Comprehensive Genomic Sequencing Research Articles

Comparative genome analysis of endophytic Bacillus amyloliquefaciens MR4: a potential biocontrol agent isolated from wild medicinal plant root tissue.

In this investigation, 396 endophytic bacterial strains from six indigenous medicinal plant species within the Xinjiang Tumor Peak National Nature Reserve were subjected to screening. The strain MR4 emerged as a noteworthy contender, demonstrating pronounced biocontrol capabilities coupled with exceptional cold tolerance. Through morphological scrutiny and comprehensive genomic sequencing, MR4 was identified as Bacillus amyloliquefaciens. Antagonistic assays revealed MR4's efficacy in suppressing the causative agents of cotton wilt and verticillium wilt, achieving inhibition rates surpassing 50%. Analyses, underpinned by PCR methodologies, indicated MR4's capacity to biosynthesize a minimum of eight distinct antimicrobial agents. The whole-genome sequencing data indicated that B. amyloliquefaciens MR4 had the genome size and GC content of 4,017,872bp and 47.14%, respectively, and 4191 coding genes were identified. The genome consists of a single chromosome and one plasmid. Moreover, it was augmented by annotations from various databases, including GO, KEGG, and COG. The pathogenicity of MR4 undergoes evaluation, while predictions concerning MR4's secondary metabolites have disclosed gene clusters for 13 varieties of these compounds, with particular emphasis on surfactins and fengycin. Comparative analyses with four paradigmatic strains shed light on MR4's genomic composition and its phylogenetic lineage within the Bacillus genus. The genomic data pertaining to MR4 have been duly submitted to the NCBI GenBank, bearing the accession numbers CP146236 (Chr1) and CP146237 (plas1). This study endeavors to furnish potent microbial resources for the biocontrol and enhancement of plant growth, thereby providing a theoretical groundwork for MR4's agronomic utilization.

Chinese expert consensus on the analytical validation of tumor comprehensive genomic profiling next generation sequencing testing (2024 edition)

In hospital laboratories-developed testing is of great significance for the clinical testing products that has not been approved by the National Medical Product Administration and is urgently needed to meet clinical practice needs. With the development of cancer precision medicine in recent years, comprehensive genomic profiling (CGP) has become an important means and method for the detection of drug targets, precise molecular typing, and immunotherapy biomarkers in cancer patients. However, there is still a lack of unified understanding and consensus on clinical testing standards and application specifications for laboratory-developed testing in the hospitals. The Molecular Pathology Collaboration Group of the Cancer Experts Committee of the Chinese Anti-Cancer Association and the Molecular Pathology Group of the Pathology Branch of the Chinese Medical Association initiated the expert consensus on relevant specifications for analytical validation of CGP next-generation sequencing (NGS) testing in Chinese hospitals. Combined with domestic clinical practice, refer to domestic and foreign literatures, from the background of the laboratory-developed testing, analytical validation scenarios, evaluation indicators and variation ranges, sample types and quantities covered by analytical validation, clinical performance and drug efficacy determination, and site personnel for analytical validation, quality control, inter-laboratory quality evaluation and document management, etc. After the discussion by the expert group, 12 expert consensuses were formed to provide reference for the analytical validation and clinical application of tumor CGP NGS testing in Chinese hospitals, so as to promote the laboratory-developed testing applications in Chinese hospitals.

The Impact of Next-generation Sequencing on Interobserver Agreement and Diagnostic Accuracy of Desmoplastic Melanocytic Neoplasms.

Next-generation sequencing (NGS) is increasingly being utilized as an ancillary tool for diagnostically challenging melanocytic neoplasms. It is incumbent upon the pathology community to perform studies assessing the benefits and limitations of these tools in specific diagnostic scenarios. One of the most challenging diagnostic scenarios faced by skin pathologists involves accurate diagnosis of desmoplastic melanocytic neoplasms (DMNs). In this study, 20 expert melanoma pathologists rendered a diagnosis on 47 DMNs based on hematoxylin and eosin sections with demographic information. After submitting their diagnosis, the experts were given the same cases, but this time with comprehensive genomic sequencing results, and asked to render a diagnosis again. Identification of desmoplastic melanoma (DM) improved by 7%, and this difference was statistically significant ( P <0.05). In addition, among the 15 melanoma cases, in the pregenomic assessment, only 12 were favored to be DM by the experts, while after genomics, this improved to 14 of the cases being favored to be DM. In fact, some cases resulting in metastatic disease had a substantial increase in the number of experts recognizing them as DM after genomics. The impact of the genomic findings was less dramatic among benign and intermediate-grade desmoplastic tumors (BIDTs). Interobserver agreement also improved, with the Fleiss multirater Kappa being 0.36 before genomics to 0.4 after genomics. NGS has the potential to improve diagnostic accuracy in the assessment of desmoplastic melanocytic tumors. The degree of improvement will be most substantial among pathologists with some background and experience in bioinformatics and melanoma genetics.

