Next-generation Sequencing Research Articles

Modulation of Haemostatic Balance in Combined von Willebrand Disease and Antithrombin Deficiency: A Comprehensive Family Study.

Maintaining the balance between procoagulant and anticoagulant factors is essential for effective haemostasis. Emerging evidence suggests a modulation of bleeding tendency by factors in the anticoagulant and fibrinolytic systems. This study investigates the clinical and laboratory characteristics of a family with combined von Willebrand disease (VWD) and antithrombin (AT) deficiency. The study focused on a 38-year-old female index patient (IP) with severe type 3 VWD and a history of bleeding disorders. Coagulation assays included VWF antigen, platelet-dependent VWF activity, factor VIII activity, thrombin generation assay (TGA) and AT activity. Molecular genetic analyses were conducted by a targeted DNA custom next generation sequencing (NGS) panel. The IP and one of her sisters suffered type 3 VWD. While the IP presents with a classical severe bleeding phenotype, the sister (II-2) exhibited less severe bleeding symptoms. Extended family members showed type 1 VWD with mild presentations. NGS revealed a homozygous deletion of exon 6 in the VWF gene in the IP and her sister (II-2). All other family members carry this genetic variant in a heterozygous state. Additionally, II-2 has a heterozygous variant in the SERPINC1 gene (c.133C>T, p.Arg45Trp). Both IP and II-2 carry a homozygous prothrombin G20210A variant. TGA results indicated reduced thrombin generation in severe VWD patients, with a pronounced thrombin burst in those with the AT and prothrombin G20210A variant. AT deficiency appears to modulate bleeding symptoms in severe VWD. This study emphasizes the importance of comprehensive genetic and phenotypic evaluation in managing complex coagulation disorders.

Precision radiotherapy with molecular-profiling of CNS tumours.

Diagnoses of CNS malignancies in the primary and metastatic setting have significantly advanced in the last decade with the advent of molecular pathology. Using a combination of immunohistochemistry, next-generation sequencing, and methylation profiling integrated with traditional histopathology, patient prognosis and disease characteristics can be understood to a much greater extent. This has recently manifested in predicting response to targeted drug therapies that are redefining management practices of CNS tumours. Radiotherapy, along with surgery, still remains an integral part of treating the majority of CNS tumours. However, the rapid advances in CNS molecular diagnostics have not yet been effectively translated into improving CNS radiotherapy. We explore several promising strategies under development to integrate molecular oncology into radiotherapy, and explore future directions that can serve to use molecular diagnostics to personalize radiotherapy. Evolving the management of CNS tumours with molecular profiling will be integral to supporting the future of precision radiotherapy.

The importance of targeted next-generation sequencing based genomic profiling at diagnosis of childhood acute myeloid leukemia: a single center experience

Background. The management of pediatric acute myeloid leukemia (AML) is based on the prognostic risk classification of initial leukemia. Targeted next-generation sequencing (NGS) is a reliable method used to identify recurrently mutated genes of pediatric AML and associated prognosis. Methods. In this study, we retrospectively evaluated the prognostic, and therapeutic utility of a targeted NGS panel covering twenty-five genes, in 21 children with de novo and 8 with relapsed or secondary AML. Results. Variants were detected in 44.8% of patients, and 63.2% of them were in the signaling pathway genes. The number of variants per patient and diversity increased with age. The panel results affected hematopoietic stem cell transplantation decisions, especially in core binding factor AML, and allowed the categorization of diseases according to current classifications. Panel results also pointed out predisposition to germline leukemia to the extent of the panel coverage. No targeted therapy was used based on the variants, and none of the variants were used to monitor minimal residual disease. Conclusions. Targeted NGS results, along with well-known genetic aberrations and treatment responses, can guide treatment modalities. The coverage of the routine panels should include proven mutations of childhood AML and germline leukemia predisposition genes.

