Utilization Of Next-generation Sequencing Research Articles

Bridging the divide: addressing discrepancies between clinical guidelines, policy guidelines, and biomarker utilization.

This paper aims to identify and address gaps in cancer treatment and diagnosis within European health services, focusing specifically on discrepancies between clinical guidelines and policy guidelines. It seeks to highlight how the underutilization of advanced diagnostic techniques recommended by medical societies contributes to missed opportunities for improving patient outcomes. A comprehensive analysis was conducted across multiple European countries to assess the compliance and integration of clinical guidelines with the availability of advanced diagnostic technologies. Secondary data related to clinical and policy guidelines in cancer care were collected and analyzed. Key indicators of adoption and utilization of next-generation sequencing and liquid biopsy were examined to evaluate their impact on health service efficiency and patient care. The analysis revealed significant discrepancies between the recommendations of medical societies regarding advanced diagnostic techniques and their adoption in health policy decisions across Europe. Country-specific assessments indicated varying levels of alignment between clinical guidelines and the availability of advanced diagnostics. These findings underscored missed opportunities for optimizing patient care and health service efficiency through better alignment and integration of clinical guidelines with policy decisions. This study concludes that there is a critical need for health policy decision-makers to prioritize the adoption of clinical guidelines in resource allocation and health service organization. Greater attention to the recommendations of medical societies regarding advanced diagnostic techniques could significantly enhance diagnostic accuracy, treatment efficacy, and overall patient outcomes in cancer care. The paper advocates for policy reforms that acknowledge and leverage the potential benefits of advanced diagnostics in improving health service performance and patient-centered care across Europe.

Association between socioeconomic factors and utilization of next-generation sequencing in metastatic breast cancer.

e13700 Background: Targeted therapies such as PI3K inhibitors have revolutionized the treatment of patients with metastatic breast cancer (MBC). Their selective use is enabled by next-generation sequencing (NGS) approaches, which help identify actionable tumor alterations. There may be socioeconomic disparities in NGS testing and NGS-guided treatment selection. This study aimed to investigate the role of socioeconomic status (SES) (race and area deprivation index [ADI]) among patients with MBC undergoing NGS. Methods: Our retrospective study included 418 adult patients (pts) with MBC treated at the Magee Women’s Cancer Center in Pittsburgh, PA between September 2016 and December 2022. Demographic information, including race and ADI, clinicopathologic information, and NGS results were collected. ADI based on zip code was derived utilizing Neighborhood Atlas. Scores range from 0-10 (higher score = higher deprivation), representing the census-based ranking of the ZIP code at the state level based on the composite of several factors, including income, education, employment, and housing quality. Descriptive statistics, chi-squared, and independent sample t tests were used. Multivariate logistic regression analysis was done to evaluate potential associations with receipt of NGS and NGS-directed therapy. Results: 89% of pts were non-Hispanic white (NHW); 11% were non-Hispanic black (NHB). A greater proportion of NHB pts were from higher ADI (6-10) neighborhoods (p=0.00001), suggesting lower SES. NHW pts were more likely to have hormone receptor (HR)+/human epidermal growth factor receptor (HER)2- tumors compared with NHB pts (p=0.022). 219 (52.4%) total pts had NGS tumor testing performed: 53% of NHW and 47.8% of NHB pts (p=0.511). 55.1% (102/185) of pts living in higher SES neighborhoods (ADI 1-5) and 50.2% (117/233) living in lower SES neighborhoods (ADI 6-10) received NGS testing (p=0.317). Of the 219 pts who got NGS testing, 62.6% (137) had a clinically actionable alteration identified, and of those, 46% (63) received corresponding targeted therapy. Of the 63 pts who received NGS-guided therapy, 88.9% were NHW and 11.1% were NHB (p=0.849), and 50.8% were from neighborhoods with ADI 1-5 and 49.2% were from neighborhoods with ADI 6-10 (p=0.571). In multivariate analysis including race, ADI, insurance status, year of MBC diagnosis, and tumor subtype, only tumor subtype (non-HR+/HER2- tumors) was significantly associated with a lower likelihood of both receiving NGS testing (p=0.032) and receiving NGS-directed therapy (p=0.001). Conclusions: There was a higher numerical rate of NGS testing and NGS-guided therapy initiation in NHW pts and pts from lower ADI (1-5 vs. 6-10) neighborhoods, but this did not reach statistical significance. Overall, in this single institution cohort limited by small numbers, there were no differences in NGS tumor testing based on race and SES.

