DNA Database Research Articles

Growing prominence of deep-sea life in marine bioprospecting

AbstractMarine bioprospecting, which involves the exploration of genetic and biochemical material from marine organisms, can be used towards addressing a broad range of public and environmental health applications such as disease treatment, diagnostics and bioremediation. Marine genetic resources are important reservoirs for such bioprospecting efforts; however, the extent to which they are used commercially for natural product discovery and the marine sources from which they are derived are not well understood. Here we introduce a comprehensive database of marine genes referenced in patent filings, the Marine Bioprospecting Patent database. It includes 92,550 protein-coding sequences associated with 4,779 patent filings, identified by analysing all relevant records from genetic sequence databases. Three companies alone—BASF, IFF and DuPont—included sequences from 949 species (more than half of referenced species with identified marine origin). Microbial life in the deep sea, a vast and remote biome predominantly beyond national jurisdiction, is already attracting substantial economic interest; the top ten patent holders have all filed marine gene patents referencing sequences from deep-sea life. Our findings provide an updated understanding of the marine bioprospecting landscape, contribute to the sustainable use of marine biodiversity and underscore the need for policymakers to ensure stewardship of deep-sea ecosystems.

Identification of Diptera Puparia in Forensic and Archeo-Funerary Contexts.

Diptera identification is fundamental in forensic entomology as well as in funerary archeoentomology, where the challenge is exacerbated by the presence of immature stages such as larvae and puparia. In these two developmental stages, specimens possess a very limited number of diagnostic features, and for puparia, there is also a lack of identification tools such as descriptions and identification keys. Morphological analysis, DNA-based techniques, and cuticular chemical analyses all show good potential for species identification; however, they also have some limitations. DNA-based identification is primarily hindered by the incompleteness of genetic databases and the presence of PCR inhibitors often co-extracted from the puparial cuticle. Chemical analysis of the cuticle is showing promising results, but this approach is also limited by the insufficient profile database and requires specific, expensive equipment, as well as trained personnel. Additionally, to ensure the repeatability of the analysis-a critical aspect in forensic investigations-and to preserve precious and unique specimens from museum collections, non-invasive protocols and techniques must be prioritized for species identification.

Cyanobacteria-cyanophage interactions between freshwater and marine ecosystems based on large-scale cyanophage genomic analysis

The disparities in harmful algal blooms dynamics are largely attributed to variations in cyanobacteria populations within aquatic ecosystems. However, cyanobacteria-cyanophage interactions and their role in shaping cyanobacterial populations has been previously underappreciated. To address this knowledge gap, we isolated and sequenced 42 cyanophages from diverse water sources in China, with the majority (n = 35) originating from freshwater sources. We designated these sequences as the “Novel Cyanophage Genome sequence Collection” (NCGC). NCGC displayed notable genetic variations, with 95 % (40/42) of the sequences representing previously unidentified taxonomic ranks. By integrating NCGC with public data of cyanophages and cyanobacteria, we found evidence for more frequent historical cyanobacteria-cyanophage interactions in freshwater ecosystems. This was evidenced by a higher prevalence of prophage integrase-related genes in freshwater cyanophages (37.97 %) than marine cyanophages (7.42 %). In addition, freshwater cyanophages could infect a broader range of cyanobacteria orders (n = 4) than marine ones (n = 0). Correspondingly, freshwater cyanobacteria harbored more defense systems per million base pairs in their genomes, indicating more frequent phage infections. Evolutionary and cyanophage epidemiological studies suggest that interactions between cyanobacteria and cyanophages in freshwater and marine ecosystems are interconnected, and that brackish water can act as a transitional zone for freshwater and marine cyanophages. In conclusion, our research significantly expands the genetic information database of cyanophage, offering a wider selection of cyanophages to control harmful cyanobacterial blooms. Additionally, we represent a pioneering large-scale and comprehensive analysis of cyanobacteria and cyanophage sequencing data, and it provides theoretical guidance for the application of cyanophages in different environments.

Morphological and Molecular Characterization of Three Myxosporean Species of the Genera Myxobolus, Henneguya, and Myxidium (Cnidaria: Myxozoa) Infecting Freshwater Fish, Isolated for the First Time in Japan.