Hybrid capture-based next-generation sequencing of new and old world Orthohantavirus strains and wild-type Puumala isolates from humans and bank voles

Orthohantaviruses, transmitted primarily by rodents, cause hemorrhagic fever with renal syndrome (HFRS) in Eurasia and hantavirus pulmonary syndrome in the Americas. These viruses, with documented human-to-human transmission, exhibit a wide case-fatality rate, 0.5–40 %, depending on the virus species, and no vaccine or effective treatment for severe Orthohantavirus infections exists. In Europe, the Puumala virus (PUUV), carried by the bank vole Myodes glareolus, causes a milder form of HFRS. Despite the reliance on serology and PCR for diagnosis, the three genomic segments of Swedish wild-type PUUV have yet to be completely sequenced.We have developed a targeted hybrid-capture method aimed at comprehensive genomic sequencing of wild-type PUUV isolates and the identification of other Orthohantaviruses. Our custom-designed panel includes >11,200 probes covering the entire Orthohantavirus genus. Using this panel, we sequenced complete viral genomes from bank vole lung tissue, human plasma samples, and cell-cultured reference strains. Analysis revealed that Swedish PUUV isolates belong to the Northern Scandinavian lineage, with nucleotide diversity ranging from 2.8 % to 3.7 % among them. Notably, no significant genotypic differences were observed between the viral sequences from reservoirs and human cases except in the nonstructural protein.Despite the high endemicity of PUUV in Northern Sweden, these are the first complete Swedish wild-type PUUV genomes and substantially increase our understanding of PUUV evolution and epidemiology. The panel's sensitivity enables genomic sequencing of human samples with viral RNA levels reflecting the natural progression of infection and underscores our panel's diagnostic value, and could help to uncover novel Orthohantavirus transmission routes.

Concurrent KRAS p.G12C mutation and ANK3::RET fusion in a patient with metastatic colorectal cancer: a case report

BackgroundColorectal cancer (CRC) frequently involves mutations in the KRAS gene, impacting therapeutic strategies and prognosis. The occurrence of KRAS mutations typically precludes the presence of RET fusions, with current medical literature suggesting a mutual exclusivity between these two genetic alterations. We present a unique case that challenges this notion.Case PresentationAn 85-year-old female with metastatic CRC was found to have a combination of genetic anomalies that is to the best of our knowledge not yet described in the medical literature: a KRAS p.G12C mutation, associated with oncogenesis and treatment resistance, and an ANK3::RET fusion, an infrequent but targetable mutation in CRC. This molecular profile was uncovered through comprehensive genomic sequencing after the patient experienced metachronous tumor dissemination. The presence of both genetic events complicates the treatment approach.ConclusionsThe identification of both a KRAS p.G12C mutation and an ANK3::RET fusion in the same CRC patient adds a new layer to the oncogenic landscape and treatment considerations for CRC. It highlights the intricate decision-making required in the era of precision medicine, where targeted therapies must be carefully chosen and potentially combined to combat complex genetic profiles. The case emphasizes the urgency of investigating the clinical effects of concurrent or sequential use of KRAS p.G12C and RET inhibitors to inform future therapeutic guidelines and improve patient outcomes in similar cases.

Cell-free DNA from nail clippings as source of normal control for genomic studies in hematologic malignancies.

Comprehensive genomic sequencing is becoming a critical component in the assessment of hematologic malignancies, with broad implications for patient management. In this context, unequivocally discriminating somatic from germline events is challenging but greatly facilitated by matched analysis of tumor:normal pairs. In contrast to solid tumors, conventional sources of normal control (peripheral blood, buccal swabs, saliva) could be highly involved by the neoplastic process, rendering them unsuitable. In this work we describe our real-world experience using cell free DNA (cfDNA) isolated from nail clippings as an alternate source of normal control, through the dedicated review of 2,610 tumor:nail pairs comprehensively sequenced by MSK-IMPACT-heme. Overall, we find nail cfDNA is a robust source of germline control for paired genomic studies. In a subset of patients, nail DNA may have tumor DNA contamination, reflecting unique attributes of the hematologic disease and transplant history. Contamination is generally low level, but significantly more common among patients with myeloid neoplasms (20.5%; 304/1482) compared to lymphoid diseases (5.4%; 61/1128) and particularly enriched in myeloproliferative neoplasms with marked myelofibrosis. When identified in patients with lymphoid and plasma-cell neoplasms, mutations commonly reflected a myeloid profile and correlated with a concurrent/evolving clonal myeloid neoplasm. For nails collected after allogeneic stem-cell transplantation, donor DNA was identified in 22% (11/50). In this cohort, an association with recent history of graft-vs-host disease was identified. These findings should be considered as a potential limitation for the use of nail as normal control but could also provide important diagnostic information regarding the disease process.