Performance of preimplantation genetic testing for aneuploidy for patients with unexplained recurrent pregnancy loss and repeated implantation failure

ObjectiveThe primary objective was to investigate whether the utilization of next-generation sequencing (NGS) for preimplantation genetic testing for aneuploidy (PGT-A) could enhance the reproductive outcomes in patients with unexplained recurrent pregnancy loss (uRPL) or unexplained repeated implantation failure (uRIF) undergoing intracytoplasmic sperm injection (ICSI) cycles. Materials and methodsWe studied the reproductive outcomes of uRPL or uRIF sufferers in Chengdu women and children's central hospital from July 2020 to Jan 2024 retrospectively. These patients were categorized into two groups based on whether they underwent PGT-A or not. As the patients in the PGT-A group all had ICSI and frozen-thawed embryo transfer (FET), only patients who underwent ICSI and FET were included in the non-PGT-A group for comparison. Demographic characteristics and reproductive outcomes were compared in uRPL or uRIF sufferers. ResultsFor uRPL group, a significant increased ongoing pregnancy rate (63.6 % vs 26.1 %, p = 0.002) and reduced pregnancy loss rate (18.4 % vs 73.3 %, p < 0.001) were found in the PGT-A group in comparison with those in the non-PGT-A group. For uRIF group, no significant difference was noted in the HCG-positive rate, ongoing pregnancy rate, or pregnancy loss rate between the two groups. It is noteworthy that the maternal age in the PGT-A group was significantly higher than that in the non-PGT-A group (p = 0.048). ConclusionsNGS-based PGT-A effectively optimized the reproductive outcomes in uRPL sufferers. Although its benefits in uRIF appeared to be limited, there is a potential advantage for those with advanced maternal age. Considering the small sample size, further randomized controlled trials are warranted to validate these findings.

Spectrum of genetic variants in bilateral sensorineural hearing loss.

Background: Hearing loss (HL) is an impairment of auditory function with identified genetic forms that can be syndromic (30%) or non-syndromic (70%). HL is genetically heterogeneous, with more than 1,000 variants across 150 causative genes identified to date. The genetic diagnostic rate varies significantly depending on the population being tested. Countries with a considerably high rate of consanguinity provide a unique resource for studying rare forms of recessive HL. In this study, we identified genetic variants associated with bilateral sensorineural HL (SNHL) using whole-exome sequencing (WES) in 11 families residing in the United Arab Emirates (UAE). Results: We established the molecular diagnosis in six probands, with six different pathogenic or likely pathogenic variants in the genes MYO15A, SLC26A4, and GJB2. One novel nonsense variant, MYO15A:p.Tyr1962Ter*, was identified in a homozygous state in one family, which has not been reported in any public database. SLC26A4 and GJB2 were found to be the most frequently associated genes in this study. In addition, six variants of uncertain significance (VUS) were detected in five probands in the genes CDH23, COL11A1, ADGRV1, NLRP3, and GDF6. In total, 12 variants were observed in eight genes. Among these variants, eight missense variants (66.7%), three nonsense variants (25.0%), and one frameshift (8.3%) were identified. The overall diagnostic rate of this study was 54.5%. Approximately 45.5% of the patients in this study came from consanguineous families. Conclusion: Understanding the genetic basis of HL provides insight for the clinical diagnosis of hearing impairment cases through the utilization of next-generation sequencing (NGS). Our findings contribute to the knowledge of the heterogeneous genetic profile of HL, especially in a population with a high rate of consanguineous marriage in the Arab population.