Screening of the key genes and signaling pathways for schizophrenia using bioinformatics and next generation sequencing data analysis

Schizophrenia is thought to be the most prevalent chronic psychiatric disorder. Researchers have identified numerous proteins associated with the occurrence and development of schizophrenia. This study aimed to identify potential core genes and pathways involved in schizophrenia through exhaustive bioinformatics and next generation sequencing (NGS) data analyses using GSE106589 NGS data of neural progenitor cells and neurons obtained from healthy controls and patients with schizophrenia. The NGS data were downloaded from the Gene Expression Omnibus database. NGS data was processed by the DESeq2 package in R software, and the differentially expressed genes (DEGs) were identified. Gene ontology (GO) enrichment analysis and REACTOME pathway enrichment analysis were carried out to identify potential biological functions and pathways of the DEGs. Protein-protein interaction network, module, micro-RNA (miRNA)-hub gene regulatory network, transcription factor (TF)-hub gene regulatory network, and drug-hub gene interaction network analysis were performed to identify the hub genes, miRNA, TFs, and drug molecules. Potential hub genes were analyzed using receiver operating characteristic curves in the R package. In this investigation, an overall 955 DEGs were identified: 478 genes were remarkably upregulated and 477 genes were distinctly downregulated. These genes were enriched for GO terms and pathways mainly involved in the multicellular organismal process, G protein-coupled receptor ligand binding, regulation of cellular processes, and amine ligand-binding receptors. MYC, FN1, CDKN2A, EEF1G, CAV1, ONECUT1, SYK, MAPK13, TFAP2A, and BTK were considered the potential hub genes. The MiRNA-hub gene regulatory network, TF-hub gene regulatory network, and drug-hub gene interaction network were constructed successfully and predicted key miRNAs, TFs, and drug molecules for schizophrenia diagnosis and treatment. On the whole, the findings of this investigation enhance our understanding of the potential molecular mechanisms of schizophrenia and provide potential targets for further investigation.

Analysis of the benefit of anti-PD-1 monotherapy according to NGS-diagnosed genetic alterations in patients with non-small cell lung cancer

Aim: Immune checkpoint inhibitors improved the survival of advanced non-small cell lung cancer. However, only 20% of patients respond to these treatments and the search for predictive biomarkers of response is still topical. The objective of this work is to analyze the anti-PD-1 monotherapy benefit based on genetic alterations diagnosed by next generation sequencing (NGS), in advanced non-small cell lung cancer. Methods: Patients with advanced non-small cell lung cancer treated with immunotherapy were retrospectively included in this monocentric study. Clinical data, immunohistochemical expression of PD-L1 and molecular data, with a 22-genes NGS panel, were collected. Results: 107 patients were included. The median age was 65 years [59; 73], 70 were men (65%), 96 had adenocarcinoma (90%), 33 were receiving a first line (31%). 54 patients had KRAS mutation (50%) and 56 had TP53 mutation (52%). The remaining mutations were present in fewer than 10 patients. There was no statistically significant differences in median of progression-free or overall survival based on KRAS-only, TP53-only or KRAS-TP53 mutations co-mutated compared to double wild-type patients (P = 0.46 and P = 0.72 respectively). Conclusions: The search for a predictive composite biomarker remains a major issue in the coming years.

A root nodule microbiome sequencing data set from red alder (Alnus rubra Bong.)

There have been frequent reports of more than one strain of the nitrogen-fixing symbiont, Frankia, in the same root nodule of plants in the genus Alnus, but quantitative assessments of their relative contributions have not been made to date. Neither has the diversity of other microbes, having potential functional roles in symbiosis, been systematically evaluated. Alnus rubra root nodule microbiota were studied using Illumina short read sequencing and kmer-based read classification. Single end 76 bp sequencing was done to a median depth of 96 million reads per sample. Reads were assigned to taxa using KrakenUniq, with taxon abundances being estimated using its companion program Bracken. This was the first high resolution study of Alnus root nodules using next generation sequencing (NGS), quantifying multiple Cluster 1 A Frankia strains in single nodules, and in some cases, a Cluster 4 strain. Root nodules were found to contain diverse bacteria, including several genera containing species known to have growth-promoting effects. Evidence was found for partitioning of some bacterial strains in older versus younger lobes.

