DNA Database Research Articles

Ethical considerations for Forensic Genetic Frequency databases: First Report conception and development

The Forensic Databases Advisory Board (FDAB), an independent board that assists the International Society for Forensic Genetics (ISFG), has presented a First Report on ethical aspects of the following Forensic Genetic Frequency Databases (FGFD): EMPOP, STRidER and YHRD. The FDAB designed an ethical framework to evaluate the content of these FGFD, and the factors to be considered for retention and acceptance of submissions. The FDAB framework proposes to categorize submissions according to the risk of having contravened the universal ethical principles outlined by international organizations, and the guidelines adopted by the ISFG. The report has been open to discussion by the scientific community since 2023. Herein we present the conception and development of the First Report along with a summary of its content, with consideration of the feedback received.

Forensic genetics associated with hair analysis as a tool for jaguar (Panthera onca) identification

Animal smuggling and illegal wildlife trade comprise one of the most common crimes being committed on an international level. This action can affect biodiversity and most certainly increases the risk of extinction of several endangered species. Wildlife taxonomic identification is becoming routine to forensic experts. The aim of this study was to identify a possible jaguar sample (Panthera onca Linnaeus, 1958) from legal evidence using hair morphology and mitochondrial DNA (mtDNA) to help in an official animal identification. Scanning and optical microscope images of hair samples were used to compare diagnostic characteristics of felines to reference studies. A preserved region, (cytochrome oxidase subunit 1 (COI)), from mtDNA was sequenced and compared to a DNA database (GenBank) to perform genetic identification. Forensic genetic and hair analysis techniques combined positively identified the sample as jaguar. These methods can help practitioners and forensics experts to identify evidence collected in wildlife crimes suspected to involve jaguars.

A RANGE-WIDE ECTOPARASITE SURVEY FOR ALLEGHENY WOODRATS (NEOTOMA MAGISTER).

Allegheny woodrats (Neotoma magister) are karst-specializing rodents that are rare or in conservation need in many states within their current range. Parasitism and habitat fragmentation have been suggested as primary reasons for declining populations. The presence, prevalence, and impact of ectoparasites, including fleas, ticks, and bots, is not fully understood rangewide. We collected Allegheny woodrat ectoparasites across 8 states in their range, identifying parasites via morphological and genetic means. Across contributions from 8 states, we discovered 2 woodrat-specific fleas parasitizing Allegheny woodrats: Orchopeas pennsylvanicus (all contributing states, n = 228) and Epitedia cavernicola (Indiana only, n = 9). The former was a new state record in New Jersey and Ohio. Woodrat specialists Ixodes woodi were morphologically identified as the dominant tick species (n = 38), and our contributions to genetic databases may ease confusion in future efforts. Three generalist species of ticks representing 8 individuals were identified as Dermacentor variabilis, Amblyomma americanum, and Ixodes scapularis. Only 2 bot fly species were recognized in Allegheny woodrats: 1 squirrel bot (Cuterebra emasculator) and 10 individuals of Cuterebra sp. not genetically conspecific to any known eastern U.S. rodent bot. The host specificity for fleas is not surprising, given that previous small-scale surveys and ticks primarily appear to be a mix of genus-specific (Ixodes woodi) and generalist species. There remains uncertainty with bots via morphological and genetic analyses. Our survey presents a wide-ranging baseline survey for Allegheny woodrats across their range, emphasizing the diversity (or specificity) of parasite groups for this species. An understanding of Allegheny woodrats and the health impact of ectoparasites is imperative because they face myriad challenges rangewide, especially considering the bot-driven demise of 1 woodrat in our study. Ectoparasites can have a marked impact on already-declining woodrat populations across their range and should not be overlooked in future surveys.