The majority of myxosporean species (Cnidaria: Myxozoa) of the genera Myxobolus (35 species), Henneguya (8 species), and Myxidium (9 species) from freshwater or brackish fish in Japan were recorded more than 30 years ago (accumulatively 81.1% [43/53]). The re-discovery and molecular-genetic characterization of these species is a current research priority. During our myxosporean survey in Japanese freshwater fish, we detected three species that had never been recorded in Japan, but in the Russian Far East (Sakhalin Island, and Maritime Province): Myxobolus tribolodonus sp. n., forming cysts in the gills of Tribolodon sachalinensis (syn. M. marinus sensu Aseeva, 2000; M. marinus sensu Sokolov et Frolova, 2015, recorded from the gills of Pseudaspius (syn. Tribolodon) spp.); Henneguya pungitii Achmerov, 1953, forming cysts in the subcutis of external skin and buccal submucosa of Pungitius sinensis; and Myxidium salvelini Konovalov et Shulman, 1966, in the urinary bladder of Oncorhynchus masou ishikawae. These new isolates were characterized by integrated taxonomic approaches, i.e., myxospore morphology and molecular-genetic characterization of the small subunit ribosomal RNA gene (SSU rDNA). These new isolates were phylogenetically differentiated from any species whose SSU rDNA sequences were deposited in the DNA databases, and concurrently compared with recorded species based on classical morphological criteria. All three species were differentiated from myxosporeans previously recorded in Japan, indicating new distribution records out of the Russian Far East. For reliable species identification, accumulation of at least SSU rDNA sequences of known species worldwide is critically important.

Biomedical literature mining: graph kernel-based learning for gene–gene interaction extraction

The supervised machine learning method is often used for biomedical relationship extraction. The disadvantage is that it requires much time and money to manually establish an annotated dataset. Based on distant supervision, the knowledge base is combined with the corpus, thus, the training corpus can be automatically annotated. As many biomedical databases provide knowledge bases for study with a limited number of annotated corpora, this method is practical in biomedicine. The clinical significance of each patient’s genetic makeup can be understood based on the healthcare provider’s genetic database. Unfortunately, the lack of previous biomedical relationship extraction studies focuses on gene–gene interaction. The main purpose of this study is to develop extraction methods for gene–gene interactions that can help explain the heritability of human complex diseases. This study referred to the information on gene–gene interactions in the KEGG PATHWAY database, the abstracts in PubMed were adopted to generate the training sample set, and the graph kernel method was adopted to extract gene–gene interactions. The best assessment result was an F1-score of 0.79. Our developed distant supervision method automatically finds sentences through the corpus without manual labeling for extracting gene–gene interactions, which can effectively reduce the time cost for manual annotation data; moreover, the relationship extraction method based on a graph kernel can be successfully applied to extract gene–gene interactions. In this way, the results of this study are expected to help achieve precision medicine.

The complete chloroplast genome of rhododendron williamsianum (ericaceae)

Rhododendron williamsianum Rehder & E. H. Wilson 1913, is a plant with important horticultural value. Here we report its chloroplast genome. The total length of the chloroplast genome was 205,424 bp, with a GC content of 35.8%. It consisted of a 107,968 bp large single copy, a 2606 bp small single copy, and a pair of 47,425 bp inverted repeats separating them. Within the chloroplast genome, there were a total of 110 unique genes, which included 76 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Our phylogenetic analyses indicated that R. williamsianum was closely genetically related to R. sutchuenense and R. jingangshanicum. The findings from this study not only contribute to the genetic database of Rhododendron plants but also have implications for evolutionary research within the family Ericaceae.

Changing Australia's trading language has enhanced the implementation of objective carcase measurement technologies.

In 2016 an Australian project, the Advanced Livestock Measurement Technologies project (ALMTech), was initiated to accelerate the development and implementation of technologies that measure lean meat yield and eating quality. This led to the commercial testing, and implementation of a range of new technologies in the lamb, beef, and pork industries. For measuring lean meat yield %, these technologies included dual energy X-ray absorptiometry, hand-held microwave systems, and 3-D imaging systems. For measuring beef rib-eye traits and intramuscular fat %, both pre- and post-chilling technologies were developed. Post-chilling, a range of camera systems and near infrared spectrophotometers were developed. While pre-chilling, technologies included insertable needle probes, nuclear magnetic resonance, and X-ray systems. Initially these technologies were trained to predict the pre-existing traits already traded upon within industry. However, this approach was limiting because the technologies could measure attributes that were either non-existent in the trading language, were superior as calibrating standards, or more accurately reflected value than the pre-existing trait. Therefore, we introduced IMF% into the trading language for both beef and sheep meat, and carcase lean%, fat%, and bone% for sheep meat. These new technologies and the traits that they predict have delivered multiple benefits. Technology provider-companies are instilled with the confidence to commercialise due to the provision of achievable accreditation standards. Processors have the confidence to invest in these technologies and establish payment grids based upon their measurements. And lastly, it has enhanced data flow into genetic databases, industry data systems (MSA), and as feedback to producers.

