bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methylated ctDNA as a biomarker for detecting previously undetectable clinically significant somatic mutations.
Authors: Ye Patrick Peiyong , Woodward Brian D. , Langpap Sydne , Viens Robb , Shelburne Katherine , Zhou Wen , Zhu Joyce , Wignall Jan , Searle Naomi , Varga Matthew Gordon , Palmer Gary A. , Tsao David , Atay Oguzhan , Husain Hatim 
Published: June 2023

e15020 Background: Treatment selection liquid biopsies can be re-run upon clinical progression to identify the new clinically significant somatic mutations that might be contributing to resistance to therapy or that can help guide the selection of an alternative therapy. However, there are not currently any biomarkers or tests that suggest an increased likelihood for the detection of new, i.e. previously undetected, clinically significant somatic mutations in a subsequent treatment selection liquid biopsy assay. Methods: We explored whether a methylation-based liquid biopsy could indicate when new clinically significant alterations are more likely to be detected in a treatment selection liquid biopsy. As part of a retrospective study of metastatic lung cancer patients (N = 75 new treatment starts), both a treatment selection assay and a therapy monitoring methylation assay were performed on plasma collected pre-treatment for a subset of patients that underwent at least two separate treatment regimens. By quantifying the number of methylated ctDNA molecules at > 500 genomic locations, the methylation assay assessed the total burden of methylated ctDNA (represented as tumor methylation score), as well as the percent of methylated molecules originating from newly methylated genomic loci, representing a change in the methylation profile. Results: When the methylation assay detected at least a 2x increase in the tumor methylation score, indicating a significant increase in the fraction of ctDNA present in the patient’s blood, new clinically significant somatic mutations (including actionable ERBB2 alterations) were found 83% of the time. This appeared to be more frequent than among patients without an increase in tumor methylation score, where new clinically significant somatic mutations were found 33% of the time. Importantly, when the increase in the methylation score was coupled with a significant change in the methylation profile, new clinically significant mutations were identified in 100% of patients. Conclusions: The preliminary data suggests that an overall increase in methylated ctDNA, in combination with a significant change in methylation profile, is correlated with detecting new, previously undetected clinically significant somatic mutations in a treatment selection assay. Leveraging this methylated ctDNA assay may inform clinicians as to when to run another treatment selection assay, thereby potentially identifying the appearance of clinically significant somatic mutations which could influence clinical decision making and affect patient clinical outcomes.
A next-generation sequencing methylation assay for sub-typing small cell lung cancer in cell-free DNA.
Authors: Huang chung-Ying , Berkebile Ashley D. , Parker Allison , Hernandez Jennifer , Meacham Frazer , Garg Kavita , Guo Jiannan 
Published: June 2023

e15021 Background: Liquid biopsy provides an easy access and minimally invasive technique to inform cancer patient management in clinics as well as clinical trials. Detecting genomic alterations in circulating tumor DNA (ctDNA) has demonstrated clinical utility and actionability in therapy selection and longitudinal monitoring. The development of a comprehensive assay that provides multi-omic information is imperative to expand the utility of liquid biopsy. Methods: Agilent Resolution ctDNA diagnostic assays can detect all four major types of actionable genomic alterations for cancer patients: SNVs, Indels, fusions, and CNVs. The Agilent Resolution ctDx FIRST assay has recently been approved by the FDA as a companion diagnostic assay for non-small cell lung cancer (NSCLC). Applying the same core technology, we developed an additional assay that enables methylation profiling in cfDNA. The custom methylation-specific panel targets informative regions to detect tumor signals and potentially profile the disease by subtype. Recent reports suggest that small cell lung cancer (SCLC) may be stratified into subtypes based on gene expression, including that of ASCL-1, NEUROD1, and POU2F3. We used the proposed SCLC subtyping model to test the feasibility of subtyping SCLC by cfDNA methylation profiles. A baseline methylation profile was established using cell-free DNA from healthy donors. Test samples included genomic DNA from SCLC cell lines and plasma samples of SCLC patients with matching tissue, where available. Results: We applied a methylation-specific bioinformatic pipeline that generates error-corrected unique molecules. The methylation workflow showed unique coverage comparable to our ctDx assay and produced consistent results from input DNA as low as 1ng. We found consistent methylation patterns in cfDNA among healthy donors. SCLC cell lines showed distinct profiles that could be classified into sub-types. When spiked into healthy donor cfDNA background, the tumor signals were distinguishable down to ~0.5%. Plasma samples from SCLC patients showed profiles consistent with that of SCLC sub-types defined by cell lines. Matching plasma and tissue samples produced concordant sub-typing results, supporting the feasibility of disease subtyping in both sample types. Samples were also tested by a custom SCLC panel to analyze genomic alterations. Prevalent variants in SCLC were detected, including SNVs in TP53, PIK3CA, RB1, and MYC amplifications. Conclusions: We showed a cfDNA methylation profiling platform that could support disease sub-typing for SCLC. This platform has great potential in disease stratification and patient management.
Somatic hereditary gene panel analysis: A pilot study from Uzbekistan.
Authors: Olimova Zilola Avazovna 
Published: June 2023