Plasma mutation profile of precursor lesions and colorectal cancer using the Oncomine Colon cfDNA Assay

BackgroundColorectal cancer (CRC) is the second leading cause of cancer death worldwide. Early detection of precursor lesions or early-stage cancer could hamper cancer development or improve survival rates. Liquid biopsy, which detects tumor biomarkers, such as mutations, in blood, is a promising avenue for cancer screening.AimTo assess the presence of genetic variants in plasma cell-free tumor DNA from patients with precursor lesions and colorectal cancer using the commercial Oncomine Colon cfDNA Assay.Material and methodsCell-free DNA (cfDNA) samples from the plasma of 52 Brazilian patients were analyzed. Eight patients did not have any significant lesions (five normal colonoscopies and three hyperplastic polyps), 24 exhibited precursor lesions (13 nonadvanced adenomas, 10 advanced adenomas, and one sessile serrated lesion), and 20 patients with cancer (CRC). The mutation profile of 14 CRC-associated genes were determined by next-generation sequencing (NGS) using the Oncomine Colon cfDNA Assay in the Ion Torrent PGM/S5 sequencer.ResultsThirty-three variants were detected in eight genes (TP53, PIK3CA, FBXW7, APC, BRAF, GNAS, KRAS, and SMAD4). No variants were detected in the AKT1, CTNNB1, EGFR, ERBB2, MAP2K1 and NRAS genes. All variants were considered pathogenic and classified as missense or truncating. The TP53 gene harbored the most variants (48.48%), followed by the KRAS gene (15.15%) and the APC gene (9.09%). It was possible to detect the presence of at least one pathogenic variant in cfDNA in 60% of CRC patients (12/20) and 25% of precursor lesions (6/24), which included variants in three patients with nonadvanced adenoma (3/13 – 23.08%) and three with advanced adenomas (3/10 – 30%). No variants were detected in the eight patients with normal findings during colonoscopy. The detection of mutations showed a sensitivity of 60% and a specificity of 100% for detecting CRC and a sensitivity of 50% and a specificity of 100% for detecting advanced lesions.ConclusionThe detection of plasma NGS-identified mutations could assist in early screening and diagnostic of CRC in a noninvasive manner.

Monogenic Type 1 Diabetes: A High Yield Pool in Which to Discover New Mechanisms and Candidate Therapeutics for Type 1 Diabetes.

Rare monogenic forms of disease provide a unique opportunity to understand novel pathways in human biology. With the rapid advances in genomics and next-generation sequencing, we now have the tools to interrogate the genomes of patients on a large scale to identify candidate genes in patients with rare monogenic forms of type 1 diabetes (T1D). These cases are more likely to represent genetic defects in critical pathways of immune tolerance, and the study of these patients provides a high-yield pool in which to discover new mechanisms of disease in T1D. These studies are also expected to have high translational impact for the T1D community by helping to identify at-risk individuals and provide compelling candidate targets for prevention and treatment.

TP53 Mutation Is the Only Robust Mutational Biomarker for Outcome Found in a Consecutive Clinical Cohort of Real-Word Patients With Primary Large B-Cell Lymphoma.

Large B-cell lymphoma (LBCL) taxonomy has moved in the direction of a molecular classification, but further clinical experience is needed. We present high-risk gene mutations, which predict outcome in an exploratory study of a consecutive real-world cohort of patients with primary LBCL treated with R-CHOP or R-CHOP-like therapy. The study was a Registry Study Research Project. Sixty-one patients with LBCL, who had a diagnostic tumor sample successfully examined with a 59-gene next-generation sequencing (NGS) panel as a part of routine clinical work, were included in an otherwise unselected cohort. Data were extracted from patient files and pathology reports. Mutations in NOTCH2 (HR 9.69; 95% CI [2.46-38.11]; p = 0.0012), PRDM1 (HR 3.54; 95% CI [1.03-12.22]; p = 0.045), and TP53 (HR 5.89; 95% CI [1.71-20.32]; p = 0.005) were significantly associated with inferior survival in patients with primary LBCL treated with intention to cure with at least three series of R-CHOP or R-CHOP-like therapy. Neither MYD88 (HR 0.66; 95% CI (0.17-2.49), p = 0.54) nor CD79B (HR 0.84;95% CI (0.18-3.88), p = 0.82) mutations were associated with inferior survival. With a targeted gene panel and NGS methodology feasible in daily diagnostic routine, we identified high-risk gene mutations with a significant prognostic impact of which TP53 mutations were reproducible across validation cohorts.

