Molecular Diagnosis Research Articles

IgE sensitization to Blo t 21 and Blo t 5 is associated with asthma in the tropics: a case-control study.

Blomia tropicalis sensitization is associated with asthma in different tropical and sub-tropical countries; however, information about the specific molecular components associated with this disease is scarce. Using molecular diagnosis, we sought to identify B. tropicalis allergens associated with asthma in Colombia. Specific IgE (sIgE) to eight B. tropicalis recombinant allergens (Blo t 2/5/7/8/10/12/13 and 21) was determined using an in-house developed ELISA system in asthmatic patients (n=272) and control subjects (n=298) recruited in a national prevalencestudy performed in Colombian cities (Barranquilla, Bogotá, Medellín, Cali and San Andrés). Sample study included children and adults (mean age: 28±SD 17 years old). Cross-reactivity between Blot 5 and Blo t 21 was evaluated by ELISA-inhibition. Sensitization to Blo t 21 (aOR: 1.9; 95% CI: 1.2 - 2.9) and Blo t 5 (aOR: 1.6; 95%CI: 1.1 - 2.5), but not Blo t 2, was associated with asthma. sIgE levels to Blo t 21 and to Blo t 5 were significantly higher in the disease group. Cross-reactivity between Blo t 21 and Blo t 5 is on average moderate; however, individual analysis indicates that may be high (>50%) in some cases. Although Blo t 5 and Blo t 21 has been described as common sensitizers, this is the first report of their association with asthma. Both components should be included in molecular panels for allergy diagnosis in the tropics.

РАННЯЯ ДИАГНОСТИКА МИОДИСТРОФИИ ДЮШЕННА: АКТУАЛЬНОСТЬ, ПРОБЛЕМЫ, ВОЗМОЖНОСТИ И ПЕРСПЕКТИВЫ

Duchenne muscular dystrophy (DMD) is an orphan neuromuscular progressive genetic disease that causes muscle breakdown and subsequent loss. Provided early diagnosis, complex standard and pathogenetic therapy significantly changes the trajectory of the disease, making it more benign. Diagnosis of DMD is a two-pillar system with creatine kinase (CK) level measured at the first stage followed by molecular genetic study in case the enzyme threshold values. The quality of genetic diagnostics in Russia has reached the best worldwide standards recently though identifying children with elevated CK levels is yet difficult. The number of diagnosed DMD patients in Russia is significantly lower than the statistically estimated global amount. The average age for diagnosis is not decreasing either. Thus, the median age for DMD and Becker muscular dystrophy (BMD) molecular diagnosis is 7 years and 8 months old. The number of identified children below the age of 2 y/o in Russia has remained consistently low over the past three years. According to the results of a familial cases survey, the correct primary diagnosis of DMD was established in less than half of all cases, 47.1%. The most common incorrect diagnoses were as follows: asymptotic hepatitis (25.1%), perinatal damage to the central nervous system (6.4%), cerebral palsy (2.7%), autism spectrum disorder (ASD) (2.7%) and flat feet, hallux valgus etc. (16% in total). The median duration between the initial DMD manifestation and molecular diagnosis is 3 years and 8 months as yet whilst the age-specific guidelines suggest prescribing standard and pathogenetic therapy during the 2 to 5 y/o period of life. Therefore, the Russia’s average age of DMD diagnosis above 7 y/o lies far beyond the optimal age for initiating of the DMD therapy with the purpose of gaining its maximum possible clinical benefit. The accumulated international and Russian experience demonstrates the possibility for improving of the primary DMD and BMD diagnosis in early preschool age and therefore requires its nationwide introduction.

