scholarly journals Embedding indigenous principles in genomic research of culturally significant species: a conservation genomics case study

2019 ◽  
Author(s):  
Levi Collier-Robinson ◽  
Aisling Rayne ◽  
Makarini Rupene ◽  
Channell Thoms ◽  
Tammy Steeves
Keyword(s):  
Genomic Data ◽  
Research Programme ◽  
Position Statement ◽  
Genomic Research ◽  
Freshwater Crayfish ◽  
Data Generation ◽  
Cultural Significance ◽  
Conservation Genomics ◽  
Ecological Data ◽  
Genomics Research

Indigenous peoples around the world are leading discussion regarding genomic research of humans, and more recently, species of cultural significance, to ensure the ethical and equitable use of DNA. Within a Māori (indigenous people of Aotearoa New Zealand) worldview, genomic data obtained from taonga (culturally significant) species has whakapapa – generally defined as genealogy, whakapapa layers the contemporary, historical and mythological aspects of bioheritage – thus genomic data obtained from taonga species are taonga in their own right and are best studied using Māori principles. We contend it is the responsibility of researchers working with genomic data from taonga species to move beyond one-off Māori consultation toward building meaningful relationships with relevant Māori communities. Here, we reflect on our experience embedding Māori principles in genomics research as leaders of a BioHeritage National Science Challenge project entitled “Characterising adaptive variation in Aotearoa New Zealand’s terrestrial and freshwater biota”. We are co-developing a culturally-responsive evidence-based position statement regarding the benefits and risks of prioritising adaptive potential to build resilience in threatened taonga species, including species destined for customary or commercial harvest. To achieve this, we co-developed a research programme with the local subtribe, Ngāi Tūāhuriri, that integrates Māori knowledge with emerging genomic technologies and extensive ecological data for two taonga species, kōwaro (Canterbury mudfish; Neochanna burrowsius) and kēkēwai (freshwater crayfish; Paranephrops zealandicus). The foundation of our research programme is an iterative decision-making framework that includes tissue sampling as well as data generation, storage and access. Beyond upholding the promises made in The Treaty of Waitangi, we contend the integration of Māori principles in genomics research will enhance the recovery of taonga species and enable the realisation of Māori values.

scholarly journals The Report of Marine Life Genomic Research

2018 ◽  
Author(s):  
Guangyi Fan ◽  
Jianwei Chen ◽  
Tao Jin ◽  
Chengcheng Shi ◽  
Xiao Du ◽  
...  
Keyword(s):  
Recent Progress ◽  
Ethical Issues ◽  
Marine Invertebrates ◽  
Marine Species ◽  
White Paper ◽  
Genomic Research ◽  
Research Progress ◽  
Biological Research ◽  
Marine Microorganisms ◽  
Genomics Research

With the continuing development of sequencing technology, genomics has been applied in a variety of biological research areas. In particular, the application of genomics to marine species, which boast a high diversity, promises great scientific and industrial potential. Significant progress has been made in marine genomics especially over the past few years. Consequently, BGI, leveraging its prominent contributions in genomics research, established BGI-Qingdao, an institute specifically aimed at exploring marine genomics. In order to accelerate marine genomics research and related applications, BGI-Qingdao initiated the International Conference on Genomics of the Ocean (ICG-Ocean) to develop international collaborations and establish a focused and coherent global research plan. Last year, the first ICG-Ocean conference was held in Qingdao, China, during which 47 scientists in marine genomics from all over the world reported on their research progress to an audience of about 300 attendees. This year, we would like to build on that success, drafting a report on marine genomics to draw global attention to marine genomics. We summarized the recent progress, proposed future directions, and we would like to enable additional profound insights on marine genomics. Similar to the annual report on plant and fungal research by Kew Gardens, and the White Paper of ethical issues on experimental animals, we hope our first report on marine genomics can provide some useful insights for researchers, funding agencies as well as industry, and that future versions will expand upon the foundation established here in both breadth and depth of knowledge.This report summarizes the recent progress in marine genomics in six parts including: marine microorganisms, marine fungi, marine algae and plants, marine invertebrates, marine vertebrates and genomics-based applications.

scholarly journals Extending TCGA queries to automatically identify analogous genomic data from dbGaP

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 319
Author(s):  
Erin K. Wagner ◽  
Satyajeet Raje ◽  
Liz Amos ◽  
Jessica Kurata ◽  
Abhijit S. Badve ◽  
...  
Keyword(s):  
Genomic Data ◽  
The Cancer Genome Atlas ◽  
Genomic Research ◽  
Reproducible Research ◽  
Software Pipeline ◽  
Individual Level ◽  
Related Data ◽  
Cancer Genome Atlas ◽  
Existing Data ◽  
Genome Atlas