e15044 Background: Molecular diagnostics is gaining importance in routine clinical practice. Availability of actionable genetic changes in hereditary panel of genes has acquired even larger interest. This study is an attempt evaluate the limited somatic genetic alterations in small population of Uzbek patients. Methods: Somatic tumor sample material was analyzed using FOUNDATIONONER CDx (F1CDx) - the NGS based in vitro diagnostic device for detection of substitutions, insertion and deletion alterations(indels), and copy numbers alterations (CNAs) in 324 genes and select gene rearrangements, as well as genomic signatures. Our focus of hereditary panel included following genes-TP53, CDH1, PTEN, STK11, PALB2, CHEK2, ATM, NBN, BARD1, BRCA1 and BRCA2. Results: Out of 76 patients analyzed 50 were found have at list one abnormal gene from the above hereditary panel. TP53 was frequent pathogenic mutation in 50 of 76 patients. Commonest hereditary gene alterations were seen in ATM gene -12/50(6%). BRCA2 mutations existed in 7 of 50(3,5%), PTEN – 6/50(3%), PALB-2 – 4/50(2%), CHEK-2 – 5/50(2,5%), NBN – 5/50(2,5%), STK11 – 3/50(1,5%), CDH1 – 2/50(1%), BRCA1-2(1%), BARD1 – 1/50(0,5%). Some patients had multiple gene combinations. One of the patients had four gene abnormality-PTEN, PALB2, CHEK2, and BRCA2.Three patients have 3(1,5%) somatic hereditary mutations, 23(11,5%) patients have two abnormal hereditary genes and 38(19%) patients had changes in single gene only. Important actionable mutations (BRCA, PALB2 and CHEK2 were found in 15(11,4%) patients. Conclusions: This is the first exploratory analysis of somatic hereditary multi-gene panel. About 11% of the patients were found to have actionable gene mutations.
Health equity challenges facing testing, evaluation, and implementation of multi-cancer early detection tests.
Authors: LeBeau Michelle M. , Kessler Larry , Guerra Carmen , Krofah Esther , Brain Kate 
Published: June 2023