Patterns of genomic instability in > 2000 patients with ovarian cancer across six clinical trials evaluating olaparib

BackgroundThe introduction of poly(ADP-ribose) polymerase (PARP) inhibitors represented a paradigm shift in the treatment of ovarian cancer. Genomic data from patients with high-grade ovarian cancer in six phase II/III trials involving the PARP inhibitor olaparib were analyzed to better understand patterns and potential causes of genomic instability.Patients and methodsHomologous recombination deficiency (HRD) was assessed in 2147 tumor samples from SOLO1, PAOLA-1, Study 19, SOLO2, OPINION, and LIGHT using next-generation sequencing technology. Genomic instability scores (GIS) were assessed in BRCA1 and/or BRCA2 (BRCA)-mutated (BRCAm), non-BRCA homologous recombination repair-mutated (non-BRCA HRRm), and non-HRRm tumors.ResultsBRCAm was identified in 1021/2147 (47.6%) tumors. BRCAm tumors had significantly higher GIS than non-BRCAm tumors (P < 0.001) and high biallelic loss (815/838; 97.3%) regardless of germline (658/672; 97.9%) or somatic (101/108; 93.5%) BRCAm status. In non-BRCA HRRm tumors (n = 121) a similar proportion were HRD-positive (GIS ≥ 42: 55/121; 45.5%) relative to HRD-negative (GIS < 42: 52/121; 43.0%). GIS was highly variable in non-BRCA HRRm (median 42 [interquartile range (IQR) 29–58]) and non-HRRm (n = 1005; median 32 [IQR 20–55]) tumors. Gene mutations with high GIS included HRR genes BRIP1 (median 46 [IQR 41–58]), RAD51C (median 58 [IQR 48–66]), RAD51D (median 62 [IQR 54–69]), and PALB2 (median 64 [IQR 58–74]), and non-HRR genes NF1 (median 49 [IQR 25–60]) and RB1 (median 55 [IQR 30–71]). CCNE1-amplified and PIK3CA-mutated tumors had low GIS (CCNE1-amplified: median 24 [IQR 18–29]; PIK3CA-mutated: median 32 [IQR 14–52]) and were predominantly non-BRCAm.ConclusionsThese analyses provide valuable insight into patterns of genomic instability and potential drivers of HRD, besides BRCAm, in ovarian cancer and will help guide future research into the potential clinical effectiveness of anti-cancer treatments in ovarian cancer, including PARP inhibitors as well as other precision oncology agents.Trial registrationThe SOLO1 trial was registered at ClinicalTrials.gov (NCT01844986) on April 30, 2013; the PAOLA-1 trial was registered at ClinicalTrials.gov (NCT02477644) on June 18, 2015 (retrospectively registered); Study 19 was registered at ClinicalTrials.gov (NCT00753545) on September 12, 2008 (retrospectively registered); the SOLO2 trial was registered at ClinicalTrials.gov (NCT01874353) on June 7, 2013; the OPINION trial was registered at ClinicalTrials.gov (NCT03402841) on January 3, 2018; the LIGHT trial was registered at ClinicalTrials.gov (NCT02983799) on November 4, 2016.

Inferring Distant Relationships From Dense SNP Data Utilizing Two Genealogy Algorithms.