Report: Establishment of a DNA Fingerprinting Database in the United Arab Emirates

DNA fingerprinting represents a pivotal advancement in forensic science since the 1980s. Recognizing its significance, the United Arab Emirates (UAE) implemented the first law pertaining to this technology through Federal Decree by Law No. (39) of 2023, titled ‘Concerning the Regulation of the Federal DNA Fingerprinting Database’. This law came into effect on 1 November 2023. The report will delve into the concept of DNA fingerprinting and its database, focusing on the administration of the Federal DNA Fingerprinting Database and its practical applications. The discussion will cover various aspects, including the origins of biological specimens, managing biological samples preservation and execution, the retention duration of DNA fingerprinting, and the measures in place to ensure legal safeguards for genetic fingerprint databases. This brief overview endeavours to offer a concise insight into the legal framework and operational factors concerning DNA fingerprinting in the context of recent legislative changes.

Long-read sequencing analysis of the chloroplast genome in sandalwood (Santalum album L.)

Abstract Santalum album L. (sandalwood) is a tree species renowned for producing essential oil with high economic value. However, the potential of S. album faces significant challenges due to unsustainable management practices within its natural population. Genetic techniques present a viable solution to mitigating S. album sustainability challenges, offering insights crucial for its conservation and long-term management. Hence, there is a recognised necessity to furnish chloroplast genome information for S. album, thereby augmenting the existing genetic database and facilitating the formulation of effective conservation strategies for the sustainability of this species. This research aims to obtain the long-read sequence data using MinION from Oxford Nanopore Technologies for generating the S. album chloroplast genome, and to analyse genetic relationships of S. album with other species through a phylogenetic tree. The study successfully generated a completed chloroplast genome of S. album, consisting of 143.261 base pairs, which has the potential to be used in various applications of genetic analysis. These applications hold promise for the future of S. album conservation, offering new avenues for sustainable management and preservation.

Value of DNA mixture-to-mixture comparisons within an operational context

Since 1995, national forensic DNA databases have used a maximum number of contributors, and a minimum number of loci to reduce the risk of providing false leads. DNA profiles of biological traces that do not meet these criteria cannot be loaded into these databases. In 2023, about 10 % of more than 15,000 trace DNA profiles analyzed in western Switzerland were not compared at the national level, even though they were considered to be interpretable, mainly because they contained the DNA from more than two persons. In this situation, police services can request local comparisons with DNA profiles of known persons and/or with other traces, but this occurs in only a small proportion of cases, so that DNA mixtures are rarely used to help detect potential series. The development of probabilistic genotyping software and its associated tools have made possible the efficient performance of this type of comparison, which is based on likelihood ratios (LR) rather than on the number of shared alleles.To highlight potential common contributors for investigation and intelligence purposes, the present study used the mixture-to-mixture tool of the software STRmix v2.7 to compare 235 DNA profiles that cannot be searched the Swiss DNA database. These DNA profiles originated from traces collected by six different police services in 2021 and 2022. Traces were selected by the police based on information that indicated that they were from potential series. Associations between profiles were compared with expected investigative associations to define the value of this approach. Among the 27,495 pairwise comparisons of DNA profiles, 88 pairs (0.3 %) showed at least one potential common contributor when using a LR threshold of 1000. Of these 88 pairs, 60 (68.2 %) were qualified by the police services as “expected” (60/88), 22 (25.0 %) as “possible”, and six (6.8 %) as “unexpected”. Although it is important to consider the limits of this approach (e.g., adventitious or missed associations, cost/benefit evaluation, integration of DNA mixture comparison in the process), these findings indicate that non CODIS loadable DNA mixtures could provide police agencies with information concerning potential series at both the local and national level.

