Advancing the ethics of paleogenomics.
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ABSTRACT:
SUBMITTER: Bardill J
PROVIDER: S-EPMC6150602 | biostudies-literature | 2018 Apr
REPOSITORIES: biostudies-literature
Publications
Advancing the ethics of paleogenomics.
Bardill Jessica J Bader Alyssa C AC Garrison Nanibaa' A NA Bolnick Deborah A DA Raff Jennifer A JA Walker Alexa A Malhi Ripan S RS
Science (New York, N.Y.) 20180426 6387
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Project description:BackgroundTo describe the ethical issues and experiences of scientists conducting mixed methods health services research and to advance empirical and conceptual discussion on ethical integrity in mixed methods health research.MethodsThe study was conducted with 64 scholars, faculty and consultants from the NIH-funded Mixed Methods Research Training Program (MMRTP) for the Health Sciences. This was a cross-sectional study. Survey results were analyzed using descriptive statistics to characterize responses and open coding to summarize strategies about eight ethical mixed methods research issues. Respondents completed an online survey to elicit experiences related to eight ethical issues (informed consent, confidentiality, data management, burden, safety, equitable recruitment, communication, and dissemination) and strategies for addressing them.ResultsOnly about one-third of respondents thought their research ethics training helped them plan, conduct, or report mixed methods research. The most frequently occurring ethical issues were participant burden, dissemination and equitable recruitment (> 70% endorsement). Despite occurring frequently, < 50% of respondents rated each ethical issue as challenging. The most challenging ethical issues were related to managing participant burden, communication, and dissemination. Strategies reported to address ethical issues were largely not specific or unique to mixed methods with the exception of strategies to mitigate participant burden and, to a lesser degree, to facilitate equitable recruitment and promote dissemination of project results.ConclusionsMixed methods health researchers reported encountering ethical issues often yet varying levels of difficulty and effectiveness in the strategies used to mitigate ethical issues. This study highlights some of the unique challenges faced by mixed methods researchers to plan for and appropriately respond to arising ethical issues such as managing participant burden and confidentiality across data sources and utilizing effective communication and dissemination strategies particularly when working with a multidisciplinary research team. As one of the first empirical studies to examine mixed methods research ethics, our findings highlight the need for greater attention to ethics in health services mixed methods research and training.
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Project description:Although most ancient DNA studies have focused on the last 50,000 years, paleogenomic approaches can now reach into the early Pleistocene, an epoch of repeated environmental changes that shaped present-day biodiversity. Emerging deep-time genomic transects, including from DNA preserved in sediments, will enable inference of adaptive evolution, discovery of unrecognized species, and exploration of how glaciations, volcanism, and paleomagnetic reversals shaped demography and community composition. In this Review, we explore the state-of-the-art in paleogenomics and discuss key challenges, including technical limitations, evolutionary divergence and associated biases, and the need for more precise dating of remains and sediments. We conclude that with improvements in laboratory and computational methods, the emerging field of deep-time paleogenomics will expand the range of questions addressable using ancient DNA.
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Project description:Despite centuries of research, much about the barbarian migrations that took place between the fourth and sixth centuries in Europe remains hotly debated. To better understand this key era that marks the dawn of modern European societies, we obtained ancient genomic DNA from 63 samples from two cemeteries (from Hungary and Northern Italy) that have been previously associated with the Longobards, a barbarian people that ruled large parts of Italy for over 200 years after invading from Pannonia in 568 CE. Our dense cemetery-based sampling revealed that each cemetery was primarily organized around one large pedigree, suggesting that biological relationships played an important role in these early medieval societies. Moreover, we identified genetic structure in each cemetery involving at least two groups with different ancestry that were very distinct in terms of their funerary customs. Finally, our data are consistent with the proposed long-distance migration from Pannonia to Northern Italy.
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Project description:The MGISEQ-2000 sequencer is widely used in various omics studies, but the performance of this platform for paleogenomics has not been evaluated. We here compare the performance of MGISEQ-2000 with the Illumina X-Ten on ancient human DNA using four samples from 1750BCE to 60CE. We found there were only slight differences between the two platforms in most parameters (duplication rate, sequencing bias, θ, δS, and λ). MGISEQ-2000 performed well on endogenous rate and library complexity although X-Ten had a higher average base quality and lower error rate. Our results suggest that MGISEQ-2000 and X-Ten have comparable performance, and MGISEQ-2000 can be an alternative platform for paleogenomics sequencing.