A highly esteemed method known as investigative genetic genealogy (IGG) has been developed to identify DNA samples from forensic crime scenes and human remains of disaster victims. With the advent of next-generation sequencing, it is now feasible to access information on millions of SNPs typed in a single sequencing run that fulfill the requirements for kinship inference. However, challenges such as the poor quality of forensic samples, the high cost associated with sequencing technology, and privacy concerns regarding large-scale genetic databases remain unresolved in this field. In the present study, we validated the identification of relationships up to the seventh degree using two genealogy algorithms (IBIS and KING) under various parameter settings. This was accomplished through whole genome sequencing data derived from two southern Chinese Han pedigrees during an initial phase, while also exploring workflows adapted for low-quality samples. To achieve this objective, low-coverage whole genome sequencing data were downsampled from high-coverage original datasets; additionally, mimic SNP array data-containing less information but offering greater accessibility-were prepared as reference samples. Through a series of experimental analyses, we not only validate the applicability of selected processing procedures and inference tools for low-coverage samples but also proposed that a meticulously crafted site filtering strategy can significantly improve the accuracy of kinship identification. This acknowledges the necessity for further systematic evidence in future research endeavors.

Rapid, multiplex and automated detection of bacteria and fungi in endophthalmitis via a microfluidic real-time pcr system

BackgroundEndophthalmitis is an ophthalmologic emergency requiring accurate and rapid diagnosis for treatment. Currently, the diagnosis commonly relies on culture and molecular biology, which falls short of clinical rapid diagnosis. The purpose of this study was to evaluate the feasibility of a self-build Microfluidic Real-time Polymerase Chain Reaction (RT-PCR) System for rapidly identifying potential pathogens of endophthalmitis.MethodsThis study included 22 patients who presented to Shenzhen Eye Hospital and the Ophthalmology Department of the Affiliated Hospital of Guizhou Medical University in China between January 2023 and March 2024. The samples were cultured using conventional methods and underwent Microfluidic RT-PCR and metagenomic next-generation sequencing (mNGS).ResultsThe Microfluidic RT-PCR System identified pathogens in 11 of 22 cases (50.00%), compared with 40.91% for microbiology culture. 14 cases (63.64%) had concordant results, and 5 cases were positive for the microfluidic system only. The agreements between culture and microfluidic system, as well as culture and mNGS were 100.00% (6/6) and 50.00% (3/6), respectively. The average waiting time for the microfluidic system was about 30 min if excepting DNA extraction time, which was much shorter than 2.88 days for culture and 1.57 days for mNGS.ConclusionThe microfluidic-based RT-PCR system was preliminarily proved to be a sensitive, easy-to-operate, and rapid in-hospital technology. It is expected to become a rapid diagnostic platform for endophthalmitis.

A Narrative Review of Molecular, Immunohistochemical and In-Situ Techniques in Dermatopathology

Skin disorders pose a significant health burden globally, affecting millions of individuals across diverse demographics. Advancements in molecular techniques have revolutionised our understanding of the underlying mechanisms of skin disorders, offering insights into their pathogenesis, diagnosis, and potential targeted treatment. Furthermore, the integration of molecular diagnostics into clinical practice has enhanced the accuracy of skin disorder diagnoses. Polymerase chain reaction (PCR), next-generation sequencing (NGS), and other molecular assays have allowed for the detection of infectious agents, assessment of genetic mutations, and profile gene expression patterns with unequalled precision. These techniques have proven instrumental in distinguishing between subtypes of skin cancers, aiding treatment strategies and prognostic assessments. Moreover, molecular profiling is increasingly guiding the selection of therapeutic agents, ensuring a personalised and effective approach to managing skin disorders. The application of PCR has revolutionised the field by enabling the identification of microbial DNA (i.e., Mycobacterium tuberculosis and Epstein-Barr Virus) in skin infections and detecting specific genetic mutations associated with dermatological disorders (e.g., BRAF). DNA sequencing technologies, such as next-generation sequencing, have facilitated the elucidation of genetic variations and mutations in skin diseases (i.e., bullous disorders), paving the way for personalised treatment approaches. Gene expression profiling techniques, such as microarrays and RNA sequencing, have provided insights into dysregulated pathways and molecular signatures associated with conditions ranging from inflammatory skin disorders to cutaneous malignancies. Immunohistochemistry and fluorescence in situ hybridization have proven invaluable in determining protein expression patterns and detecting chromosomal abnormalities, respectively, aiding in the characterization of skin lesions in conjunction with the molecular data. Proteomic studies have contributed to understanding the intricate protein networks involved in dermatological conditions (i.e., psoriasis), while epigenetic analyses have shed light on the role of epigenetic modifications in gene regulation within skin cancer (i.e., Malignant Melanoma). Together, these molecular techniques have laid the groundwork for targeted therapies and precision medicine in dermatology, with implications for improved diagnostics and treatment outcomes. This review focuses on the routinely employed molecular techniques within dermatopathology, with a focus on cutaneous malignancies, autoimmune diseases, infectious diseases, and neonatal screening which can be implemented in the diagnosis and contribute to improved patient care.

