Changes In Allele Frequencies Research Articles

Canine hyper-sociability structural variants associated with altered three-dimensional chromatin state

Strong selection on complex traits can lead to skewed trait means and reduced trait variability in populations. An example of this phenomenon can be evidenced in allele frequency changes and skewed trait distributions driven by persistent human-directed selective pressures in domesticated species. Dog domestication is linked to several genomic variants; however, the functional impacts of these variants may not always be straightforward when found in non-coding regions of the genome. Four polymorphic transposable elements (TE) found within non-coding sites along a 5 Mb region on canine CFA6 have evolved due to directional selection associated with heightened human-directed hyper-sociability in domesticated dogs. We found that the polymorphic TE in intron 17 of the canine GTF2I gene, which was previously reported to be negatively correlated with canid human-directed hyper-sociability, is associated with altered chromatin looping and hence distinct cis-regulatory landscapes. We reported supporting evidence of an E2F1-DNA binding peak concordant with the altered loop and higher expression of GTF2I exon 18, indicative of alternative splicing. Globally, we discovered differences in pathways regulating the extra-cellular matrix with respect to TE copy number. Overall, we reported evidence suggesting an intriguing molecular convergence between the emergence of hypersocial behaviors in dogs and the same genes that, when hemizygous, produce human Williams Beuren Syndrome characterized by cranio-facial defects and heightened social behaviors. Our results additionally emphasize the often-overlooked potential role of chromatin architecture in social evolution.

Circulating tumor DNA dynamics reveal KRAS G12C mutation heterogeneity and response to treatment with the KRAS G12C inhibitor divarasib in solid tumors.

To inform prognosis, treatment response, disease biology, and KRAS G12C mutation heterogeneity, we conducted exploratory circulating tumor DNA (ctDNA) profiling on 134 patients with solid tumors harboring a KRAS G12C mutation treated with single-agent divarasib (GDC-6036) in a phase 1 study. Plasma samples were collected for serial ctDNA profiling at baseline (Cycle 1 Day 1 prior to treatment) and multiple on-treatment time points (Cycle 1 Day 15 and Cycle 3 Day 1). KRAS G12C ctDNA was detectable from plasma samples in 72.9% (43/59) and 92.6% (50/54) of patients with non-small cell lung cancer and colorectal cancer, respectively, the majority of whom were eligible for study participation based on a local test detecting the KRAS G12C mutation in tumor tissue. Baseline ctDNA tumor fraction was associated with tumor type, disease burden, and metastatic sites. A decline in ctDNA level was observed as early as Cycle 1 Day 15. Serial assessment showed a decline in ctDNA tumor fraction associated with response and progression-free survival. Except for a few cases of KRAS G12C sub-clonality, on-treatment changes in KRAS G12C variant allele frequency mirrored changes in the overall ctDNA tumor fraction. Across tumor types, the KRAS G12C mutation likely represents a truncal mutation in the majority of patients. Rapid and deep decline in ctDNA tumor fraction was observed in patients responding to divarasib treatment. Early on-treatment dynamics of ctDNA were associated with patient outcomes and tumor response to divarasib treatment.

RB1 circulating-tumor DNA in the blood of Retinoblastoma patients increases in untreated patients.

Circulating tumor DNA (ctDNA) in plasma has been identified in many cancers, including retinoblastoma at diagnosis. We have previously shown that with treatment (enucleation or ophthalmic artery chemosurgery (OAC)) all ctDNA disappears; and if there is persistent plasma ctDNA after treatment metastases develop. The purpose of this study was to determine how the ctDNA RB1 variant allele frequency (VAF) changes in patients with retinoblastoma who have delayed treatment. Circulating tumor DNA RB1 was detected and VAF was measured at diagnosis and again prior to any intervention at some time later ranging from 2 to 28 days. Four patients with five ctDNA RB1 mutations were detected at diagnosis and VAF was increased on re-evaluation of the same RB1 mutations in ctDNA. In this small cohort, every patient (4) and every RB1 mutation (5) plasma level VAF% increased when measured at two time periods before treatment was instituted suggesting that growing tumors demonstrate increasing plasma ctDNA.

Historical museum samples reveal signals of selection and drift in response to changing insecticide use in an agricultural pest moth.

In response to environmental and human-imposed selective pressures, agroecosystem pests frequently undergo rapid evolution, with some species having a remarkable capacity to rapidly develop pesticide resistance. Temporal sampling of genomic data can comprehensively capture such adaptive changes over time, for example, by elucidating allele frequency shifts in pesticide resistance loci in response to different pesticides. Here, we leveraged museum specimens spanning over a century of collections to generate temporal contrasts between pre- and post-insecticide populations of an agricultural pest moth, Helicoverpa armigera. We used targeted exon sequencing of 254 samples collected across Australia from the pre-1950s (prior to insecticide introduction) to the 1990s, encompassing decades of changing insecticide use. Our sequencing approach focused on genes that are known to be involved in insecticide resistance, environmental sensation, and stress tolerance. We found an overall lack of spatial and temporal population structure change across Australia. In some decades (e.g., 1960s and 1970s), we found a moderate reduction of genetic diversity, implying stochasticity in evolutionary trajectories due to genetic drift. Temporal genome scans showed extensive evidence of selection following insecticide use, although the majority of selected variants were low impact. Finally, alternating trajectories of allele frequency change were suggestive of potential antagonistic pleiotropy. Our results provide new insights into recent evolutionary responses in an agricultural pest and show how temporal contrasts using museum specimens can improve mechanistic understanding of rapid evolution.

