Peter Frandsen

Endometrial carcinoma (EC) is a common gynecological cancer with rising incidence driven by obesity and aging populations. Accurate and timely molecular classification is critical for guiding personalized oncology treatment, especially in early-stage high-grade endometrioid carcinoma. Here we present a large scale, retrospective multicenter validation of a novel POLE-POLD1 mutation assay for use in molecular characterization of EC. We evaluated the analytical performance and robustness of the novel Idylla™ POLE-POLD1 Mutation Assay, a cartridge-based PCR platform optimized for FFPE tissue. Performance comparators were established NGS reference methods. Overall, 544 formalin-fixed, paraffin embedded (FFPE) EC cases from diagnostic pathology of ten centers in Europe and North America were included. Of 544 samples, 520 revealed POLE-POLD1 test and comparator results, yielding an overall concordance of 97% (PPA of 0.96 and NPA of 0.98). Discordance was limited to a small number of variants and was often associated with low input material or the detection of multiple concurrent variants. The assay demonstrated robust performance across variable FFPE slice thickness (4–10 μm), number of Sects. (1–6), and tumor cell percentage (from 10% to 100%), with an assay invalid rate of only 2.76%. Moreover, the Idylla™ platform offers rapid results (~ 2 h) with minimal workflow complexity. The Idylla™ POLE-POLD1 Mutation Assay is a reliable and rapid diagnostic assay for clinically relevant molecular classification of EC, demonstrating high concordance with NGS and robust performance under routine pathology conditions. Whereas NGS provides comprehensive genomic profiling, including rare variants of unknown pathogenic significance, the Idylla™ assay targets treatment relevant pathogenic variants with rapid turnaround time, supporting timely, individualized treatment decisions.

Summary: Establishing the genetic and geographic structure of populations is fundamental both to understand their evolutionary past and preserve their future, especially for endangered species. Nevertheless, the patterns of genetic population structure are unknown for most endangered species, including some of our closest living relatives. This is the case of bonobos ( Pan paniscus ) which together with chimpanzees ( Pan troglodytes ) are humans’ closest living relatives. Chimpanzees live across equatorial Africa and are classified into four subspecies (Groves, 2001), with some genetic population substructure even within subspecies. Conversely, bonobos live exclusively in the Democratic Republic of Congo and are considered a homogeneous group with low genetic diversity (Fischer et al. 2011) despite some population structure inferred from mtDNA. Nevertheless, mtDNA aside, their genetic structure remains unknown, hampering our understanding of the species and conservation efforts. Placing bonobos’ genetics in space is however challenging because, being endangered, only non-invasive sampling is possible for wild individuals. Here, we jointly analyse the exomes and mtDNA from 20 wild-born bonobos, the whole-genomes of 10 captive bonobos and the mtDNA of 61 wild individuals. We identify three genetically distinct bonobo groups of inferred Central, Western and Far-Western geographic origin within the bonobo range. We estimate the split time between the central and western populations to ∼145,000 years ago, and genetic differentiation to be in the order of that of the closest chimpanzee subspecies. We identify putative signatures of differential genetic adaptation among populations for genes associated with homeostasis, metabolism and the nervous system. Furthermore, our estimated long-term N _e for Far-West (∼3,000) is among the lowest estimated for any great ape lineage. Our results highlight the need of attention to bonobo substructure, both in terms of research and conservation. Highlights: – We identified three genetically distinct populations of bonobos, inferred as having Central, Western and Far-Western geographic origin within the species range. The estimated split time is ∼145,000 years ago for the Central and Western populations, and ∼60,000 years ago for the two Western populations. – The genetic differentiation between the Central and Far-Western bonobo populations is in the order of that between Central and Eastern chimpanzee subspecies, while the genetic differentiation among Western bonobo populations is similar to that among human groups. – Once substructure is accounted for, we infer a long-term effective population size ( N _e ) of only ∼3,000 for Far-Western bonobos, genetic isolation and inbreeding.

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.