Discordance of Penta D x.4 microvariant alleles results between three capillary electrophoresis and one massively parallel sequencing short tandem repeat kits

Forensic Biology is contingent upon matching DNA profiles between a crime sample and a reference sample. There are several capillary electrophoresis kits available to generate a short tandem repeat (STR) profile from DNA samples, while newer methods using massively parallel sequencing are slowly being implemented in forensic laboratories worldwide. During evaluation of a newer capillary electrophoresis kit, Applied Biosystems™ VeriFiler™ Plus, a discordance was observed in the Penta D locus. The previous kit, Promega PowerPlex 21® System produced a 13.4,14 genotype, whilst VeriFiler™ Plus produced a 14,14 genotype. An expanded investigation into Penta D microvariant alleles revealed that multiple discordances were observed for DNA profiles containing larger x.4 variants. There was full concordance between PowerPlex® 21 and QIAGEN Investigator® 26plex, however discordances were observed between VeriFiler™ Plus and the other three kits tested, including the massively parallel sequencing kit, Verogen ForenSeq® MainstAY. Notably, four of these discordances resulted in null alleles with the VeriFiler™ Plus kit. A review of the Penta D DNA sequences in MainstAY revealed fully concordant microvariant alleles involved deletions within the repeat region, whilst variability in the discordances observed were dependent on the location of the variation outside the repeat region and the analysis method used. Variations observed within the 5’ flanking region produced the same allele designation across all capillary electrophoresis kits. However, deletions within the 3’ region either produced a null allele for VeriFiler™ Plus where the deletion is thought to overlap the primer binding site, or microvariant alleles for the PowerPlex® 21 and Investigator 26plex kits, which produced longer Penta D amplicons. The discovery of these variations in the Penta D flanking sequences is informative as it increases the awareness of Penta D discordances between different kit chemistries in nominated reference DNA profile comparisons and DNA database searching and matching alike, and provides support for this phenomenon when providing evidence as to the admissibility of such results in trial proceedings.

Genetic Characteristics of a Large Pediatric Cohort of Patients with Inborn Errors of Immunity: Single-Center Experience.

More than 450 genetic defects result in inborn errors of immunity (IEI). Their individual prevalence in specific cohorts is influenced by national characteristics and other factors. We present results of genetic testing conducted in 1809 Russian children with IEI. Genetic defects confirming IEI were found in 1112 out of 1809 (61.5%) probands. These defects included variants in 118 single genes (87.9% of patients) and aberrations in 6 chromosomes (11.8%). Notably, three patients harbored pathogenic variants in more than one IEI gene. Large deletions constituted 5% of all defects. Out of the 799 original variants, 350 (44%) have not been described previously. Rare genetic defects (10 or fewer patients per gene) were identified in 20% of the patients. Among 967 probands with germline variants, defects were inherited in an autosomal dominant manner in 29%, X-linked in 34%, and autosomal recessive in 37%. Four females with non-random X-inactivation exhibited symptoms of X-linked diseases (BTK, WAS, CYBB, IKBKG gene defects). Despite a relatively low rate of consanguinity in Russia, 47.9% of autosomal recessive gene defects were found in a homozygous state. Notably, 28% of these cases carried "Slavic" mutation of the NBN gene or known hot-spot mutations in other genes. The diversity of IEI genetic forms and the high frequency of newly described variants underscore the genetic heterogeneity within the Russian IEI group. The new variants identified in this extensive cohort will enrich genetic databases.

Novel Variants in ABCA4-Related Retinopathies with Structural Re-Assessment of Variants of Uncertain Significance

Introduction: Conclusive molecular genetic diagnoses in inherited retinal diseases remains a major challenge due to the large number of variants of uncertain significance (VUS) identified in genetic testing. Here, we determined the genotypic and phenotypic spectrum of ABCA4 gene variants in a cohort of Canadian inherited retinal dystrophy subjects. Methods: This retrospective study evaluated 64 subjects with an inherited retinal dystrophy diagnosis with variants in the ABCA4 gene. Pathogenicity of variants was assessed by comparison to genetic databases and in silico modelling. ABCA4 variants classified as VUS were further evaluated using a cryo-electron structural model of the ABCA4 protein to predict impact on protein function and were also assessed for evolutionary conservation. Results: Conclusive disease-causing biallelic ABCA4 variants were detected in 52 subjects with either Stargardt’s disease, cone-rod dystrophy, macular dystrophy, or pattern dystrophy. A further 14 variants were novel comprising 1 nonsense, 1 frameshift, 3 splicing, and 9 missense variants. Based on in silico modelling, protein modelling and evolutionary conservation from human to zebrafish, we re-classified 5 of these as pathogenic and a further 3 as likely pathogenic. We also added to the ABCA4 phenotypic spectrum seen with four known pathogenic variants (c.2161-2A>G; Leu296Cysfs*4; Arg1640Gln; and Pro1380Leu). Conclusions: This study expands the genotypic and phenotypic spectrum of ABCA4 disease-associated variants. By panel-based genetic testing, we identified 14 novel ABCA4 variants of which 8 were determined to be disease-causing or likely disease-causing. These methodologies could circumvent somewhat the need for labour intensive in vitro and in vivo assessments of novel ABCA4 variants.

