Gene Frequencies Research Articles

Examining the Frequency of bla CTX-M and bla TEM Genes in Escherichia Coli Isolates with Multiple Drug Resistance Isolated from Patients Hospitalized in Ahvaz University Hospitals

Background and Objectives In the last few decades, Escherichia coli strains producing extended-spectrum beta-lactamases (ESBLs) have increased and are now considered a major problem in hospitalized patients. The aim of this study was to investigate the prevalence of blaCTX-M and blaTEM genes in Escherichia coli with multiple drug resistance. Subjects and Methods This study was conducted from October 2021 to May 2022. The research site included the microbiology laboratories of Golestan, Imam Khomeini, and Shahid Beqai hospitals where isolates suspected of Escherichia coli were isolated from urine culture samples of patients with urinary tract infection. All Escherichia coli samples were identified by conventional biochemical and molecular methods. The antibiotic sensitivity of the isolates was determined by disk diffusion method. Then, in order to finally confirm the presence of blaCTX-M and blaTE genes, PCR method was used. Results Out of the 160 bacterial isolates examined, 138 (86.3%) showed multidrug resistance (MDR). The highest and lowest percentage of resistance was related to Amoxicillin-Clavonic acid (84.1%) and Meropenem (5.8%), respectively. Based on the combined disk method, 96 isolates (69.6%) were positive for Beta-lactamase enzymes (ESBLs). Among the 96 ESBL-positive isolates, 85 (88.5%) and 38 (39.6%) carried blaCTX-M and blaTEM genes, respectively. Conclusion Given the significant prevalence of Escherichia coli strains that are resistant to multiple drugs and carrying ESBLs beta-lactamase genes in hospital, there is a need for effective surveillance measures to prevent the further spread of drug resistance in these isolates.

Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis

BackgroundDomestic goose breeds are descended from either the Swan goose (Anser cygnoides) or the Greylag goose (Anser anser), exhibiting variations in body size, reproductive performance, egg production, feather color, and other phenotypic traits. Constructing a pan-genome facilitates a thorough identification of genetic variations, thereby deepening our comprehension of the molecular mechanisms underlying genetic diversity and phenotypic variability.ResultsTo comprehensively facilitate population genomic and pan-genomic analyses in geese, we embarked on the task of 659 geese whole genome resequencing data and compiling a database of 155 RNA-seq samples. By constructing the pan-genome for geese, we generated non-reference contigs totaling 612 Mb, unveiling a collection of 2,813 novel genes and pinpointing 15,567 core genes, 1,324 softcore genes, 2,734 shell genes, and 878 cloud genes in goose genomes. Furthermore, we detected an 81.97 Mb genomic region showing signs of genome selection, encompassing the TGFBR2 gene correlated with variations in body weight among geese. Genome-wide association studies utilizing single nucleotide polymorphisms (SNPs) and presence-absence variation revealed significant genomic associations with various goose meat quality, reproductive, and body composition traits. For instance, a gene encoding the SVEP1 protein was linked to carcass oblique length, and a distinct gene-CDS haplotype of the SVEP1 gene exhibited an association with carcass oblique length. Notably, the pan-genome analysis revealed enrichment of variable genes in the “hair follicle maturation” Gene Ontology term, potentially linked to the selection of feather-related traits in geese. A gene presence-absence variation analysis suggested a reduced frequency of genes associated with “regulation of heart contraction” in domesticated geese compared to their wild counterparts. Our study provided novel insights into gene expression features and functions by integrating gene expression patterns across multiple organs and tissues in geese and analyzing population variation.ConclusionThis accomplishment originates from the discernment of a multitude of selection signals and candidate genes associated with a wide array of traits, thereby markedly enhancing our understanding of the processes underlying domestication and breeding in geese. Moreover, assembling the pan-genome for geese has yielded a comprehensive apprehension of the goose genome, establishing it as an indispensable asset poised to offer innovative viewpoints and make substantial contributions to future geese breeding initiatives.

The Influence of Traditional Opera Culture on the Development of Ethnic Vocal Music Art under Deep Learning Modeling

Abstract In this paper, according to the characteristics and development trend of traditional opera, based on the deep learning model, we use a convolutional neural network to extract the opera features, combined with an SVM classifier to construct a CNN-SVM classification model. For the two classification algorithm models of logistic regression and deep confidence network, combined with two types of feature parameters of timbre and melody, six groups of experiments are designed to extract the time-frequency features of traditional opera. The CNN-SVM classification model is used to categorize the emotion of traditional opera, which aims to divide the musical features by multi-feature selection. Analyze the timbre feature parameter MFCC to investigate the impact of traditional opera timbre on ethnic vocal singing. For the logistic regression model, the coefficient of MFCCs is 0.5588, and the classification accuracy is only 0.5301 when the feature parameters are selected as melodic features, i.e., gene frequency, resonance peak, and band energy, and 0.6228 when the feature parameters are selected as a combination of timbral and melodic features. The diversity of the traditional opera timbres contributes to the development of ethnic vocal art with the trend of inclusiveness.

