Next-generation Sequencing In Patients Research Articles

The genomic landscape of papillary thyroid carcinoma on next-generation sequencing in patients undergoing total thyroidectomy.

Thyroidectomy is increasingly performed for suspected malignancy. This cohort study aimed to identify genetic markers associated with malignancy and determine the molecular landscape of papillary thyroid carcinoma (PTC) through next-generation sequencing (NGS) in patients undergoing total thyroidectomy. Among 116 surgical candidates, 103 patients (age=42.9±13.7years; Male: Female=14:89) with benign or malignant thyroid nodules were eligible. Live thyroid tissue samples harvested intraoperatively with adequate DNA and RNA yield were subjected to NGS on the Illumina NovaSeq 6000 platform for genomic and transcriptomic analysis, respectively. Histopathology comprised 20 malignant (19.4%) and 83 benign (80.6%) cases, including 16 PTC (15.5%) cases. On NGS, single nucleotidepolymorphisms (SNPs) in NTRK1 at NC_000001.11:156879016 on chromosome 1 and ALK at NC_000002.12:29717663 on chromosome 2 were frequent in malignant lesions (p<0.05). A SNP in ALK at NC_000002.12:29193706 was consistently a homozygous alternate alleleacross the cohort. DNA-sequencing of PTC lesions identified recurrentsomatic mutations in BRAF (100%), ALK (56.3%), RET (18.8%), PIK3CA (12.5%), NTRK1 (12.5%), NTRK2 (87.5%), NTRK3(12.5%), NRAS(6.3%), and PTCH1 (31.3%) genes. RNA sequencing revealednovelfusiongenes, including MKRN1-BRAF, RN7SL1-CDH1, IRF2BPL-MED12, MED12-IRF2BPL, CPM-MDM2, and AC005895.3-PDGFRB. Inreceiveroperative characteristics analysis, the AUCs ofALKmutationpredictingrecurrence and metastases were 0.818 and 0.783. This Indian study identified novel somatic mutations and fusion genes in PTC, revealing a distinct genomic landscape with implications in precision diagnostics and personalized therapies. NGS with intraoperative live sampling shows promise in prognostication and therapeutic optimization of advanced/metastatic PTC cases. CTRI/2020/09/027607dt 04/09/2020; REF/2020/08/036119.

The clinical management and efficacy of metagenomic next-generation sequencing in patients with pyogenic spinal infection: a single-center cohort study

ObjectiveThis study aims to evaluate the clinical management and effectiveness of metagenomic next-generation sequencing (mNGS) in patients with pyogenic spinal infections.MethodsWe conducted a retrospective review of 17 patients diagnosed with pyogenic spinal infections and treated at our institution between October 2022 and February 2024. The cohort included 8 males and 9 females, with a mean age of 63.59 ± 10.18 years (range: 41–71 years). The infections comprised 9 epidural abscesses, 6 intervertebral space infections, and 2 deep abscesses. All patients underwent open surgical procedures and mNGS-based bacterial identification using intraoperative pus or tissue specimens, in addition to conventional blood bacterial cultures. Clinical outcomes were assessed using CRP, PCT, WBC inflammatory markers, and VAS scores postoperatively.ResultsAll 17 patients with pyogenic spinal infections underwent open surgery and mNGS bacterial detection at our institution. Among the 17 patients, mNGS yielded positive results in 14 cases (82.4%), significantly higher than the 5.9% positivity rate of conventional bacterial cultures (p < 0.001). The mNGS test time was notably shorter than conventional cultures (1.0 vs. 5.88 days, p < 0.001). Postoperative antibiotic therapy was adjusted based on mNGS findings. There were significant reductions in postoperative VAS, WBC, PCT, and CRP values compared to preoperative levels (p < 0.01).ConclusionMetagenomic next-generation sequencing is effective in managing pyogenic spinal infections by facilitating rapid and sensitive detection of pathogens. This technique improves the timeliness and accuracy of diagnosis, highlighting its potential for broader clinical use.

Somatic Variants of KRT1/KRT10 Identified by Next-generation Sequencing in Patients with Epidermal Nevi.