Perspectives on sperm donor anonymity: insights from donor-conceived adults in Belgium.

Are donor-conceived adults in Belgium interested in obtaining donor information, and do these interests vary based on their family backgrounds? Donor-conceived adults express a significant interest in obtaining donor-related information, with the highest interest reported by offspring from heterosexual couples compared to those from lesbian couple-parented or single-parent families. In Belgium, sperm donation is mainly anonymous, but the rise of direct-to-consumer genetic testing challenges this anonymity. This was a cross-sectional study involving an online nationwide survey conducted from July 2022 to October 2023. Participants, aged 18years and older and being aware of their anonymous sperm donor-conceived status, were recruited through various channels. A total of 203 participants were included: 62.6% grew up in heterosexual families with infertile fathers, 26.1% with lesbian couples, 8.4% with single parents, and 3.0% in various or diverse family structures. The survey was available in both French and Dutch and consisted of 43 questions, including a mix of yes/no questions and multiple-choice items. The average age of disclosure was 16.5 years, with notably later disclosure in heterosexual couple-parented households. A substantial 82.8% of donor-conceived individuals expressed a keen interest in obtaining non-personally identifiable donor information, while 69% were curious about personally identifiable donor data. Furthermore, 61.6% conveyed a desire for personal contact with their donors, and 26.6% advocated for the inclusion of the donor's name on their birth certificates. Participants raised in lesbian two-parent families exhibited the lowest level of interest in donor-related information compared with those raised in other family structures. An overwhelming 90.1% wondered about the possibility of having half-siblings from the same sperm donor. Analysis of survey responses on DNA database registration revealed that 55.2% of donor-conceived offspring were already registered, with 68.8% discovering the same donor offspring and 30.4% successfully locating their donors. Compared to individuals from other family structures, those raised in heterosexual couple-parented households exhibit a less positive attitude toward their conception through anonymous sperm donation. About 61.6% of donor-conceived individuals reported experiencing distinct emotions compared to their peers, while 44.1% encountered psychological difficulties related to anonymous sperm donation, primarily attributed to late disclosure. The majority supported the idea of informing the donor about the number of children he facilitated to conceive. Lastly, the study highlighted that 21.2% of donor-conceived adults considered becoming donors themselves, and 31.3% expressed willingness to use an anonymous donor whenever faced with fertility challenges. Our sample size may not fully represent all adults conceived through anonymous sperm donation in Belgium. Participation bias may have influenced the results, especially due to the overrepresentation of participants from heterosexual couples. Additionally, an association exists between individuals raised by heterosexual couples and late disclosure, complicating the analysis by introducing a confounding factor. The findings of this study contribute to a better understanding of the needs and preferences of donor-conceived adults, with significant potential impact on patient education and healthcare policy. Study funding was not obtained for this research. There are no conflicts of interest to disclose. N/A.

Allelic frequency of pathogenic α1-antitrypsin variants in the Japanese population: Results from a survey of open Japanese genetic variation databases

α1-antitrypsin deficiency (AATD) is a hereditary disorder with a global prevalence that differs across regions. AATD is highly prevalent in Europe and North America but rarely found in Asian countries, including Japan, possibly because of the founder effect of the pathogenic SERPINA1 variants PI*Z and PI*S. However, AATD remains underdiagnosed even in high-prevalence and low-prevalence regions, possibly because of lack of awareness. In this study, we surveyed open Japanese genetic variation databases to estimate AATD prevalence in Japan. We identified allelic frequencies (AFs) of 5 among the 14 major pathogenic SERPINA1 variants from three datasets, collectively derived from 63,119 Japanese participants. The mean AF was determined to be 8.56 × 10−4 (95% confidence interval [CI]: 6.43 × 10−4 to 1.12 × 10−3). Given that this represents the entire Japanese population, one AATD patient was speculated to be born per 1.37 × 106 births (95% CI: 7.97 × 105 to 2.42 × 106) in Japan. Our results support the prevailing notion that AATD is extremely rare in Japan.