Plasma-activated water regulated transcriptome gene expression leading to high germination and growth of mung beans

BackgroundPlasma-activated water (PAW) is a solution created by exposing water to cold atmospheric plasma discharge, resulting in a biocidal agent with unique biochemical properties attributed to highly reactive oxygen and nitrogen species (RONS). Plasma-activated water (PAW) has been the subject of research for its potential in promoting seed germination. While it has shown promising results, the exact mechanism by which PAW promotes seed growth remains unclear. This study aims to investigate the role of PAW in promoting mung bean germination, including its effects on vitality improvement and the triggering of plant stress responses to promote crop growth. Through the utilization of next-generation sequencing, we aim to explore the interaction between the properties of PAW and gene expression in mung beans. By deciphering the nature of PAW and analyzing gene expression patterns, we hope to uncover the underlying mechanisms that govern their interaction.ResultsThe results revealed that nitrogen plasma-activated water (NPAW) treatment improves the vitality and hypocotyl length of mung beans and leads to a good overall growth state. Moreover, we identified numerous differentially expressed genes (DEGs), including genes related to stress responses, growth regulation, and metabolic processes, that were upregulated or downregulated in response to PAW treatment. As a result of APAW treatment, 168 genes were upregulated and 90 genes were downregulated. Furthermore, 179 genes were upregulated in the NPAW compared to 125 genes that were downregulated in the control group. Gene expression analysis revealed involvement in stress signaling and metabolic processes.ConclusionsPAW treatment can promote crop growth and serve as a reference for other seeds. This research provides insights into the regulatory mechanisms and benefits of PAW in sustainable agriculture.Graphical

Development of New Diagnostic Methods for Early Detection of Cancer: Integration of Genomic and Bioinformatics Technologies

The relentless pursuit of improved cancer diagnostics has led to the development of novel methods for early detection. This article explores the integration of genomic and bioinformatics technologies to propel advancements in cancer diagnostics. With the increasing understanding of cancer as a molecular disease, genomic technologies play a pivotal role in unraveling the intricate genetic alterations associated with various cancer types. The utilization of next-generation sequencing (NGS) allows for comprehensive genomic profiling, enabling the identification of specific genetic mutations, alterations, and aberrations indicative of early-stage cancer.&#x0D; Bioinformatics, as a complementary field, becomes crucial in managing and interpreting the vast datasets generated by genomic technologies. Advanced computational algorithms and machine learning models are employed to analyze genomic data, identify biomarkers, and discern subtle patterns that may serve as early indicators of cancer. The integration of these technologies offers a holistic approach, combining the power of genomics with sophisticated computational analyses to enhance the sensitivity and specificity of cancer diagnostics.&#x0D; Moreover, the article explores the potential of liquid biopsy as a non-invasive method for early cancer detection. By analyzing circulating tumor DNA (ctDNA) and other biomolecules in bodily fluids, liquid biopsy provides a minimally invasive means to monitor molecular changes associated with cancer progression. The integration of liquid biopsy with genomic and bioinformatics technologies further amplifies the scope of early cancer detection, offering a real-time, dynamic assessment of the evolving cancer landscape.&#x0D; In conclusion, the amalgamation of genomic and bioinformatics technologies represents a paradigm shift in cancer diagnostics, facilitating the identification of molecular alterations at an unprecedented level of detail. This integrated approach holds great promise for the early detection of cancer, paving the way for more effective and personalized therapeutic interventions. The article underscores the transformative potential of these technologies in reshaping the landscape of cancer diagnosis and emphasizes the need for ongoing research and technological innovation in the relentless pursuit of improved cancer care.

Primary cardiac sarcoma: demographics, genomic study correlation, and survival benefits of surgery with adjuvant therapy in U.S. population.