Frequency and functional characterization of fusion genes in squamous cell carcinoma of the lung

IntroductionIn contrast to lung adenocarcinoma (LUAD), targetable genetic alterations are less frequently detected in squamous cell carcinoma of the lung (LUSC). Over the last years, gene fusions have become promising targets in many solid cancers. Here, we analysed a cohort of LUSC, identified recurrent fusion genes and functionally characterised these tumour genomes. MethodsA subset of 1608 squamous cell carcinomas of the lung was analysed by means of the FusionPlex® Lung Panel to identify potentially targetable gene fusions using targeted next-generation sequencing. Cases harbouring recurrent gene fusions were further analysed using FISH, Cytoscan HD arrays and cell culture experiments. ResultsWe found both, known and novel gene fusions in about 3 % of the cases. Known fusions occurring in lung cancer included ALK::EML4, EGFRvIII, EZR::ROS1 and FGFR3::TACC. We further identified recurrent gene fusions of currently unknown biological function, involving EGFR::VSTM2A and NSD3::FGFR1 and showed that the occurrence of the EGFR::VSTM2A fusion is accompanied by high-level amplification of EGFR. Our analyses further revealed that the genomes of these LUSC patients are chromosomally unstable, which leads us to believe that such non-actionable genomic rearrangements may be a result of “chromosomal chaos” most probably not representing exclusive cancer-driving genes in this cancer entity. ConclusionsWe emphasise that caution should be taken when novel fusions are found and that the appearance of new gene fusions should always be interpreted in the molecular context of the respective disease.

Diagnosis and treatment of ovarian cancer in the light of modern molecular genetic achievements

The purpose of the study was to systematize and summarize the literature data on the study of clinical and genetic aspects, molecular pathogenesis, as well as new trends in the diagnosis and treatment of ovarian cancer.Material and Methods. A literature search was conducted using Web of science, scopus, medline, pubmed, and elibrary databases.Results. Ovarian cancer is the leading cause of death in women diagnosed with gynecological cancer. ovarian cancer is a heterogeneous disease composed of different types of tumors, each of which has differences in pathogenesis, spectrum and mutation frequencies in characteristic genes, response to therapy and prognosis of the disease. more than 80 % of all malignant ovarian tumors are of epithelial origin (carcinomas) and about 26 % of all cases of ovarian cancer are caused by germline mutations found in the BRCA1/BRCA2 genes. to date, the priority areas in the study of ovarian cancer are the improvement of diagnostic methods, algorithm of examination of women, identification of new biomarkers, study of tumor microenvironment and composition of ascitic fluid to detect cancer at early stages and prescribe appropriate therapy. Recent advances in targeted therapy based on the molecular profile of the tumor have made it possible to personalize treatment and increase its effectiveness. Achievements in molecular genetic, cytological, immunological and biochemical studies contribute to the development of novel approaches to the diagnosis and treatment of ovarian cancer.Conclusion. With the advent of new novel approaches to the diagnosis and treatment of ovarian cancer, it is becoming increasingly clear that the tumor microenvironment can significantly affect the success of chemotherapy. New biomarkers can help identify the best candidates for ovarian cancer treatment. Further basic and applied research is needed to explore the use of different diagnostic and therapeutic agents in ovarian cancer.

Exploration of molecular markers related to chemotherapy efficacy of hepatoid adenocarcinoma of the stomach.

Preoperative neoadjuvant chemotherapy may not improve the prognosis of patients with hepatoid adenocarcinoma of the stomach (HAS), a rare pathological type of gastric cancer. Thus, the study aimed at the genomic and transcriptomic impacts of preoperative chemotherapy on HAS. Patients with HAS who underwent surgical resection at Peking University Cancer Hospital were retrospectively included in this study. Whole exome sequencing and transcriptome sequencing were performed on pre-chemotherapy, non-chemotherapy and post-chemotherapy samples. We then compared the alterations in molecular markers between the post-chemotherapy and non-chemotherapy groups, and between the chemotherapy-effective and chemotherapy-ineffective groups, respectively. A total of 79 tumor samples from 72 patients were collected. Compared to the non-chemotherapy group, the mutation frequencies of several genes were changed after chemotherapy, including TP53. In addition, there was a significant increase in the frequency of frameshift mutations and cytosine transversion to adenine (C > A), appearance of COSMIC signature 6 and 14, and a reduced gene copy number amplification. Interestingly, the same phenomenon was observed in chemotherapy-ineffective patients. In addition, many HAS patients had ERBB2, FGFR2, MET and HGF gene amplification. Moreover, the expression of immune-related genes, especially those related to lymphocyte activation, was down-regulated after chemotherapy. Chemotherapy is closely associated with changes in the molecular characteristics of HAS. After chemotherapy, at genomic and transcriptome level, many features were altered. These changes may be molecular markers of poor chemotherapeutic efficacy and play an important role in chemoresistance in HAS. In addition, ERBB2, FGFR2, MET and HGF gene amplification may be potential therapeutic targets for HAS.

INCIDENCE AND CHARACTERISTICS OF NEOVASCULAR AGE-RELATED MACULAR WITH OVER A 12-MONTH REMISSION AFTER THREE MONTHLY AFLIBERCEPT ADMINISTRATION: 60 Months Results of a Pro Re Nata Regimen.