e15051 Background: The development of Multi Cancer Early Detection markers may herald a new approach to screening and detection of multiple cancers simultaneously via various biological assays. At each stage of development and evaluation of these tests, and especially at implementation, challenges to ensuring equitable access to advancements in cancer prevention, screening, diagnosis, and treatment arise. Diverse research study populations and methods are key when investigating the efficacy of screening tools in practice. Health equity encompasses all parts of research study and design, particularly increasing diversity in research study populations and methods to reflect intended populations of study and document how MCEDs may impact demographic groups differently. Methods: The MCED Consortium is a not-for-profit group of volunteers, advisors, and companies from the US and the UK spanning a wide range of expertise in biomarker evaluation and implementation, with a special focus on clinical practice, health equity, and communication ( https://www.mced.info/ ). We are developing recommendations for the evaluation of test utility, appropriate prioritized populations for screening or early detection, downstream actions in health systems, achieving health equity, and addressing the communication challenges related to this new, potentially revolutionary generation of tests. Results: The MCED consortium has made recommendations in the domains of investigator, participant level, and study design features. The Consortium also has identified key questions for MCED researchers and users regarding equitable access, acceptance, and follow-up. An emerging challenge relates to the release of these tests to selected populations via the laboratory-developed test pathway; which will almost certainly disproportionately increase access to insured and higher socioeconomic status populations. Conclusions: In this MCED Consortium presentation, we will discuss the barriers to ensuring adequate clinical trial diversity and evaluation of MCEDs and how to optimize equity during their current and near-term distribution.
Systematic review and meta-analysis of accuracy of tumor origin detection in blood cell-free DNA (cfDNA)-based multi-cancer early detection (MCED) assays in the general population.
Authors: Park Joo Hee , Oh Youjin , Chung Liam Il-Young , Duan Richard , Djunadi Trie Arni , Yoon Sung Mi , Shah Zunairah , Jung Chan Mi , Hong Ilene , Kim Leeseul , Choi Horyun , Chae Young Kwang 
Published: June 2023

e15053 Background: Among recently developed blood-based MCED tests, the ability to determine the location of tumors is pivotal to guiding appropriate treatment. We systematically reviewed and statistically examined the accuracy of tumor of origin predictions among blood-based MCED tests. Methods: Original articles were searched from Pubmed, Cochrane, and Embase for blood-based screening tests, multiple cancer types, and asymptomatic human subjects. We excluded studies with small samples (n < 30), non-screening, and non-blood-based tests. For cfDNA-based assays, measurements of diagnostic accuracy were pooled for meta-analysis. Results: Of 1,074 records identified and screened, five case-control studies and one cohort study that used cfDNA-based diagnostic tests were analyzed. Accuracy of tissue-of-origin (TOO) prediction for 3,895 cancer samples across cancer types was 0.79 (95% CI 0.66 - 0.90). Among six cancer types, colorectal cancers had the highest accuracy and liver & bile duct cancers had the lowest, although the difference was statistically insignificant (0.89 (95% CI 0.79-0.97) vs. 0.68 (95% CI 0.40-0.90)). Additionally, cases were most frequently misclassified as colorectal cancer (Table 1). The information for localizing TOO was derived from methylation patterns of cfDNA in four studies, fragmentation profiles of cfDNA in another study, and combination of mutations in cfDNA and protein markers in the last study. Conclusions: Our results demonstrate that the primary site of cancers was accurately discerned in 79% of cases by MCED tests. However, performance varies across cancer types. Further research on performance based on cancer stages and in combination with other molecular profiling is warranted. [Table: see text]
Feasibility and clinical utility of cancer whole-genome sequencing in adult solid tumors.
Authors: Kwon Minsuk , Kim Ryul , Oh Baek-Lok , Kim Seokhwi , Roh Jin , Hur Hoon , Yu Woo Sik , Kim Chang Woo , Lee Jeong Seok , Ju Young Seok 
Published: June 2023