Mapping quantitative trait loci for seminal root angle in a selected durum wheat population.

Seminal root angle (SRA) is an important root architectural trait associated with drought adaptation in cereal crops. To date, all attempts to dissect the genetic architecture of SRA in durum wheat (Triticum durum Desf.) have used large association panels or structured mapping populations. Identifying changes in allele frequency generated by selection provides an alternative genetic mapping approach that can increase the power and precision of QTL detection. This study aimed to map quantitative trait loci (QTL) for SRA by genotyping durum lines created through divergent selection using a combination of marker-assisted selection (MAS) for the major SRA QTL (qSRA-6A) and phenotypic selection for SRA over multiple generations. The created 11 lines (BC1F2:5) were genotyped with genome-wide single-nucleotide polymorphism (SNP) markers to map QTL by identifying markers that displayed segregation distortion significantly different from the Mendelian expectation. QTL regions were further assessed in an independent validation population to confirm their associations with SRA. The experiment revealed 14 genomic regions under selection, 12 of which have not previously been reported for SRA. Five regions, including qSRA-6A, were confirmed in the validation population. The genomic regions identified in this study indicate that the genetic control of SRA is more complex than previously anticipated. Our study demonstrates that selection mapping is a powerful approach to complement genome-wide association studies for QTL detection. Moreover, the verification of qSRA-6A in an elite genetic background highlights the potential for MAS, although it is necessary to combine additional QTL to develop new cultivars with extreme SRA phenotypes.

Polygenic selection to a changing optimum under self-fertilisation.

Many traits are polygenic, affected by multiple genetic variants throughout the genome. Selection acting on these traits involves co-ordinated allele-frequency changes at these underlying variants, and this process has been extensively studied in random-mating populations. Yet many species self-fertilise to some degree, which incurs changes to genetic diversity, recombination and genome segregation. These factors cumulatively influence how polygenic selection is realised in nature. Here, we use analytical modelling and stochastic simulations to investigate to what extent self-fertilisation affects polygenic adaptation to a new environment. Our analytical solutions show that while selfing can increase adaptation to an optimum, it incurs linkage disequilibrium that can slow down the initial spread of favoured mutations due to selection interference, and favours the fixation of alleles with opposing trait effects. Simulations show that while selection interference is present, high levels of selfing (at least 90%) aids adaptation to a new optimum, showing a higher long-term fitness. If mutations are pleiotropic then only a few major-effect variants fix along with many neutral hitchhikers, with a transient increase in linkage disequilibrium. These results show potential advantages to self-fertilisation when adapting to a new environment, and how the mating system affects the genetic composition of polygenic selection.

Selection with two alleles of X-linkage and its application to the fitness component analysis of OdsH in Drosophila.

In organisms with the XY sex-determination system, there is an imbalance in the inheritance and transmission of the X chromosome between males and females. Unlike an autosomal allele, an X-linked recessive allele in a female will have phenotypic effects on its male counterpart. Thus, genes located on the X chromosome are of particular interest to researchers in molecular evolution and genetics. Here we present a model for selection with two alleles of X-linkage to understand fitness components associated with genes on the X chromosome. We apply this model to the fitness analysis of an X-linked gene, OdsH (16D), in the fruit fly Drosophila melanogaster. The function of OdsH is involved in sperm production and the gene is rapidly evolving under positive selection. Using site-directed gene targeting, we generated functional and defective OdsH variants tagged with the eye-color marker gene white. We compare the allele frequency changes of the two OdsH variants, each directly competing against a wild-type OdsH allele in concurrent but separate experimental populations. After twenty generations, the two genetically modified OdsH variants displayed a 40% difference in allele frequencies, with the functional OdsH variant demonstrating an advantage over the defective variant. Using maximum likelihood estimation (MLE), we determined the fitness components associated with the OdsH alleles in males and females. Our analysis revealed functional aspects of the fitness determinants associated with OdsH, and that sex-specific fertility and viability consequences both contribute to selection on an X-linked gene.

Genome-wide allele frequency changes reveal that dynamic metapopulations evolve differently.