To investigate the characteristics of patients with over a 12-month remission after 3 monthly intravitreal aflibercept injections followed by a pro re nata regimen for exudative age-related macular degeneration (AMD). One hundred forty-four eyes with exudative AMD were included. All patients received 3 monthly intravitreal aflibercept injections as a loading dose, followed by an as-needed regimen for 60 months. Patients were classified into the remission and recurrence groups depending on the presence or absence of a 12-month remission. ARMS2 A69S and CFH I62V were genotyped in all cases. During the study, 82 eyes (56.9%) showed 12 months or more remission at least once. The cumulative incidence rate of a 12-month remission showed a plateau pattern and converged to 60% (y = -166.26x-2.172 + 0.6, R2 = 0.8168). Patients in the remission group were younger than those in the recurrence group (P < 0.001) and had less risk allele frequency of the ARMS2 gene than the recurrence group (P < 0.001). The longer the remission interval was prolonged, the better visual acuity was achieved at the 60-month visit (P < 0.001). Fifty-seven percent of patients showed a 12-month remission or more at least once during a 60-month follow-up, suggesting that patients with no reactivation can prolong the treatment interval.

Abstract 16838: Relation of Clinical Status in Heart Failure to Cardiac Lysophosphatidylethanolamine Accumulation in Hypertrophic Cardiomyopathy

Background: Patients with hypertrophic cardiomyopathy (HCM) represents diverse symptoms, morphology, and cardiovascular events. Although myocardium metabolism in patients with HCM has been studied, it is not well elucidated. In this study, we assessed the association between biomarkers, heart failure-related findings, genetic mutations, and myocardium lipid metabolism in HCM patients using imaging mass spectrometry. Method: We prospectively enrolled patients with HCM in Hamamatsu University hospital from July 2020 to October 2022. All patients underwent endomyocardial biopsy and genetic analysis. Obtained myocardial specimens were analyzed using a desorption electrospray ionization source attached to a mass spectrometer. Differences among groups were statistically evaluated with the Fisher’s exact test and Mann-Whitney U test. Correlations between the two values were analyzed using Spearman’s correlation coefficient values. Results: A total of 31 Japanese patients were enrolled in this study. These patients included 18 (58.0%) women, and the mean age was 67.6 ± 10.6 years. Genetic analysis revealed that six (19.4%) patients had pathogenic or likely pathogenic variant. (Frequency of causal genes was as follows: MYBPC3 2 [6.5%], TNNI3 2 [6.5%], MYH7 1 [3.2%], and MYOZ2 1 [3.2%].) We divided the patients into two groups according to their median intensity of candidate molecule to reveal between group differences. The group of high lysophosphatidylethanolamine (LPE) showed lower N-terminal pro-brain natriuretic peptide (NT-proBNP) levels (330.0 [147.0-614.0] pg/mL vs. 933.0 [699.5-2576.5] pg/mL, P = 0.001). A correlation was observed between the intensity of LPE and the NT-proBNP levels (r = -0.455, P = 0.012). There was no association between the presence of genetic mutations and New York Heart Association class and LPE intensity. Conclusion: HCM patients with the high intensity of LPE in myocardial tissue had relatively low NT-proBNP levels.

Assessment of Staphylococcal toxins acting as superantigens in different nasal specimens in the etiology of chronic rhinosinusitis

The mechanism of development of chronic rhinosinusitis(CRS) is not fully known. However, bacteria are thought to play an important role in this clinic. It has been suggested that toxins with superantigen(SAgs) properties produced by one of these bacteria, Staphylococcus aureus(S.aureus), play a role in the development of inflammation associated with sinusitis. In this study, S.aureus was isolated by taking endoscopic sinus biopsy samples and nasal swab samples from patients with CRS and the control group. It was aimed to examine the frequency of S.aureus presence in the samples taken, the presence of toxin genes showing superantigen quality in these isolated bacteria, and to evaluate the roles of these parameters in the development of CRS. More S.aureus was isolated in the samples taken from patients with CRS than in the control group. The isolated S.aureus samples were analysed by real-time PCR method. The presence of enterotoxin A, B, C and D genes in the S.aureus samples isolated from the patient group were found at the rates of 54%, 32%, 16% and 16%, respectively, while these rates were 46%, 24%, 14% and 14% in the control group. The Toxic Shock Syndrome Toxin-1(TSST-1) gene was detected in 20% of the samples isolated from the patient and 46% in the control group bacteria. The fact that S.aureus was isolated in 20% of the patients shows that this bacterium is not necessary for CRS. The frequency of superantigen toxin genes in S.aureus isolates shows that these toxins are not necessary for the development of the disease.

Signatures of adaptation in myopia-related genes on the sunlight exposure hypothesis

BackgroundMyopia is a common eye disorder that results from gene-environment interactions. The prevalence of myopia varies across populations, and exposure to bright sunlight may prevent its development. We hypothesize that local adaptation to light environments during human migration played a role in shaping the genetic basis of myopia, and we aim to investigate how the environment influences the genetic basis of myopia.MethodWe utilized the whole-genome variant data of the 1000 Genomes Project for analysis. We searched myopia-associated loci that were under selection in Europeans using population branch statistics and the number of segregating sites by length statistics. The outliers of these statistics were enriched in the Kyoto Encyclopedia of Genes and Genomes pathways and the gene ontology biological process terms in searching for pathways that were under selection. We applied Bayesian inference to estimate the correlation between environmental factors and allele frequencies of the selected loci and performed causal inference of myopia using two-sample Mendelian randomization analysis.ResultsWe detected signatures of adaptation in vision and light perception pathways, supporting our hypothesis of sunlight adaptation. We discovered a strong correlation between latitude and allele frequencies in genes that are under significant selection, and we found pleiotropic effects of pigmentation or circadian rhythm genes on myopia, indicating that sunlight exposure influences the genetic diversity of myopia.ConclusionsMyopia genes involved in light perception showed signs of selection. Local adaptation during human migration shaped the genetic basis of myopia and may have influenced its global prevalence distribution.