Cardiac sarcomas are rare and aggressive tumors with little known about the demographics, genetics, or treatment outcomes. The objectives of this study were to characterize the demographics, treatment modality, and survival associated with cardiac sarcomas and evaluate the potential for mutation-directed therapies. All cases from 2000 to 2018 of cardiac sarcoma were extracted from the SEER database. Genomic comparison utilized The Cancer Genome Atlas (TCGA) database, as well as reviews and re-analysis of past applicable genomic studies. Cardiac sarcomas occurred most often in White patients, compared with national census data cardiac sarcomas occurred at a significantly higher rate in Asians. The majority of cases were undifferentiated (61.7%) and without distant metastases (71%). Surgery was the most common primary treatment modality and offered survival benefit (HR 0.391 (p = 0.001) that was most pronounced and sustained as compared to patients who received chemotherapy (HR 0.423 (p = 0.001) or radiation (HR 0.826 (p = 0.241) monotherapy. There was no difference in survival when stratified by race or sex; however, younger patients (< 50) had better survival. Genomics data on histologically undifferentiated cardiac sarcomas revealed a significant number were likely poorly differentiated pulmonary intimal sarcomas and angiosarcomas. Cardiac sarcoma is a rare disease with surgery continuing to be a cornerstone of therapy followed by traditional chemotherapy. Case studies have indicated the potential for therapies directed to specific genetic aberrations to improve survival for these patients and utilization of next-generation sequencing (NGS) will help improve both classification and these therapies for cardiac sarcoma patients.

(419) In Vivo Next Generation Sequencing Identifies More Isolates vs. Standard Culture During Revision Inflatable Penile Prosthesis Insertion: A Single Center Experience

Abstract Introduction The presence of biofilm at the inflatable penile prosthesis (IPP) component sites, which resists eradication, likely increases postoperative infection rates in revision surgery. The microbiome of (IPP) revision surgery has been shown to be increasingly complex and the weak microbe Staph epidermidis is no longer prevailing and was previously considered the major causative agent for overt infections. Furthermore, next generation sequencing (MicrogenDx, Lubbock, TX, USA) has been used recently to demonstrate that in certain scenarios such as mechanical malfunction, erosion, and infection, specific microbes dominate. Due to the disastrous complications with postoperative IPP infection, it is paramount to provide additional evidence for increased utilization of next generation sequencing over traditional cultures during IPP revision surgery. This will serve to guide postoperative treatment if necessary. Objective We investigated a cohort of IPP revision patients receiving intraoperative low concentration chlorhexidine (CHG) lavage to see whether next generation sequencing or traditional cultures of the pump space reveals more isolates. Methods A total of 31 patients with indwelling IPPs underwent revision surgery for both infectious and noninfectious reasons between May 2021 and March 2022 by a single, high volume implant surgeon who solely uses 0.05% CHG dip and irrigation. Once the pump capsule was entered, swabs were taken from the pump space and sent for traditional culture and next generation sequencing. All cultures were obtained prior to irrigation with 0.05% chlorhexidine (CHG) solution (Irrimax corporation, Lawrenceville, GA, USA). All patients received perioperative clindamycin, gentamicin, and fluconazole. Results 1 patient was excluded due to missing next generation sequencing results. Of the 30 remaining patients, 4 presented with infectious and 26 with noninfectious etiologies. 93% (28/30) patients had negative traditional cultures prior to irrigation with 0.05% CHG; however, 21% (6/28) of these patients had isolates on next generation sequencing. Only 7% (2/30) had positive preop irrigation cultures and isolates on next generation sequencing. Both of these patients presented with infection. 1 of these patients had a concordant next generation sequencing result. However, the other patient had multiple isolates. The traditional culture showed only pseudomonas a. On NGS, it was the third most abundant on NGS at only 4% compared to the most and second most abundant being E. coli at 83% and Klebsiella p. at 12%. Conclusions These results suggests that a greater number of isolates are obtained using next generation sequencing compared to traditional cultures during IPP revision surgery. Consequently, this may lead to better prevention and/or better guide treatment of postoperative IPP infection in the setting of IPP replacement. Although, further studies are needed prior to universally adopting this modality. Disclosure Yes, this is sponsored by industry/sponsor: MicrogenDx. Clarification Industry funding only - investigator initiated and executed study. Any of the authors act as a consultant, employee or shareholder of an industry for: MicrogenDx.