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Usefulness of endoscopic ultrasound with bronchoscope-guided fine-needle aspiration for next-generation sequencing in patients with non-small cell lung cancer: A comparison with other bronchoscopic techniques

BackgroundNext-generation sequencing (NGS) is essential in treating advanced lung cancer. However, the effectiveness of endoscopic ultrasound with bronchoscope-guided fine-needle aspiration (EUS-B-FNA) in NGS remains unclear. This study examined the usefulness of EUS-B-FNA in lung cancer NGS cases where EUS-B-FNA was performed for specimen submission in a nationwide genomic screening platform (LC-SCRUM-Asia) and compared specimens collected using other bronchoscopy methods (endobronchial ultrasound-guided transbronchial needle aspiration [EBUS-TBNA] and EBUS-guided transbronchial biopsy with a guide sheath [EBUS-GS-TBB]) during the same period. MethodsWe retrospectively compared the NGS success rates of NGS, DNA and RNA yields for EUS-B-FNA, EBUS-TBNA, and EBUS-GS-TBB from the records of the patients recruited for the Lung Cancer Genomic Screening Project for Individualized Medicine (LC-SCRUM)-Asia. ResultsFifty-one patients were enrolled, and the NGS success rates were comparable for samples obtained by EUS-B-FNA, EBUS-TBNA, and EBUS-GS-TBB (100%, 90.9%, and 81.0%, respectively). Genetic alterations were detected in 73.7%, 90.9%, and 85.7% of patients, respectively, with druggable genetic alterations found in 31.6%, 72.7%, and 61.9% of patients, respectively. The DNA and RNA yields were significantly higher in EUS-B-FNA samples than in EBUS-GS-TBB samples (50.4 (interquartile range (IR): 15.45–72.35) ng/μl and 33.9 (IR: 9–76.8) ng/μl from EUS-B-FNA, and 3.3 (IR: 1.4–7.1) ng/μl and 15.1 (IR: 8.3–31.5) ng/μl from EBUS-GS-TBB, respectively, p < 0.05). ConclusionEUS-B-FNA emerges as a promising bronchoscopic method for obtaining adequate samples for NGS in advanced lung cancer cases.

Clinical diagnostic value of metagenomic next-generation sequencing in patients with acute infection in emergency department

ObjectiveTo explore the value of metagenomic next-generation sequencing (mNGS) and culture in microbial diagnosis of patients with acute infection. MethodsWe retrospectively analyzed 206 specimens from 163 patients who were admitted to the emergency department of The First Affiliated Hospital of Sun Yat-sen University between July 2020, and July 2021. We evaluated the diagnostic efficacy of mNGS and in-hospital traditional culture. ResultsThe total positive rate of mNGS was significantly higher than that culture methods (71.4 % vs 40.8 %, p < 0.001), while the sensitivity and accuracy of mNGS were found to be 92.9 % and 88.2 % respectively. However, culture exhibited superior specificity with a value of 92.6 % compared to 75.9 % for mNGS. The detection efficiency of mNGS and culture for fungi was comparable, but mNGS showed superior performance for bacterial detection. In the analysis of sepsis samples, mNGS outperformed traditional culture methods in diagnosing various types of samples, especially for sputum and bronchoalveolar lavage fluid. Among the identified infections, bacterial infections were the most common single infection (37.5 %). Additionally, bacterial-fungal infections represented the most prevalent form of mixed infection (77.3 %). Candida albicans and Staphylococcus aureus were identified as the predominant pathogens in the survival and death groups, respectively. No significant differences in microbial diversity were observed. ConclusionCompared to culture methods, mNGS demonstrates superior positive rates, sensitivity, and accuracy in the rapid detection of acute infections, particularly in critically ill patients such as those with sepsis. This capability establishes a foundation for the swift and precise identification of pathogens, allowing for the analysis of clinical indicators and patient prognosis based on the extensive data generated from mNGS.

Analysis of the clinical factors affecting the negative rate of metagenomic next-generation sequencing in patients with spinal infection.