99P Comprehensive genomic sequencing as an ancillary diagnostic tool for pathologists

99P Comprehensive genomic sequencing as an ancillary diagnostic tool for pathologists

Dramatic, durable response to therapy in gBRCA2-mutated pancreas neuroendocrine carcinoma: opportunity and challenge

Poorly differentiated pancreatic neuroendocrine tumors (PDNEC), are a subtype of pancreatic cancer encompassing both small cell and large cell neuroendocrine carcinoma subtypes, and are characterized as distinct in terms of biology and prognosis compared to the more common pancreatic adenocarcinoma. Until recently, there has been a paucity of data on the genomic features of this cancer type. We describe a male patient diagnosed with PDNEC and extensive metastatic disease in the liver at diagnosis. Genomic analysis demonstrated a germline pathogenic variant in BRCA2 with somatic loss-of-heterozygosity of the BRCA2 wild-type allele. Following a favorable response to platinum-based chemotherapy (and the addition of immunotherapy), the patient received maintenance therapy with olaparib, which resulted in a further reduction on follow-up imaging (Fig. 1). After seventeen months of systemic control with olaparib, the patient developed symptomatic central nervous system metastases, which harboured a BRCA2 reversion mutation. No other sites of disease progression were observed. Herein, we report an exceptional outcome through the incorporation of a personalized management approach for a patient with a pancreatic PDNEC, guided by comprehensive genomic sequencing.

Abstract CT089: Molecular-guided therapy for the treatment of patients with relapsed and refractory childhood cancers: a Beat Childhood Cancer Research Consortium trial

Abstract Background: Children with relapsed CNS tumors, neuroblastoma, sarcomas, and other rare solid tumors face poor outcomes. Here we describe a study to determine the feasibility of leveraging genomic profiling results within a molecular tumor board (MTB) to make real-time treatment decisions for children with relapsed/refractory solid tumors. Methods: Subjects were divided to 3 strata: Strata 1: Relapsed/refractory neuroblastoma, Strata 2: Relapsed/refractory CNS tumors, and Strata 3: Relapsed/refractory rare solid tumors. Samples were sent for tumor/normal whole exome (WES) and tumor whole transcriptome sequencing, and the genomic data were used in a MTB to make real-time treatment decisions. The MTB recommended plan allowed for a combination of up to 4 agents. Feasibility was measured by time to completion of genomic sequencing, MTB review and initiation of treatment. Response was assessed after every 2 cycles using Response Evaluation Criteria in Solid Tumors (RECIST). Patient benefit was calculated by the sum of the CR, PR, SD, and NED subjects divided by the sum of CR, PR, SD, NED, and PD subjects. Grade 3 and higher related and unexpected adverse events (AEs) were tabulated for safety evaluation. Results: 144 eligible subjects were enrolled with 144 evaluable for safety and 124 evaluable for response. Tumor types included neuroblastoma (n=31), CNS tumors (n=41), and rare tumors (n=72). Sarcomas (n=40) were the most common tumor type in the rare tumor stratum. The average time from biopsy to completion of DNA/RNA sequencing was 10 days (range 2-31 days); to completed analysis and drug prediction report, 17 days (8-41); 23 days (10-66) to MTB decisions; and 38 days (18-146) to initiation of the 4-drug combination agreed upon by the MTB. Treatments were selected on DNA and RNA findings in 19.5% of cases and in 80.5% on RNA alone. Patient benefit was exhibited in 70% of all subjects, 85% of neuroblastoma subjects, 73% of CNS tumor subjects, and 62% of rare tumor subjects. AEs occurred in &amp;lt;1% of the subject cohort. Grade 3 leukopenia was the only unexpected hematologic AE. There were 7 occurrences of unexpected non-hematologic AEs: grade 4 elevated ALT (1), grade 3 elevated AST (1), grade 3 dehydration (1), grade 3 infection (2), grade 3 oral mucositis (1), and grade 3 pancreatitis (1). Conclusions: It has been well-established that comprehensive genomic sequencing is the future of precision medicine. Here, we have demonstrated the feasibility, efficacy, and safety of a comprehensive sequencing model to guide targeted therapy for patients with any relapsed/refractory solid malignancies. Targeted therapy was well tolerated, and the response benefit rate of 70% in these heavily pretreated populations suggests that this treatment could be an effective option for relapsed and refractory pediatric cancers. Citation Format: Giselle L. Saulner Sholler, Jacqueline Kraveka, Genevieve Bergendahl, Elizabeth Lewis, William Ferguson, Abhinav Nagulapally, Karl Dykema, Valerie Brown, Michael Isakoff, Joseph Junewick, Deanna Mitchell, Don Eslin, Virginia Harrod, William Roberts, Javier Oesterheld, Randy Wada, Jawhar Rawwas, Devang Pastakia, Kevin Ginn, Raya Saab, Kevin Bielamowicz, Jason Glover, Eugenia Chang, Gina Hanna, Daniel Enriquez, Tyler Izatt, Rebecca Halperin, Sara Byron, William Hendricks, Jeffrey Trent. Molecular-guided therapy for the treatment of patients with relapsed and refractory childhood cancers: a Beat Childhood Cancer Research Consortium trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr CT089.