Advancing human genotyping: The Infinium HTS iSelect Custom microarray panel (Rita) development study

Single Nucleotide Polymorphisms (SNPs), as the most prevalent type of variation in the human genome, play a pivotal role in influencing human traits. They are extensively utilized in diverse fields such as population genetics, forensic science, and genetic medicine. This study focuses on the 'Rita' BeadChip, a custom SNP microarray panel developed using Illumina Infinium HTS technology. Designed for high-throughput genotyping, the panel facilitates the analysis of over 4000 markers efficiently and cost-effectively. After careful clustering performed on a set of 1000 samples, an evaluation of the Rita panel was undertaken, assessing its sensitivity, repeatability, reproducibility, precision, accuracy, and resistance to contamination. The panel’s performance was evaluated in various scenarios, including sex estimation and parental relationship assessment, using GenomeStudio data analysis software. Findings show that over 95 % of the custom BeadChip assay markers were successful, with better performance of transitions over other mutations, and a considerably lower success rate for Y chromosome loci. An exceptional call rate exceeding 99 % was demonstrated for control samples, even with DNA input as low as 0.781 ng. Call rates above 80 % were still obtained with DNA quantities under 0.1 ng, indicating high sensitivity and suitability for forensic applications where DNA quantity is often limited. Repeatability, reproducibility, and precision studies revealed consistency of the panel's performance across different batches and operators, with no significant deviations in call rates or genotyping results. Accuracy assessments, involving comparison with multiple available genetic databases, including the 1000 Genome Project and HapMap, denoted over 99 % concordance, establishing the Rita panel's reliability in genotyping. The contamination study revealed insights into background noise and allowed the definition of thresholds for sample quality evaluation. Multiple metrics for differentiating between negative controls and true samples were highlighted, increasing the reliability of the obtained results. The sex estimation tool in GenomeStudio proved highly effective, correctly assigning sex in all samples with autosomal loci call rates above 97 %. The parental relationship assessment of family trios highlighted the utility of GenomeStudio in identifying genotyping errors or potential Mendelian inconsistencies, promoting the application of arrays such as Rita in kinship testing. Overall, this evaluation confirms the Rita microarray as a robust, high-throughput genotyping tool, underscoring its potential in genetic research and forensic applications. With its custom content and adaptable design, it not only meets current genotyping demands but also opens avenues for further research and application expansion in the field of genetic analysis.

Genetic Researchers’ Use of and Interest in Research With Diverse Ancestral Groups

Genetic researchers must have access to databases populated with data from diverse ancestral groups to ensure research is generalizable or targeted for historically excluded communities. To determine genetic researchers' interest in doing research with diverse ancestral populations, which database stewards offer adequate samples, and additional facilitators for use of diverse ancestral data. This survey study was conducted from June to December 2022 and was part of an exploratory sequential mixed-methods project in which previous qualitative results informed survey design. Eligible participants included genetic researchers who held US academic affiliations and conducted research using human genetic databases. Internet-administered survey to genetic research professionals. The survey assessed respondents' experience and interest in research with diverse ancestral data, perceptions of adequacy of diverse data across database stewards (ie, private, government, or consortia), and identified facilitators for encouraging use of diverse ancestral data. Descriptive statistics, χ2 tests, and z tests were used to describe respondents' perspectives and experiences. A total of 294 researchers (171 men [58.5%]; 121 women [41.2%]) were included in the study, resulting in a response rate of 20.4%. Across seniority level, 109 respondents (37.1%) were senior researchers, 85 (28.9%) were mid-level researchers, 71 (24.1%) were junior researchers, and 27 (9.2%) were trainees. Significantly more respondents worked with data from European ancestral populations (261 respondents [88.8%]) compared with any other ancestral population. Respondents who had not done research with Indigenous ancestral groups (210 respondents [71.4%]) were significantly more likely to report interest in doing so than not (121 respondents [41.2%] vs 89 respondents [30.3%]; P < .001). Respondents reported discrepancies in the adequacy of ancestral populations with significantly more reporting European samples as adequate across consortium (203 respondents [90.6%]), government (200 respondents [89.7%]), and private (42 respondents [80.8%]) databases, compared with any other ancestral population. There were no significant differences in reported adequacy of ancestral populations across database stewards. A majority of respondents without access to adequate diverse samples reported that increasing the ancestral diversity of existing databases (201 respondents [68.4%]) and increasing access to databases that are already diverse (166 respondents [56.5%]) would increase the likelihood of them using a more diverse sample. In this survey study of US genetic researchers, respondents reported existing databases only provide adequate ancestral samples for European populations, despite their interest in other ancestral populations. These findings suggest there are specific gaps in access to and composition of genetic databases, highlighting the urgent need to boost diversity in research samples to improve inclusivity in genetic research practices.