ОСОБЕННОСТИ НУТРИТИВНОГО СТАТУСА ДЕТЕЙ С МУКОВИСЦИДОЗОМ РАЗЛИЧНЫХ ЭТНИЧЕСКИХ ГРУПП СЕВЕРНОГО КАВКАЗА

Adequate nutritional status in a patient with cystic fibrosis (CF) positively correlates with the normal function of the bronchopulmonary system. Many domestic and foreign studies have been conducted so far to assess the nutritional status of children and adults with CF. However, there is no data as yet on the phenotypic characteristics of children from different ethnic groups of the North Caucasus depending on their genotype. The purpose of this research was to study the peculiarities of nutritional status in children with CF of the following Russia’s North Caucasus ethnic groups: Chechen, Karachay-Circassian, Dagestani, Ingush and Ossetian-Alanian. Materials and methods used: a single-center open prospective study of 117 children with CF aged 2 months to 17 years old (Me 6 y/o) of various North Caucasus ethnic groups was conducted. All patients have undergone molecular diagnosis and assessment of both nutritional status and exocrine pancreatic function. Results: 50.4% of pediatric patients with CF in the Russia’s North Caucasus have had pathological mutations in c.1545_1546delTA, p.(Tyr515*) and c.3846G>A, p.(Trp1282*) in homozygous state. These mutations were most often found in the Ingush (100%) and Chechen (82%) ethnic groups and somewhat less frequently in the Dagestani (57.1%) and Karachay-Circassian (54%) ethnic groups. In the Chechen and Ossetian-Alanian ethnic groups, when these mutations were detected, severe pancreatic insufficiency was established in 40.5% and 100% of cases, respectively. Pseudo-Bartter syndrome was diagnosed in 60% of cases with this genetic variant in a homozygous or compound heterozygous states during the patients’ first years of life. Indicators for the nutritional status of children with CF from different ethnic groups were significantly lower compared to those recorded officially in the 2021 Russian National Register of Patients with CF. Conclusion: it is necessary to study the course of CF and the state of nutritional status separately in each population and its connection with the identified genetic characteristics of the Russia’s North Caucasus ethnic groups. The genotype and phenotype patterns for these patients were the reason for the development of disorders of the exocrine function of the pancreas and pseudo-Bartter syndrome at an early age, which in its turn could lead to further development of nutritional deficiency.

Genome Sequencing for Diagnosing Rare Diseases

BackgroundGenetic variants that cause rare disorders may remain elusive even after expansive testing, such as exome sequencing. The diagnostic yield of genome sequencing, particularly after a negative evaluation, remains poorly defined.MethodsWe sequenced and analyzed the genomes of families with diverse phenotypes who were suspected to have a rare monogenic disease and for whom genetic testing had not revealed a diagnosis, as well as the genomes of a replication cohort at an independent clinical center.ResultsWe sequenced the genomes of 822 families (744 in the initial cohort and 78 in the replication cohort) and made a molecular diagnosis in 218 of 744 families (29.3%). Of the 218 families, 61 (28.0%) — 8.2% of families in the initial cohort — had variants that required genome sequencing for identification, including coding variants, intronic variants, small structural variants, copy-neutral inversions, complex rearrangements, and tandem repeat expansions. Most families in which a molecular diagnosis was made after previous nondiagnostic exome sequencing (63.5%) had variants that could be detected by reanalysis of the exome-sequence data (53.4%) or by additional analytic methods, such as copy-number variant calling, to exome-sequence data (10.8%). We obtained similar results in the replication cohort: in 33% of the families in which a molecular diagnosis was made, or 8% of the cohort, genome sequencing was required, which showed the applicability of these findings to both research and clinical environments.ConclusionsThe diagnostic yield of genome sequencing in a large, diverse research cohort and in a small clinical cohort of persons who had previously undergone genetic testing was approximately 8% and included several types of pathogenic variation that had not previously been detected by means of exome sequencing or other techniques. (Funded by the National Human Genome Research Institute and others.)

DSC-PWI presurgical differentiation of grade 4 astrocytoma and glioblastoma in young adults: rCBV percentile analysis across enhancing and non-enhancing regions.

The presurgical discrimination of IDH-mutant astrocytoma grade 4 from IDH-wildtype glioblastoma is crucial for patient management, especially in younger adults, aiding in prognostic assessment, guiding molecular diagnostics and surgical planning, and identifying candidates for IDH-targeted trials. Despite its potential, the full capabilities of DSC-PWI remain underexplored. This research evaluates the differentiation ability of relative-cerebral-blood-volume (rCBV) percentile values for the enhancing and non-enhancing tumor regions compared to the more commonly used mean or maximum preselected rCBV values. This retrospective study, spanning 2016-2023, included patients under 55 years (age threshold based on World Health Organization recommendations) with grade 4 astrocytic tumors and known IDH status, who underwent presurgical MR with DSC-PWI. Enhancing and non-enhancing regions were 3D-segmented to calculate voxel-level rCBV, deriving mean, maximum, and percentile values. Statistical analyses were conducted using the Mann-Whitney U test and AUC-ROC. The cohort consisted of 59 patients (mean age 46; 34 male): 11 astrocytoma-4 and 48 glioblastoma. While glioblastoma showed higher rCBV in enhancing regions, the differences were not significant. However, non-enhancing astrocytoma-4 regions displayed notably higher rCBV, particularly in lower percentiles. The 30th rCBV percentile for non-enhancing regions was 0.705 in astrocytoma-4, compared to 0.458 in glioblastoma (p = 0.001, AUC-ROC = 0.811), outperforming standard mean and maximum values. Employing an automated percentile-based approach for rCBV selection enhances differentiation capabilities, with non-enhancing regions providing more insightful data. Elevated rCBV in lower percentiles of non-enhancing astrocytoma-4 is the most distinguishable characteristic and may indicate lowly vascularized infiltrated edema, contrasting with glioblastoma's pure edema.