Analysis of the clinical factors affecting the negative rate of metagenomic next-generation sequencing in patients with spinal infection.

Next-generation sequencing in patients with lung cancer undergoing immunotherapy: Retrospective analysis.

e15071 Background: Identifying targetable oncogenic drivers and resistance mechanisms by Next-generation sequencing (NGS) is critical in Non-Small Cell Lung Cancer (NSCLC). Methods: We conducted a retrospective study at the University of Vermont Center to assess the utilization of NGS in NSCLC. We examined the medical records of NSCLC patients who received Immune Checkpoint Inhibitors (ICIs) as a first-line therapy between January 2017 and June 2022. We collected demographic data, including age, sex, ethnicity, cancer stage, NGS, mutations and survival data. Survival analysis was performed for the most common mutation by measuring the Hazard Ratio (HR) via Cox regression of different mutations compared to the whole cohort. Results: We identified 95 NSCLC patients with 52.6% males, 94.7% whites and a mean age of 63.4 years (Standard Deviation (SD): 11.34). 67.4 % received Pembrolizumab and 30.5% got Durvalumab. Most patients had stage 4 and stage 3 cancers, with 54.7% and 35.8%, respectively. Mean ECOG of 0.9 (SD: 0.7), 34% had average body mass index, and overall mortality was 41%. PD L1 expression and NGS were reported in 81% of cases. NGS was reported in 88.5% of stage 4 and 76.5% of stage 3 categories. 41.8% had a type of KRAS mutation, with KRAS p.G12C being the most common. 24.1% of cases had no mutation. The mean survival months ranged from 7.6 months in MET to 52.4 months in RET mutation. Survival analysis showed decreased mortality in EGFR mutation, as seen in Table. Conclusions: The rate of NGS testing at our rural academic center in Vermont is on the higher side of the national average NGS testing, but the turnaround time (TAT) of 28 days is suboptimal compared to NCI centers. Strategies to reduce TAT need to be implemented to get timely essential for tailoring therapies in patients with NSCLC. Further research is needed to explore the prognostic utility of mutations in NSCLC patients undergoing ICIs. [Table: see text]

Germline targeted next-generation sequencing in patients with adrenal incidentalomas

Germline targeted next-generation sequencing in patients with adrenal incidentalomas

Mutational Profiling by Next-Generation Sequencing in Patients with Metastatic Non-Small Cell Lung Carcinoma: Our Experience

Introduction According to GLOBOCAN 2020, overall lung cancer is the second most common cancer in both sexes (11.4%) accounting for highest cancer-related mortality (18%).1 Adenocarcinoma subtype of non-small cell lung cancer (NSCLC) is the most common subtype and is divided into further molecular subtypes based on oncogenic driver mutations. Overall survival in these patients is poor with the use of conventional platinum-based double chemotherapy and various recent studies on targeted therapy studies have showed improved survival. Therefore, broad panel-based testing like next-generation sequencing (NGS) is strongly recommended to identify these targetable driver mutations. Aims and Objectives The aim of this study was to evaluate the mutational profile in patients with metastatic NSCLC (mNSCLC) by NGS method. Materials and Methods A hospital-based prospective observational study done on 88 patients under the Department of Medical Oncology, State Cancer Institute during a period of 1 year. All patients above 18 years of age diagnosed as mNSCLC having Eastern Cooperative Oncology Group performance status 0 to 2 and evaluated for mutational profiling by NGS method were included. Five gene panel tests including endothelial growth factor receptor (EGFR), echinoderm microtubule-associated protein-like 4 and anaplastic lymphoma kinase (EML4-ALK), BRAF, mesenchymal epithelial transition (MET), and ROS proto-oncogene 1 (ROS1) were used. Results and Observations Majority of mNSCLC cases were in the age group of 41 to 50 years (n = 30, 34.1%) with average age at presentation being 53.74 years. Male: female ratio was 1.14:1 and most patients were nonsmokers. Adenocarcinoma subtype of mNSCLC cases had the highest mutational burden (n = 55, 62.5%). EGFR (n = 32, 56.14%) was the most common mutation followed by EML4-ALK (n = 19, 33.33%). Most common EGFR mutation was in Exon 19. Other rare mutations were ROS1 (n = 4), BRAF V600E (n = 1), and MET (n = 1). Skeleton was the most common site of metastasis across all driver mutations. Conclusion EGFR and EML4-ALK were the commonest targetable mutations detected in the study. As there is very limited data from North Eastern region of India regarding mutational status in mNSCLC, this study opens up possibilities for further studies targeting multiple mutations to give us more comprehensive understanding of the mutational landscape of mNSCLC in this era of precision medicine.