B-cell lineage neoplasms transdifferentiating into histiocytic/dendritic cell neoplasms: diversity, differentiation lineage, genomic alterations, and therapy: Report from the 2021 SH/EAHP Workshop

To report findings from the 2021 Society for Hematopathology/European Association for Haematopathology Workshop within the category of B-cell lineage neoplasms' transdifferentiation into histiocytic/dendritic cell neoplasms (HDCNs). The workshop panel reviewed 29 cases, assigned consensus diagnoses, and summarized findings. The specific diagnoses of transdifferentiated HDCN tumors were histiocytic sarcoma (16); Langerhans cell histiocytosis/sarcoma (5); indeterminate DC tumor (1); and HDCN, unclassifiable (1). Approximately one-third of the patients reviewed had follicular lymphoma; lymphoblastic leukemia/lymphoma; or another B-cell lymphoma, most commonly chronic lymphocytic leukemia/small lymphocytic lymphoma. There was a 3:1 preponderance toward women, median patient age was 60 years, and the median interval between the initial diagnosis of B-cell lineage neoplasm and HDCN was 4 to 5 years. The submitted cases have demonstrated substantial heterogeneity as well as overlapping immunophenotypic and other features. Comprehensive genomic DNA sequencing revealed alterations enriched in the MAPK pathway. Based on shared and distinct alterations seen in HDCNs and the preceding lymphomas, both linear and divergent clonal evolutionary pathways were inferred. Furthermore, RNA sequencing performed in a subset of cases yielded new insights into markers that could be useful for more precise cell lineage identification. The panel has thus proposed an updated algorithm for HDCN lineage assignment. The outcome of transdifferentiated HDCNs was poor, but the MAPK signaling pathway emerges as a potentially attractive therapeutic target. Transdifferentiated HDCNs demonstrate heterogeneity and pose diagnostic challenges with regard to exact classification, but the in-depth characterization of the submitted cases have added to our understanding of the secondary HDCNs transdifferentiated from B-cell lymphoma/leukemia. Continuous efforts focusing on deciphering the specific cell lineage and differentiation state of these tumors will be critical for their accurate classification. Comprehensive molecular characterization of HDCNs may be informative in this regard. With the list of novel pharmacologic inhibitors of the MAPK pathway continuing to expand, improved outcomes for HDCN can be expected.

Application of Comprehensive Genomic Profiling-Based Next-Generation Sequencing Assay to Improve Cancer Care in a Developing Country.

Identifying actionable oncogenic mutations have changed the therapeutic landscape in different types of tumors. This study investigated the utility of comprehensive genomic profiling (CGP), a hybrid capture-based next-generation sequencing (NGS) assay, in clinical practice in a developing country. In this retrospective cohort study, CGP was performed on clinical samples from patients with different solid tumors recruited between December 2016 and November 2020, using hybrid capture-based genomic profiling, at the individual treating physicians' request in the clinical care for therapy decisions. Kaplan-Meier survival curves were estimated to characterize the time-to-event variables. Patients median age was 61years (range: 14-87years), and 64.7% were female. The most common histological diagnosis was lung primary tumors, with 90 patients corresponding to 52.9% of the samples (95% CI 45.4-60.4%). Actionable mutations with FDA-approved medications for specific alterations correspondent to tumoral histology were identified in 58 cases (46.4%), whereas other alterations were detected in 47 different samples (37.6%). The median overall survival was 15.5months (95% CI 11.7months-NR). Patients who were subjected to genomic evaluation at diagnosis reached a median overall survival of 18.3months (95% CI 14.9months-NR) compared to 14.1months (95% CI 11.1months-NR) in patients who obtained genomic evaluation after tumor progression and during standard treatment (P = .7). CGP of different types of tumors identifies clinically relevant genomic alterations that have benefited from targeted therapy and improve cancer care in a developing country to guide personalized treatment to beneficial outcomes of cancer patients.

Clinical impact of mutations in driver oncogenes and TP53/RB1 in advanced prostate cancer.