Ropeginterferon Alfa-2b for Pre-Fibrotic Primary Myelofibrosis and DIPSS Low/Intermediate-1 Risk Myelofibrosis: Durable Responses and Evidence of Disease Modification

Background Most patients with primary myelofibrosis (PMF) in pre-/early fibrotic stage (pre-PMF) and at low or intermediate-1 risk by the dynamic international prognostic scoring system (DIPSS) will progress to higher risks or overt MF. There is currently no consensus on the optimal treatment for these patients. Ropeginterferon alfa 2b (ropeg) is a next-generation monopegylated interferon alfa-2b developed specifically to treat myeloproliferative neoplasms (MPN). Aims P1101MF is an on-going multicenter phase 2 study of ropeg in patients with pre-PMF and DIPSS low/intermediate-risk PMF. Methods Key eligibility included morphologically confirmed pre-PMF, overt PMF, post-polycythemia vera MF (PPV-MF) or post-essential thrombocythaemia MF (PET-MF), DIPSS low/intermediate-1 risk, and the need for cytoreduction. The primary outcome were responses in haemoglobin (Hb, from 10 g/dL to upper reference range), white blood cell (WBC, &amp;lt; 10 x 10 9/L) and platelet (≤ 400 x 10 9/L) at 24 and 48 weeks. Secondary outcomes included adverse events (AEs), changes in mutant allele frequencies (MAF) of driver and non-driver genes as assessed by droplet digital polymerase chain reaction (ddPCR), quality-of-life (QOL), cytokine profiles and bone marrow morphology. Patients received ropeg at a dose of 250 mcg at week 1, followed by 350 mcg at week 2 and 500 mcg every 2 weeks from week 4 onwards. Results At the data cut-off of 30 June 2023, 37 men and 29 women with a median age of 59 (range: 30-86) years were enrolled. The diagnoses were pre-PMF (=46, 69.6%); overt PMF (N=6, 9.1%); PPV-MF (N=5, 7.5%); and PET-MF (N=9, 13.6%). Mutational profile of driver genes was JAK2V617F (N=46, 69.6%); CALR mutations (type 1/type-1 like, N=13, 19.7%; type 2/type 2-like, N=4, 6.1%); MPL mutation (N=1, 1.5%); and triple-negative (N=3, 4.5%). The median time from diagnosis to treatment was 5.8 (1-271) months. The median baseline parameters were white blood cell count (WBC): 6.49 (3.25-33.95) x 10 9/L; haemoglobin (Hb): 12.5 (7.1-15.9) g/dL; platelet count: 495 (113-1114) x 10 9/L; and lactate dehydrogenase: 277 (136-1146) IU/L. The median follow-up was 69 (4-69) weeks, with 61 patients (92%) and 51 patients (77%) having completed 24 and 48 weeks of treatment respectively. Responses in Hb, WBC and platelet were 75%, 82% and 74% respectively at 24 weeks, and 82%, 80% and 71% respectively at 48 weeks. Reduction of MAF at 24 and 48 weeks was achieved for JAK2V617F in 50% (19/38) of patients (≥50%, N=10, 26%; complete, N=3, 8%) and 79% (22/28) of patients (≥50%, N=6, 21%; complete, N=1, 4%) respectively; and for CALR in 44% (7/16) of patients (≥50%, N=1, 6%) and 50% (5/10) of patients (≥50%, N=1, 10%) respectively. Forty-six patients (69.6%) had bone marrow biopsies serially performed, with 42 patients (91%) having stable/improved marrow fibrosis. Eight patients (17.4%) had resolution of marrow fibrosis by 48 weeks. There were 5 discontinuations (personal reasons, N=1; intractable pruritus, N=1; symptom/spleen size progression, N=3). Disease progression (pre-PMF to overt PMF; development of accelerated/blast phase) was not observed. Non-haematological AEs included transaminitis (grade 1-2, N=34); malaise (grade 1-2, N=27; grade 3-4, N=1) and hair loss (grade 1-2, N=21). The most common haematological AE was anaemia (grade 1-2, N=15; grade 3-4, N=6). Conclusion: Ropeg was well-tolerated, effective in cytoreduction and induced molecular and morphologic responses in patients with pre-PMF and low/intermediate-1-risk MF.