Timing of genetic testing in BRCA1/2 and PALB2-Associated breast cancer: Preoperative result disclosure increases uptake of risk-reducing mastectomy and reduces unnecessary exposure to radiotherapy

IntroductionThe impact of timing of genetic testing on uptake of risk reducing mastectomy (RRM) in affected female BRCA1/2 or PALB2 carriers remains an area of evolving interest, particularly with the introduction of mainstream genetic testing initiatives. MethodsWomen with stage I-III breast cancer and a confirmed germline pathogenic variant in BRCA1/2 or PALB2 between 2000 and 2023 were identified from an institutional genetics database. Uptake of RRM was evaluated according to disclosure of genetic testing results before or after index surgery for a first diagnosis of breast cancer. ResultsThe cohort included 287 female BRCA1/2 or PALB2 carriers with a median age of 44 years (IQR, 36–52). Overall, 155 (54 %) carriers received genetic testing results before and 132 (46 %) after index breast surgery. Receipt of genetic testing results before surgery was associated with a higher rate of index bilateral mastectomy (58.7 % vs. 7.6 %, p < 0.001) and a commensurate decrease in adjuvant radiation (41.9 % vs. 74.2 %, p < 0.001). At a median follow up of 4.4 years after genetic testing, 219 (76.3 %) affected carriers had undergone bilateral RRM, including 83.9 % with preoperative knowledge and 67.4 % of patients with postoperative knowledge of their germline pathogenic variant (log rank, p < 0.001). On multivariate regression, disclosure of genetic testing results before index breast surgery was independently associated with long-term uptake of bilateral mastectomy (HR 1.69, 95 % CI 1.21–2.38). ConclusionGenetic testing results delivered prior to index breast surgery increase uptake of bilateral RRM in affected BRCA1/2 and PALB2 carriers. Efforts to mainstream genetic testing would help optimize surgical decision-making.

The Value of Forensic DNA Database

This paper explores the importance and impact of DNA databases in forensic investigations. It responds to a recent publication by Kostiuchenko, Vynohradova, Sereda, Svoboda, and Polunina (2024), highlighting challenges in setting up and using DNA databases. These challenges include logistical, staffing, legal, security, growth, public interest, and international cooperation issues. By examining South Africa's successful NFDD implementation, the authors stress the need for thorough planning and implementing a comprehensive value chain. Drawing insights from South Africa's successful NFDD implementation, the authors emphasise the importance of meticulous planning and implementing a value chain. This value chain should cover DNA evidence collection, follow-up investigations, and presenting evidence in court.

Enhanced pan-genomic resources at the maize genetics and genomics database.

Pan-genomes, encompassing the entirety of genetic sequences found in a collection of genomes within a clade, are more useful than single reference genomes for studying species diversity. This is especially true for a species like Zea mays, which has a particularly diverse and complex genome. Presenting pan-genome data, analyses, and visualization is challenging, especially for a diverse species, but more so when pan-genomic data is linked to extensive gene model and gene data, including classical gene information, markers, insertions, expression and proteomic data, and protein structures as is the case at MaizeGDB. Here, we describe MaizeGDB's expansion to include the genic subset of the Zea pan-genome in a pan-gene data center featuring the maize genomes hosted at MaizeGDB, and the outgroup teosinte Zea genomes from the Pan-Andropoganeae project. The new data center offers a variety of browsing and visualization tools, including sequence alignment visualization, gene trees and other tools, to explore pan-genes in Zea that were calculated by the pipeline Pandagma. Combined, these data will help maize researchers study the complexity and diversity of Zea, and to use the comparative functions to validate pan-gene relationships for a selected gene model.