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Project description:Ancient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. In particular, molecular data from extinct Holocene island faunas have revealed surprising biogeographic scenarios. Here, we recovered partial mitochondrial (mt) genomes for 1300-1400 year old specimens (n = 2) of the extinct "horned" crocodile, Voay robustus, collected from Holocene deposits in southwestern Madagascar. Phylogenetic analyses of partial mt genomes and tip-dated timetrees based on molecular, fossil, and stratigraphic data favor a sister group relationship between Voay and Crocodylus (true crocodiles). These well supported trees conflict with recent morphological systematic work that has consistently placed Voay within Osteolaeminae (dwarf crocodiles and kin) and provide evidence for likely homoplasy in crocodylian cranial anatomy and snout shape. The close relationship between Voay and Crocodylus lends additional context for understanding the biogeographic origins of these genera and refines competing hypotheses for the recent extinction of Voay from Madagascar.
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Project description:OBJECTIVE:The general purpose for ethics consultations is to deliberate on issues on medical and scientific research and act towards the safeguard of the patient's rights and dignity. With the implementation of European Union (EU) Regulation 536/2014 on clinical trials and cost and time-optimization, the nature of consultations and the bodies they are carried out might be to some extent affected. Accordingly, we sought to gain an updated perspective on the current role and current practices of ethics consultations nationwide in both clinical and research settings. METHODS:The study was carried forth by a three-step mixed-method approach: i) review of policies/regulations for ethics committee (EC) nationwide; ii) a structured survey on ethics consultation activity completed by each EC during 2016; iii) incorporated into the third part, a qualitative assessment with a selected sample of 8 key-informants for a semi-structured interview, discussing EC history, the ethics consultation function, and the professional experience of consultants. RESULTS:Review of the policies/regulations promoted by ECs showed that 72,6% (n = 69) of all the ECs (N = 95) being actually capable of providing ethics consultation service by policy. 71 ECs (74.7%) responded to the survey on ethics consultation requests; among them, 48 (67.6%) provided ethics consultations of which 23 (23/48) actually received requests for this service in the year 2016. Many ECs did not have a structured database in place to provide precise figures of requests received in the last year nor of their contents. CONCLUSION:To date, ethics consultation in clinical and research practice is largely underappreciated and not well understood by users. The consultants themselves lack a comprehensive vision of work carried out in their field, and bioethics training programs to keep them updated. Despite clinical ethics consultation services should not necessarily be mandatory, following the recent EU Regulation on clinical trials, institutional ethics consultation bodies should be re-evaluated.
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Project description:Ethics are the moral values of human behavior and the principles which govern these values. The situation becomes challenging for a doctor when he assumes the role of researcher. The doctor-researcher has to serve both the roles and at times the zeal of an investigator has the potential to cloud the morality of the physician inside. It is very important to realize that exploiting the faith of patients is an offence that tantamount to a crime. Medical science is one discipline where the advancement of knowledge is hugely guided by research and mankind has benefitted from many experiments. However benefit and risk are the two faces of the same coin. Various unethical human experiments made us realize that the whims of researchers need to be reined and led to the evolution of the first guidelines for researcher, the Nuremberg code. Thereafter the Good Clinical Practice guidelines serve as the guiding doctrine of clinical research. The principles of ethics rest on the four pillars of autonomy, beneficence, justice, non-maleficence and recently two more pillars are added which includes, confidentiality and honesty. Ethics committees serve as a guardian of these principles. The multidisciplinary Ethics Committee ensures a competent review of the ethical aspects of the project proposal submitted and does it free from any bias or external influence. Ethical review of clinical trial applications follows a decentralized process in India, and requires Ethics Committee approval for each trial site. All Ethics committees have to be registered with Drug Controller General of India (DCGI) without which they cannot approve any clinical trial protocol and has come into effect from 25th February 2013.
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Project description:Researchers in areas as diverse as computer science and political science must increasingly navigate the possible risks of their research to society. However, the history of medical experiments on vulnerable individuals influenced many research ethics reviews to focus exclusively on risks to human subjects rather than risks to human society. We describe an Ethics and Society Review board (ESR), which fills this moral gap by facilitating ethical and societal reflection as a requirement to access grant funding: Researchers cannot receive grant funding from participating programs until the researchers complete the ESR process for their proposal. Researchers author an initial statement describing their proposed research's risks to society, subgroups within society, and globally and commit to mitigation strategies for these risks. An interdisciplinary faculty panel iterates with the researchers to refine these risks and mitigation strategies. We describe a mixed-method evaluation of the ESR over 1 y, in partnership with a large artificial intelligence grant program at our university. Surveys and interviews of researchers who interacted with the ESR found 100% (95% CI: 87 to 100%) were willing to continue submitting future projects to the ESR, and 58% (95% CI: 37 to 77%) felt that it had influenced the design of their research project. The ESR panel most commonly identified issues of harms to minority groups, inclusion of diverse stakeholders in the research plan, dual use, and representation in datasets. These principles, paired with possible mitigation strategies, offer scaffolding for future research designs.
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