Second Line Treatment with Bruton Tyrosine Kinase Inhibitor (BTKi) or Bcl-2 Inhibitor (Bcl-2i) in Patients with Chronic Lymphocytic Leukemia (CLL): Primary Analysis of the Czech Study Group for CLL (CSCLL)

Introduction: Venetoclax in combination with rituximab (VenR) along with either ibrutinib or acalabrutinib monotherapy represent the most common regimens currently used for the treatment of relapsed/refractory (RR) chronic lymphocytic leukemia (CLL) in the Czech Republic. As all of these regimens are approved for identical indications in RR CLL, the selection of the most appropriate treatment depends on the drug toxicity profile and patient´s comorbidities. Methods: We conducted a retrospective analysis of data from the Czech National Registry of CLL patients (CLLEAR). Patients were treated in one of eight Czech hematological centres between December 2015 and June 2023. Only those who received chemoimmunotherapy in the first-line and Bruton tyrosine kinase inhibitor (BTKi) or Bcl-2 inhibitor (Bcl-2i) in the second-line treatment were included in the study. All patients fulfilled iwCLL diagnostic criteria and had provided informed consent before their data were captured in the CLLEAR. Key CLL-related clinical and laboratory parameters were obtained from the database (Table 1). Ibrutinib and acalabrutinib monotherapy were given at standard doses until disease progression (PD) or unacceptable toxicity. The combination of venetoclax and rituximab (VenR) was administered in the regular dosing schedule for 24 months. Results: Out of 291 patients included in the study, 70.1% (204/291) were treated with ibrutinib, 8.9% (26/291) received acalabrutinib and 20.9% (61/291) VenR. The median age at the start of the second-line treatment was 72.1 and 70.6 years, respectively (BTKi and Bcl-2i). There were no significant differences in sex, clinical stage, CIRS, creatinine clearance and time since diagnosis until the beginning of the second-line treatment. Bendamustine and rituximab followed by fludarabine, cyclophosphamide and rituximab were the most common regimens used in the firs-line treatment. Deletion (del) 17p and/or TP53 mutation, and del 11q were more frequent in the BTKi cohort, while unmutated IGVH gene was detected similarly in both groups (Table 1). Median follow-up was longer in BTKi than in Bcl-2i group (19.2 vs. 11.5 months). The overall response rate (ORR) was evaluated in 191 patients treated with BTKi and in 42 patients treated with Bcl-2i for at least six months. The ORR was comparable between the BTKi and Bcl-2i cohort, 90.6% (173/191) vs. 92.9% (39/42) (p = 0.774). More complete remissions (CR) were seen in Bcl-2i group, 12.0% (23/191) vs. 42.9% (18/42) (p&amp;lt;0.001). Median progression-free survival (mPFS) was 37.4 (31.4 - 43.35) months vs. not reached (BTKi vs Bcl-2i), HR 1.07 (95% CI, 0.59 - 1.94) (p = 0.833, Figure 1). Median overall survival (mOS) was 64.3 (37.2 - 91.5) months vs. not reached (BTKi vs Bcl-2i), HR 1.35 (95% CI 0.70 - 2.63) (p=0.371, Figure 1). Similar results were observed in the subgroup with del17p and/or TP53 mutation (mPFS: 35.6 months vs. not reached, HR 1.80, 95% CI, 0.69 - 4.69), as well as in the subgroup with unmutated IGVH gene (mPFS: 35.6 months vs. not reached, HR 1.36, 95% CI, 0.72 - 2.55). At the time of data analysis, hematological toxicity and infectious complications were premature for comparison (data were assessed in 31.3% of BTKi and 57.4% of Bcl-2i patients). Grade III-IV hypertension and other non-hematological toxicity (excluding infections) prevailed in BTKi cohort (19.2% BTKi, 9.6% Bcl-2i). The median treatment duration of BTKi and Bcl-2i was 14.7 (0.7 - 53.4) and 9.7 (0.3 - 25.8) months, respectively. Early discontinuation was observed more frequently post BTKi compared to post Bcl-2i administration, 43.9% (101/230) vs. 26.2% (16/61) (p&amp;lt;0.001). Except for the progression (24.8% BTKi, 18.8% Bcl-2i), the most common causes leading to premature discontinuation were death (23.8% BTKi, 12.5% Bcl-2i), infection (9.99% BTKi, 37.5% Bcl-2i), and non-hematological toxicity (24.8% BTKi, 6.3% Bcl-2i). Conclusion: In terms of high-risk prognostic markers, a higher prevalence of del 17p and/or TP53 mutation, and del 11q were observed in the BTKi cohort. In contrast, frequency of the unmutated IGVH gene was comparable in both groups. Difference in median PFS and OS was not statistically significant within the current follow-up period. However, premature termination of treatment was more commonly seen in BTKi group. To confirm our primary outcomes, longer follow-up is warranted.

Genomic Profiles and Associated Survival Prognosticators in Black Patients with Acute Myeloid Leukemia