263 Background: Prostate cancer (PCa) is characterized by considerable genetic heterogeneity, and complex genomic features may influence prognosis and treatment response. We created a database of aggressive PCa that integrates comprehensive genomic sequencing with detailed clinical outcomes to better understand the optimal use of genomic sequencing. Methods: From 4/2005-7/2021, PCa cancer patients older than 18 years of age underwent tissue collection for tumoral RNA-sequencing and tumor/normal whole exome sequencing at our institution (HUM00046018, HUM00048105, HUM00067928, SU2C). Genomic and transcriptomic sequencing data was processed using Turnkey Precision Oncology. Genetic alterations, including ETS fusions, SPOP, FOXA1 class 1, and CDK12 mutations, as well as TP53 and RB1 mutations were analyzed. Clinical data was collected from 05/2021-01/2022, and clinical associations (metastasis free survival (MFS), time to castrate resistant prostate cancer (CRPC), and overall survival (OS)) were determined. Results: Data was available for 325 men. Median follow up from diagnosis was 106 months (IQR, 90-121), median age at diagnosis was 61 (IQR, 54-67), and most (91%) presented with PCa adenocarcinoma (n=292/325). At diagnosis, 51% (n=165) had localized, 5% (n=18) had clinical node positive, and 40% (n=128) had de-novo M1 disease. At time of tissue sampling, 87% (n=283) had metastatic disease, and 59% (n=192) were castrate resistant. Established PCa driver mutations included 140 ETS fusions (49%), 26 SPOP mutations (9%), 22 FOXA1 class 1 mutations (8%), and 15 (5%) CDK12 mutations. For men with localized disease at diagnosis (n=197/325), ETS fusion was associated with improved MFS (HR: 0.55; 95% CI: 0.37-0.81), time to CRPC (HR: 0.53; 0.35-0.80), and OS (HR: 0.56; 0.35-0.89). SPOP mutations were also associated with improved prognosis in this population (n=197/325): MFS (HR: 0.45; 0.24-0.84), time to CRPC (HR: 0.36; 0.18-0.73), and OS (HR: 0.46; 0.21-0.99). TP53 mutations were identified in 38% (n=122) of all patients and were associated with worse OS from the time of biopsy after adjusting for PCa castration state and disease spread at biopsy (HR: 2.2; 1.7-2.9, p&lt;0.001). RB1 mutations were identified in 12% (n=40; 24/40 also TP53 mutants). OS from the time of biopsy was worse in the presence of dual TP53/RB1 mutants when compared to TP53 or RB1 mutants alone, independent of the disease state at time of biopsy (HR, 4.3; 95%CI: 2.7-7.0). Conclusions: In a cohort of aggressive PCa, oncogenic driver mutations were associated with significant differences in prognosis. ETS fusions and SPOP mutations correlated with improved outcomes for men with localized disease at presentation. TP53 loss was associated with worse prognosis, as was the combination with RB1 loss, across the disease spectrum. Future efforts will focus on correlating sensitivity to PCa treatments with genetic alterations throughout the disease course.

The evolution of targeted therapy in pediatric AML: gemtuzumab ozogamicin, FLT3/IDH/BCL2 inhibitors, and other therapies.

Despite the maximum intensification of chemotherapy and the increased use of hematopoietic stem cell transplantation (HCT) in pediatric patients with acute myeloid leukemia (AML), nearly 40% of patients still experience relapse, and cure in this setting remains a significant challenge. Recent improvements in AML characterization, including advances in flow cytometry and comprehensive genomic sequencing, have led to a better understanding of AML biology and the identification of multiple potential therapeutic targets. Novel agents targeting genomic lesions, cell surface antigens, and other mechanisms that permit oncogenesis or immune escape are being incorporated into current treatment strategies or are under investigation in efforts to improve outcomes and decrease the toxicities and late effects associated with traditional intensive chemotherapeutic and HCT treatment. However, multiple challenges still exist, including the biologic and immunophenotypic heterogeneity of childhood AML, the differences in underlying biology as compared to adult AML, and the significant potential for on-target/off-tumor toxicity associated with therapies directed at targets common to myeloid cells, both leukemic and normal. This article reviews the current landscape of genomic and cell surface targets for children with AML with a focus on the currently available targeted therapeutic agents, those in active clinical investigation, and those still in development.

Comprehensive Genomic Sequencing–Based Screening for Hearing Loss in the Neonatal Intensive Care Setting—Is It Time?

Comprehensive Genomic Sequencing–Based Screening for Hearing Loss in the Neonatal Intensive Care Setting—Is It Time?