Two important characteristics of metapopulations are extinction-(re)colonization dynamics and gene flow between subpopulations. These processes can cause strong shifts in genome-wide allele frequencies that are generally not observed in "classical" (large, stable, panmictic) populations. Subpopulations founded by one or a few individuals, the so-called propagule model, are initially expected to show intermediate allele frequencies at polymorphic sites until natural selection and genetic drift drive allele frequencies toward a mutation-selection-drift equilibrium characterized by a negative exponential-like distribution of the site frequency spectrum (SFS). We followed changes in SFS distribution in a natural metapopulation of the cyclically parthenogenetic pond-dwelling microcrustacean Daphnia magna using biannual pool-seq samples collected over a five-year period from 118 ponds occupied by subpopulations of known age. As expected under the propagule model, SFSs in newly founded subpopulations trended toward intermediate allele frequencies and shifted toward right skewed distributions as the populations aged. Immigration and subsequent hybrid vigor altered this dynamic. We show that the analysis of SFS dynamics is a powerful approach to understand evolution in metapopulations. It allowed us to disentangle evolutionary processes occurring in a natural metapopulation, where many subpopulations evolve in parallel. Thereby, stochastic processes like founder and immigration events lead to a pattern of subpopulation divergence, while genetic drift, leads to converging SFS distributions in the persisting subpopulations. The observed processes are well explained by the propagule model and highlight that metapopulations evolve differently from classical populations.

Biotic interactions promote local adaptation to soil in plants

Although different ecological factors shape adaptative evolution in natural habitats, we know little about how their interactions impact local adaptation. Here we used eight generations of experimental evolution with outcrossing Brassica rapa plants as a model system, in eight treatment groups that varied in soil type, herbivory (with/without aphids), and pollination mode (hand- or bumblebee-pollination), to study how biotic interactions affect local adaptation to soil. First, we show that several plant traits evolved in response to biotic interactions in a soil-specific way. Second, using a reciprocal transplant experiment, we demonstrate that significant local adaptation to soil-type evolved in the “number of open flowers”, a trait used as a fitness proxy, but only in plants that evolved with herbivory and bee pollination. Whole genome re-sequencing of experimental lines revealed that biotic interactions caused a 10-fold increase in the number of SNPs across the genome with significant allele frequency change, and that alleles with opposite allele frequency change in different soil types (antagonistic pleiotropy) were most common in plants with an evolutionary history of herbivory and bee pollination. Our results demonstrate that the interaction with mutualists and antagonists can facilitate local adaptation to soil type through antagonistic pleiotropy.

A Path Integral Approach for Allele Frequency Dynamics Under Polygenic Selection.

Many phenotypic traits have a polygenic genetic basis, making it challenging to learn their genetic architectures and predict individual phenotypes. One promising avenue to resolve the genetic basis of complex traits is through evolve-and-resequence experiments, in which laboratory populations are exposed to some selective pressure and trait-contributing loci are identified by extreme frequency changes over the course of the experiment. However, small laboratory populations will experience substantial random genetic drift, and it is difficult to determine whether selection played a roll in a given allele frequency change. Predicting how much allele frequencies change under drift and selection had remained an open problem well into the 21st century, even those contributing to simple, monogenic traits. Recently, there have been efforts to apply the path integral, a method borrowed from physics, to solve this problem. So far, this approach has been limited to genic selection, and is therefore inadequate to capture the complexity of quantitative, highly polygenic traits that are commonly studied. Here we extend one of these path integral methods, the perturbation approximation, to selection scenarios that are of interest to quantitative genetics. In particular, we derive analytic expressions for the transition probability (i.e., the probability that an allele will change in frequency from , to in time ) of an allele contributing to a trait subject to stabilizing selection, as well as that of an allele contributing to a trait rapidly adapting to a new phenotypic optimum. We use these expressions to characterize the use of allele frequency change to test for selection, as well as explore optimal design choices for evolve-and-resequence experiments to uncover the genetic architecture of polygenic traits under selection.

A randomized study evaluating tailoring of advanced/metastatic colorectal cancer (mCRC) therapy using circulating tumor DNA (ctDNA): TACT-D.