“The truth should not be hidden”: Experiences and recommendations of individuals making NPE discoveries through genetic genealogy databases

PurposeFueled by direct-to-consumer (DTC) genetic testing and genetic-relative finder services, some participants in genetic genealogy databases are making “not parent expected” (NPE) discoveries. To better understand experiences of this phenomenon, we surveyed a large cohort of users of genetic relative finder (GRF) services concerning their experiences after an NPE discovery. MethodsUsing thematic analysis, we analyzed responses from a cohort of GRF users (n = 646) to open-ended survey items to understand these experiences and their recommendations for DTC genetic testing companies and other GRF users. ResultsWe found that individuals had both positive and negative emotional experiences related to the NPE discovery. Positive aspects included deeper self-understanding, connecting with new family members, and uncovering answers to questions. Negative aspects included rejection by new genetic relatives, inability to seek answers from relatives who had already died, and impairment of family relationships, especially with mothers. For many participants, the challenges after the discovery nevertheless felt worthwhile because the truth was uncovered. Perhaps notably, some participants suggested enhanced warnings prediscovery and improved support after discovery from companies who provide DTC genetic testing services. ConclusionGRF services are powerful tools for family research and genealogy. Despite some possible positive and worthwhile experiences arising from making an NPE discovery, GRF users risk dealing with this potentially life-altering experience without adequate support. Participants in this study recommended an increase in resources from DTC genetic testing companies that could help users anticipate and navigate an NPE discovery.

P-566 Addressing ethnic underrepresentation in carrier screening: prioritizing comprehensive variant curation over ClinVar-based automated analysis

Abstract Study question How does the use of a ClinVar-based approach in Carrier Genetic Screening (CGS) affect the efficiency and accuracy of carrier detection analysis? Summary answer For CGS, comprehensive variant curation, not automated analysis alone, addresses risk from under-representation of diverse populations in genetic databases. What is known already Next-generation sequencing (NGS) analyses in Carrier Screening (CS) yield numerous variants per patient requiring interpretation for pathogenicity assessment. Public variant databases aid in the curation process, clinical interpretation, and genomic data sharing, reducing error risks and diagnostic delays. Consequently, an increasing number of genetic laboratories are integrating these databases into their workflows. However, over-representation of certain ethnic groups persists due to genetic inequality, as these databases primarily contain variants previously reported in patients and manually recorded. This lack of ethnic diversity in human genomic studies and databases can lead to inaccurate risk assessment and inadequate interventions in under-studied populations. Study design, size, duration Retrospective analysis involved 3886 patients of various ethnicities examined between June 2021 and March 2023. They were grouped according to self-reported ethnicity: African(54), Asian(43), Mediterranean(689), European/Caucasian(2402), Latino(449) and not reported(249). Participants/materials, setting, methods Patients were categorized based on their self-reported ethnicity after undergoing analysis with a Carrier Screening (CS) panel of 300 genes, which included autosomal recessive and X-linked disorders, using Next-Generation Sequencing (NGS). Complete variant curation (CCV) was conducted using the American College of Medical Genetics and Genomics(ACMG) and ClinGen guidelines for variant interpretation. The average number of variants per patient was calculated for both the automated process using only the ClinVar database and the CCV performed. Main results and the role of chance Upon evaluating the number of variants identified per patient,, 1.51 variants/patient (v/p) were observed when CCV, while 1.27 v/p would have been detected using only ClinVar (automated process). In summary, ClinVar accounted for 88% of all variants identified with CCV. Significant differences in variant detection were observed across ethnicities. The percentage of variants not detected by the automatic process were as follows: 21.95% in Asian ethnicity, 17.84% in African, 13.99% in Latino, 11.88% in Mediterranean, 10.97% in European/Caucasian and 10.70% in patients who did not report ethnicity. Among these, Asian and African ethnic groups had the lowest percentage of variants detected by ClinVar 78.05% and 82.16%, respectively. In the Asian group, 0.95 v/p were identified, while in the African group, 1.70 v/p were identified. Limitations, reasons for caution Data was collected based on self-reported ethnicity, which may not always accurately reflect true ancestry. Additionally, the sample size for certain ethnicities was relatively small. Variant classification relied on information available in databases or literature at the time of the study, potentially subject to updates or revisions in the future. Wider implications of the findings This study underscores the limitations of automated analysis in detecting all variants identified by CCV across ethnicities, highlighting genetic disparities present in mutation databases like ClinVar. The findings emphasize the importance of implementing CCV in Carrier Screening tests to effectively mitigate reproductive risks across diverse ethnic groups. Trial registration number not applicable