Background Our knowledge of the genomics of acute myeloid leukemia (AML), which serves as the basis of clinically used prognostic biomarkers and therapeutic advances (including targeted therapies), is almost exclusively based on data from patients (pts) of European ancestry. Methods We analyzed the exomes and transcriptomes of 100 Black AML pts at diagnosis who received intensive induction chemotherapy on Alliance for Clinical Trials in Oncology (Alliance) protocols. African Ancestry was confirmed by SNP analysis. We established their genetic landscape including somatic gene mutations, structural variants, gene fusions and associated gene expression. Somatic mutation frequency was compared to whole-exome sequencing of 741 White pts at diagnosis from the Beat AML cohort analyzed by identical workflow. Survival of Black pts was compared to 1,519 White pts treated on the same Alliance protocols. Multivariable analysis was used to identify clinical and molecular features associated with outcomes. Results We identified 162 recurrently mutated genes in Black AML pts. We detected different mutation frequencies for AML-associated genes based on ancestry, and mutations in genes not previously implicated in AML, including PHIP alterations in 7% of this cohort. 38 genes were mutated in 3-5% of Black pts but in &amp;lt;1% of White pts . Of the 162 recurrently mutated genes in Black pts, only 41 (25%) were recurrently mutated in White pts, while 121 genes (75%) were mutated in ≤1 White patient. Only 1/741 White AML pts did not have a mutation in at least 1/ 56 recurrently mutated AML genes assessed by clinical NGS panels. By comparison, 10% of Black pts had no mutations in these genes. Analysis of gene fusions showed recurrent, cryptic CBFA2T3 fusions in 4 pts and a recurrent GGNBP2:: MYO19 fusion involving chromosome 17 not previously described in AML in 2 pts. The CBFA2T3 fusions did not cluster with CBF-AMLs by gene expression, suggesting biological differences. t-SNE visualization of gene expression showed that Black and White AML pts clustered together by known driver mutations. We identified a t-SNE cluster enriched for pts with myelodysplasia-related (MR) mutations. Notably, Black pts in this cluster were significantly younger than White pts [50 vs 58-years (y), p=0.04], suggestive of intrinsic and/or extrinsic dysplasia-causing stressors. When matched for age, performance status and study date, Black pts had higher relapse rates (63% vs 48%, p=0.05), worse disease-free (DFS, 3-y rates, 30% vs 47%, p=0.01) and overall survival (OS, 3-y rates, 31% vs 47%, p=0.007) compared to White pts. In a multivariable analysis, MR mutations (HR=2.06, p=0.03) and mutations in NPM1 (HR=2.29, p=0.009) and NRAS (HR=1.95, p=0.04) were associated with shorter DFS. Using the recently published iScore as a proxy for inflammation, we detected an enrichment of high inflammation in Black pts harboring NPM1 mutations compared to Whites (iScore high vs low; Black, 69% vs 31%, White, 45% vs 55%; p=0.08). Furthermore, when we classified pts into LSC17 prognostic groups, only 13% of Black pts in the prognostically favorable low LSC17 group were NPM1-mutated, compared with to 38% of White pts, suggesting ancestry-associated differences in the biological impact of NPM1 mutations. Mutations in IDH1/2 associated with shorter OS (HR=1.73, p=0.05) in Black pts identifying ancestry-specific risk markers. Finally, we show that the current ELN 2022 risk stratification system can be significantly improved by including NPM1, NRAS and IDH1/2 mutations as ancestry-specific adverse risk markers for Black pts ( Figure 2). Mutations in NPM1, NRAS, and IDH1/2 were enriched in a cohort of 43 Black relapsed/refractory (R/R)-AML pts via MSK-IMPACT supporting their adverse prognostic risk in Black pts. Conclusions Our work demonstrates ancestry-related differences in the genomic profiles of AML pts and calls for additional studies of ancestry-diverse populations to understand the landscape of somatic genetic alterations in AML. Further, our results emphasize the need to include ancestry-associated variants in clinical testing panels and to refine genetic risk assessment of AML by incorporating ancestry-specific prognostic biomarkers. Support: U10CA180821, U10CA180882, U24CA196171; Clinicaltrials.gov Identifiers: NCT00048958, NCT00899223, NCT00900224. https://acknowledgments.alliancefound.org.

Clinical Characteristics and Prognosis of Acute Myeloid Leukemia Patients with Protein Tyrosine Phosphatase Non-Receptor Type 11 Gene Mutation.

The purpose of our study was to investigate the clinical characteristics, molecular biological characteristics and prognosis of acute myeloid leukemia (AML) patients with protein tyrosine phosphatase non-receptor type 11 (PTPN11) gene mutation. The clinical data of 30 newly diagnosed adult AML patients with PTPN11 gene mutation were analyzed retrospectively. Kaplan-Meier and Cox proportional risk regression model were examined for prognostic analysis and prognostic factor screening. High-frequency mutation sites of PTPN11 gene are located in exon 3 of chromosome 12, which are D61 and A72 (16.7%), followed by E76 (13.3%). The median variant allele frequency (VAF) of PTPN11 mutant gene is 18.4%. The patients were divided into two groups according to PTPN11 VAF 35.3% (upper quartile). We observed that the peripheral blood leukocyte count in patients with VAF ≥35.3% was significantly higher than patients with VAF < 35.3% (p = 0.019) and also closely related to M5 (p = 0.016) and internal tandem duplication (ITD) of FMS-like tyrosine kinase 3 (FLT3) (FLT3-ITD) mutation (p = 0.048). Taking PTPN11 VAF 20% and 35.3% as the cutoff value, the patients were divided into two groups, and the overall survival and event-free survival (EFS) of the two groups were not significant. Multivariate analysis of Cox risk ratio model showed that white blood cell count and Eastern Cooperative Oncology Group (ECOG) physical status score were independent risk factors affecting the EFS. Our study observed that PTPN11 VAF may not be a prognostic factor in patients with PTPN11mut AML. Newly diagnosed high white blood cell count and poor performance status were independent risk factors for EFS in PTPN11mut AML.

CYP2D6 genotyping and the clinical impact on outcomes in breast cancer tamoxifen-treated patients.