LBA3557 Background: Identifying non-responders to expensive salvage therapies with modest benefits and substantial treatment related adverse events (TRAEs) (e.g. regorafenib [Reg] or TAS102 [Tas] in mCRC) is key to precision care. Retrospective studies suggest that ctDNA changes at timepoints (4-10 weeks [wks] into therapy) before radiographic assessment may predict treatment outcomes. However, prospective studies assessing early ctDNA changes are lacking and clinical utility remains uncertain. Methods: TACT-D is a randomized study to validate early dynamic changes in ctDNA (ΔctDNA: change in either maximum variant allele frequency (maxVAF) or mean VAF in predicting treatment response/resistance. Patients (pts) with mCRC clinically eligible for Reg/Tas were randomly assigned 2:1 to either standard of care (SOC) or ctDNA arm. All pts had ctDNA sequencing by Guardant360 CDx assay on cycle 1 day 1 (C1D1) and C1D15. On SOC arm, pts were restaged at 8 wks. On ctDNA arm, ΔctDNA (C1D15 - C1D1) was run in real-time and increase in ctDNA (ΔctDNA > 0) triggered early radiographic restaging. Therapy was continued for responders (RECISTv1.1 stable disease/response) and stopped for progression (non-responders). Co-primary endpoints were: 1) comparison of TRAEs among study arms and 2) association of ΔctDNA and objective response rate (RR). Key secondary endpoints were progression free (PFS) and overall (OS) survival. Study was powered (82%; 2-sided α = .05) to detect 30% decrease in toxicity. Results: Between 4/2019 and 8/2023, 100 pts were randomized; 80 evaluable had median age of 56 years, 46% were females, 44% and 56% received Tas and Reg, respectively. Baseline ctDNA levels (ρ 0.90) and ΔctDNA (ρ 0.68) using maxVAF (reported below) and mean VAF showed strong correlation (P < .001). Median ΔctDNA for entire cohort was -47% with no significant difference by treatment arms (SOC -45% v Exp -58%, P = .79) and therapy (Tas -71 v Reg -44, P = .19). ΔctDNA increased in 18% pts. Grade 3/4 TRAEs (32% v 40%, P = .62) did not differ significantly between arms. No significant association was seen between ΔctDNA and RR (OR .88, P = 1.0), PFS (HR .99, P = .88) and OS (HR 1.00, P = .64). Notably, higher baseline maxVAF was strongly associated with response (median maxVAF: 21.8% in non-responders v 3.4% in responders), PFS (HR 1.02) and OS (HR 1.03) (all P < .001). After adjusting for baseline maxVAF, ΔctDNA was found to be associated with both PFS (HR 1.87, P = .038) and OS (HR 3.55, P = .001). Conclusions: In the first prospective study of clinical utility of monitoring ctDNA in mCRC, baseline ctDNA was strongly prognostic for clinical benefit from salvage therapies in mCRC. Adjusted for this prognostic impact, ΔctDNA between C1D1 and C1D15 was predictive of clinical outcomes. Efforts are needed to establish novel signatures, optimal cutoffs/intervals for assessing ctDNA response in mCRC, tailored to pts and their therapy. Clinical trial information: NCT03844620 .

Suggested mechanism of CCR5Δ32, CCR2-64I and SDF 1-3'A allele frequency change in Polish and Lithuanian gene pools from the perspective of passing time.

The study aimed to determine the frequency of the alleles associated with hereditary immune response in 16 historical populations and assess which evolutionary forces may have contributed to the observed frequency fluctuation. The analysed polymorphic sites are located in three genes - CCR5, CCR2 and SDF 1 (CXCL12). Protein products are involved in the innate immune response and are also involved in various types of infections, autoimmune diseases and tumours. The frequency of the alleles found in the DNA of the studied individuals was determined by the Sanger methodology and was compared with the data obtained for modern populations. To confirm the authenticity of the obtained results, mtDNA HVRI haplotypes of all the studied samples were obtained and compared with the genetic database of the laboratory personnel who came into contact with the studied material. Based on the variability of allele frequency, advanced biostatistical analysis was used to distinguish the effect of natural selection from genetic drift, i.e. the forces operating on the polymorphic sites studied. All procedures were performed according to the guidelines for working with ancient DNA to avoid contamination with modern DNA molecules. 681 samples from 39 archaeological sites in Poland and Lithuania dated to the 40th century BC and the 19th century were studied. The biostatistical analysis showed that the fluctuations in the frequency of CCR5Δ32 in the analysed time interval could be mainly the effect of genetic drift. Nevertheless, for CCR2-64I and SDF 1-3'A, the results confirm the suggestion of negative selection as the mechanism involved. Since all the polymorphic sites encode the elements of innate immune response that are indirectly associated with the process of an HPV infection and the development of cervical cancer, the human papillomavirus may be a good candidate for a selection coefficient affecting the frequency of CCR2-64I and SDF 1-3'A. However, for CCR5Δ32, selection was not detected despite its proven role in the molecular mechanism involved in the response to an HPV infection. The presented work seems to be the first in which the problem of the pattern of CCR5Δ32, CCR2-64I and SDF 1-3'A frequency fluctuations in a temporal perspective was discussed, proposing HPV as a factor influencing the occurrence of the CCR2 and SDF1 alleles.

Phase 2 study of the lysine-specific demethylase 1 (LSD1) inhibitor bomedemstat in patients with polycythemia vera (PV).