Clinical practice recommendations for the use of next-generation sequencing in patients with solid cancer: a joint report from KSMO and KSP.

In recent years, next-generation sequencing (NGS)-based genetic testing has become crucial in cancer care. While its primary objective is to identify actionable genetic alterations to guide treatment decisions, its scope has broadened to encompass aiding in pathological diagnosis and exploring resistance mechanisms. With the ongoing expansion in NGS application and reliance, a compelling necessity arises for expert consensus on its application in solid cancers. To address this demand, the forthcoming recommendations not only provide pragmatic guidance for the clinical use of NGS but also systematically classify actionable genes based on specific cancer types. Additionally, these recommendations will incorporate expert perspectives on crucial biomarkers, ensuring informed decisions regarding circulating tumor DNA panel testing.

Perspectives for next generation sequencing in patients with follicular lymphoma

Aim. To study the prognostic significance of gene mutations and intracellular signaling pathways involved in lymphomagenesis in patients with follicular lymphoma using next generation sequencing (NGS).Materials and methods. The prospective study included 26 patients with a median age of 51.5 years. Mutational screening was performed for cohort using custom NGS Panel of 118 genes. Gene set enrichment analysis (GSEA) was performed using Metascape. The data was analyzed in SPSS Statistics 26 and R 4.2.2.Results. The highest mutation frequency was noted in the genes: KMT2C – 50 %, KMT2D – 50 %, CREBBP – 31 %, NOTCH2 – 31 %, GNAS – 23 %. Missense mutations occurred with a frequency of 84.3 %. ARID1A gene mutation is an unfavorable prognostic factor according to progressive-free (p = 0.014) and event-free (p = 0.029) survival analysis. Tumor mutation burden (TMB) was defined as the number of mutations per megabase (Mb) of the coding sequence, the median TMB was 5.0 (3.3–8.3) mutations/Mb. The TMB threshold of 6 mutations/Mb divided patients into groups with high (44 %) and low (56 %) TMB. In the high TMB group, 2-year event-free survival was 27.3 % (95 % confidence interval 6.0–61.0), which was significantly lower than in low TMB group – 72.7 % (95 % confidence interval 41.9–91.6; p = 0.037). The most enriched cellular pathways according to GSEA results were regulation of cell activation (–log10(q-value) = 6.357), chromatin remodeling (–log10(q-value) = 5.707), histone modification (–log10(q-value) = 4.569). We have also demonstrated other possibilities of GSEA using follicular lymphoma as an example.Conclusion. TMB is a significant prognostic factor in patients with follicular lymphoma. We have shown that mutations in the MYC, CREBBP, EZH2, KMT2D genes lead to dysregulation in several intracellular processes, mediating complex molecular changes. The most enriched intracellular pathways in follicular lymphoma are those of chromatin remodeling, regulation of cell activation and histone modification.

Diagnostic Efficacy of Metagenomic Next-Generation Sequencing in Patients with Spinal Infections: A Retrospective Study

Diagnostic Efficacy of Metagenomic Next-Generation Sequencing in Patients with Spinal Infections: A Retrospective Study

Clinical Practice Recommendations for the Use of Next-Generation Sequencing in Patients with Solid Cancer: A Joint Report from KSMO and KSP.