Quality assurance for next-generation sequencing diagnostics of rare neurological diseases in the European Reference Network.

In the past decade, next-generation sequencing (NGS) has revolutionised genetic diagnostics for rare neurological disorders (RND). However, the lack of standardised technical, interpretative, and reporting standards poses a challenge for ensuring consistent and high-quality diagnostics globally. To address this, the European Reference Network for Rare Neurological Diseases (ERN-RND) collaborated with the European Molecular Genetics Quality Network (EMQN) to establish an external quality assessment scheme for NGS-based diagnostics in RNDs. The scheme, initiated in 2021 with a pilot involving 29 labs and followed by a second round in 2022 with 42 labs, aimed to evaluate the performance of laboratories in genetic testing for RNDs. Each participating lab analysed genetic data from three hypothetical cases, assessing genotyping, interpretation, and clerical accuracy. Despite a majority of labs using exome or genome sequencing, there was considerable variability in gene content, sequencing quality, adherence to standards, and clinical guidance provision. Results showed that while most labs provided correct molecular diagnoses, there was significant variability in reporting technical quality, adherence to interpretation standards, reporting strategies, and clinical commentary. Notably, some labs returned results with the potential for adverse medical outcomes. This underscores the need for further harmonisation, guideline development, and external quality assessment in the evolving landscape of genomic diagnostics for RNDs. Overall, the experience with the scheme highlighted the generally good quality of participating labs but emphasised the imperative for ongoing improvement in data analysis, interpretation, and reporting to enhance patient safety.

Clinical and molecular features of patients with IDH1 wild-type primary glioblastoma presenting unexpected short-term survival after gross total resection.

This study investigated the factors influencing short-term survivors (STS) after gross total resection (GTR) in patients with IDH1 wild-type primary glioblastoma. We analyzed five independent cohorts who underwent GTR, including 83 patients from Kitasato University (K-cohort), and four validation cohorts of 148 patients from co-investigators (V-cohort), 66 patients from the Kansai Molecular Diagnosis Network for the Central Nervous System tumors, 109 patients from the Cancer Genome Atlas, and 40 patients from the Glioma Longitudinal AnalySiS. The study defined STS as those who had an overall survival ≤ 12months after GTR with subsequent radiation therapy, and concurrent and adjuvant temozolomide (TMZ). The study included 446 patients with glioblastoma. All cohorts experienced unexpected STS after GTR, with a range of 15.0-23.9% of the cases. Molecular profiling revealed no significant difference in major genetic alterations between the STS and non-STS groups, including MGMT, TERT, EGFR, PTEN, and CDKN2A. Clinically, the STS group had a higher incidence of non-local recurrence early in their treatment course, with 60.0% of non-local recurrence in the K-cohort and 43.5% in the V-cohort. The study revealed that unexpected STS after GTR in patients with glioblastoma is not uncommon and such tumors tend to present early non-local recurrence. Interestingly, we did not find any significant genetic alterations in the STS group, indicating that such major alterations are characteristics of GB rather than being reliable predictors for recurrence patterns or development of unexpected STS.

Infectious optic neuropathy (ION), how to recognise it and manage it.

Optic neuropathy can be of infectious or non-infectious/idiopathic aetiology. Many infectious organisms can cause optic neuropathy that can be of varied presentation including papillitis, retrobulbar optic neuritis, neuroretinitis, and optic perineuritis. Detailed history, ocular, systemic/neurologic examination along with appropriate laboratory evaluation can help clinicians to identify the infectious agent causing optic neuropathy. In spite of recent advanced techniques in serological testing and molecular diagnostics like polymerase chain reaction (PCR), the identification of these pathogens is still a diagnostic challenge. It is ideal to have an infectious disease (ID) consultant in the management team, as most of these infections are multisystem involving diseases. Most infectious agents can be effectively treated with specific antibiotics, with or without corticosteroid therapy, but visual recovery is highly variable and depends entirely on early diagnosis of the causative agent. This review article will provide an overview of common pathogens involved in ION and will describe their management paradigms.

Revolutionizing Leishmaniasis Treatment with Cutting Edge Drug Delivery Systems and Nanovaccines: An Updated Review.