TPS6595 Background: PV is a myeloproliferative neoplasm (MPN) characterized by clonal erythrocytosis that is driven by mutations in JAK2. Currently available treatments reduce thrombotic risk and symptom burden but have little impact on disease course or risk of progression to post-PV myelofibrosis (PPV-MF) or acute myeloid leukemia (AML). There remains a need for novel treatments that can alter the natural history of PV. LSD1 is an enzyme that regulates megakaryocytes and erythrocyte maturation. Bomedemstat is an irreversible inhibitor of LSD1 that has been shown to have manageable safety and clinically relevant activity in other JAK2-mutation–prevalent MPNs (essential thrombocythemia and myelofibrosis). Here, we describe the methods for an open-label phase 2 study (NCT05558696) that has been designed to evaluate the efficacy and safety of bomedemstat in patients with PV who are resistant to or intolerant of standard cytoreductive therapy. Methods: Eligible patients are ≥18 years, have a confirmed diagnosis of PV per World Health Organization 2016 diagnostic criteria, a bone marrow fibrosis score of grade 0 or 1, an ECOG performance status of 0-2, a platelet count of ≥250 × 109/L, an absolute neutrophil count of ≥1.5 × 109/L, and resistance to or intolerance of ≥1 standard cytoreductive therapy. All patients will receive bomedemstat at a starting dose of 40 mg/d by mouth for 36 weeks, with dose titration to a hematocrit target of <45% with no grade ≥1 thrombocytopenia. Treatment with bomedemstat can continue beyond week 36 in patients deriving clinical benefit. Clinic visits will occur every 2 weeks until week 12 and monthly thereafter. Adverse events will be graded per NCI CTCAE version 5.0 criteria and will be monitored for up to 30 days after treatment end. Transfusions or phlebotomy can be administered during treatment as needed. The primary end points are safety and the proportion of patients who achieve a reduction in hematocrit to <45% without phlebotomy by week 36. Secondary end points will be the durability of reduction in hematocrit <45% without phlebotomy; the incidence and durability of reduction in platelet count to ≤450 × 109/L and white blood cell count to <10 × 109/L; the incidence of new thrombotic or major hemorrhagic events; reduction in spleen volume by week 36 in patients with an enlarged spleen at baseline; progression to PPV-MF or myelodysplastic syndrome or transformation to AML; pharmacokinetics; and change in patient-reported symptom burden assessed using the MSAF v4.0 and PGIC. Exploratory end points include change in the concentration of circulating inflammatory cytokines and growth factors, change in mutant allele frequency of JAK2and other mutations, and change in bone marrow fibrosis grade. Approximately 20 patients will be enrolled. Recruitment for this study is currently underway in Australia, the United Kingdom, and the United States. Clinical trial information: NCT05558696 .

Spectrum of Resistance Mechanisms to ALK TKIs in NSCLC: Largest Single-Center Experience from India

Abstract Introduction Anaplastic lymphoma kinase (ALK) rearranged non-small cell lung carcinoma (NSCLC) has emerged as a distinct entity with growing number of potent ALK tyrosine kinase inhibitors (TKIs). Despite showing durable responses and promising survival rates, resistance to these ensue. This is the largest series of repeat biopsies from patients of ALK-positive NSCLC progressing on ALK-directed therapy from this part of the world. Using a combinatorial approach of genomics and histology, we describe the spectrum of various resistance mechanisms encountered. Methods This is a cross-sectional study recruiting ALK-positive NSCLC cases who have progressed on any line ALK TKI and have undergone repeated biopsies followed by genomic sequencing by next-generation sequencing (NGS). Results Thirty-two ALK-positive NSCLC patients progressed on TKI were enrolled. Median age was 53 years (range: 36–75 years) with a male predilection (male:female 1.3:1). Twenty-seven (84.4%) cases harbored an additional resistance mechanism. Eighteen of these harbored an on-target ALK alteration, with L1196M gatekeeper mutation being the most common, in 11 cases, and G1202 alteration in 3 cases. In 9 cases an off-target alteration was detected, the most frequent being TP53 mutation in 8 cases, KRAS mutation in 4 cases and MET amplification in 3 cases. Four patients underwent sequential NGS testing and allele frequency changes in ALK fusion and resistance mechanisms were demonstrated. Sixteen patients have been offered lorlatinib therapy, the median progression-free survival of which has not yet been reached. Conclusion This is the largest series depicting ALK resistance mechanisms from a single center to date. The SPACEWALK study which demonstrated ALK TKI resistance mechanisms using plasma-based genotyping was a multicentric study. The spectrum encountered in this study is distinct from the rest of the world, thus highlighting heterogeneity within ALK-rearranged tumors. Comprehensive clinical evaluation at disease progression coupled with NGS-based genotyping will pave the way for lucid understanding of disease biology, thus aiding in the institution of optimal therapy.

Allele frequency dynamics under sex-biased demography and sex-specific inheritance in a pedigreed jay population.

Sex-biased demography, including sex-biased survival or migration, can alter allele frequency changes across the genome. In particular, we can expect different patterns of genetic variation on autosomes and sex chromosomes due to sex-specific differences in life histories, as well as differences in effective population size, transmission modes, and the strength and mode of selection. Here, we demonstrate the role that sex differences in life history played in shaping short-term evolutionary dynamics across the genome. We used a 25-year pedigree and genomic dataset from a long-studied population of Florida Scrub-Jays (Aphelocoma coerulescens) to directly characterize the relative roles of sex-biased demography and inheritance in shaping genome-wide allele frequency trajectories. We used gene dropping simulations to estimate individual genetic contributions to future generations and to model drift and immigration on the known pedigree. We quantified differential expected genetic contributions of males and females over time, showing the impact of sex-biased dispersal in a monogamous system. Due to female-biased dispersal, more autosomal variation is introduced by female immigrants. However, due to male-biased transmission, more Z variation is introduced by male immigrants. Finally, we partitioned the proportion of variance in allele frequency change through time due to male and female contributions. Overall, most allele frequency change is due to variance in survival and births. Males and females make similar contributions to autosomal allele frequency change, but males make higher contributions to allele frequency change on the Z chromosome. Our work shows the importance of understanding sex-specific demographic processes in characterizing genome-wide allele frequency change in wild populations.