In recent years, next-generation sequencing (NGS)-based genetic testing has become crucial in cancer care. While its primary objective is to identify actionable genetic alterations to guide treatment decisions, its scope has broadened to encompass aiding in pathological diagnosis and exploring resistance mechanisms. With the ongoing expansion in NGS application and reliance, a compelling necessity arises for expert consensus on its application in solid cancers. To address this demand, the forthcoming recommendations not only provide pragmatic guidance for the clinical use of NGS but also systematically classify actionable genes based on specific cancer types. Additionally, these recommendations will incorporate expert perspectives on crucial biomarkers, ensuring informed decisions regarding circulating tumor DNA panel testing.

T(11;14) status is stable between diagnosis and relapse and concordant between detection methodologies based on fluorescence in situ hybridization and next-generation sequencing in patients with multiple myeloma.

Multiple myeloma (MM) is associated with a wide variety of recurrent genomic alterations. The most common translocation in MM is t(11;14). In this retrospective, single-center, non-interventional study, patients' bone marrow samples were examined at diagnosis and at relapse(s) following treatment with anti-myeloma regimens to determine whether t(11;14) status was stable over time. This stability cohort consisted of 272 patients, of whom 118 were t(11;14)-positive at diagnosis and 154 were negative. All patients in the stability cohort retained the same t(11;14) status at relapse that they had at diagnosis of MM. Sixteen patients who had t(11;14)-positive MM at diagnosis had multiple longitudinal assessments by fluorescence in situ hybridization (FISH) at relapse events and remained t(11;14)-positive across all timepoints. Patients who had t(11;14)-positive disease at diagnosis of monoclonal gammopathy of unknown significance or smoldering MM also retained t(11;14) positivity through MM diagnosis and relapse. The t(11;14) fusion patterns also remained constant for 90% of patients. For detection of t(11;14), results from FISH and next-generation sequencing (NGS) were compared to determine the rate of concordance between these two methods. This concordance cohort contained 130 patients, of whom 66 had t(11;14)-positive disease and 64 were t(11;14)-negative. In this sample set, the concordance between FISH- and NGS-based detection of t(11;14) was 100%. These results strongly suggest that the t(11;14) rearrangement remains stable during the full disease course in patients with MM and can be detected by FISH- and NGS-based methodologies.

Detecting circulating microbial cell-free DNA by next-generation sequencing in patients with Mycobacterium avium complex-lung disease: A pilot study.

Determining a diagnosis for non-Tuberculous mycobacterium (NTM)-lung disease (LD) remains difficult. The value of circulating cell-free DNA (cfDNA) secreted from microbes has been established in the detection of pathogens in septic patients. However, it is unknown whether NTM-derived cfDNA is detectable in plasma from patients with NTM-LD and whether this is associated with the disease status of NTM-LD, especially in patients with Mycobacterium avium complex (MAC)-LD. In this pilot study, from 2018 to 2019, we enrolled adult patients with MAC-LD at Taipei Veterans General Hospital in Taiwan for the detection of circulating cfDNA. We performed cfDNA extraction from plasma, next-generation sequencing (NGS) for nonhuman cfDNA, and sequence matching to a microbial database and then assessed the association between pathogen cfDNA and MAC-LD. Two (40%) plasma samples from MAC-LD patients had detectable MAC-specific cfDNA, namely one instance of DNA polymerase III alpha subunit and one instance of ATP-binding cassette transporters permease. The plasma samples from the three other MAC-LD cases and the one tuberculosis control were negative for either NTM-derived cfDNA or tuberculosis-related cfDNA. In addition to MAC-specific cfDNA, Ralstonia solanacearum, Staphylococcus aureus, and Pasteurella multocida were the most observed bacteria in our patients. The two patients with MAC-cfDNA positivity yielded higher radiographic scores (P = 0.076) and presented a higher number of nonhuman reads than those without MAC-cfDNA positivity (P = 0.083). Using NGS method, we demonstrated MAC-cfDNA was detectable in patients with MAC-LD. Further large-scale research is warranted to assess the clinical value of detecting MAC-specific cfDNA in MAC-LD patients.