Evaluation of genetic markers for the metabarcoding of Australian marsupials from predator scats

Context DNA recovered from predator faeces (scats) can be used to determine the presence of fauna and shed light on their life histories and inter-species interactions. DNA metabarcoding, which involves concurrent amplification and sequencing of DNA from multiple taxa, represents an important advance by enabling the simultaneous detection of multiple species from such samples. Although an attractive proposition, metabarcoding requires ‘universally’ applicable genetic markers that can discriminate among a broad range of taxa, while also targeting sequences that are sufficiently short to be amplified from degraded DNA. Aims To identify, evaluate, and test metabarcoding DNA markers suitable for the detection of marsupials and other Australian fauna from terrestrial predator scats found in nature. Methods We apply a bioinformatic approach using publicly available DNA databases and a locally derived and marker-specific reference-DNA database to evaluate the diagnostic ability and likelihood of amplification of candidate metabarcoding markers for marsupials and other taxa that may be consumed by predators. Key results We identify two markers (12SV5 and 16SMam) that are suitable for use and successfully identify marsupial sequences at a high level of resolution. These markers work best in combination because they bring complementary levels of primer specificity and diagnostic ability in detecting multiple prey species as well as the predator. We also show that these samples work well in predator scats sampled from the wild in Tasmania. Conclusions These markers provide a useful tool for surveying mammalian predators and their prey and could also be applied to eDNA analyses from other sample types. Improvements to the reference database and further development of markers targeting different taxonomic groups will improve the resolution and usefulness of this approach. Implications Metabarcoding of predator scats provides a potent approach to non-invasive wildlife survey that offers the opportunity for the detection of multiple species across all vertebrates.

The advent of forensic DNA databases: It’s time to agree on some international governance principles!

National forensic DNA databases are a valuable investigative tool, that have the potential to increase the efficacy of criminal investigations. Their unfettered expansion in recent years raises unsettling ethical issues that require close attention. DNA database expansion threatens the rights to privacy, non-discrimination, and equality, and can undermine public trust in government. This perspective piece relies on data from an international mapping study of Forensic DNA Databases to document the expansion of these databases, highlight the ethical issues they raise, and propose key recommendations for more responsible use of this infrastructure.

Disruptive data: How access and benefit-sharing discourses structured ideas and decisions during the Convention on Biological Diversity negotiations over digital sequence information from 2016 to 2022

In 2016, negotiations of the Convention on Biological Diversity on access and benefit-sharing policies were shaken up by the emergence of digital sequence information (DSI) as policy issue. Open access to DSI on genetic resources in genetic databases is standard practice in data-driven biological research, but such access was argued to bypass access and benefit-sharing policies of the Convention. As Parties and observers had to take a position on governing DSI, this research investigated the influence of discourses on the negotiations through argumentative discourse analysis. Actors in international environmental negotiations mobilize ‘background’ discourses – both consciously and unconsciously – to define and ‘foreground’ issues, which in turn shape negotiation and decision-making processes. The analysis shows that existing discourses on access and benefit-sharing and biodiversity structured actors’ statements aimed at defining DSI, thus applying and redefining access and benefit-sharing principles in the context of DSI. Actors with similar and slightly varying interests formed discourse-coalitions on the basis of shared storylines. Developing countries formed a separate discourse-coalition to push for DSI regulation wherein ideas about sustainable development and environmental justice were integrated, and to a lesser extent about biopiracy (the notion that open access to DSI enables the misappropriation of genetic resources and associated traditional knowledge). In response, developed countries adopted narratives put forward by industry and research, advocating that open access to DSI is essential for science, biodiversity conservation and sustainable development. A third coalition, consisting of Indigenous peoples and local communities and civil society, also mobilized environmental justice and biopiracy discourses, but more prominently a unique holistic discourse on nature. Finally, holistic and biopiracy discourses were marginalized in official negotiation documents, while scientific and sustainable development discourses were adopted in official negotiation documents. The research provides a novel understanding of the DSI-negotiations as discursive politics, and highlights how different positionalities in discourses structure and are structured by statements in this political arena.