Deep genotyping reveals specific adaptation footprints of conventional and organic farming in barley populations—an evolutionary plant breeding approach

Sustainable food production for a growing world population will pose a central challenge in the coming decades. Organic farming is among the feasible approaches to achieving this goal if the yield gap to conventional farming can be decreased. However, uncertainties exist to which extend—and for which phenotypes in particular—organic and conventional agro-ecosystems require differentiated breeding strategies. To answer this question, a heterogeneous spring barley population was established between a wild barley and an elite cultivar to examine this question. This initial population was divided into two sets and sown one in organic and the other in conventional managed agro-ecosystems, without any artificial selection for two decades. A fraction of seeds harvested each year was sown the following year. Various generations, up to the 23th were whole-genome pool-sequenced to identify adaptation patterns towards ecosystem and climate conditions in the allele frequency shifts. Additionally, a meta-data analysis was conducted to link genomic regions’ increased fitness to agronomically related traits. This long-term experiment highlights for the first time that allele frequency pattern difference between the conventional and organic populations grew with subsequent generations. Further, the organic-adapted population showed a higher genetic heterogeneity. The data indicate that adaptations towards new environments happen in few generations. Drastic interannual changes in climate are manifested in significant allele frequency changes. Particular wild form alleles were positively selected in both environments. Clustering these revealed an increased fitness associated with biotic stress resistance, yield physiology, and yield components in both systems. Additionally, the introduced wild alleles showed increased fitness related to root morphology, developmental processes, and abiotic stress responses in the organic agro-ecosystem. Concluding the genetic analysis, we demonstrate that breeding of organically adapted varieties should be conducted in an organically managed agro-ecosystem, focusing on root-related traits, to close the yield gap towards conventional farming.

Selection leads to remarkable variability in the outcomes of hybridisation across replicate hybrid zones.

Hybrid zones have been viewed as an opportunity to see speciation in action. When hybrid zones are replicated, it is assumed that if the same genetic incompatibilities are maintaining reproductive isolation across all instances of secondary contact, those incompatibilities should be identifiable by consistent patterns in the genome. In contrast, changes in allele frequencies due to genetic drift should be idiosyncratic for each hybrid zone. To test this assumption, we simulated 20 replicates of each of 12 hybrid zone scenarios with varied genetic incompatibilities, rates of migration, selection and different starting population size ratios of parental species. We found remarkable variability in the outcomes of hybridisation in replicate hybrid zones, particularly with Bateson-Dobzhansky-Muller incompatibilities and strong selection. We found substantial differences among replicates in the overall genomic composition of individuals, including admixture proportions, inter-specific ancestry complement and number of ancestry junctions. Additionally, we found substantial variation in genomic clines among replicates at focal loci, regardless of locus-specific selection. We conclude that processes other than selection are responsible for some consistent outcomes of hybridisation, whereas selection on incompatibilities can lead to genomically widespread and highly variable outcomes. We highlight the challenge of mapping between pattern and process in hybrid zones and call attention to how selection against incompatibilities will commonly lead to variable outcomes. We hope that this study informs future research on replicate hybrid zones and encourages further development of statistical techniques, theoretical models and exploration of additional axes of variation to understand reproductive isolation.

Abstract PO4-14-10: Circulating Tumor DNA as a Biomarker for ADCs in Metastatic Breast Cancer