Utilization of Next-Generation Sequencing in Conjunction With Immunohistochemistry to Predict Exceptional Response to Combination Immune Checkpoint Therapy in a Heavily Pretreated Patient With Castration-Resistant Prostate Cancer.

Utilization of Next-Generation Sequencing in Conjunction With Immunohistochemistry to Predict Exceptional Response to Combination Immune Checkpoint Therapy in a Heavily Pretreated Patient With Castration-Resistant Prostate Cancer.

Current trends and insights on EMS mutagenesis application to studies on plant abiotic stress tolerance and development.

Ethyl methanesulfonate (EMS)-induced mutagenesis is a powerful tool to generate genetic resource for identifying untapped genes and characterizing the function of genes to understand the molecular basis of important agronomic traits. This review focuses on application of contemporary EMS mutagenesis in the field of plant development and abiotic stress tolerance research, with particular focuses on reviewing the mutation types, mutagenesis site, mutagen concentration, mutagenesis duration, the identification and characterization of mutations responsible for altered stress tolerance responses. The application of EMS mutation breeding combined with genetic engineering in the future plant breeding and fundamental research was also discussed. The collective information in this review will provide good insight on how EMS mutagenesis is efficiently applied to improve abiotic stress tolerance of crops with the utilization of Next-generation sequencing (NGS) for mutation identification.

Identification of novel exonic variants contributing to hereditary breast and ovarian cancer in west Indian population

Breast and ovarian cancers are the most common cancer types in females worldwide and in India. Patients with these cancers require an early diagnosis which is essential for better prognosis, treatment and improved patient survival. Recently, the utilization of next-generation sequencing (NGS)-based screening has accelerated molecular diagnosis of various cancers. In the present study, we performed whole-exome sequencing (WES) of 30 patients who had a first or second-degree relative with breast or ovarian cancer and are tested negative for BRCA1/2 or other high and moderate-risk genes reported for HBOC. WES data from patients were analyzed and variants were called using bcftools. Functional annotation of variants and variant prioritization was performed by Exomiser. The clinical significance of variants was determined as per ACMG classification using Varsome tool. The functional analysis of genes was determined by STRING analysis and disease association was determined by open target tool. We found novel variants and gene candidates having significant association with HBOC conditions. The genes identified by exomiser (phenotype score > 0.75) are associated with various biological processes such as DNA integrity maintenance, transcription regulation, cell cycle regulation, and apoptosis. Our findings provide novel and prevalent gene variants associated with the HBOC condition in the West Indian population which could be further studied for early diagnosis and better prognosis of HBOC.

Utilization of next generation sequencing (NGS) in stage IV gastrointestinal (GI) cancer patients (pts) and efficacy of electronic reminder notification (ERN) in improving utilization of NGS in the private practice community-based setting.

