Assessment of the effectiveness of the EUROFORGEN NAME and Precision ID Ancestry panel markers for ancestry investigations

The EUROFORGEN NAME panel is a regional ancestry panel designed to differentiate individuals from the Middle East, North Africa, and Europe. The first version of the panel was developed for the MassARRAY system and included 111 SNPs. Here, a custom AmpliSeq EUROFORGEN NAME panel with 102 of the original 111 loci was used to sequence 1098 individuals from 14 populations from Europe, the Middle East, North Africa, North-East Africa, and South-Central Asia. These samples were also sequenced with a global ancestry panel, the Precision ID Ancestry Panel. The GenoGeographer software was used to assign the AIM profiles to reference populations and calculate the weight of the evidence as likelihood ratios. The combination of the EUROFORGEN NAME and Precision ID Ancestry panels led to fewer ambiguous assignments, especially for individuals from the Middle East and South-Central Asia. The likelihood ratios showed that North African individuals could be separated from European and Middle Eastern individuals using the Precision ID Ancestry Panel. The separation improved with the addition of the EUROFORGEN NAME panel. The analyses also showed that the separation of Middle Eastern populations from European and South-Central Asian populations was challenging even when both panels were applied

Lab Retriever: a software tool for calculating likelihood ratios incorporating a probability of drop-out for forensic DNA profiles

BACKGROUND: Technological advances have enabled the analysis of very small amounts of DNA in forensic cases. However, the DNA profiles from such evidence are frequently incomplete and can contain contributions from multiple individuals. The complexity of such samples confounds the assessment of the statistical weight of such evidence. One approach to account for this uncertainty is to use a likelihood ratio framework to compare the probability of the evidence profile under different scenarios. While researchers favor the likelihood ratio framework, few open-source software solutions with a graphical user interface implementing these calculations are available for practicing forensic scientists. RESULTS: To address this need, we developed Lab Retriever, an open-source, freely available program that forensic scientists can use to calculate likelihood ratios for complex DNA profiles. Lab Retriever adds a graphical user interface, written primarily in JavaScript, on top of a C++ implementation of the previously published R code of Balding. We redesigned parts of the original Balding algorithm to improve computational speed. In addition to incorporating a probability of allelic drop-out and other critical parameters, Lab Retriever computes likelihood ratios for hypotheses that can include up to four unknown contributors to a mixed sample. These computations are completed nearly instantaneously on a modern PC or Mac computer. CONCLUSIONS: Lab Retriever provides a practical software solution to forensic scientists who wish to assess the statistical weight of evidence for complex DNA profiles. Executable versions of the program are freely available for Mac OSX and Windows operating systems. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-015-0740-8) contains supplementary material, which is available to authorized users

Evaluation of the Precision of Ancestry Inferences in South American Admixed Populations

Ancestry informative markers (AIMs) are used in forensic genetics to infer biogeographical ancestry (BGA) of individuals and may also have a prominent role in future police and identification investigations. In the last few years, many studies have been published reporting new AIM sets. These sets include markers (usually around 100 or less) selected with different purposes and different population resolutions. Regardless of the ability of these sets to separate populations from different continents or regions, the uncertainty associated with the estimates provided by these panels and their capacity to accurately report the different ancestral contributions in individuals of admixed populations has rarely been investigated. This issue is addressed in this study by evaluating different AIM sets. Ancestry inference was carried out in admixed South American populations, both at population and individual levels. The results of ancestry inferences using AIM sets with different numbers of markers among admixed reference populations were compared. To evaluate the performance of the different ancestry panels at the individual level, expected and observed estimates among families and their offspring were compared, considering that (1) the apportionment of ancestry in the offspring should be closer to the average ancestry of the parents, and (2) full siblings should present similar ancestry values. The results obtained illustrate the importance of having a good balance/compromise between not only the number of markers and their ability to differentiate ancestral populations, but also a balanced differentiation among reference groups, to obtain more precise values of genetic ancestry. This work also highlights the importance of estimating errors associated with the use of a limited number of markers. We demonstrate that although these errors have a moderate effect at the population level, they may have an important impact at the individual level. Considering that many AIM-sets are being described for inferences at the individual level and not at the population level, e.g., in association studies or the determination of a suspect’s BGA, the results of this work point to the need of a more careful evaluation of the uncertainty associated with the ancestry estimates in admixed populations, when small AIM-sets are used.LG was supported by the Ellen og Aage Andersen’s Foundation, Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq (ref. 306342/2019-7), and Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro – FAPERJ(CNE-2018)

Children, play, and the built environment : what can we learn from co-creation and embodied cognitive science?

The emphasis on creating cities and buildings that take children’s needs and perspectives seriously has gained strength across the international built environment community in recent years. Manifested through agendas such as child-friendly environments and the rise of participatory design approaches involving adolescents and children, it highlights a shift in viewing children as active rather than passive agents in the design and creation of spaces. In parallel, the growing concerns regarding the built environments’ impact on children’s physical and mental health have contributed to the resurgence of interest in play and playful learning as a key factor in children’s holistic and healthy development. This research is a first step towards the generation of a sound knowledge base on how to better design child-friendly environments and spaces that encourage children’s play, learning through play, and children’s holistic development. Moreover, it considers how processes of co-creation can assist in the pursuit of more child-friendly built environments. Accordingly, the aim of the research project was to critically explore existing scholarship on children, play, playful learning, and creativity in the built environment (i.e. architectural and urban spaces) in order to identify the state-of-the-art in research as well as examples of practice internationally. Our report synthesizes the key collection of academic literature and vocabulary associated with “children in the city” and “play in the built environment” to develop a systematic understanding of: (1) the different components associated with designer-child collaboration in the built environment as well as (2) a variety of novel approaches and methods for conceptualizing and investigating children’s interactions with the built environment. Based on the critical reading and analysis of the 159 academic papers and 20 cases, we present a series of findings that unpack the relationship between children and the built environment from the complimentary perspectives of embodied cognitive science and co-creation. Through these lenses, we posit a number of research gaps and suggestions for future investigation on the themes presented. Our report presents a seminal study, which for the first time, links children, play, playful learning, and creativity with the built environment, co-creation, and embodied cognitive science. At present, this field is not yet well established, representing an emerging area of scholarship and academic interest. While existing research on the subject hold value, connections between co-creation and embodied cognitive science in the built environment are in their infancy, thus there is a need for further testing to corroborate the outcomes of the review with additional empirical research belonging to a number of specific areas. Through these gaps, we highlight opportunities for developing stronger theoretical and empirical research on how different spaces afford and invite children’s play across the play spectrum as well as how designer-child collaboration can potentially influence place-making to more readily enable child-friendly design approaches in cities. We put forward, that children can—and should—be considered as co-producers of spaces and places through play and their own practices in the built environment. Designer-child collaboration—if executed with due care and consideration—can act as the bridge and translation process to ensure that this environment is designed collectively and a rich landscape of affordances for play are provided