Leishmaniasis, one of the most overlooked tropical diseases, is a life-threatening illness caused by the parasite Leishmania donovani that is prevalent in underdeveloped nations. Over 350 million individuals in more than 90 different nations worldwide are at risk of contracting the disease, which has a current fatality rate of 50 000 mortalities each year. The administration of liposomal Amp B, pentavalent antimonials, and miltefosine are still considered integral components of the chemotherapy regimen. Antileishmanial medications fail to treat leishmaniasis because of their numerous drawbacks. These include inadequate effectiveness, toxicity, undesired side effects, drug resistance, treatment duration, and cost. Consequently, there is a need to overcome the limitations of conventional therapeutics. Nanotechnology has demonstrated promising outcomes in addressing these issues because of its small size and distinctive characteristics, such as enhanced bioavailability, lower toxicity, biodegradability, and targeted drug delivery. This review is an effort to highlight the recent progress in various nanodrug delivery systems (nDDSs) over the past five years for treating leishmaniasis. Although the preclinical outcomes of nDDSs have shown promising treatment for leishmaniasis, further research is needed for their clinical translation. Advancement in three primary priority domains─molecular diagnostics, clinical investigation, and knowledge dissemination and standardization─is imperative to propel the leishmaniasis field toward translational outcomes.

Delayed diagnosis of mild mucopolysaccharidosis type IVA

BackgroundMucopolysaccharidosis IVA (MPS IVA) is a lysosomal storage disease caused by biallelic variants in the N-acetylgalactosamine-6-sulfatase (GALNS) gene and is characterized by progressive and multi-system involvements, dominantly with skeletal deformities. A mild form of MPS IVA often presents with atypical symptoms and can go unrecognized for years.MethodsThe diagnosis of MPS IVA was confirmed via GALNS enzyme activity testing in leukocytes. Clinical features were collected. Molecular analysis was performed by next generation sequence and Sanger sequencing of the GALNS gene. The pathogenicity of the deep intron variant was verified by mRNA analyses.ResultsThirteen patients with mild MPS IVA from six families were included. All probands first visit pediatric orthopedists and it took 5.6 years to be diagnosed after the disease onset. The most common symptoms in our series were waddling gait (85%), short neck (69%) and flat feet (62%). Radiologic findings indicated skeletal abnormalities in all patients, especially modification of the vertebral bodies (100%) and acetabular and femoral head dysplasia (100%). Five novel GALNS variants, including c.121-2_121-1insTTTGCTGGCATATGCA, E2 deletion, c.569 A > G, c.898 + 2 T > A, and c.1139 + 2 T > C, were identified. The most common variant, a deep intron variant NM_000512.5: c.121–210 C > T (NM_001323544.2: c.129 C > T, p.G43G), was revealed to result in an 11 bp deletion (c.128_138delGCGATGCTGAG, p.Gly43Aspfs*5) on GALNS mRNA in the GALNS transcript of NM_001323544.2.ConclusionsThis study provides significant insights into the clinical features and molecular characteristics that contribute to the early diagnosis of mild MPS IVA. On the basis of our cohort, orthopedists need to be able to recognize signs and symptoms of mild MPS IVA as well as the molecular and biochemical diagnosis so that an early diagnosis and treatment can be instituted.

Molecular Genetic Diagnosis with Targeted Next Generation Sequencing in a Cohort of Turkish Osteogenesis Imperfecta Patients and Their Genotype-phenotype Correlation.

Osteogenesis imperfecta (OI) is a group of phenotypically and genetically heterogeneous connective tissue disorders that share similar skeletal anomalies causing bone fragility and deformation. This study aimed to investigate the molecular genetic etiology and determine the relationship between genotype and phenotype in OI patients with targeted next-generation sequencing (NGS). In patients with OI, a targeted NGS analysis panel (Illumina TruSight One) containing genes involved in collagen/bone synthesis was performed on the Illumina Nextseq550 platform. Fifty-six patients (female/male: 25/31) from 46 different families were enrolled in the study. Consanguinity between parents was noted in 15 (32.6%) families. Clinically according to Sillence classification; 18(33.1%) patients were considered to type I, 1(1.7%) type II, 26(46.4%) type III and 11(19.6%) type IV. Median body weight was -1.1 (-6.8, - 2.5) SDS, and height was -2.3 (-7.6, - 1.2) SDS. Bone deformity was detected in 30 (53.5%) of the patients, while 31 (55.4%) were evaluated as mobile. Thirty-six (60.7%) patients had blue sclera, 13 (23.2%) had scoliosis, 12 (21.4%) had dentinogenesis imperfecta (DI), and 2 (3.6%) had hearing loss. Disease-causing variants in COL1A1 and COL1A2 genes were found in 24 (52.1%) and 6 (13%) families, respectively. In 8 (17.3%) of the remaining 16 (34.7%) families, the NGS panel revealed disease-causing variants in three different genes (FKBP10, SERPINF1, and P3H1). Nine (23.6%) of the variants detected in all investigated genes were not previously reported in the literature and were classified to be pathogenic according to ACMG guidelines pathogenity scores. In ten (21.7%) families, a disease-related variant was not found in a total of 13 OI genes included in the panel. Genetic etiology was found in 38 (82.6%) of 46 families by targeted NGS analysis. In addition, 9 new variants were assessed in known OI genes which is a significant contribution to the literature.