Aims: To report the distribution of allele frequencies of CYP2D6 gene and to evaluate their influence on the clinical outcomes of a group of breast cancer patients receiving adjuvant tamoxifen treatment from Uruguay. Patients & methods: 199samples were genotyped through real-time polymerase chain reaction assays. Metabolization profiles were inferred from the genotypes. Correlations were evaluated using Pearson's χ2 test. Results: Phenotype frequencies were0.65 normal (NM), 0.30 intermediate (IM)and 0.05 poor metabolizers (PM). Similar clinical outcomes between NM and (PM+IM) patient groups (odds ratio=1.011, 95% CI=0.2703-3.7826;p=0.987) were found. Conclusion: CYP2D6 allele frequencies were analyzed for the first time in a cohort from Uruguay. Results did not support any impact of CYP2D6 gene polymorphisms on clinical outcomes.

Customized targeted massively parallel sequencing enables the identification of novel pathogenic variants in Tunisian patients with developmental and epileptic encephalopathy.

To develop a high-throughput sequencing panel for the diagnosis of developmental and epileptic encephalopathy in Tunisia and to clarify the frequency of disease-causing genes in this region. We developed a custom panel for next-generation sequencing of the coding sequences of 116 genes in individuals with developmental and epileptic encephalopathy from the Tunisian population. Segregation analyses and in silico studies have been conducted to assess the identified variants' pathogenicity. We report 12 pathogenic variants in SCN1A, CHD2, CDKL5, SZT2, KCNT1, GNAO1, PCDH19, MECP2, GRIN2A, and SYNGAP1 in patients with developmental and epileptic encephalopathy. Five of these variants are novel: "c.149delA, p.(Asn50MetfsTer26)" in CDKL5; "c.3616C > T, p.(Arg1206Ter)" in SZT2; "c.111_113del, p.(Leu39del)" in GNAO1; "c.1435G>C, p.(Asp479His)" in PCDH19; and "c.2143delC, p.(Arg716GlyfsTer10)" in SYNGAP1. Additionally, for four of our patients, the genetic result facilitated the choice of the appropriate treatment. This is the first report of a custom gene panel to identify genetic variants implicated in developmental and epileptic encephalopathy in the Tunisian population as well as the North African region (Tunisia, Egypt, Libya, Algeria, Morocco) with a diagnostic rate of 30%. This high-throughput sequencing panel has considerably improved the rate of positive diagnosis of developmental and epileptic encephalopathy in the Tunisian population, which was less than 15% using Sanger sequencing. The benefit of genetic testing in these patients was approved by both physicians and parents.

Implications of combined NOD2 and other gene mutations in autoinflammatory diseases.

NOD-like receptors (NLRs) are intracellular sensors associated with systemic autoinflammatory diseases (SAIDs). We investigated the largest monocentric cohort of patients with adult-onset SAIDs for coinheritance of low frequency and rare mutations in NOD2 and other autoinflammatory genes. Sixty-three patients underwent molecular testing for SAID gene panels after extensive clinical workups. Whole exome sequencing data from the large Atherosclerosis Risk in Communities (ARIC) study of individuals of European-American ancestry were used as control. Of 63 patients, 44 (69.8%) were found to carry combined gene variants in NOD2 and another gene (Group 1), and 19 (30.2%) were carriers only for NOD2 variants (Group 2). The genetic variant combinations in SAID patients were digenic in 66% (NOD2/MEFV, NOD2/NLRP12, NOD2/NLRP3, and NOD2/TNFRSF1A) and oligogenic in 34% of cases. These variant combinations were either absent or significantly less frequent in the control population. By phenotype-genotype correlation, approximately 40% of patients met diagnostic criteria for a specific SAID, and 60% had mixed diagnoses. There were no statistically significant differences in clinical manifestations between the two patient groups except for chest pain. Due to overlapping phenotypes and mixed genotypes, we have suggested a new term, "Mixed NLR-associated Autoinflammatory Disease ", to describe this disease scenario. Gene variant combinations are significant in patients with SAIDs primarily presenting with mixed clinical phenotypes. Our data support the proposition that immunological disease expression is modified by genetic background and environmental exposure. We provide a preliminary framework in diagnosis, management, and interpretation of the clinical scenario.

Establishment of AA-NAT, SCD, PROP1, and IGFBP3 gene frequency distributions in Karacabey Merino and Kivircik Sheep Breeds

Thus, the aim of the current study was to investigate the genotypic dispersion of AA-NAT, SCD, PROP1, and IGFBP3 genes in the target population. Primarily, the genomic DNA was isolated from blood samples by the phenol/chloroform method. The genomic analyses were performed on a total of 160 Karacabey Merino (KM) sheep (n=80) and Kivircik (n=80). The PCR-RFLP method was used to determine the genotype of the SNPs. Deviation from Hardy–Weinberg equilibrium (HWE) and population genetic assays such as observed (Ho) and expected (He) heterozygosities, effective allele numbers (Ne), and the polymorphism information content (PIC) were calculated for each gene in the population. As a result, there was no deviation from HWE was determined except SCD and PROP1 gene in KM. The most frequent genotypes were found AA (66,25% and 87,50%) for AA-NAT gene, CC (93,75% and 91,25%) for SCD gene and CC genotype (70,00% and 56,25%) for PROP1 gene in KM and Kivircik sheep. All breeds were detected monomorphic in terms of the IGFBP3 gene. In conclusion, the other regions of the IGFBP3 gene which were determined as monomorphic in the studied flock could be researched. Moreover, further studies should be necessary for defining the effects of investigated genes on related traits in KM and Kivircik sheep in terms of polymorphic genes specified.