73 Background: NGS testing allows for identification of genetic mutations/alterations that can be important in determining treatment options for advanced cancer pts. The National Comprehensive Cancer Network (NCCN) includes NGS testing as part of standard of care for many tumor types including stage IV pancreatic cancer, colon cancer, and rectal cancer and all other GI solid tumor types. Previous reports have described the utilization of NGS in clinical practice at academic centers. To our knowledge this is the first report in the private practice setting. Methods: For the historical portion, we established baseline data to quantify NGS testing frequency in stage IV GI tumor pts in our community based oncology practice by performing a retrospective chart review. In the prospective portion, the intervention of an ERN was used to alert treating physicians if NGS had not been done. Primary endpoint is the percent (%) of pts with NGS sent compared to historical control. Secondary endpoint is the % of pts with targeted therapy options made available to them. Results: In a private practice multi-office setting, 200 charts of pts with stage IV GI cancer using Flatiron’s OncoEMR software were reviewed for the retrospective cohort between July 1 to December 31, 2020. Of the 200, 44.5% (89 pts) had colon cancer, 17.5% (35 pts) had pancreatic cancer, 15% (30 pts) had rectal cancer, and 23% (46 pts) had other types of GI cancer. Of these, 87 (43.5%) pts had NGS testing; of which 41 of 89 (46.0%) are colon pts, 13 of 35 (37.1%) are pancreatic pts and 16 of 30 (53.3%) are rectal pts. For the prospective portion, between July 1 and August 15, 2021 each physician’s schedule was evaluated and an ERN was sent shortly before each Stage IV GI pt was to be seen. A total of 114 pts were reviewed, and 92 (79%) had NGS sent. Of these, 47 pts of 54 (87%) are colon pts, 12 of 15 (80%) are pancreatic pts, 16 of 21(76%) are rectal pts, and 17 of 24 (70%) are pts with other GI cancer. 2% of pts with NGS testing had a potentially actionable mutation identified. Conclusions: NGS testing is standard of care for pts with stage IV GI cancer that wish to pursue therapy. ERN was minimally helpful in increasing NGS testing. This may be in part due to the effect of the practice's emphasis on NGS testing, which increased its baseline prospective testing rate. Increased use of a team based approach in the office would be a key element to increasing compliance with the current workflow as well as use of pathways which embed the NGS testing into the treatment plan. A more robust EMR would also be vital in increasing NGS testing rates by the use of automatic reminders or order sets. Better support of the physician and use of multiple touch points is necessary until full automation is utilized for NGS testing.

Whole-exome sequencing identified a novel mutation in CHM of a Chinese family

Choroideraemia (CHM) is a rare X-linked progressive-inherited retinal disease. In this study, we diagnosed and explored the genetic cause in a Chinese pedigree exhibiting nyctalopia and decreased visual acuity in early life. Clinical data and peripheral blood samples were collected from available family members. Sanger sequencing of RPGR and RP2 genes, and subsequently whole-exome sequencing was carried out to investigate the molecular cause. The proband was initially diagnosed as retinitis pigmentosa and experienced night blindness at an early age and decreased visual acuity in teens. The other affected males in this family suffered from the same problem. Direct sequencing failed to reveal the genetic cause and hence a novel hemizygous mutation c.861_862insGCTT was detected by WES in CHM gene resulting in a premature stop codon and a truncated protein. Subsequently, it was confirmed by Sanger sequencing and cosegregation analysis. We describe a novel mutation c.861_862insGCTT in CHM gene in a Chinese pedigree with choroideraemia. Our study emphasizes the utilization of next-generation sequencing in the diagnosis and genetic analysis of retinal diseases.

Association Between Medicare's National Coverage Determination and Utilization of Next-Generation Sequencing.