Hybrid Assembly of Complete Genomes of &lt;I&gt;Yersinia pestis&lt;/I&gt; Strains

The aim of the study was to assemble full-length nucleotide sequences of the chromosome and plasmids for 13 Yersinia pestis strains from 11 natural plague foci located in the Russian Federation, using data from two sequencing technologies.Materials and methods. Y. pestis strains were grown on Hottinger’s agar (pH 7.2) at 37 °C. DNA was isolated using phenol-chloroform extraction. For the MinIon genetic analyzer (Oxford Nanopore), DNA fragments were prepared by ligation according to a modified protocol. For the Ion S5 genetic analyzer (IonTorrent), sample preparation was carried out according to the standard protocol for obtaining a library with a DNA fragment size of 400 nucleotide pairs (bp). The resulting single reads were filtered by average quality Q30 for IonTorrent and Q7 for Oxford Nanopore.Results and discussion. DNA fragments containing 50 000 or more nucleotide pairs were prepared for subsequent sequencing using nanopore sequencing technology (Oxford Nanopore). The Trycycler algorithm was applied for hybrid assembly of the genome of Y. pestis strains and correction of errors arising during this process, allowing the obtainment of full-length nucleotide sequences of the chromosome and plasmids for each genome of the strain. The nucleotide sequences of the chromosomes of 13 Y. pestis strains from 11 natural foci of plague located in the Russian Federation have been deposited in the international genetic database NCBI GenBank. It has been established that to assemble full-length genomes of Y. pestis strains, a significant number of reads with a size of 50 000 bp or more is required, and the use of the Trycycler algorithm allows one to generate a more accurate assembly of complete bacterial genomes.

Establishing forensic DNA databases in Africa.

Establishing forensic DNA databases in Africa.

Genetic polymorphism and frequency study at 15 short tandem repeat loci in the North and East Indian populations for use in personal identification and applications in India

Allele frequency is a crucial factor in estimating the weight of evidence (WoE) for an individual’s involvement in a DNA sample. To determine the allele and genotype frequencies within the populations of the northern and eastern states of India, 15 short tandem repeats (STRs) were used, including Penta E, CSF1PO, D18S51, D7S820, D21S11, TH01, D3S1358, Vwa, FGA, TPOX, D8S1179, D16S539, D13S317, Penta D, and D5S818. The study involved 509 randomly selected individuals, analyzed using the PowerPlex 16 System Kit. Various statistical parameters of forensic significance were calculated using Forensic Statistic Analysis Toolbox (FORSTAT) software, including the typical paternity index (TPI), power of exclusion (PE), matching probability (MP), power of discrimination (PD), polymorphism information content (PIC), and observed (Hobs) and expected heterozygosities (Hexp). The analysis revealed a maximum allele frequency of 0.4282 at TPOX, with a minimum frequency of 0.0009 observed at different loci. FGA was found to be the most polymorphic loci among the 15 loci analyzed in the North and East Indian populations. Furthermore, no divergence from the Hardy‐Weinberg equilibrium (HWE) was observed. The results serve as a valuable source of information for establishing a DNA database for North and East Indian populations, providing essential information for population genetics studies and forensic casework in India.

Public Perspectives on Investigative Genetic Genealogy: Findings from a National Focus Group Study

Background Investigative genetic genealogy (IGG) is a technique that involves uploading genotypes developed from perpetrator DNA left at a crime scene, or DNA from unidentified remains, to public genetic genealogy databases to identify genetic relatives and, through the creation of a family tree, the individual who was the source of the DNA. As policymakers demonstrate interest in regulating IGG, it is important to understand public perspectives on IGG to determine whether proposed policies are aligned with public attitudes. Methods We conducted eight focus groups with members of the public (N = 72), sampled from four geographically diverse US regions, to explore general attitudes and perspectives regarding aspects of IGG practices, applications, and policies. Five major topics were explored in each focus group: when IGG should be used; who should perform IGG; how to approach consent for genetic database users; what systems of oversight should govern IGG practitioners; and whether to notify database users if their data are involved in law enforcement (LE) matching. Results Participants were supportive of IGG in most scenarios, especially for cold and violent cases. The favorable attitudes toward IGG were, however, tempered by distrust of law enforcement among some participants. All participants agreed that databases must inform users if IGG is allowed, but they did not agree on how individual database users should be allowed to opt out or whether to notify them if their data are involved in specific investigations. All participants agreed that IGG should be subject to some prescriptive guidelines, regulations, or accountability mechanisms. Conclusions These findings suggest broad public support for IGG, and interest in developing systems of accountability for its practice. Our study provides useful insight for policy makers, genomic database stewards, law enforcement, and other stakeholders in IGG’s practice, and suggests multiple directions for future research.