Adequacy of EUS–guided fine-needle aspiration and fine-needle biopsy for next-generation sequencing in pancreatic malignancies: A systematic review and meta-analysis

ABSTRACT Background and Objectives A majority of pancreatic malignancies are unresectable at the time of presentation and require EUS–guided fine-needle aspiration or fine-needle biopsy (EUS-FNA/FNB) for diagnosis. With the advent of precision therapy, there is an increasing need to use EUS-FNA/FNB sample for genetic analysis. Next-generation sequencing (NGS) is a preferred technology to detect genetic mutations with high sensitivity in small specimens. We performed a meta-analysis to evaluate the adequacy of EUS-FNA/FNB for NGS in pancreatic malignancies. Methods PubMed, Embase, Cochrane Library, and Web of Science were searched from database inception to November 11, 2023. The primary outcome was the proportion of sufficient sample acquired by EUS-FNA/FNB in pancreatic malignancies for NGS. Secondary outcomes were the proportion of sufficient sample for NGS in pancreatic ductal adenocarcinoma (PDAC) and the detection rates of mutations in KRAS, TP53, CDKN2A, and SMAD4 and actionable mutations in PDAC. The pooled proportions were calculated using a random-effects model. Potential sources of heterogeneity were investigated with subgroup analyses and meta-regression. Results Twenty studies with 881 samples were included. The pooled adequacy of EUS-FNA/FNB sample for NGS was 89.9% (95% CI, 80.8%–96.7%) in pancreatic malignancies and 92.0% (95% CI, 81.3%–98.8%) in PDAC. Screening sample suitability before NGS testing was associated with lower adequacy in subgroup analysis (79.7% vs. 98.4%, P = 0.001). The pooled prevalences of mutations in KRAS, TP53, CDKN2A, and SMAD4 in PDAC were 87.4% (95% CI, 83.2%–91.2%), 62.6% (95% CI, 53.2%–71.7%), 20.6% (95% CI, 11.9%–30.8%), and 19.4% (95% CI, 11.2%–29.1%), respectively. The pooled prevalence of potentially actionable mutations in PDAC was 14.5% (95% CI, 8.2%–22.0%). Conclusions In the majority of cases, EUS-FNA/FNB can acquire adequate sample for NGS and identify tumor-specific mutations in patients with pancreatic malignancies. Strict pre-analysis screening criteria may negatively impact the sample adequacy and the success rate for NGS.