Data sharing is critical to advance genomic research by reducing the demand to collect new data by reusing and combining existing data and by promoting reproducible research. The Cancer Genome Atlas (TCGA) is a popular resource for individual-level genotype-phenotype cancer related data. The Database of Genotypes and Phenotypes (dbGaP) contains many datasets similar to those in TCGA. We have created a software pipeline that will allow researchers to discover relevant genomic data from dbGaP, based on matching TCGA metadata. The resulting research provides an easy to use tool to connect these two data sources.

scholarly journals Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data

2019 ◽  
Author(s):  
Kate Chkhaidze ◽  
Timon Heide ◽  
Benjamin Werner ◽  
Marc J. Williams ◽  
Weini Huang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Tumour Growth ◽  
Evolutionary Dynamics ◽  
Clonal Selection ◽  
Genomic Data ◽  
Confounding Factors ◽  
Data Generation ◽  
Next Generation ◽  
Sequencing Data ◽  
Generation Sequencing

AbstractQuantification of the effect of spatial tumour sampling on the patterns of mutations detected in next-generation sequencing data is largely lacking. Here we use a spatial stochastic cellular automaton model of tumour growth that accounts for somatic mutations, selection, drift and spatial constrains, to simulate multi-region sequencing data derived from spatial sampling of a neoplasm. We show that the spatial structure of a solid cancer has a major impact on the detection of clonal selection and genetic drift from bulk sequencing data and single-cell sequencing data. Our results indicate that spatial constrains can introduce significant sampling biases when performing multi-region bulk sampling and that such bias becomes a major confounding factor for the measurement of the evolutionary dynamics of human tumours. We present a statistical inference framework that takes into account the spatial effects of a growing tumour and allows inferring the evolutionary dynamics from patient genomic data. Our analysis shows that measuring cancer evolution using next-generation sequencing while accounting for the numerous confounding factors requires a mechanistic model-based approach that captures the sources of noise in the data.SummarySequencing the DNA of cancer cells from human tumours has become one of the main tools to study cancer biology. However, sequencing data are complex and often difficult to interpret. In particular, the way in which the tissue is sampled and the data are collected, impact the interpretation of the results significantly. We argue that understanding cancer genomic data requires mathematical models and computer simulations that tell us what we expect the data to look like, with the aim of understanding the impact of confounding factors and biases in the data generation step. In this study, we develop a spatial simulation of tumour growth that also simulates the data generation process, and demonstrate that biases in the sampling step and current technological limitations severely impact the interpretation of the results. We then provide a statistical framework that can be used to overcome these biases and more robustly measure aspects of the biology of tumours from the data.

scholarly journals From symptomatic to pre-symptomatic patient: the tide of personal genomics

2011 ◽  
Vol 10 (03) ◽  
pp. C03
Author(s):  
Marina Levina ◽  
Roswell Quinn
Keyword(s):  
Human Subjects ◽  
Genomic Data ◽  
Symptomatic Patient ◽  
Privacy Rights ◽  
Personal Genomics ◽  
Direct To Consumer ◽  
Marketing Social ◽  
Genomics Research ◽  
Definition Of ◽  
Consumer Marketing

Personal Genomics Companies are an emerging form of biotechnology startup that bring rapidly advancing whole genome technologies to a variety of commercial venues. With a combination of direct-to-consumer marketing, social media, and Web 2.0 applications these companies seek to create novel uses, including entertainment, for what is described as predictive medicine – that is the use of genetic marketers to create health forecasts that would allow individual’s healthcare to be tailored to their individual genomic data. In this brief piece, the authors use a critical cultural approach to question how this combination of genomics research, marketing, and communications technologies may alter both patient experiences and research processes. In it we argue these companies radically expand the definition of a patient by claiming all consumers are simply pre-symptomatic patients. Moreover, by placing genomic data on both the marketplace and cyberspace, personal genomic companies seek to create new avenues of research that alter how we define (and access) research agendas and human subjects. Therefore, beyond commonly discussed issues of ethics and privacy rights, Personal Genomics has the potential to alter both healthcare priorities and distribution.

scholarly journals Alaska Native genomic research: perspectives from Alaska Native leaders, federal staff, and biomedical researchers

2020 ◽  
Vol 22 (12) ◽  
pp. 1935-1943
Author(s):  
Vanessa Y. Hiratsuka ◽  
◽  
Michael J. Hahn ◽  
R. Brian Woodbury ◽  
Sara Chandros Hull ◽  
...  
Keyword(s):  
Alaska Native ◽  
Genomic Research ◽  
Health Board ◽  
Socially Responsible ◽  
Health Organizations ◽  
Research Partnerships ◽  
Cultural Considerations ◽  
Research Perspectives ◽  
National Human ◽  
Genomics Research