The utility of trace DNA within forensic science for investigative and intelligence purposes

AbstractForensic science not only provides evidence to support criminal investigations, but also contributes to knowledge surrounding criminal phenomena. Forensic scientists are in the unique position to strategically combine information gained from traces to create intelligence that can assist the security space in keeping our communities safe. Research into the use of traces for more than just criminal investigations, with a focus on the greater “utility” of a trace, has pointed to the broader problem‐solving potential of traces when more fully exploited. Alongside this, there has continued to be an exponential increase of the use of biological traces for criminal investigations, in particular the collection of trace DNA specimens. The potential for identification, among other information, trace DNA can provide is vast, however much of the previous research has predominately focused on recovery rates which does not provide a holistic view of the value of trace DNA. This paper summarizes the current knowledge on the utility of trace DNA, as well as makes suggestions toward the creation of a decision‐making model that can inform scene of crime officers in regards to trace selection and decisions about trace analysis.This article is categorized under: Forensic Biology &gt; DNA Databases and Biometrics Crime Scene Investigation &gt; From Traces to Intelligence and Evidence

Identification of HDAC9 and ARRDC4 as potential biomarkers and targets for treatment of type 2 diabetes

We aimed to identify the key potential insulin resistance (IR)-related genes and investigate their correlation with immune cell infiltration in type 2 diabetes (T2D). The GSE78721 dataset (68 diabetic patients and 62 controls) was downloaded from the Gene Expression Omnibus database and utilized for single-sample gene set enrichment analysis. IR-related genes were obtained from the Comparative Toxicology Genetics Database, and the final IR-differentially expressed genes (DEGs) were screened by intersecting with the DEGs obtained from the GSE78721 datasets. Functional enrichment analysis was performed, and the networks of the target gene with microRNA, transcription factor, and drug were constructed. Hub genes were identified based on a protein–protein interaction network. Least absolute shrinkage and selection operator regression and Random Forest and Boruta analysis were combined to screen diagnostic biomarkers in T2D, which were validated using the GSE76894 (19 diabetic patients and 84 controls) and GSE9006 (12 diabetic patients and 24 controls) datasets. Quantitative real-time polymerase chain reaction was performed to validate the biomarker expression in IR mice and control mice. In addition, infiltration of immune cells in T2D and their correlation with the identified markers were computed using CIBERSORT. We identified differential immune gene set regulatory T-cells in the GSE78721 dataset, and T2D samples were assigned into three clusters based on immune infiltration. A total of 2094 IR-DEGs were primarily enriched in response to endoplasmic reticulum stress. Importantly, HDAC9 and ARRDC4 were identified as markers of T2D and associated with different levels of immune cell infiltration. HDAC9 mRNA level were higher in the IR mice than in control mice, while ARRDC4 showed the opposite trend. In summary, we discovered potential vital biomarkers that contribute to immune cell infiltration associated with IR, which offers a new sight of immunotherapy for T2D.

Abstract 3903: Discovery of ULBP6 as a novel immuno-oncology target using pleiotropic signals from 23andMe’s genetic and health survey database

Abstract 23andMe has assembled one of the largest platforms for human genetics research that combines genotypes from 14 million individuals, 80% of which are consented to participate in research, with billions of phenotypic data points collected from health survey data. Using these large scale genetic and phenotypic datasets, we have developed a unique target discovery platform that has identified hundreds of pleiotropic genetic variants with opposing directionality of effects in cancer and immune diseases. These immune-oncology (I/O) genetic associations point to already clinically validated immune checkpoint receptors (e.g., CTLA4) and those currently in clinical trials (e.g., CD200R1). This suggests that these I/O genetic associations could be linked to genes that are broadly utilized by tumor cells to evade the immune system and could be used to identify novel therapeutic targets involved in regulating anti-tumor immune response. Here, we utilized expression quantitative trait loci (eQTLs) and annotation of coding single nucleotide polymorphisms (SNPs) to link one of these signals to a causal gene, and identified ULBP6, a stress-induced ligand for the activating immunoreceptor NKG2D found on NK and T cells. ULBP6 is known to be shed from the cell surface of tumor cells to block its interaction with NKG2D to evade immune surveillance. Expression profiling of ULBP ligands in various tumor types using MSD, IHC, bulk and single-cell RNA-seq revealed tumor-intrinsic up-regulation of ULBP6 in squamous cancer subtypes. Collectively, these data suggest that ULBP6 is a promising therapeutic target, and that can potentially enhance anti-tumor immunity. Citation Format: Susanne Tilk, Pierre Fontanillas, Wei-Jen Chung, Clifford Hom, Shi Shi, Anh Diep, Kim Gerrick, Mauro Poggio, Pranidhi Sood. Discovery of ULBP6 as a novel immuno-oncology target using pleiotropic signals from 23andMe’s genetic and health survey database [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3903.