Western chimpanzees ( Pan troglodytes verus ) are Critically Endangered and Guinea is a key stronghold for this subspecies. However, Guinea is also rich in minerals with some of the highest‐grade iron‐ore deposits in the world. Specifically, the Nimba Mountains, home to western chimpanzees, is one of the sites under consideration for mining activities. To assess the impact of mining activities in the area, we used non‐invasive genetic sampling to estimate chimpanzee population size, sex ratio, community composition, and range boundaries on the western flank of the massif. The level of genetic diversity and affinity between communities was estimated and recommendations for future genetic censusing provided. Between 2003 and 2018, we collected 999 fecal samples of which 663 were analyzed using a panel of 26 microsatellites. We identified a minimum of 136 chimpanzees in four communities, with evidence of migratory events, a high level of shared ancestry and genetic diversity. We assessed sampling intensities and capture rates for each community. Saturation was reached in two communities with sampling between 3.2 and 4.3 times the estimated number of chimpanzees. Our findings highlight the utility of genetic censusing for temporal monitoring of ape abundance, as well as capturing migratory events and gauging genetic diversity and population viability over time. We recommend genetic sampling, combined with camera trapping, for use in future Environmental and Social Impact Assessments, as these methods can yield robust baselines for implementing the mitigation hierarchy, future biomonitoring and conservation management.

Background: Numerous Ebola virus outbreaks have occurred in Equatorial Africa over the past decades. Besides human fatalities, gorillas and chimpanzees have also succumbed to the fatal virus. The 2004 outbreak at the Odzala-Kokoua National Park (Republic of Congo) alone caused a severe decline in the resident western lowland gorilla ( Gorilla gorilla gorilla ) population, with a 95% mortality rate. Here, we explore the immediate genetic impact of the Ebola outbreak in the western lowland gorilla population. Results: Associations with survivorship were evaluated by utilizing DNA obtained from fecal samples from 16 gorilla individuals declared missing after the outbreak (non-survivors) and 15 individuals observed before and after the epidemic (survivors). We used a target enrichment approach to capture the sequences of 123 genes previously associated with immunology and Ebola virus resistance and additionally analyzed the gut microbiome which could influence the survival after an infection. Our results indicate no changes in the population genetic diversity before and after the Ebola outbreak, and no significant differences in microbial community composition between survivors and non-survivors. However, and despite the low power for an association analysis, we do detect six nominally significant missense mutations in four genes that might be candidate variants associated with an increased chance of survival. Conclusion: This study offers the first insight to the genetics of a wild great ape population before and after an Ebola outbreak using target capture experiments from fecal samples, and presents a list of candidate loci that may have facilitated their survival.

Populations of the common chimpanzee (Pan troglodytes) are in an impending risk of going extinct in the wild as a consequence of damaging anthropogenic impact on their natural habitat and illegal pet and bushmeat trade. Conservation management programmes for the chimpanzee have been established outside their natural range (ex situ), and chimpanzees from these programmes could potentially be used to supplement future conservation initiatives in the wild (in situ). However, these programmes have often suffered from inadequate information about the geographical origin and subspecies ancestry of the founders. Here, we present a newly designed capture array with ~60,000 ancestry informative markers used to infer ancestry of individual chimpanzees in ex situ populations and determine geographical origin of confiscated sanctuary individuals. From a test panel of 167 chimpanzees with unknown origins or subspecies labels, we identify 90 suitable non-admixed individuals in the European Association of Zoos and Aquaria (EAZA) Ex situ Programme (EEP). Equally important, another 46 individuals have been identified with admixed subspecies ancestries, which therefore over time, should be naturally phased out of the breeding populations. With potential for future re-introduction to the wild, we determine the geographical origin of 31 individuals that were confiscated from the illegal trade and demonstrate the promises of using non-invasive sampling in future conservation action plans. Collectively, our genomic approach provides an exemplar for ex situ management of endangered species and offers an efficient tool in future in situ efforts to combat the illegal wildlife trade.

The most frequent chromosomal aneuploidy in humans, trisomy 21 (T21), has only been reported twice in the common chimpanzee (Pan troglodytes). In both cases, phenotypical traits were comparable to human T21 traits and were formally diagnosed through conventional techniques like chromosomal staining. Here, we present the first application of sequencing data as a diagnostic tool to compare chromosomal dosage imbalances in chimpanzees. By calculating the ratio of mapped reads on each chromosome between a case and a control, we observe a trisomic dosage imbalance on chromosome 21 in the case individual. While case numbers remain too low to be conclusive, evidence suggests that prevalence of T21 in chimpanzees could be lower than in humans. In future genetic testing of captive ape populations, the genetic diagnostic methods presented here will allow for a reliable and time-efficient assessment of the global prevalence of chromosomal dose imbalances in chimpanzees and other great apes.