióticos/administração & dosagem , Helmintíase/imunologia , Helmintíase/prevenção & controle , Humanos , Animais , Microbioma Gastrointestinal/fisiologia , Microbioma Gastrointestinal/efeitos dos fármacos , Epigênese Genética/efeitos dos fármacos

RESUMO

Low-pass whole genome sequencing (LP-WGS) has been applied as alternative method to detect copy number variants (CNVs) in the clinical setting. Compared with chromosomal microarray analysis (CMA), the sequencing-based approach provides a similar resolution of CNV detection at a lower cost. In this study, we assessed the efficiency and reliability of LP-WGS as a more affordable alternative to CMA. A total of 1363 patients with unexplained neurodevelopmental delay/intellectual disability, autism spectrum disorders, and/or multiple congenital anomalies were enrolled. Those patients were referred from 15 nonprofit organizations and university centers located in different states in Brazil. The analysis of LP-WGS at 1x coverage (>50kb) revealed a positive testing result in 22% of the cases (304/1363), in which 219 and 85 correspond to pathogenic/likely pathogenic (P/LP) CNVs and variants of uncertain significance (VUS), respectively. The 16% (219/1363) diagnostic yield observed in our cohort is comparable to the 15%-20% reported for CMA in the literature. The use of commercial software, as demonstrated in this study, simplifies the implementation of the test in clinical settings. Particularly for countries like Brazil, where the cost of CMA presents a substantial barrier to most of the population, LP-WGS emerges as a cost-effective alternative for investigating copy number changes in cytogenetics.

Assuntos

Variações do Número de Cópias de DNA , Sequenciamento Completo do Genoma , Humanos , Variações do Número de Cópias de DNA/genética , Sequenciamento Completo do Genoma/economia , Sequenciamento Completo do Genoma/métodos , Brasil , Masculino , Feminino , Criança , Deficiência Intelectual/genética , Deficiência Intelectual/diagnóstico , Análise Custo-Benefício , Análise em Microsséries/economia , Análise em Microsséries/métodos , Transtorno do Espectro Autista/genética , Transtorno do Espectro Autista/diagnóstico , Pré-Escolar , Anormalidades Múltiplas/genética , Anormalidades Múltiplas/diagnóstico , Países em Desenvolvimento , Adolescente , Transtornos do Neurodesenvolvimento/genética , Transtornos do Neurodesenvolvimento/diagnóstico , Testes Genéticos/economia , Testes Genéticos/métodos

RESUMO

Comprehensive genomic profiling is highly recommended for treatment decision in nonsquamous, non-small cell lung cancer (NSCLC). However, rare genomic alterations are still being unveiled, with scarce data to guide therapy. Herein, we describe the treatment journey of a 56-year-old, never-smoker Caucasian woman with a metastatic NSCLC harboring a CD47-MET fusion, initially classified as a variant of unknown significance. She had undergone 3 lines of therapy over the course of 3 years, including chemotherapy, immunotherapy, and anti-angiogenic therapy. After reanalysis of her next-generation sequencing data in our service, the fusion was reclassified as likely oncogenic. The patient was started with fourth-line capmatinib, with a good tolerance so far and a complete metabolic response in the active sites of disease, currently ongoing for 18 months. In conclusion, we highlight the sensitivity of a novel MET fusion to capmatinib and emphasize the need for comprehensive panels in NSCLC and molecular tumor board discussions with specialized centers when rare findings arise.

Assuntos

Adenocarcinoma de Pulmão , Neoplasias Pulmonares , Proteínas Proto-Oncogênicas c-met , Humanos , Feminino , Pessoa de Meia-Idade , Adenocarcinoma de Pulmão/tratamento farmacológico , Adenocarcinoma de Pulmão/genética , Adenocarcinoma de Pulmão/patologia , Neoplasias Pulmonares/tratamento farmacológico , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patologia , Proteínas Proto-Oncogênicas c-met/genética , Acrilamidas/uso terapêutico , Benzamidas/uso terapêutico , Proteínas de Fusão Oncogênica/genética , Triazinas/uso terapêutico , Imidazóis

RESUMO

BACKGROUND: Breast cancer (BC) is the world's largest tumor species in which hormone receptor-positive patients have relatively good prognosis. However, majority of patients will develop late resistance, one of the important factors is due to the loss of the original estrogen receptor (ER) expression. METHODS: We conducted this study in 115 patients with BC who experienced second biopsy at Jiangsu Province Hospital (JSPH) and divided patients into two subgroups ER + to - and ER + to + . First, clinicopathological characteristics between two groups were evaluated. Second, we explored candidate genes related to BC ER intratumor heterogeneity by applying next-generation sequencing (NGS) in 42 patients. Multi-omics integrative analysis of tumor transcriptomic, cancer-related pathway, diagnostic and prognostic value and immune profile were conducted. Besides, preliminary assay were also used to evaluate the correlation between KMT2C and ERα (ESR1) expression. The CCK-8, 5-Ethynyl-2'-deoxyuridine (EdU) assays, Transwell assays and the wound scratch tests were applied to explore the cellular interactions between KMT2C and BC. RESULTS: We find the histological type (p = 0.008) and disease-free survival (DFS) (p = 0.004) were significantly different in two subgroups. In Cox survival analysis, metastasis (Hazard ratio (HR) > 1, p = 0.007) and neo-adjuvant (HR < 1, p < 0.001) are independent prognostic factors of DFS. Besides, by analyzing NGS results, we found four genes KMT2C, FGFR19, FGF1 and FGF4 were highly mutated genes in ER + to - subgroup. Furthermore, the gene KMT2C displayed significant diagnostic value and prognostic value in BC and pan-cancer. In addition, a positive correlation between KMT2C expression and immune infiltrating levels of T cell CD4 + , macrophage and neutrophil was found. In the end, Western blot and RT-qPCR assay were used and found KMT2C and ERα (ESR1) expressions are strongly positive correlated in mRNA and protein level. Inhibition of KMT2C significantly reduced proliferation, invasion, and migration of MCF7 cells. CONCLUSION: People in two cohorts from JSPH presented different clinical characteristics and prognosis. The gene KMT2C may affect the progression of BC by regulating the molecular, epigenetic activity and immune infiltration. It may also serve as a novel prognostic biomarker for BC patients who underwent ER status converted from positive to negative.