Abstract 2375: 23ME-01473, a novel anti-ULBP6/2/5 monoclonal antibody, reinvigorates anti-tumor NK cell function through NKG2D and FcγRIIIa activation

Abstract Using genome-wide association studies (GWAS) of the 23andMe genetic and healthy survey database across all phenotypes as part of our unique target discovery platform, we identified immuno-oncology (I/O)-related genetic variants as those with opposing directionality of effects on cancer and immunological phenotypes, which comprise the I/O signature. This I/O signature identified ULBP6 as a potential cancer therapeutic target. ULBP6 is a stress-induced cell surface ligand found on cancer cells, that binds to the activating receptor, NKG2D, on NK and T cells to induce tumor cell killing. However, as a mechanism of immune escape, tumors shed ULBP6 to produce a soluble form that attenuates NKG2D activation and is elevated in cancers. Given that the 2 allelic variants of ULBP6 have the highest binding affinity to NKG2D of all human NKG2D ligands, ULBP6 may be the most immunosuppressive soluble NKG2D ligand and a critical regulator of anti-tumor response. Accordingly, soluble ULBP6 exhibited significant suppression of IFNγ release and detectable cell surface NKG2D expression on healthy donor PBMCs using in vitro cell-based assays. Moreover, the overexpression of human ULBP6 in a genetically modified MC38 murine model resulted in decreased infiltration of NK, NKT, and CD8 T cells in vivo. As such, we developed a novel humanized monoclonal antibody, 23ME-01473, that binds with high affinity to ULBP6, and due to the high sequence homology, to ULBP2 and ULBP5, to block their interaction with NKG2D. By preventing the binding of soluble ULBP6 to NKG2D on PBMCs in vitro, 23ME-01473 restored NKG2D activation as measured by increased detectable cell surface NKG2D expression, IFNγ and granzyme B release, and tumor cell killing by PBMCs. To further leverage the binding of 23ME-01473 to ULBP6/2/5, 23ME-01473 was designed to have an afucosylated Fc domain that enhances its binding affinity to the activating Fc receptor, FcγRIIIa, on NK cells to induce ADCC against tumor cells. The combination of NKG2D and FcγRIIIa activation resulted in synergistic PBMC-mediated IFNγ secretion and enhanced tumor cell killing, compared to activation of either NKG2D or FcγRIIIa. Taken together, these results reveal ULBP6 as a novel cancer therapeutic target, and given the dual activation of NKG2D and FcγRIIIa, suggest the potential of 23ME-01473 to activate NK cells and elicit anti-tumor immunity. Citation Format: Joel Benjamin, Abigail Jarret, Shashank Bharill, Shruti Yadav, Dina Ayupova, Clifford Hom, Zahra Bahrami Dizicheh, I-Ling Chen, Anh Diep, Shi Shi, Caroline Bonnans, Danielle Kellar, Germaine Fuh, Maike Schmidt, Kimberline Gerrick, Patrick Koenig, Mauro Poggio. 23ME-01473, a novel anti-ULBP6/2/5 monoclonal antibody, reinvigorates anti-tumor NK cell function through NKG2D and FcγRIIIa activation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2375.