Abstract Background: Breast cancer is a complex disease characterized by heterogeneity, and the analysis of circulating tumor DNA (ctDNA) holds promise for capturing this heterogeneity. Recently, ctDNA testing has been employed in clinical practice to guide targeted therapies for metastatic breast cancer, particularly in cases of hormone receptor-positive disease with mutations in PIK3CA and ESR1. This approach becomes necessary when traditional tumor biopsies are inadequate for next-generation sequencing (NGS) testing or fail to capture the full extent of the cancer's heterogeneity. Moreover, the utilization of antibody-drug conjugates (ADC) in addressing tumor heterogeneity continues to expand. However, there has been no biomarker, outside of HER2 protein expression, to predict ADC response. In this project, we test the hypothesis that ctDNA can be utilized as a biomarker to predict response to novel therapies such as ADCs. Methods: We analyzed a subset of patients from the Dallas Metastatic Breast Cancer Study comprised of patients with metastatic breast cancer (n= 109) who underwent ctDNA testing using the Tempus xF liquid biopsy ctDNA sequencing panel. This panel detects 105-genes that are known oncogenic drivers and resistance mutations. The data was collected from a single academic medical center between the initial year of ctDNA collection in 2019 and 2023. Results: Among these patients, 85 (77.9%) had hormone receptor-positive disease, 13 (11.9%) had triple-negative breast cancer, and 11 (10.0%) had HER2-positive disease (including 3 (2.75%) patients with triple-positive disease). Only 22 of these patients had tissue biopsies that underwent NGS testing. Analysis of all patients revealed that the most common gene alteration was PIK3CA, which was identified in 70 patients. Specifically, the most frequently observed alteration was PIK3CA p.545K, found in 25 patients. Table 1 further details the frequency of each gene in this subset of patients. Among the patients, 34 out of 109 (31%) received an ADC, while only 8 out of 109 (7%) received immunotherapy. Patients with CDKN2A achieved the longest progression-free survival (PFS) on an ADC, with a median PFS of 7 months, whereas patients carrying mutations in TP53, PIK3R1, PIK3CA, PTEN, NF1, BRAF, RHOA, FGFR4, KRAS, TERT, GATA3, HNF1A, FB1, STOP had median PFSs of 2 months or less. Table 2 provides additional information on the response of patients with specific mutations to ADCs. Notably, only one patient received sequential ctDNA testing, and in that case, there was a gain of TP53 p.N239S following sacituzumab govitecan administration compared to the baseline ctDNA test, followed by a gain of PIK3CA p.P449_L455del after trastuzumab deruxtecan administration. Conclusions: As we observe changes in subtypes following treatment progression, researchers are actively seeking biomarkers to better characterize real-time changes in tumor biology that can predict response and resistance to treatments. Further studies are needed to identify additional genes present in ctDNA that can provide mechanistic insights into why certain patients respond favorably to ADCs while others do not. We are currently enrolling patients for a prospective study that aims to assess baseline ctDNA levels and monitor changes in variant allele frequency following treatment with ADCs and immunotherapy. Table 2 Median PFS on ADC by Gene Citation Format: Hannah Chang, Isabela Anawate, Alyssa Low, Shao-Po Huang, Julia Maues, Christine Hodgdon, Isaac Chan. Circulating Tumor DNA as a Biomarker for ADCs in Metastatic Breast Cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-14-10.

Abstract PO3-23-11: Multiomics analysis of ER+ breast cancer with matched primaries, lymph node metastases and recurrent cancers on adjuvant endocrine therapy

Abstract Background: 80% of all breast cancers (BCs) are ER-positive (ER+). A significant number develop endocrine therapy resistance (ETR) . Clones develop in lymph nodes (LNs) which differ from the primary and these are implicated in ETR. A multiomics analysis of primary ER+ breast cancers, matched LN metastasis (LN+), if present, and matched recurrences (primary, nodal or distant) has been performed. Patients and Methods: The patients included are: Cohort A: 95 patients with matched primary and recurrent ER+ BC on different endocrine therapies. 35% had involved LNs at diagnosis. Recurrences: local in 59/95, concurrent local and nodal in 33/95, LN-only in 3/95. Median time to recurrence 4.5 years. Cohort B: 18 patients with ER+ LN+ BC who developed multiple recurrences (local and/or nodal, >3 consecutive recurrences/patient) on different lines of sequential endocrine therapy. Cohort C: 7 patients with ER+ breast cancer with multiple involved LNs treated with 3-6 months of neoadjuvant ET before surgery. Biopsies of primary and matched LNs performed at diagnosis and throughout treatment (3-4 timepoints/patient). Clinical response by serial ultrasound. Primary and LN samples (mean 12 samples/patient) were analysed together with normal DNA. Targeted RNAseq and DNA exome sequencing and whole-genome expression analysis was performed. Somatic mutations and copy number alterations (CNA) were determined, and differential gene expression analysis was performed. Validation of pathways implicated in ETR was by spatial NanoString GeoMx. All patients have long term follow-up. Results: Cohort A: A mean of 6 potential driver mutations identified by DNA sequencing in each primary BC (range 1-16). Most commonly mutated genes were PIK3CA, TP53, ERBB4, MAP3K1 and ERBB3. Multiple aberrations and a highly diverse mutational landscape were observed in all recurrences. In the majority of recurrences significant changes in variant allele frequency (VAF) were identified across several ETR-implicated genes and in over 50% new gains/losses were identified. Most frequently, losses were seen in ERBB3, ARID1A, HRAS and FOXA1 with gains in CDH1, NF1, PIK3CA, ESR1, TBX3 and GATA3 in recurrences vs primaries. Transcriptomic analysis revealed differentially expressed pathways including ER, HER2, GATA3, AKT, RAS and p63 signalling. Integrated analysis revealed several driver mutations with corresponding changes in upstream pathway activity. 33 patients had concurrent local and nodal recurrences and 52% had similar somatic mutation profiles in both with only minor variance in VAF. In 48%, 1 or more new potential driver mutations was identified in axillary nodes compared to recurrent primary cancers with losses in AKT1, CDH1 and TP53 being most common. Multiomics profiling of Cohorts B and C is complete and analysis underway. Discussion: This multiomics study is the largest cohort to-date of matched early and recurrent ER+/HER2- cancers. It sheds new light on the complex somatic and transcriptomic changes in local and nodal recurrent disease. The mechanisms of ETR are diverse and underlying mechanisms and clinically meaningful biomarkers including potentially actionable mutations and targets have been identified. Cohort C will uniquely capture and compare clonal evolution of breast cancer in primary and multiple matched lymph during neoadjuvant ET. Citation Format: Carlos Martinez-Perez, Charlene Kay, Rebecca Swan, Lorna Renshaw, J Michael Dixon, Arran K Turnbull. Multiomics analysis of ER+ breast cancer with matched primaries, lymph node metastases and recurrent cancers on adjuvant endocrine therapy [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-23-11.