Abstract PL03-05: A framework for community-engaged participatory research in cancer genomic sequencing: A collaborative with sovereign tribal nations in the American southwest

Abstract While American Indian Tribes and communities are highly diverse in ethnicity, language, and culture, there is one unfortunate characteristic they share: profound cancer health disparities. Compounded by low rates of cancer screening and more limited access to healthcare, American Indians are more often diagnosed at later stages of disease and have the poorest outcomes in all types of cancer when compared to any other racial and ethnic group in the United States (Jamal et al. JNCI 2017; Sep; 109(9)). American Indians and Alaskan Natives (AI/AN) across the U.S. are impacted by a significantly higher incidence of several cancers when compared to non-Hispanic Whites (NHW): hepatocellular carcinoma; renal cell carcinoma; and cancers of the biliary tree (gall bladder and cholangiocarcinoma). In terms of mortality, AI/AN have the nation’s highest rate of death from liver cancer (2.2-fold &amp;gt; NHW) and a 1.9-fold higher rate of death from kidney cancer. The incidence of colorectal cancer in AI/AN communities has also increased significantly. The cause of these significant cancer disparities is undoubtedly multifactorial. In addition to low rates of cancer screening, other contributing factors include differences in access to healthcare and timely interventions; distinct cultural perspectives and beliefs regarding cancer etiology, screening, and treatment; differences in diet, obesity, metabolism, and risk behaviors (including tobacco, alcohol, and intravenous drug use); variable rates of vaccination and treatment for Hepatitis, HPV, and other viruses; ancestry-related biologic and genetic factors; and differences in environmental exposures. In the American Southwest, exposure of Tribal communities to environmental and carcinogenic toxins, including exposure to toxins such as aristolochic acid and aflatoxin, and to mining wastes from abandoned hard rock and uranium mines must also be considered. Experimental and epidemiologic studies have linked exposure to mining wastes that contaminate western watersheds (containing highly toxic metal mixtures of arsenic, uranium, cadmium, and other metals) to increased cancer risk in Tribal and non-Tribal communities (Environ Health Perspect. 2014;122(4):363; Cancer Epidemiol Biomark Prev. 2013;22(11):1944.).A virtually unexplored factor which may also contribute to cancer health disparities in AI/AN communities is whether the cancers that arise in American Indians have a distinct spectrum of somatic and germline genomic mutations (somatic and germline) resulting from these factors. Unfortunately, AI/AN cancer patients have been strikingly understudied to date, accounting for &amp;lt; 0.5% of all patients studied in national cancer genomic initiatives. Cancer genomic studies previously conducted by our team of investigators in the NCI TARGET Project (https://ocg.cancer.gov &amp;gt; programs &amp;gt; target) focused on high-risk acute lymphoblastic leukemia (ALL) discovered that patients with a high degree of indigenous genetic ancestry had a unique spectrum of mutations in genes encoding tyrosine kinases or genes regulating tyrosine kinase pathways. All patients with this mutation spectrum had a significantly poorer overall outcome, despite treatment with intensive therapies. Recent studies have found a unique spectrum and frequency of mutations and mutational signatures in kidney cancers arising in indigenous communities (Trent, J. et al; unpublished). Our NCI-funded Participant Engagement-Cancer Genome Sequencing (PE-CGS) Research Center (NCI U2C CA252973: Engagement of American Indians of Southwestern Tribal Nations in Cancer Genomic Sequencing; MPIs: Willman and Jeffrey Trent, PhD) is seeking to overcome this knowledge gap through direct participant engagement and collaborative research partnerships with Tribal nations and communities. A proper framework for engagement of indigenous Tribal Nations and tribal participants in research includes respect for Tribal sovereignty; engagement of participants and communities in project selection and oversight; assuring that the research is beneficent; the use of culturally-appropriate approaches for informed consent; appropriate data sharing, assurance of data privacy, and data interpretation and communication, including the need to engage AI/AN participants and communities in the development of culturally appropriate interpretive data narratives; sensitivities regarding collection and approval for use of biospecimens, particularly future use; concerns over genetic privacy, protection of individual identity, and assurance that molecular means of ancestry determination in individual Tribal members will not interfere with Tribal means of cultural identify and their Tribal membership; and joint sharing in intellectual property and the benefits of discoveries. It is our hypothesis that through appropriate participant and community engagement and comprehensive genomic sequencing, we will discover novel somatic and germline mutations, differences in the spectrum and/or frequency of cancer-promoting mutations, and genome-wide mutational signatures reflective of behaviors and exposures, that can ultimately be translated to improved cancer screening, precision prevention, and therapeutic intervention in American Indian participants and communities. Citation Format: Cheryl L. Willman. A framework for community-engaged participatory research in cancer genomic sequencing: A collaborative with sovereign tribal nations in the American southwest [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr PL03-05.