Abstract 2359: New insights into targeting the CD200R1 pathway in T and NK cells using 23ME-00610 as a single agent or in combination

Abstract 23ME-00610 is a monoclonal antibody that is being evaluated as a single agent in a Phase 1/2a clinical trial for advanced solid malignancies (NCT05199272). It binds with high affinity (KD &amp;lt; 0.1 nM) to CD200R1, a promising immune-oncology (IO) target identified by surveying the 23andMe genetic and health survey database. CD200R1 is an inhibitory receptor that when bound to its ligand CD200, reduces pro-inflammatory cytokine production, and leads to an immunosuppressive tumor environment. To gain further insight into the mechanism of action of 23ME-00610 and its potential for combination therapy, we profiled CD200R1 and other immune inhibitory receptors in human dissociated solid tumor samples using spectral flow cytometry. CD200R1 was broadly expressed across tumor-infiltrating immune cells, including T cells and NK cells, cytotoxic cell types with known antitumor functions. Notably, CD200R1 expression pattern was differentiated from PD-1, which is mostly restricted to T cells, indicating differences in patient populations that could potentially benefit from anti-CD200R1 and anti-PD-1 treatments. The ligand, CD200 was broadly expressed, including on tumor cells and endothelial cells. The differential expression profiles of CD200R1 and PD-1 on immune cells, along with CD200 expression on endothelial cells, suggest that combining 23ME-00610 with other clinically validated immunomodulatory agents could enhance antitumor responses. Follow-up experiments were conducted to validate and extend these findings. In an in vitro assay with cancer patient-derived PBMCs, 23ME-00610 promoted higher production of IFNγ, a key functional antitumor cytokine, compared to anti-PD-1 in 9 of 10 donors. Subsequent attempts were made to pinpoint immune cells responsible for 23ME-00610's anti-tumor activity. 23ME-00610 reversed CD200-mediated suppression of chronically stimulated primary T cells and CD200-mediated inhibition of NK cell degranulation, suggesting that 23ME-00610 can mediate tumor cell killing through at least two different cell types. To test the potential of 23ME-00610 to combine with anti-PD-1 to enhance T cell function, an artificial antigen-presenting cell (aAPC) line overexpressing PD-L1 and CD200 was co-cultured with chronically stimulated primary human T cells. Anti-PD-1 and 23ME-00610 each independently enhanced IFNy secretion levels compared to isotype control, yet their combination resulted in a more than additive effect. Taken together, these data demonstrate that 23ME-00610 can enhance both NK and T cell antitumor effector functions, and 23ME-00610 could synergize with anti-PD-1 to further increase the activity of T cells against cancer cells. The results of this study provide evidence that 23ME-00610 could expand IO treatment options for patients with advanced solid malignancies as a single agent or in combination with other anti-tumor therapeutics. Citation Format: Mithra R. Kumar, Shiteng Duan, Shruti Yadav, Abigail Jarret, Zhonghao Yan, Jill Fenaux, Martin Kinisu, Zuoan Yi, Mauro Poggio, Patrick Collins, Antony Symons, Lorena Riol Blanco, Maike Schmidt, Sophia Majeed, Anh Diep, Clarissa Lee. New insights into targeting the CD200R1 pathway in T and NK cells using 23ME-00610 as a single agent or in combination [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2359.

Abstract 5025: Extracellular vesicle DNA as a potential biomarker for cancer detection: A comparative analysis with ctDNA