AbstractMeaningful engagement of Alaska Native (AN) tribes and tribal health organizations is essential in the conduct of socially responsible and ethical research. As genomics becomes increasingly important to advancements in medicine, there is a risk that populations not meaningfully included in genomic research will not benefit from the outcomes of that research. AN people have historically been underrepresented in biomedical research; AN underrepresentation in genomics research is compounded by mistrust based on past abuses, concerns about privacy and data ownership, and cultural considerations specific to this type of research. Working together, the National Human Genome Research Institute and two Alaska Native health organizations, Southcentral Foundation and the Alaska Native Health Board, cosponsored a workshop in July 2018 to engage key stakeholders in discussion, strengthen relationships, and facilitate partnership and consideration of participation of AN people in community-driven biomedical and genomic research. AN priorities related to translation of genomics research to health and health care, return of genomic results, design of research studies, and data sharing were discussed. This report summarizes the perspectives that emerged from the dialogue and offers considerations for effective and socially responsible genomic research partnerships with AN communities.

scholarly journals Prediction of condition-specific regulatory genes using machine learning

2020 ◽  
Vol 48 (11) ◽  
pp. e62-e62 ◽  
Author(s):  
Qi Song ◽  
Jiyoung Lee ◽  
Shamima Akter ◽  
Matthew Rogers ◽  
Ruth Grene ◽  
...  
Keyword(s):  
Machine Learning ◽  
Transcription Factors ◽  
Single Cell ◽  
Control Cell ◽  
Genomic Data ◽  
Regulatory Genes ◽  
Genomic Research ◽  
Open Chromatin ◽  
Data Set ◽  
Better Than

Abstract Recent advances in genomic technologies have generated data on large-scale protein–DNA interactions and open chromatin regions for many eukaryotic species. How to identify condition-specific functions of transcription factors using these data has become a major challenge in genomic research. To solve this problem, we have developed a method called ConSReg, which provides a novel approach to integrate regulatory genomic data into predictive machine learning models of key regulatory genes. Using Arabidopsis as a model system, we tested our approach to identify regulatory genes in data sets from single cell gene expression and from abiotic stress treatments. Our results showed that ConSReg accurately predicted transcription factors that regulate differentially expressed genes with an average auROC of 0.84, which is 23.5–25% better than enrichment-based approaches. To further validate the performance of ConSReg, we analyzed an independent data set related to plant nitrogen responses. ConSReg provided better rankings of the correct transcription factors in 61.7% of cases, which is three times better than other plant tools. We applied ConSReg to Arabidopsis single cell RNA-seq data, successfully identifying candidate regulatory genes that control cell wall formation. Our methods provide a new approach to define candidate regulatory genes using integrated genomic data in plants.

scholarly journals Next generation tools for genomic data generation, distribution, and visualization

2010 ◽  
Vol 11 (1) ◽  
Author(s):  
David A Nix ◽  
Tonya L Di Sera ◽  
Brian K Dalley ◽  
Brett A Milash ◽  
Robert M Cundick ◽  
...  
Keyword(s):  
Genomic Data ◽  
Data Generation ◽  
Next Generation

scholarly journals Human genetics and genomics research in Ecuador: historical survey, current state, and future directions

2019 ◽  
Vol 13 (1) ◽  
Author(s):  
Marlon S. Zambrano-Mila ◽  
Spiros N. Agathos ◽  
Juergen K. V. Reichardt
Keyword(s):  
Human Genetics ◽  
Genetic Diseases ◽  
Historical Record ◽  
Genomic Research ◽  
Current Status ◽  
Forensic Sciences ◽  
Resource Limited ◽  
Genomics Research ◽  
Comprehensive Picture ◽  
Genetics And Genomics

Abstract Background In South America, the history of human genetics is extensive and its beginnings go back to the onset of the twentieth century. In Ecuador, the historical record of human genetics and genomics research is limited. In this context, our work analyzes the current status and historical panorama of these fields, based on bibliographic searches in Scopus, Google Scholar, PubMed, and Web of Science. Results Our results determined that the oldest paper in human genetics coauthored by an Ecuadorian institution originates from the Central University of Ecuador in 1978. From a historical standpoint, the number of articles has increased since the 1990s. This growth has intensified and it is reflected in 137 manuscripts recorded from 2010 to 2019. Areas such as human population genetics, phylogeography, and forensic sciences are the core of genetics and genomics-associated research in Ecuador. Important advances have been made in the understanding of the bases of cancer, some genetic diseases, and congenital disorders. Fields such as pharmacogenetics and pharmacogenomics have begun to be explored during the last years. Conclusions This work paints a comprehensive picture and provides additional insights into the future panorama of human genetic and genomic research in Ecuador as an example of an emerging, resource-limited country with interesting phylogeographic characteristics and public health implications.

scholarly journals Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes

2020 ◽  
Vol 5 ◽  
pp. 3 ◽  
Author(s):  
Kirstyn Brunker ◽  
Gurdeep Jaswant ◽  
S.M. Thumbi ◽  
Kennedy Lushasi ◽  
Ahmed Lugelo ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Data ◽  
Genomic Research ◽  
Whole Genome ◽  
Middle Income ◽  
Endemic Disease ◽  
Middle Income Countries ◽  
Virus Genomes ◽  
Low And Middle Income

Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.

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