First-Line Fixed-Duration Ibrutinib Plus Venetoclax (Ibr+Ven) Versus Chlorambucil Plus Obinutuzumab (Clb+O): 55-Month Follow-up from the Glow Study

Introduction : In the GLOW trial (NCT03462719), fixed-duration Ibr+Ven treatment has shown superiority to Clb+O in progression-free survival (PFS), better sustained undetectable minimal residual disease (uMRD) responses, and overall survival (OS) benefit in patients with previously untreated chronic lymphocytic leukemia (CLL) who are older and/or have comorbidities (CU Niemann, et al. Blood. 2022;140[suppl 1]:228-230). In this analysis, we report clinical outcomes, including PFS, OS, and MRD analysis, from the Ibr+Ven combination in GLOW with a median follow-up of 55 months, including subgroup analyses by IGHV and MRD. Methods : Patients aged ≥ 65 years or 18 to 64 years with a Cumulative Illness Rating Scale score &amp;gt; 6 or creatinine clearance &amp;lt; 70 mL/min were randomized 1:1 to Ibr+Ven (3 cycles of Ibr lead-in, followed by 12 cycles of Ibr+Ven; N = 106) or 6 cycles of Clb+O (N = 105). Each cycle was 28 days. Patients were excluded if they had del17p or known TP53 mutations at screening. End points included investigator-assessed PFS, uMRD rates, time to next treatment (TTNT), and OS. MRD was assessed sequentially over time in peripheral blood by next-generation sequencing for patients with partial response (PR) or better. Patients with &amp;lt; 1 CLL cell per 10,000 leukocytes (&amp;lt; 10 -4) were considered to have uMRD, whereas patients with ≥ 1 CLL cell per 10,000 leukocytes (≥ 10 -4) were considered to have detectable MRD (dMRD). All p values reported were nominal. Safety was not further assessed, as all patients were already past the treatment period in previous analyses. Results of updated analyses : With a median follow-up of 55 months, PFS remained superior for Ibr+Ven (hazard ratio [HR] 0.239 [95% confidence interval (CI), 0.159-0.359]; p &amp;lt; 0.0001); 54-month PFS rates were 65.8% for Ibr+Ven and 19.1% for Clb+O. In the Ibr+Ven arm, for patients with unmutated IGHV (uIGHV; n = 67) and mutated IGHV (mIGHV; n = 32), 54-month PFS rates were 58% and 90%, respectively. Also in the Ibr+Ven arm, PFS rates at 3 years post-treatment were 82% in patients who achieved uMRD at 3 months after end of treatment (EOT+3; n = 58) and 73% for patients with dMRD (n = 31). Among patients with uIGHV, PFS rates at 3 years post-treatment were 81% for those achieving uMRD at EOT+3 (n = 40) and 56% for those with dMRD (n = 16). In patients with mIGHV, PFS rates at 3 years post-treatment were ≥ 92% regardless of MRD status at EOT+3. Overall, at 38 months after end of treatment (EOT+38), 32.1% of patients had uMRD in the Ibr+Ven arm. Of the patients who achieved uMRD at EOT+3 (n = 58), 53.4% sustained uMRD status at EOT+38 in the Ibr+Ven arm. In addition, TTNT was prolonged for patients receiving Ibr+Ven versus Clb+O. The risk of needing second-line therapy was significantly reduced by 83% with first-line Ibr+Ven versus Clb+O (HR 0.174 [95% CI, 0.088-0.342]; p &amp;lt; 0.0001), and by 85% among patients with uIGHV (HR 0.146 [95% CI, 0.069-0.310]) compared with a 29% risk reduction in those with mIGHV (HR 0.708 [95% CI, 0.118-4.256]). In the Ibr+Ven arm, 4 patients received single-agent ibrutinib as subsequent therapy as part of the study; while 1 patient had not yet had a disease assessment, the best response for the other 3 patients were complete response (n = 1) and PR (n = 2). Finally, Ibr+Ven continues to demonstrate improved OS versus Clb+O, reducing the risk of death by 58% (HR 0.421 [95% CI, 0.237-0.747]; p = 0.0023). Estimated 54-month OS rates were 84.5% for the Ibr+Ven arm and 63.1% for the Clb+O arm. Conclusion : With prolonged follow-up of 55 months in the GLOW study, all-oral, once-daily, fixed-duration Ibr+Ven continues to show superior PFS versus Clb+O. Among patients treated with Ibr+Ven, benefit in PFS was particularly observed in patients with uIGHV who achieved uMRD at EOT+3 and in patients with mIGHV regardless of MRD status at EOT+3. Moreover, Ibr+Ven fixed-duration combination treatment continues to demonstrate an OS advantage versus chemoimmunotherapy in patients with previously untreated CLL.