Abstract Background: Liquid biopsy testing has been implemented in clinical practice because of recent advancements in detecting and characterizing circulating tumor DNA (ctDNA). The Food and Drug Administration (FDA) has approved three ctDNA liquid biopsy tests that detect mutations in cancers, which can aid clinicians in choosing the most effective treatments. While ctDNA has been validated for clinical applications, the same is not true for extracellular vesicle (EV)-associated DNA, which is another promising biomarker. Previously, our laboratory developed the Extracellular Vesicle-Associated DNA Database (EV-ADD) to provide validated experimental details and data extracted from peer-reviewed published literature on EV-DNA. The aim of our study was to investigate the potential clinical utility of EV-DNA in liquid biopsy for tumor detection by surveying studies on EV-ADD that compared ctDNA and EV-DNA. Methods: We searched the entire EV-ADD to selectively identify studies that compared cell-free DNA (cfDNA) or ctDNA and EV-DNA in cancer patients (inclusion criteria). The sensitivity and specificity of cancer detection, the concentrations of DNA, and the methods of detection were compared between ct/cfDNA and EV-DNA. We define sensitivity as the ability to detect mutations in ctDNA/EV-DNA from patient blood when the mutations are known. Specificity is defined as the proportion of true negatives from the sum of true negatives and false positives. A true negative case occurs when no driver mutation is detected in ctDNA/EV-DNA of a patient whose tumor does not have the mutation either. A false positive case occurs when a driver mutation is detected in ctDNA/EV-DNA of a patient whose tumor does not have the mutation. Results: Of 97 studies in the database, 20 met our inclusion criteria. From 12 studies that matched our definition of sensitivity, the sensitivity of EV-DNA and ctDNA ranged from 19% to 95% and 14% to 97%, respectively. From the same 12 studies, the specificity of EV-DNA and ctDNA ranged from 89% to 100% and 80% to 100%, respectively. Other studies that met our inclusion criteria but did not match our definition of sensitivity either calculated sensitivity differently (2 studies), calculated sensitivity the same way in pleural effusions (2 studies), in bronchoalveolar lavage fluid (2 studies), analyzed mitochondrial DNA (1 study), or did not calculate sensitivity (1 study). The concentrations of EV-DNA and ctDNA in blood ranged from 0.8 - 118.4 ng/ml and 4.0 - 236.5 ng/ml, respectively. Digital droplet PCR (ddPCR) and sequencing were the most common methods (45% and 35%, respectively) for detecting cancer mutations. Conclusions: Since EV-DNA performed comparably to ctDNA in detecting cancer DNA in the blood of patients, EV-DNA should be seriously considered as a potential biomarker and complementary tool for detecting and monitoring cancer tumors. Citation Format: Tad Wu, Thupten Tsering, Yunxi Chen, Amélie Nadeau, Julia V. Burnier. Extracellular vesicle DNA as a potential biomarker for cancer detection: A comparative analysis with ctDNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5025.

Combining Molecular, Macroevolutionary, and Macroecological Perspectives on the Generation of Diversity.

Charles Darwin presented a unified process of diversification driven by the gradual accumulation of heritable variation. The growth in DNA databases and the increase in genomic sequencing, combined with advances in molecular phylogenetic analyses, gives us an opportunity to realize Darwin's vision, connecting the generation of variation to the diversification of lineages. The rate of molecular evolution is correlated with the rate of diversification across animals and plants, but the relationship between genome change and speciation is complex: Mutation rates evolve in response to life history and niche; substitution rates are influenced by mutation, selection, and population size; rates of acquisition of reproductive isolation vary between populations; and traits, niches, and distribution can influence diversification rates. The connection between mutation rate and diversification rate is one part of the complex and varied story of speciation, which has theoretical importance for understanding the generation of biodiversity and also practical impacts on the use of DNA to understand the dynamics of speciation over macroevolutionary timescales.

Exploring the bidirectional relationship between metabolic syndrome and thyroid autoimmunity: a Mendelian randomization study.

Observational studies have reported a possible association between metabolic syndrome (MetS) and thyroid autoimmunity. Nevertheless, the relationship between thyroid autoimmunity and MetS remains unclear. The objective of this research was to assess the causal impact of MetS on thyroid autoimmunity through the utilization of Mendelian randomization (MR) methodology. We performed bidirectional MR to elucidate the causal relationship between MetS and their components and thyroid autoimmunity (positivity of TPOAb). Single nucleotide polymorphisms (SNPs) of MetS and its components were obtained from the publicly available genetic variation summary database. The Thyroidomics Consortium conducted a genome-wide association analysis, which provided summary-level data pertaining to thyroid autoimmunity. The study included several statistical methods, including the inverse variance weighting method (IVW), weighted median, simple mode, weight mode, and MR-Egger methods, to assess the causal link. In addition, to ensure the stability of the results, a sensitivity analysis was conducted. IVW showed that MetS reduced the risk of developing thyroid autoimmunity (OR = 0.717, 95% CI = 0.584 - 0.88, P = 1.48E-03). The investigation into the causative association between components of MetS and thyroid autoimmune revealed a statistically significant link between triglycerides levels and the presence of thyroid autoimmunity (IVW analysis, OR = 0.603, 95%CI = 0.45 -0.807, P = 6.82E-04). The reverse analysis did not reveal any causal relationship between thyroid autoimmunity and MetS, including its five components. We have presented new genetic evidence demonstrating that MetS and its triglyceride components may serve as potential protective factors against thyroid autoimmunity.