Modular CRISPR/Cas12a synergistic activation platform for detection and logic operations.

The revolutionary technology of CRISPR/Cas has reshaped the landscape of molecular biology and molecular engineering. This tool is of interest to researchers in multiple fields, including molecular diagnostics, molecular biochemistry circuits, and information storage. As CRISPR/Cas spreads to more niche areas, new application scenarios and requirements emerge. Developing programmability and compatibility of CRISPR/Cas becomes a critical issue in the new phase. Here, we report a redundancy-based modular CRISPR/Cas12a synergistic activation platform (MCSAP). The position, length, and concentration of the redundancy in the split DNA activators can finely regulate the activity of Cas12a. With the redundant structure as an interface, MCSAP serves as a modular plug-in to seamlessly integrate with the upstream molecular network. MCSAP successfully performs three different tasks: nucleic acid detection, enzyme detection, and logic operation. MCSAP can work as an effector for different molecular networks because of its compatibility and programmability. Our platform provides powerful yet easy-to-use tools and strategies for the fields of DNA nanotechnology, molecular engineering, and molecular biology.

Molecular Diagnosis of Chlamydia trachomatis in Women with Frequent Abortions

Molecular Diagnosis of Chlamydia trachomatis in Women with Frequent Abortions

N2M2/NOA-20: Phase I/IIa umbrella trial of molecularly matched targeted therapies plus radiotherapy in patients with newly diagnosed glioblastoma without MGMT promoter hypermethylation.

2000 Background: Patients with glioblastoma without MGMT promoter hypermethylation are unlikely to benefit from temozolomide (TMZ). Trials aiming at replacing TMZ with targeted agents in not molecularly selected patient populations have failed. Methods: This phase I/IIa umbrella trial aimed at showing safety, feasibility, and preliminary efficacy of targeted compounds in addition to standard radiotherapy initiated within 42 days postoperatively. Molecular diagnostics and bioinformatic evaluation are performed within 28 days after surgery. Stratification for treatment takes place in five subtrials, including alectinib, idasanutlin, palbociclib, vismogedib and temsirolimus, according to the best matching molecular alteration. Patients without matching alterations are randomized between subtrials without strong biomarkers using atezolizumab and asunercept and TMZ as standard of care. Primary objective of the phase I parts of the trial was dose finding or dose validation. In the phase IIa trials, centrally determined progression-free survival at six months (PFS-6) is used as endpoint for efficacy with interim analyses for futility ( H0: p=0.231). Results: From May 2018 through July 2022, 301 patients were enrolled and 228 treated in 13 German NOA sites. The alectinib and vismodegib subtrials were closed since no molecularly matching patients were accrued; the idasanutlin subtrial was closed prior to the optimal dose at nine patients at discretion of the company providing the drug. The TMZ subtrial showed a PFS-6 of 18.52% (10/54 patients) (p=0.831) and a median overall survival (OS) of 12.1 months. Asunercept: PFS-6 of 15.4% (4/26) (p=0.8825) and OS of 12.8 months. Atezolizumab: PFS-6 of 21.4% (9/42) (p=0.660) and OS of 11.7 months. Palbociclib with patients demonstrating CDK4 amplification or CDKN2A/B codeletion: PFS-6 of 24.4% (10/41) (p=0.4823) and OS of 12.6 months. Temsirolimus with patients demonstrating mTOR activation: PFS-6 of 39.1% (18/46) (p=0.0109) and OS of 15.4 months. The regimen-limiting toxicity (RLT)-rate is 34.8%, which is insignificantly above the predefined unacceptable rate for RLTs of 30%. Most RLTs had severity grade 3, one RLT had severity grade 4. No RLTs resulted in death. Conclusions: N2M2 allows for elaborate molecular testing being integrated into the treatment decision and efficient determination of treatment activity for patients with newly diagnosed glioblastoma. There is clinical activity of temsirolimus in patients with tumors harboring an activated mTOR pathway although this is not positively prognostic without mTOR inhibition; there is no clinical activity for asunercept and atezolizumab in not molecularly selected patients and also palbociclib in molecularly selected patients. Clinical trial information: NCT03158389 .