Analysis of Correlation Between Coronary Heart Disease and Genetic Polymorphism Detected by Gold Magnetic Nanoparticles Chromatography.

It aimed to explore the correlation of Glu504Lys locus mutation of aldehyde dehydrogenase-2 (ALDH2) with coronary heart disease (CHD) based on gold magnetic nanoparticles (GMNPs) chromatography and amplification refractory mutation system-PCR (ARMS-PCR). 120 CHD patients admitted to the cardiovascular Department of Wenling First People's Hospital affiliated to Wenzhou Medical University from December 2020 to December 2021 were selected as Case group and 80 non-CHD patients admitted during the same period were selected as Ctrl group. The venous blood and indexes of Total Cholesterol (TC), Triglyceride (TG), Low Density Lipoprotein Cholesterol (LDL-C), High Density Lipoprotein Cholesterol (HDL-C), and Fasting Blood Glucose (FBS) were collected. The ARMS-PCR GMNPs chromatography based on ARMS-PCR and immunochromatography assay was adopted to detect gene polymorphism of ALDH2. Correlation between ALDH2 gene polymorphism and risk factors of CHD was analyzed via logistic regression. In contrast to Ctrl group, the genotypes of GG, GA, and AA in Case group were evidently different (P < 0.05), and the frequency of A allelic gene was obviously increased (P < 0.05). Under the dominant model, frequency of GA + AA genotype in Case group was remarkably higher in contrast to Ctrl group (P < 0.05). Under the recessive model, there was no obvious difference in genotype frequency between two groups. In contrast to Ctrl group, TC, LDL-C, and FBS in Case group were notably increased (P < 0.05), while HDL-C was notably decreased (P < 0.05). The distribution frequency of abnormal LDL-C, HDL-C, and FBS in Case group was notably higher in contrast to Ctrl group (P < 0.05). LDL-C and FBS had no obvious effect on the genotypes and frequency distribution of alleles in CHD patients. However, the frequency distribution of genotypes of GA and AA and A allelic gene in patients with abnormal HDL-C was notably lower in contrast to those with normal HDL-C (P < 0.05). Logistic regression analysis showed that abnormal HDC-C with A allelic gene were independent risk factors for CHD (P = 0.001, OR = 1.934). The gene polymorphism of Glu504Lys locus of ALDH2 was closely related to the pathogenesis of CHD, A allelic gene may be a susceptibility gene for CHD, and patients with abnormal HDC-C and carried A allelic gene had relatively higher incidence of CHD.

DNMT1 SNPs (rs2114724 and rs2228611) associated with positive symptoms in Chinese patients with schizophrenia

ObjectiveSchizophrenia is a serious mental disorder with complex clinical manifestations, while its pathophysiological mechanism is not fully understood. Accumulated evidence suggested the alteration in epigenetic pathway was associated with clinical features and brain dysfunctions in schizophrenia. DNA methyltransferases (DNMTs), a key enzyme for DNA methylation, are related to the development of schizophrenia, whereas the current research evidence is not sufficient. The aim of study was to explore the effects of gene polymorphisms of DNMTs on the susceptibility and symptoms of schizophrenia.MethodsThe study was case–control study that designed and employed the Diagnostic and Statistical Manual of Mental Disorders-Fifth Edition (DSM-5) as the diagnostic standard. 134 hospitalized patients with schizophrenia in the Third People's Hospital of Zhongshan City from January 2018 to April 2020 (Case group) as well as 64 healthy controls (Control group) from the same region were involved. Single nucleotide polymorphisms (SNPs) of DNMT1 genes (r s2114724 and rs 2228611) and DNMT3B genes (rs 2424932, rs 1569686, rs 6119954 and rs 2424908) were determined with massARRAY. Linkage disequilibrium analysis and haplotype analysis were performed, and genotype and allele frequencies were compared. The Hardy–Weinberg equilibrium was tested by the Chi-square test in SPSS software (version 20.0, SPSS Inc., USA). The severity of clinical symptoms was assessed by the Positive and Negative Syndrome Scale (PANSS). The correlation between DNMT1 genes (rs 2114724 and rs 2228611) and DNMT3B genes (rs2424932, rs1569686, rs6119954 and rs2424908) and clinical features was analyzed.ResultsThere were no significant differences in genotype, allele frequency and haplotype of DNMT1 genes (rs 2114724 and rs 2228611) and DNMT3B genes (rs 2424932, rs 1569686, rs 6119954 and rs 2424908) between the case and healthy control group. There were significant differences in the PANSS total positive symptom scores, P3 (hallucinatory behavior), P6 (suspicious/persecution), G7 (motor retardation), and G15 (preoccupation) in patients with different DNMT1 gene rs 2114724 and rs 2228611 genotypes. The linkage disequilibrium analysis of gene polymorphic loci revealed that rs 2114724–rs 2228611 was complete linkage disequilibrium, and rs 1569686–rs 2424908, rs 2424932–rs 1569696 and rs 2424932–rs 2424908 were strongly linkage disequilibrium.ConclusionThe polymorphisms alteration in genetic pathway may be associated with development of specific clinical features in schizophrenia.