In 2018, Medicare issued a national coverage determination (NCD) providing reimbursement for next-generation sequencing (NGS) tests for beneficiaries with advanced or metastatic cancer and no previous NGS testing. We examined the association between NCD implementation and NGS utilization trends in Medicare beneficiaries versus commercially insured patients. This was a retrospective study of patients with advanced non-small-cell lung cancer (aNSCLC), metastatic colorectal cancer (mCRC), metastatic breast cancer (mBC), or advanced melanoma with a de novo or recurrent advanced diagnosis from January 1, 2011, through December 30, 2019, using a nationwide US electronic health record-derived deidentified database. Patients were classified by insurance and by advanced diagnosis date. NGS testing was assessed by receipt of first NGS test result ≤ 60 days of advanced diagnosis. Interrupted time series analysis assessed NGS utilization pre- and post-NCD effective date by insurance type. The utilization and repeat NGS testing analysis included 70,290 and 4,295 patients, respectively. Use of NGS rose from < 1% in 2011 to > 45% in Q4 2019 in aNSCLC while remaining < 20% in mBC and advanced melanoma. Among patients with aNSCLC, mCRC, or mBC, NGS testing increased post-NCD versus pre-NCD (P < .05). There was no significant difference in trends pre- and post-NCD between Medicare beneficiaries and commercially insured patients in any tumor. Repeat NGS testing was similar before the NCD (Medicare v commercial: 24.8% v 28.5%). Post-NCD, fewer Medicare beneficiaries had repeat NGS testing (27.7% v 36.0%; P < .01). Trends in NGS utilization significantly changed post-NCD, although the magnitude of change was not significantly different by insurance type, indicating private insurers may also be incorporating NCD guidance. Implementation of the NCD may have limited use of repeat NGS testing in Medicare beneficiaries.

EP444 - Utilization of next generation sequencing to characterize duplications identified through chromosomal microarray

eP444 - Utilization of next generation sequencing to characterize duplications identified through chromosomal microarray

Next-Generation Sequencing Reveals a Novel Emaravirus in Diseased Maple Trees From a German Urban Forest.

While the focus of plant virology has been mainly on horticultural and field crops as well as fruit trees, little information is available on viruses that infect forest trees. Utilization of next-generation sequencing (NGS) methodologies has revealed a significant number of viruses in forest trees and urban parks. In the present study, the full-length genome of a novel Emaravirus has been identified and characterized from sycamore maple (Acer pseudoplatanus) – a tree species of significant importance in urban and forest areas – showing leaf mottle symptoms. RNA-Seq was performed on the Illumina HiSeq2500 system using RNA preparations from a symptomatic and a symptomless maple tree. The sequence assembly and analysis revealed the presence of six genomic RNA segments in the symptomatic sample (RNA1: 7,074 nt-long encoding the viral replicase; RNA2: 2,289 nt-long encoding the glycoprotein precursor; RNA3: 1,525 nt-long encoding the nucleocapsid protein; RNA4: 1,533 nt-long encoding the putative movement protein; RNA5: 1,825 nt-long encoding a hypothetical protein P5; RNA6: 1,179 nt-long encoding a hypothetical protein P6). Two independent NGS sequencing runs from the same symptomatic maple tree detected the same genome segments. For one of these sequencing runs the cDNA library was prepared using a primer targeting the conserved genome terminal region, known to be shared between emaraviruses genome segments. We suggest, therefore, that the six identified genome segments represent the complete genome of a novel emaravirus from maple, which we tentatively name maple mottle-associated virus (MaMaV). Phylogenetic and sequence homology analyses place this virus on the distinct “subgroup a” clade within the Emaravirus genus along with – among others – rose rosette virus, Actinidia emaravirus 2, and fig mosaic virus. Validation RT-PCR assays performed on symptomatic and non-symptomatic trees suggest that MaMaV may be the symptom-inducing virus in the diseased trees. To our knowledge, this is the first time an Emaravirus is described from maple and is fully genetically characterized. With the discovery of MaMaV, the genus Emaravirus comprising negative-sense single-stranded viruses with very divergent genomes – that were until recently overlooked – has substantially increased counting 22 established and putative members.

Utilization of next generation sequencing in ovarian and endometrial cancers at a single institution

Objective: An increasing number of targeted therapies have been approved by the FDA for gynecologic malignancies. The expanded availability of affordable next-generation sequencing has allowed for widespread tumor testing for pathogenic mutations. We sought to describe the most frequent genetic mutations associated with common histologic subtypes of a selected cohort of ovarian and endometrial cancer patients at a single large academic medical center.

A precision medicine approach to management of acute myeloid leukemia in older adults.