D-Glucose-Mediated Gold Nanoparticle Fabrication for Colorimetric Detection of Foodborne Pathogens.

Gold nanoparticle (AuNP) fabrication via the oxidation of D-glucose is applied for detecting two foodborne pathogens, Enterococcus faecium (E. faecium) and Staphylococcus aureus (S. aureus). D-glucose is used as a reducing agent due to its oxidation to gluconic acid by sodium hydroxide (NaOH), resulting in the formation of AuNPs. Based on this mechanism, we develop AuNP-based colorimetric detection in conjunction with loop-mediated isothermal amplification (LAMP) for accurately identifying the infectious bacteria. Here, Au+ ions bind to the base of double-stranded DNA. In the presence of D-glucose and NaOH, the LAMP amplicon-Au+ complex maintains its bound state at 65 °C for 10 min while it is reduced to AuNPs in a dispersed form, exhibiting a red color. We aimed to pre-mix D-glucose with LAMP reagents before amplification and induce successful colorimetry without inhibiting amplification to simplify the experimental process and decrease the reaction time. Therefore, the entire process, including LAMP and colorimetric detection, is accomplished in approximately 1 h. The limit of detection of E. faecium and S. aureus is confirmed using the introduced method as 101 CFU/mL and 100 fg/μL, respectively. We expect that colorimetric detection using D-glucose-mediated AuNP synthesis offers an application for simple and immediate molecular diagnosis.

Somatic STK11 mosaicism in a Turkish patient with Peutz-Jeghers syndrome.

Peutz-Jeghers syndrome (PJS) is an autosomal dominant disorder, caused by germline variants in the serine/threonine kinase 11 (STK11) gene. However, mosaic variants in STK11 gene have been rarely described. A 25-year-old woman diagnosed with PJS due to multiple hamartomatous polyps in the gastrointestinal tract was referred to our clinic. In the molecular diagnosis, the patient was evaluated using the STK11 gene sequence analysis and multiplex ligation-dependent probe amplification (MLPA) method, which suggested no pathogenic variant to account for the clinical picture. Given that the clinical findings of the patient were consistent with those of PJS, the raw data from next-generation sequencing (NGS) were re-examined for mosaicism which led to the detection of a novel mosaic c.920 + 1G > T variant in STK11 gene with a rate of 23% (1860x). Deep read-level NGS was performed on buccal mucosa and polyp samples to determine mosaicism levels in other tissues. Variant frequencies were 29% (710x) and 31% (1301x), respectively. Mosaicism should be considered in cases with clear clinical diagnostic criteria, such as PJS, where the pathogenic variant cannot be detected by sequence analysis and MLPA methods. Identification of mosaicism in these patients is very important as it can have an impact on patient follow-up and genetic counseling for relatives.

Proteogenomic profiling of clonal hematopoiesis in the solid tumor microenvironment.