Percutaneous Image-Guided Biopsy for a Comprehensive Hybridization Capture-Based Next-Generation Sequencing in Primary Lung Cancer: Safety, Efficacy, and Predictors of Outcome

IntroductionTo evaluate factors associated with successful comprehensive genomic sequencing of image-guided percutaneous needle biopsies in patients with lung cancer using a broad hybrid capture-based next-generation sequencing assay (CHCA). MethodsWe conducted a single-institution retrospective review of image-guided percutaneous transthoracic needle biopsies from January 2018 to December 2019. Samples with confirmed diagnosis of primary lung cancer and for which CHCA had been attempted were identified. Pathologic, clinical data and results of the CHCA were reviewed. Covariates associated with CHCA success were tested for using Fisher’s exact test or Wilcoxon ranked sum test. Logistic regression was used to identify factors independently associated with likelihood of CHCA success. ResultsCHCA was requested for 479 samples and was successful for 433 (91%), with a median coverage depth of 659X. Factors independently associated with lower likelihood of CHCA success included small tumor size (OR = 0.26 [95% confidence interval (CI): 0.11–0.62, p = 0.002]), intraoperative inadequacy on cytologic assessment (OR = 0.18 [95% CI: 0.06–0.63, p = 0.005]), small caliber needles (≥20-gauge) (OR = 0.22 [95% CI: 0.10–0.45, p < 0.001]), and presence of lung parenchymal abnormalities (OR = 0.12 [95% CI: 0.05–0.25, p < 0.001]). Pneumothorax requiring chest tube insertion occurred in 6% of the procedures. No grade IV complications or procedure-related deaths were reported. ConclusionsPercutaneous image-guided transthoracic needle biopsy is safe and has 91% success rate for CHCA in primary lung cancer. Intraoperative inadequacy, small caliber needle, presence of parenchymal abnormalities, and small tumor size (≤1 cm) are independently associated with likelihood of failure.

Opening up safely: public health system requirements for ongoing COVID-19 management based on evaluation of Australia\u2019s surveillance system performance

BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) community transmission was eliminated in Australia from 1/11/2020 to 30/6/2021, allowing evaluation of surveillance system performance in detecting novel outbreaks, including against variants of concern (VoCs). This paper aims to define system requirements for coronavirus disease 2019 (COVID-19) surveillance under future transmission and response scenarios, based on surveillance system performance to date.MethodsThis study described and evaluated surveillance systems and epidemiological characteristics of novel outbreaks based on publicly available data, and assessed surveillance system sensitivity and timeliness in outbreak detection. These findings were integrated with analysis of other critical COVID-19 public health measures to establish future COVID-19 management requirements.ResultsTwenty-five epidemiologically distinct outbreaks and five distinct clusters were identified in the study period, all linked through genomic sequencing to novel introductions from international travellers. Seventy percent (21/30) were detected through community testing of people with acute respiratory illness, and 30% (9/30) through quarantine screening. On average, 2.07% of the State population was tested in the week preceding detection for those identified through community surveillance. From 17/30 with publicly available data, the average time from seeding to detection was 4.9 days. One outbreak was preceded by unexpected positive wastewater results. Twenty of the 24 outbreaks in 2021 had publicly available sequencing data, all of which identified VoCs. A surveillance strategy for future VoCs similar to that used for detecting SARS-CoV-2 would require a 100–1000-fold increase in genomic sequencing capacity compared to the study period. Other essential requirements are maintaining outbreak response capacity and developing capacity to rapidly engineer, manufacture, and distribute variant vaccines at scale.ConclusionsAustralia’s surveillance systems performed well in detecting novel introduction of SARS-CoV-2 while community transmission was eliminated; introductions were infrequent and case numbers were low. Detection relied on quarantine screening and community surveillance in symptomatic members of the general population, supported by comprehensive genomic sequencing. Once vaccine coverage is maximised, future COVID-19 control should shift to detection of SARS-CoV-2 VoCs, requiring maintenance of surveillance systems and testing all international arrivals, alongside greatly increased genomic sequencing capacity. Effective government support of localised public health response mechanisms and engagement of all sectors of the community is crucial to current and future COVID-19 management.

Epidemiological and clinical features of Panton-Valentine Leukocidin positive Staphylococcus aureus bacteremia: A case-control study.

Panton-Valentine Leukocidin (PVL) toxin in Staphylococcus aureus has been associated with both severe pneumonia and skin and soft tissue infections. However, there are only limited data on how this virulence factor may influence the clinical course or complications of bacteremic S. aureus infections. Between September 2016 and March 2018, S. aureus isolates from clinical cultures from hospitals in an academic medical center underwent comprehensive genomic sequencing. Four hundred sixty-nine (29%) of 1681 S. aureus sequenced isolates were identified as containing the genes that encode for PVL. Case patients with one or more positive blood cultures for PVL were randomly matched with control patients having positive blood cultures with lukF/lukS-PV negative (PVL strains from a retrospective chart review). 51 case and 56 control patients were analyzed. Case patients were more likely to have a history of injection drug use, while controls more likely to undergo hemodialysis. Isolates from 78.4% of case patients were methicillin resistant as compared to 28.6% from control patients. Case patients had a higher incidence of pneumonia and skin and soft tissue infection and longer duration of fever without differences in length of bacteremia. Clinical cure or expiration was comparable. These results are consistent with prior observations associating the PVL toxin with both community-acquired MRSA strains as well as severe staphylococcal pneumonia. The presence of the PVL toxin does not appear to otherwise influence the natural history of bacteremic S. aureus disease other than in prolonging the duration of fever.