A patient with concurrent EBV-negative diffuse large B-cell lymphoma and angioimmunoblastic T-cell lymphoma: a case report

IntroductionDiffuse large B-cell lymphoma (DLBCL) is an aggressive form of non-Hodgkin lymphoma that accounts for approximately a quarter of all lymphomas in the United States. It is rare to have co-occurring T cell lymphoma with DLBCL as they often develop following treatment of DLBCL rather than concomitantly.Case presentationWe report a 71-year-old male patient diagnosed with Epstein–Barr virus (EBV) -negative DLBCL with concurrent angioimmunoblastic T-cell lymphoma (AITL). A right inguinal lymph node biopsy demonstrated aggressive B-cell lymphoma consistent with DLBCL with the non-germinal center immunophenotype that was EBV-negative. Furthermore, abnormal T-cells with irregular nuclear contours were found in T cell receptor sequencing with monoclonal gamma and beta T cells. A bone marrow biopsy demonstrated occasional large atypical CD3+PD1+ T cells with corresponding identical T-cell receptor clones in the lymph node biopsy. Next-generation sequencing from the lymph node biopsy demonstrated dual inactivating TET2 mutations.ConclusionComposite DLBCL and AITL is a rare occurrence and the absence of EBV is even more so. Given the rare nature of having these two hematologic malignancies simultaneously, no standard of care exists. However, R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone) is a regimen commonly used in both malignancies individually, and therefore this patient was treated using this approach achieving a partial remission after four cycles of therapy. Unfortunately, he developed refractory disease 1 month after completion of six cycles of R-CHOP.

Case report: Exploring Lynch Syndrome through genomic analysis in a mestizo Ecuadorian patient and his brother

Lynch Syndrome (LS) is a hereditary disorder characterized by genetic mutations in DNA mismatch repair genes, affecting approximately 0.35% of the population. LS primarily increases the risk of colorectal cancer (CRC), as well as various other cancer types like endometrial, breast, and gastric cancers. Microsatellite instability, caused by MMR gene mutations, is a key feature of LS, impacting genes such as MLH1, MSH2, MSH6, and PMS2. Pathology tests studying microsatellite instability and immunohistochemical staining are used to diagnose LS. Furthermore, next-generation sequencing (NGS) allows for a thorough investigation of cancer susceptibility genes. This approach is crucial for identifying affected individuals and managing their care effectively. This study evaluated two siblings who harbored a mutation in the MLH1 gene associated with LS. The older brother was diagnosed with CRC at 24, while the younger brother remains asymptomatic at 7 years old. Genetic testing confirmed the presence of the MLH1 mutation in both siblings. Ancestry analysis showed a mix of African, European, and Native American heritage, common among Ecuadorians. Both siblings shared a family history of cancer, suggesting hereditary factors. Treatment involved surgery and chemotherapy for the older brother, emphasizing the importance of genetic testing for siblings with a cancer family history. NGS plays a pivotal role in identifying genetic mutations and guiding treatment decisions, demonstrating its significance in managing LS and other hereditary cancers.

Preferential Genetic Pathways Lead to Relapses in Adult B-Cell Acute Lymphoblastic Leukemia

Adult B-cell acute lymphoblastic leukemia (B-ALL) is characterized by genetic heterogeneity and a high relapse rate, affecting over 40% of adults. However, the mechanisms leading to relapse in adults are poorly understood. Forty-four adult B-ALL patients were studied at both diagnosis and relapse by next-generation sequencing (NGS). Four main genetic pathways leading to relapse in adults were identified: IKZF1plus genetic profile, RAS mutations and TP53 alterations in Ph-negative B-ALL and acquisition of ABL1 mutations in Ph-positive patients. The most frequently deleted gene at diagnosis was IKZF1 (52%), and 70% of these patients had IKZF1plus profile. Notably, 88% of patients with IKZF1plus at diagnosis retained this genetic profile at relapse. Conversely, the acquisition of RAS mutations or the expansion of subclones (normalized variant allele frequency &lt; 25%) present from diagnosis were observed in 24% of Ph-negative patients at relapse. In addition, 24% of relapses in the Ph-negative cohort could potentially be driven by TP53 alterations. Of these cases, five presented from diagnosis, and four emerged at relapse, mostly as “double-hit” events involving both TP53 deletion and mutation. In Ph-positive B-ALL, the main genetic finding at relapse was the acquisition of ABL1 mutations (86%). Three clonal evolution patterns were identified: the persistent clone trajectory (25%), the expanding clone trajectory (11%) and the therapy-boosted trajectory (48%). Our results reveal the presence of preferential biological pathways leading to relapse in adult B-ALL. These findings underscore the need for personalized therapeutic strategies to improve clinical outcomes in adult patients with B-ALL.