Identification of Potential Genomic Alterations Using Pan-Cancer Cell-Free DNA Next-Generation Sequencing in Patients With Gastric Cancer.

Molecular cancer profiling may lead to appropriate trials for molecularly targeted therapies. Cell-free DNA (cfDNA) is a promising diagnostic and/or prognostic biomarker in gastric cancer (GC). We characterized somatic genomic alterations in cfDNA of patients with GC. Medical records and cfDNA data of 81 patients diagnosed as having GC were reviewed. Forty-nine and 32 patients were tested using the Oncomine Pan-Cancer Cell-Free Assay on the Ion Torrent platform and AlphaLiquid 100 kit on the Illumina platform, respectively. Tier I or II alterations were detected in 64.2% (52/81) of patients. Biomarkers for potential targeted therapy were detected in 55.6% of patients (45/81), and clinical trials are underway. ERBB2 amplification is actionable and was detected in 4.9% of patients (4/81). Among biomarkers showing potential for possible targeted therapy, TP53 mutation (38.3%, 35 variants in 31 patients, 31/81) and FGFR2 amplification (6.2%, 5/81) were detected the most. Next-generation sequencing of cfDNA is a promising technique for the molecular profiling of GC. Evidence suggests that cfDNA analysis can provide accurate and reliable information on somatic genomic alterations in patients with GC, potentially replacing tissue biopsy as a diagnostic and prognostic tool. Through cfDNA analysis for molecular profiling, it may be possible to translate the molecular classification into therapeutic targets and predictive biomarkers, leading to personalized treatment options for patients with GC in the future.

Efficacy of olaparib in advanced cancers with germline or somatic mutations in BRCA1, BRCA2, CHEK2 and ATM, a Belgian Precision tumor-agnostic phase II study

The Belgian Precision initiative aims to maximize the implementation of tumor-agnostic next-generation sequencing in patients with advanced cancer and enhance access to molecularly guided treatment options. Academic tumor-agnostic basket phase II studies are part of this initiative. The current investigator-driven trial aimed to investigate the efficacy of olaparib in advanced cancers with a (likely) pathogenic mutation (germline or somatic) in a gene that plays a role in homologous recombination (HR). This open-label, multi-cohort, phase II study examines the efficacy of olaparib in patients with an HR gene mutation in their tumor and disease progression on standard of care. Patients with a somatic or germline mutation in the same gene define a cohort. For each cohort, a Simon minimax two-stage design was used. If a response was observed in the first 13 patients, 14 additional patients were included. Here, we report the results on four completed cohorts: patients with a BRCA1, BRCA2, CHEK2 or ATM mutation. The overall objective response rate across different tumor types was 11% in the BRCA1-mutated (n= 27) and 21% in the BRCA2-mutated (n= 27) cohorts. Partial responses were seen in pancreatic cancer, gallbladder cancer, endocrine carcinoma of the pancreas and parathyroid cancer. One patient with a BRCA2 germline-mutated colon cancer has an ongoing complete response with 19+ months on treatment. Median progression-free survival in responding patients was 14+ months (5-34+ months). The clinical benefit rate was 63% in the BRCA1-mutated and 46% in the BRCA2-mutated cohorts. No clinical activity was observed in the ATM (n= 13) and CHEK2 (n= 14) cohorts. Olaparib showed efficacy in different cancer types harboring somatic or germline mutations in the BRCA1/2 genes but not in ATM and CHEK2. Patients with any cancer type harboring BRCA1/2 mutations should have access to olaparib.