e15055 Background: As sequencing costs decrease, whole-genome sequencing (WGS) is expected to be utilized in actual cancer patient care. However, there is insufficient evidence that WGS can be applied to the real-world cancer patient care, and how it can help in the diagnosis and treatment process. Methods: This prospective cohort study was designed to evaluate the feasibility and clinical utility of WGS in adult solid cancer care at a tertiary hospital. All solid cancer patients who were scheduled to undergo biopsy or surgery for diagnosis or treatment were eligible for the study. Either fresh or formalin-fixed paraffin-embedded tissue with match peripheral blood were obtained. Tumors were sequenced to depth of 40x, and WGS data were curated by Genome Insight Inc. The WGS reports were provided to clinician through a web-based, user-browsable reporting system in real time. Results: 97 patients were enrolled between Sep 2022 and Jan 2023. Besides 10 QC failed cases, 87 patients were provided WGS reports. Median turn-around-time was 14 day (range 12-23). The clinical utility of WGS was evaluated in 77 cancer patients, excluding 10 cases with estimated cancer cell fraction less than 15%. 31 patients (40.3%) had more than one actionable alteration targeted by on-label drugs. 49 patients (63.6%) also had more than one actionable alteration targeted by either on-label or off-label drugs. In selected cases (N = 6), WGS could suggest the diagnosis for cancer of unknown origin or the revision of pathologic diagnosis that was regarded as a double primary cancer into a metastasis of a single cancer. By providing information of total mutation counts, whole-genome-wide mutational signature analysis, copy number variation with high accuracy, germline alterations, detection of homologous recombination deficiency, and presence of loss-of-heterozygosity, WGS could further refine the actionable mutations in 39% cases, and estimate the etiology of cancer (genomic or environmental) or to determine hereditary or sporadic cancer in 60% cases. In 90% cases, WGS demonstrated clinical utility with supporting diagnosis, informing carcinogenesis, or annotating actionable alterations. Conclusions: WGS was applicable in real-world cancer care. WGS demonstrated clinical utility in the diagnosis and treatment of adult cancer patients. Clinical trial information: KCT0008118 . [Table: see text]
Physician-reported barriers and strategies to using tumor mutational burden (TMB) testing in oncology care: An interview based study.
Authors: Jones Gieira S , Szamreta Elizabeth A. , Lee Liam , Iyer Radhika , Jackson Bianca , Ning Ning , Stephens Jennifer , Hussain Arif 
Published: June 2023

e15063 Background: Despite the availability of genomic technologies to inform treatment for oncology patients, widespread adoption of genomic testing in the U.S. has been challenging. Little information is available about the factors that influence clinical decision making regarding the use of TMB testing. The purpose of this study was to identify barriers to the adoption of TMB testing and preferred strategies to increase testing from the physician’s perspective. Methods: Semi-structured video-based interviews were conducted with a sample of U.S. physicians (N = 11), including 6 general medical oncologists, 3 surgical oncologists, and 2 gynecologic oncologists. Physicians were asked about practice characteristics, perceived barriers to testing, and potential strategies for alleviating these barriers. Results: Eighty-two percent (N = 9) of physicians reported utilizing TMB testing in their routine clinical practice. Reimbursement was the most commonly reported barrier (64%) including coverage policy language indicating the testing as “experimental”/“unproven”, patients having to pay out of pocket, and unclear/inconsistent payer policies (27% each) [Table 1]. Knowledge, resource-related, and logistical barriers were reported among the same proportion of physicians (45%). Suggested strategies to improve TMB testing uptake rates among physicians included better understanding of clinical utility of the test and corresponding therapies, integrating results into electronical medical records, incorporating TMB into routine testing, and shorter turnaround time for results. Conclusions: This qualitative study of physicians identified barriers to TMB testing of oncology patients. Results suggest that challenges around reimbursement, knowledge, resources, and logistics are key barriers to use of TMB testing for physicians. The findings of this study provide insights for future research and strategies to increase the adoption of TMB testing. [Table: see text]
Characterizing non-small cell lung cancer driven by mutations in ARAF and CRAF family members.
Authors: Okimoto Tamio , Amann Joseph , Elliott Andrew , Liu Stephen V. , Ma Patrick C. , Vanderwalde Ari M. , Radovich Milan , Sledge George W. , Coppola Vincenzo , Carbone David Paul 
Published: June 2023