Predictive Molecular Biomarkers of Bladder Cancer Identified by Next-Generation Sequencing—Preliminary Data

Background: The majority of patients with bladder cancer suffer from tumour recurrence. Identifying prognostic factors for tumour recurrence is crucial for treatment and follow-up in affected patients. The study aimed to assess the impact of somatic mutations in bladder cancer on patient outcomes and tumour recurrence. Methods: The study group comprised 46 patients with urothelial bladder cancers referred for transurethral resection of the tumour. A molecular study on tumour-derived DNA was performed using next-generation sequencing. Somatic mutations were screened in 50 genes involved in carcinogenesis. Results: We identified 81 variants in 23 genes, including 54 pathogenic mutations, 18 likely pathogenic variants, and 9 variants of unknown significance. The most frequently mutated genes were FGFR3, PIK3CA, and TP53 in 52%, 35%, and 24% of tumours, respectively. The average tumour-free survival was significantly longer in cases with mutations in the PIK3CA gene (p = 0.02), and mutations in the PIK3CA gene were associated with a decreased risk of tumour recurrence (Hazard Ratio = 0.26; 95% CI: 0.11–0.62; p = 0.018). Conclusions: The PIK3CA gene was shown to be a predictive marker of a low risk of bladder tumour recurrence. Molecular screening of bladder cancers supported predictive biomarkers of tumour recurrence and showed that tumour-free survival is molecularly determined.

Experimental tests challenge the evidence of a healthy human blood microbiome.

The advent of next-generation sequencing (NGS) technologies has made it possible to investigate microbial communities in various environments, including different sites within the human body. Therefore, the previously established belief of the sterile nature of several body sites, including human blood, has now been challenged. However, metagenomics investigation of areas with an anticipated low microbial biomass may be susceptible to misinterpretation. Here, we critically evaluate the results of 16S targeted amplicon sequencing performed on total DNA collected from healthy donors' blood samples while incorporating specific negative controls aimed at addressing potential bias to supplement and strengthen the research in this area. We prepared negative controls by increasing the initial DNA quantity through sequences that can be recognized and subsequently discarded. We found that only three organisms were sporadically present among the samples, and this was mostly attributable to bacteria ubiquitously present in laboratory reagents. Despite not fully confirming or denying the existence of healthy blood microbiota, our results suggest that living bacteria, or at least their residual DNA sequences, are not a common feature of human blood in healthy people. Finally, our study poses relevant questions on the design of controls in this research area that must be considered in order to avoid misinterpreted results that appear to contaminate current high-throughput research.

Advancements and Challenges in Preimplantation Genetic Testing for Aneuploidies: In the Pathway to Non-Invasive Techniques

The evolution of preimplantation genetic testing for aneuploidy (PGT-A) techniques has been crucial in assisted reproductive technologies (ARTs), improving embryo selection and increasing success rates in in vitro fertilization (IVF) treatments. Techniques ranging from fluorescence in situ hybridization (FISH) to next-generation sequencing (NGS) have relied on cellular material extraction through biopsies of blastomeres at the cleavage stage on day three or from trophectoderm (TE) cells of the blastocyst. However, this has raised concerns about its potential impact on embryo development. As a result, there has been growing interest in developing non-invasive techniques for detecting aneuploidies, such as the analysis of blastocoel fluid (BF), spent culture medium (SCM), and artificial intelligence (AI) models. Non-invasive methods represent a promising advancement in PGT-A, offering the ability to detect aneuploidies without compromising embryo viability. This article reviews the evolution and principles of PGT-A, analyzing both traditional techniques and emerging non-invasive approaches, while highlighting the advantages and challenges associated with these methodologies. Furthermore, it explores the transformative potential of these innovations, which could optimize genetic screening and significantly improve clinical outcomes in the field of assisted reproduction.