Abstract PO1-05-07: Circulating tumor DNA dynamics in acelERA Breast Cancer: a Phase II study of giredestrant for estrogen receptor-positive, HER2-negative, previously treated advanced breast cancer

Abstract BACKGROUND Giredestrant (GIR) is a highly potent, oral, selective estrogen receptor antagonist and degrader (SERD) that exhibits robust estrogen receptor (ER) occupancy. The Phase II, randomized, open-label acelERA Breast Cancer (BC) study (NCT04576455) assessed GIR vs physician’s choice of endocrine therapy (PCET) in second- or third-line ER-positive, HER2-negative advanced BC (ER+, HER2– aBC). The study did not reach statistical significance for the primary endpoint of investigator-assessed progression-free survival (PFS); however, the benefit of GIR was of larger magnitude among patients (pts) with ESR1-mutated tumors (ESR1m; a common cause of acquired resistance to endocrine therapy [ET]). We present an exploratory biomarker analysis of circulating tumor (ct)DNA dynamics. METHODS Pts (n = 303) were randomized 1:1 to GIR or PCET (75% of pts had fulvestrant [FUL]; 25%, an aromatase inhibitor). Partial response (PR), stable disease (SD), and progressive disease (PD) were categorized by RECIST v1.1. Plasma samples taken at Cycle 1, Day 1 (C1D1; n = 229), while on treatment (tx) at C2D1 (n = 220), and at the end of therapy (EOT; n = 155) were evaluated with the FoundationOne Liquid CDx next-generation sequencing assay. Gene mutations were defined as variants with known or likely impact on protein function. Composite tumor fraction (cTF) was defined as the total estimated tumor ctDNA content in each sample, and was only evaluable for a subset of samples (137 C1D1; 136 C2D1; 99 EOT). cTF or ESR1 mutant allele frequency (MAF) changes were calculated as a percent change from C1D1. ESR1m clonality was estimated as variant tumor fraction/estimated tumor fraction. Statistical significance was evaluated using the Mann–Whitney test. RESULTS The overall mutation landscape remained relatively unchanged with GIR tx at C2D1 or EOT, except for ESR1m prevalence, which declined from 43% at C1D1 to 26% on tx and 27% at EOT. With PCET, ESR1m prevalence decreased from 34% at C1D1 to 29% on tx, but increased to 43% by EOT. There were no concordant changes for other top mutated genes in this study, including PIK3CA, TP53, or DNMT3A. cTF decreased on tx in 38/65 (59%) and 32/59 (54%) of evaluable pts with GIR and PCET, respectively; the median change from C1D1 was –23% with GIR compared with –5% with PCET or –15% with FUL. The median change in cTF levels on tx with GIR was significantly greater in pts with a PR (–88%) vs PD (+6%, p = 0.002) or SD (–19%, p = 0.004). The degree of cTF decline on tx with GIR was significantly higher in pts with baseline ESR1m (median change –58%) vs no ESR1m detected (+5%, p = 0.012). Pts with a clonal ESR1m had higher levels of cTF decline on tx vs pts with subclonal ESR1m, suggesting cTF dynamics are a function of tumor heterogeneity. ESR1 MAF decreased on tx in 93% of pts with baseline ESR1m on GIR, vs 60% with PCET and 70% with FUL. ESR1 MAF decline on tx was significantly higher with GIR vs PCET at both C2D1 and EOT (p < 0.0001). The average ESR1 MAF decline on tx with GIR was greater in pts with a PR (–97%) vs PD (–54%, p = 0.025) or SD (–48%, p = 0.051), and all seven GIR-treated pts with a PR showed a near or total loss of ESR1 MAF by C2D1. The ESR1m variants D538G and Y537X had a significantly greater decline in MAF on tx with GIR vs PCET or FUL (p < 0.0001). CONCLUSIONS Data show that cTF and ESR1m ctDNA dynamics were associated with clinical response to GIR in ER+, HER2– aBC. ESR1 MAF decline was significantly greater with GIR vs PCET or FUL. ESR1 MAF declined to a greater degree with GIR compared with cTF, which is consistent with the larger magnitude of PFS benefit seen with GIR in pts with ESR1m tumors. The specific ESR1 variants D538G and Y537X showed greater sensitivity to GIR compared with PCET or FUL. Citation Format: Ann Collier, Aditya Bardia, Joo Hyuk Sohn, Elgene Lim, Marianna Chavez, Miguel Martín, Jorge Martinalbo, Pablo Perez-Moreno, Heather Moore. Circulating tumor DNA dynamics in acelERA Breast Cancer: a Phase II study of giredestrant for estrogen receptor-positive, HER2-negative, previously treated advanced breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-05-07.