RAB20 Promotes Proliferation via G2/M Phase through the Chk1/cdc25c/cdc2-cyclinB1 Pathway in Penile Squamous Cell Carcinoma.

Simple SummaryThere is no available biomarker that could be used to predict the prognosis or progression of penile squamous cell carcinoma (PSCC) currently. Here, we conducted comprehensive genomic sequencing on eight pairs of PSCC tissues and found that RAB20 was upregulated in tumors, especially in metastatic lymph nodes. We then detected the expression of RAB20 in a large cohort of 259 PSCC cases using IHC assay and analyzed the association between the RAB20 expression and clinical features. We found that high RAB20 expression predicted poor prognosis and advanced clinicopathological features. Further in vitro and in vivo tumorigenesis assays revealed that RAB20 regulates cell proliferation at the G2/M cell cycle phase through the Chk1/cdc25c/cdc2-cyclinB1 pathway. Our results indicated that RAB20 could be a promising prognostic biomarker of advanced PSCC with poor survival and could be a potential therapeutic target.RAB20, a member of the RAS GTPase oncogene family, is overexpressed in several cancers with poor outcomes, promoting tumorigenesis and inducing genomic instability. Here, we performed comprehensive genomic sequencing on eight penile squamous cell carcinoma (PSCC) and normal tissue pairs and found that RAB20 was upregulated in tumors, especially in metastatic lymph nodes. RAB20 overexpression in tumors was further verified by qPCR, Western blotting, and immunohistochemistry of our newly established PSCC cell lines and paired tissues. The clinical significance of RAB20 was validated in 259 PSCC patients, the largest cohort to date, and high RAB20 expression positively correlated with the T, N, M status, extranodal extension, and clinical stage (all p < 0.01). RAB20 was an unfavorable independent prognostic indicator in the survival analysis (p = 0.011, HR = 2.090; 95% Cl: 1.183–4.692), and PSCC patients with high RAB20 expression experienced shorter 5-year cancer-specific survival times (p < 0.001). Furthermore, tumorigenesis assays demonstrated that RAB20 knockdown inhibited cell proliferation, migration, and colony formation in vitro and tumor growth in vivo. RAB20 depletion also induced PSCC cell cycle arrest at G2/M by increasing Chk1 expression and promoting cdc25c phosphorylation to reduce cdc2-cyclinB1 complex formation. Our study revealed an oncogenic role for RAB20 in promoting PSCC cell proliferation at the G2/M phase via the Chk1/cdc25c/cdc2-cyclinB1 pathway. Thus, RAB20 could be a promising prognostic biomarker of advanced PSCC with poor patient survival outcomes and could be a potential therapeutic target.

Integrating comprehensive genomic sequencing of non-small cell lung cancer into a public healthcare system

ObjectivesStandard molecular testing for patients with stage IV non-small cell lung cancer (NSCLC) in the Canadian publicly funded health system includes single gene testing for EGFR, ALK, and ROS-1. Comprehensive genomic profiling (CGP) may broaden treatment options for patients. This study examined the impact of CGP in a publicly funded health system. MethodsConsenting patients with stage IV NSCLC without known targetable alterations underwent CGP on diagnostic samples. Patients that had progressed on targeted therapy were also eligible. The CGP assay was a hybrid capture next generation sequencing (NGS) panel (Oncomine Comprehensive Assay Version 3, ThermoFisher). The number of actionable alterations, changes in treatment, clinical trial eligibility and costs as a result of CGP were evaluated and patient willingness-to-pay. ResultsOf 182 screened patients,134 (74%) had successful CGP testing. Twenty percent had received prior targeted therapy. Incremental actionable alterations were identified in 31% of patients. The most common novel targets identified were mutations in ERBB2 (exon 20 insertions), MET (exon 14 skipping) and KRAS (G12C). At data cut off (31/12/2020), 16% of patients had a change in treatment as a result of CGP. Additional clinical trial options were identified for 75% of patients. The incremental direct laboratory cost for CGP beyond public reimbursement for single gene tests was $747 CAD/case. ConclusionCGP identifies additional actionable targets beyond single gene tests with a direct impact on patient treatment and increased clinical trial eligibility. These benefits highlight the value of CGP in patients with NSCLC in public health systems.