Therapy selection in older adults with acute myeloid leukemia (AML) can be challenging because of a higher incidence of high-risk cytogenetic and molecular features conferring chemoresistance and poor functional status leading to increased treatment-related toxicities. The purpose of this review is to highlight the recent advances in precision medicine in AML that have shown promise to improve outcomes of older adults. The utilization of next generation sequencing to identify and target actionable mutations can influence therapy selection in one-third of patients and can result in higher response rates as well as survival compared with those who do not receive targeted therapy. Oral targeted agents are available for AML with IDH 1, IDH2, or FLT3 mutations. Low-intensity venetoclax-based regimens have shown high rates of responses in AML, particularly among those with NPM1 and IDH2 mutations; responses are often durable and associated with minimal residual disease (MRD) negativity. Multiple studies have demonstrated the prognostic significance of flow cytometric MRD, with potential implications for subsequent therapy. Novel approaches for AML risk-stratification, MRD assessment, and a precision medicine approach offer significant promise to improve survival and quality of life of older adults.

Novel Treatment Paradigms in Acute Myeloid Leukemia.

Acute myeloid leukemia (AML) is a heterogeneous disease marked by the presence of several driver mutations and molecular subgroups even in a single patient. The genetic and molecular heterogeneity is also reflected by a progressive shift from a morphologic classification to one informed by causative genomic changes. Cytogenetic results and somatic mutations are increasingly being utilized to guide use of intensive chemotherapy and low-intensity chemotherapy, particularly among older adults. Utilization of next-generation sequencing in AML has led to increasing use of targeted treatments for actionable mutations. Quantitative real-time polymerase chain reaction-based mutational analysis and multicolor flow cytometry offer sensitive assays that can detect minimal residual disease (MRD). Several studies have shown that MRD negativity, as defined by specified cutoff values, is highly prognostic with potential therapeutic implications. The last 3years mark an unprecedented history in the drug development in AML with approval of 8 new drugs and large portfolio of ongoing early and late-phase trials of several promising drugs. Multiple combinatorial trials of approved agents and approval of newer agents in the future will continue to change the therapeutic landscape of AML.

Utilization of next-generation sequencing and associated systemic therapy initiation in metastatic prostate cancer.

e19308 Background: There is emerging evidence for using clinical genomic classifiers for prognostication and to guide treatment choice in metastatic prostate cancer (mPC). While clinical-grade next generation sequencing (NGS) tests are increasingly available, how NGS has impacted systemic therapy selection for mPC is unclear. Methods: We performed retrospective observational study using the nationwide US Flatiron Health EHR-derived de-identified database. We identified patients with mPC diagnosed between January 1, 2013 and September 31, 2019. Receipt of NGS testing was chart-confirmed. “Short-interval” systemic therapy initiation in association with NGS testing was defined as line of therapy start within 30 days of documented NGS test result date. Results: A total 11548 mPC patients were included in our cohort, of which 1034 patients (8.9%) had documented NGS after metastatic diagnosis. There were 1210 documented NGS tests total, with 146 (14.1%) patients documented as undergoing NGS testing on more than one occasion. Median time from metastatic diagnosis to initial NGS test results was 560 days (IQR 194 to 1016 days). NGS test documentation increased from 7.1% of cases diagnosed in 2013 to 12.1% of cases diagnosed in 2017 (p &lt; 0.001). A new line of systemic therapy was initiated within 30 days for 207 NGS test results (17.1%). Although the percent of NGS tests associated with short-interval initiation of a new line of therapy increased from 11.1% in 2013-2014 to 16.5% in 2018-2019, the difference was not statistically significant (p = 0.540). The most common systemic therapies initiated within 30 days after NGS testing were docetaxel (18.8%), cabazitaxel (16.8%), and abiraterone (15.4%). Conclusions: While there has been an increase in documented NGS tests in mPC, rates of short-interval systemic therapy initiation after NGS did not change significantly from 2013-2019. Further study is needed as to whether this will increase in years to come, as well as potential improvements in clinical outcomes due to therapy change.