2567 Background: Clonal hematopoiesis (CH) is caused by somatic mutations that provide a fitness advantage in hematopoietic stem cells, contributing to inflammation and disease. CH is common in solid tumor patients, and has shown context-dependent associations with survival; however, its contribution to the tumor microenvironment (TME) remains unclear. Here, we employ proteogenomic methods to define CH-associated alterations in the TME. Methods: We tested 1,550 patients across 10 primary, treatment-naïve cancers in the Clinical Proteomic Tumor Analysis Consortium cohort. CH calls were derived from peripheral blood and tumour whole exome sequencing (WES) data, and CH was defined as the presence of a somatic driver mutation at variant allele frequency (VAF) ≥2% in blood. Overall survival (OS) analysis was conducted using Cox proportional hazard models, controlled for age, sex, tumor type, metastatic status, and smoking. Tumor bulk RNA-sequencing and mass spectrometry proteomics data were processed for differential expression and gene set enrichment analyses. Abundance of immune cell populations was estimated with CibersortX. Results: 349 CH mutations were identified in 283 patients (18.3%). CH was strongly associated with age and mutations were mostly found in the epigenetic regulators DNMT3A(37.8%, n=132) and TET2(20.6%, n=72). CH was most prevalent in ovarian cancer (30%, n=27/90) and colorectal cancer (CRC; 28.3%, n=30/106). 103 blood CH mutations were also detected in tumor WES (CHTum), with presence in the tumor associated with higher tumor immune infiltration and peripheral blood VAF ≥10%. CHTum, but not CH, was associated with worse OS (CHTum HR = 1.74 [1.13-2.69]; CH HR = 1.12 [0.83-1.50]). CHTum was also associated with a reduced likelihood of patients being classified as tumor free at follow up (OR = 0.39 [0.19-0.82]). We did not identify a pan-cancer proteogenomic signature of CH in the TME. At the tumor-specific level, we consistently observed associations between CH and its subtypes with dysregulated inflammation, with high transcriptomic-proteomic concordance. In CRC, TET2-mutant CH was associated with greater infiltration of CD4+ T cells, monocyte/macrophages, NK cells, and B cells, alongside an inflammatory response characterized by IL6/JAK/STAT3 signalling, TNF signalling via NFκB, and IL2/STAT5 signalling. Conclusions: CH is common, even prior to therapy, in solid tumor patients and the infiltration of CH-mutant immune clones into the TME is linked with poor outcomes. Beyond confounding molecular tumor diagnostics, CH in the TME also dysregulates the anti-tumor immune response, highlighting the value of a blood reference in precision oncology. The lack of a pan-cancer CH signature in the TME supports a tumor-specific influence of CH. Further study is needed for mechanistic discovery and biomarker development to realize the potential of CH in immuno-oncology and improve patient outcomes.

Relationship of adaptive subtyping and tumour heterogeneity of treatment response to neoadjuvant therapy in hormone receptor–positive HER2-negative early breast cancer: PENELOPE-B.

566 Background: The concept of intrinsic subtyping has been an important step for understanding of breast cancer (BC) as a heterogenous disease. However, these subtypes are not adapted to therapy-induced molecular plasticity. We have evaluated a high-risk luminal BC clinical trial cohort to identify new additional adaptive BC subtypes based on molecular alterations induced during neoadjuvant chemotherapy (NACT). Methods: A total of 1250 ER+/HER2- BC patients (pts) with residual disease after NACT and increased risk (CPS-EG score of ≥3 or 2 with ypN+) were randomized into the PENELOPE-B (NCT01864746) trial to receive palbociclib or placebo. Biomarker analysis was performed in 1411 pre- or postNACT tumor samples including 540 paired samples using the HTG EdgeSeq Oncology Biomarker Panel targeting 2549 genes (HTG Molecular Diagnostics Inc.), with assessment of the absolute assignment of breast cancer intrinsic molecular subtype (AIMS). For a subcohort of 29 pts, we evaluated triplicate samples before and after NACT as well as at the time of metastatic disease. Results: In paired biopsies, a total of 335 genes were significantly different between the pre- and the postNACT cohort. With hierarchical unsupervised clustering of these 335 genes, we characterized five different tumor subtypes with highly significant iDFS survival differences (p<0.0001, n=539). We identified two large groups of tumors with excellent prognosis (adaptive cluster AC1 and AC2, together n=284, 6 events), as well as two groups with a poor prognosis; AC-3 (n=163, 82 events) and AC-4 (n=78, 29 events). The worst prognosis was observed in a small group of tumors with a pre-NACT Basal/HER2E AIMS subtype (n=14, 11 events). AC1 and AC3 are enriched for tumors with an AIMS subtype change from LumB to LumA during NACT, with improved iDFS for AC1. AC2 and AC4 are enriched for tumors with a constant LumA AIMS subtype before and after NACT, with improved iDFS for AC2. The low-risk adaptive subtypes AC1 and AC2 cover a total of 52.7% of pts with a combined event rate of 2.1%. In contrast, the best pretherapeutic conventional AIMS-subtype, preNACT LumA, covers 51.7% of pts, but still has an event rate of 15.4%. This suggests that adaptive subtypes are superior to classical AIMS subtypes for prediction of survival after NACT in luminal BC. Conclusions: Classical approach of intrinsic subtyping relies on constant gene expression, limiting its scope. Adaptive subtyping can complement the classical approach, focusing on those genes that are changed during therapy. Comparison of paired samples before and after therapy is superior to classical subtyping of baseline samples. This approach identified large subgroups of pts with excellent prognosis after NACT despite clinical high risk. This can be an important step to focus on high-risk pts for new neoadjuvant and post-neoadjuvant therapy concepts.

Plasma mutational burden in PIK3CA and TP53 independently predicts early progression in patients with HR+/HER2- metastatic breast cancer (MBC) enrolled in the GEICAM/2014-12 FLIPPER trial.