e15085 Background: Cancer genome screening is becoming standard clinical practice, but the number of actionable mutations detected is limited. To expand on our previous report of the possibility that ARAF S214C and CRAF S257L located in the conserved region 2 (CR2) were actionable driver mutations, we investigated responses to targeted therapies in mouse models and the prevalence of these alterations across many cancer types represented in a large real-world database of molecularly profiled patient tumors. Methods: Conditional transgenic mice that expressed human ARAF S214C or CRAF S257L in their lungs were established and treated with sorafenib or trametinib. Activation of the MAPK pathway following sorafenib or trametinib treatment was assessed in vitro by phospho-ERK IHC. DNA sequencing (592-gene or whole exome) was performed for patient samples submitted to Caris Life Sciences (Phoenix, AZ), and the prevalence of ARAF/CRAF variants was determined for each cancer type. Results: Both ARAF S214C and CRAF S257L dimerized to activate the MAPK pathway. Although a low concentration of sorafenib promoted ERK phosphorylation, a high concentration of sorafenib inhibited ERK phosphorylation. Transgenic mice rapidly developed lung adenocarcinoma when the mutant proteins were expressed. Sorafenib treatment induced tumor necrosis in both ARAF- and CRAF-mutated tumors, and 3 months of sorafenib treatment prolonged the survival of CRAF-mutant mice. Pan-tumor analysis of real-world patient samples revealed that ARAF and CRAF mutations in CR2 were found in 0.125% and 0.234% of tumors, respectively. ARAF mutations in CR2 were found in 0.415% of cholangiocarcinoma, 0.132% of colorectal cancer, and 0.173% of non-small cell lung cancer (NSCLC). CRAF mutations in CR2 were found in 0.509% of colorectal cancer, 0.502% of gastric cancer, 0.303% of NSCLC, and 0.978% of melanoma. The most prevalent CR2 mutations were ARAF S214F and CRAF S257L. Conclusions: Our in vitro results suggest ARAF S214C and CRAF S257L mutations are rare driver mutations that may be effectively treated with RAF inhibitors and warrant further investigation. [Table: see text]
Single-stranded linear amplification library preparation method for highly sensitive and low input amount ctDNA detection.
Authors: Hu Juan , Chen Meihong , Li Zihao , Xiao Shanshan , Wang Tao 
Published: June 2023

e15096 Background: Detection of circulating tumor DNA (ctDNA) or minimum residual disease (MRD) through somatic variant identifications in plasma samples has emerged as a promising approach for monitoring the clinical outcomes after surgical resections or other therapies. However, due to very low ctDNA levels in the early-stage cancers and tumor remissions after therapies, or low plasma volumes and DNA degradation caused low qualities in clinical practice, to sensitively identify somatic mutations with low allele frequencies in those samples remains a challenging technology task. Methods: In this study, we developed a single-stranded, linear amplification based library preparation sequencing (SLA-Seq) method. In the experimental workflow, double stranded molecular templates will be converted into single strands to construct libraries, thus minimize the loss of irregular double stranded DNA molecules. Adapter ligation was carried out in two steps. During the first step, P7 adapters with unique molecular identifiers(UMI) were ligated to the 3’ end of the molecular templates, and the DNA molecules were amplified by linear amplification to improve the DNA utilization efficiency. In the second step, P5 adapters were ligated to the linear amplified PCR products, then amplified by the pre-PCR. The pre-library was enriched by hybridization and magnetic-beads capturing and then subjected to high-throughput sequencing. 30ng of the cfDNA reference standard samples containing mutations of 0.3% and 0.1% allele frequencies were used to validate the performance. Results: In the SLA-Seq method, adapter sequences were carefully optimized to eliminate adapter dimers and thus improved the DNA ligation efficiency. Compared with the double-stranded library preparation method, SLA-seq showed overall higher effective depths after removing duplications if the same start amount of the DNA was used, which indicated that the higher DNA utilization rate was achieved. To evaluate the performance, we applied SLA-Seq on 11 reference standard samples with only 30ng start amount DNA. Among them, 6 samples were diluted to 0.3% allele frequency and 5 samples were diluted to 0.1% allele frequency. Totally they had 24 and 35 mutations, respectively. The sensitivity at the 0.3% allele frequency was 100% (24/24) and it was 94.29% (33/35) at the 0.1% mutation level, which also showed the higher sensitivity achieved by SLA-Seq than double-stranded library preparation method. Conclusions: We developed a single-stranded, linear amplification based library preparation method to improve difficult sample situations such as low input amount and low qualities, and achieved high single site sensitivity at the 0.1% allele frequency. Such features imply SLA-Seq has important clinical significance in the ctDNA/MRD detection.