Diagnostic value of plasma and blood cells metagenomic next-generation sequencing in patients with sepsis

BackgroundSeveral studies have investigated the detection of plasma cell-free DNA (cfDNA) using metagenomic next-generation sequencing (mNGS). However, to our knowledge, no study has evaluated the diagnostic value of mNGS detection using blood cells. In this study, we aimed to evaluate the performance of a whole blood mNGS assay which includes the results of plasma and blood cells mNGS detection. MethodsWe selected a panel of seven microorganisms to validate both the plasma and blood cells assay for their limits of detection (LoD), linearity, precision, and robustness to interference. In a multicentered prospective study conducted from January 2021 to April 2022, we tested 253 septic patients with plasma and blood cells mNGS and compared it with blood cultures (BCs). The performance of pathogen detection was compared between mNGS and BCs. ResultsThe LoD for plasma and blood cells mNGS was 8.3–140 genome equivalents (GE)/mL and 26 to 534 colony-forming units (CFU) or copies/mL, respectively. The inter- and intra-assay reproducibility of both plasma and blood cells mNGS was 100%. Compared to plasma mNGS alone, the sensitivity of whole blood mNGS was increased by 18.04% when using BCs as the standard (67.21% vs 85.25%). Furthermore, the sensitivity of whole blood mNGS in diagnosing bloodstream infections (BSIs) was 85.21%, which was significantly higher than that of BCs (36.09%, P＜0.0001) and plasma mNGS (69.82%; P = 0.0007). Additional analysis showed that blood cells mNGS was able to detect bacteria missed by plasma mNGS, while plasma mNGS was effective at detecting viruses. ConclusionsOur findings indicate that whole blood mNGS shows great potential as a promising diagnostic technique for BSIs owing to its ability to identify pathogens with higher sensitivity.

Mutation Profile via Next-Generation Sequencing in Patients with Colorectal Adenocarcinoma and Its Clinicopathological Correlation.

Recent studies that reveal the molecular profiles of colorectal carcinomas have demonstrated tumor heterogeneity. Characterization of colorectal carcinoma-specific genomic alterations is essential for developing more successful and targeted treat- ment protocols. Moreover, it is vital in elucidating the pathogenesis and mechanisms of resistance against treatment and predicting prognosis. The study included 73 cases diagnosed with colorectal carcinomas and subjected to molecular analysis by the next-generation sequencing. The association between the clinicopathologic parameters and pathogenic mutations detected in 32 genes was evaluated. Pathogenic mutations were determined in a total of 24 genes. The Cell Division Cycle 27 (CDC27), Kirsten rat sarcoma viral proto-oncogene (KRAS), serine/threonine protein kinase B-raf (BRAF), phosphatase and tensin homolog, breast cancer 2 (BRCA2), and phosphotidylinositol-4,5-biphosphate 3-kinase (PIK3CA) mutations were determined at higher rates, with the adenomatous polypo- sis coli mutation determined at a lower rate than in the literature. There were significant positive correlations between CDC27 and phosphatase and tensin homolog (PTEN), PTEN and BRCA2, and PTEN and adenomatous polyposis coli (APC) concomitant muta- tions, whereas negative correlations were present between BRAF and KRAS. Statistically significant relationships were present between KRAS exon 2 and mucinous morphology, PIK3CA and absence of perineural invasion, BRAF and tumor differentiation/localization, MutS homolog 3 (MSH3) and tumor diameter, and BRCA2 and absence of lymph node metastasis. It is necessary to have a comprehensive database of genomic alterations of colorectal carcinomas to interpret mutations more accurately clinically. There are no studies on the frequency of mutations in colorectal carcinomas in the Turkish population; thus, follow-up and treatment protocols are organized following the European and American databases and guidelines. A comprehensive study of the colorectal carcinoma patients' mutation profile in the Turkish patient cohort by the next-generation sequencing method will help to provide significant therapeutic, prognostic, and predictive data and design more successful treatment and follow-up strategies.