1029 Background: There is an unmet need for molecular diagnostics to predict therapy outcomes using blood-based biomarker monitoring to guide treatments in HR+/HER2- MBC patients. Here, we report initial results of serial ctDNA analyses in a trial of Fulvestrant (F) + CDK4/6 inhibitor (CDK4/6i) Palbociclib (Pa) vs. F + Placebo (Pl). Endocrine therapy + CDK4/6i are currently the cornerstones of treatment for HR+/HER2- MBC. However, between 10–30% of patients suffer primary resistance. Thus, early identification of HR+/HER2- MBC patients that progress during CDK4/6i treatment is required. Methods: The GEICAM FLIPPER trial (NCT02690480) is a multicenter, double-blind, randomized, phase II study comparing F+Pa vs F+Pl in postmenopausal women with HR+/HER2- MBC. Sequential plasma was collected from 187 patients at baseline, 12, 24, 36, and 48 weeks on treatment and at progression. In total, 903 samples were analyzed using the Plasma-SeqSensei BC IVD kit (Sysmex Inostics) that identifies and quantifies ctDNA mutations in six BC-related genes. The mutant allele frequency (MAF) of PIK3CA and TP53 variants was assessed in baseline samples (median value as cutoff). These variants, identified as the most prevalent, were used as surrogate markers for mutational burden. The Kaplan-Meier method was used to estimate median (m) PFS and overall survival (OS). Hazard ratio (HR) and odds ratio (OR) were calculated with 95% confidence interval (CI) using Cox proportional hazards regression model and logistic regression respectively, unadjusted or adjusted by age, site of disease, disease presentation at study entry and clinical subtype. Results: Previously we showed that F+Pa improved 1-year PFS (83.5% vs. 71.9%, p=0.064) and mPFS (31.8 vs. 22.0 months, p=0.001) vs F+Pl. Here, ctDNA analyses revealed that having ≥1 mutation in PIK3CA + TP53 was prognostic of early (≤12 months) progression (OR 2.37; 95% CI 1.1-5.12, p=0.0274) independent of treatment arm. Furthermore, having ≥2 mutations was associated with treatment resistance (not achieving objective response; OR 3.55; 95% CI 1.28-9.87, p=0.0151). Additionally, worse mPFS and mOS were seen in patients with ≥2 mutations in PIK3CA + TP53 (PFS: HR 3.6; 95% CI 2.25-5.76, p<0.0001; OS: HR 2.92; 95% CI 1.66-5.12, p=0.002) and in patients with high MAF (PFS: HR 2.43; 95% CI 1.6-3.68, p<0.0001; OS: HR 2.83; 95% CI 1.75-4.58, p<0.0001). Finally, having ≥2 mutations in PIK3CA + TP53 was predictive of early progression (OR 22.32; 95% CI 4.12-120.9, p<0.0001) and worse mOS (61.8 vs. 34.79 months) in the F+Pl arm (HR 5.91; 95% CI 2.65-13.16, p<0.0001) but not in the F+Pa arm. Conclusions: Baseline plasma mutational burden in both PIK3CA and TP53 genes was significantly associated with Fulvestrant +/- Palbociclib treatment outcome in HR+/HER2- MBC and appeared to be predictive of Palbociclib benefit. Clinical trial information: NCT02690480 .

Elucidating Mycotoxin-Producing Aspergillus Species in River Water: An Advanced Molecular Diagnostic Study for the Assessment of Ecological Health and Contamination Risk

The primary goal of this research is to isolate mycotoxin-producing fungus from the Nagavali River. Examining isolated fungi involved analyzing their mycelium growth on culture media and detailed microscopic inspection. We employed PCR analysis utilizing universal primers ITS1 and ITS4 to accurately identify the species. Furthermore, we sequenced the amplified ITS region and rigorously analyzed the sequences using NCBI-BLASTn and the ITS2 database. The analysis found a high 96.38% genetic similarity to the Aspergillus flavus strain, resulting in a 600-base pair fragment size. The sequence was given the accession number OR536222 in the NCBI GenBank database. Phylogenetic analysis was performed to ascertain the particular strain of A. flavus and its source. Remarkably, this analysis led to the identification of a single new strain gene, which represents a novel discovery in the field of fungal research. These results underscore the vital significance of molecular techniques in promptly and precisely identifying organisms. This research enhances our understanding of mycotoxin contamination in water, providing valuable insights to improve detection and prevention strategies. It accentuates the overarching importance of conserving our water resources and upholding ecological equilibrium, ultimately safeguarding the well-being of both humanity and the environment.