scholarly journals An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Yun Sung Cho ◽  
Hyunho Kim ◽  
Hak-Min Kim ◽  
Sungwoong Jho ◽  
JeHoon Jun ◽  
...  
Keyword(s):  
Large Scale ◽  
New Technologies ◽  
Reference Genome ◽  
Genomic Structure ◽  
Genome Project ◽  
Personal Genome ◽  
Personal Genomic ◽  
Personal Reference ◽  
Scale Population ◽  
Genome Assemblies

Abstract Human genomes are routinely compared against a universal reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or personal reference. Here we report a hybrid assembly of a Korean reference genome (KOREF) for constructing personal and ethnic references by combining sequencing and mapping methods. We also build its consensus variome reference, providing information on millions of variants from 40 additional ethnically homogeneous genomes from the Korean Personal Genome Project. We find that the ethnically relevant consensus reference can be beneficial for efficient variant detection. Systematic comparison of human assemblies shows the importance of assembly quality, suggesting the necessity of new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity.

scholarly journals Ethnically relevant consensus Korean reference genome towards personal reference genomes

2016 ◽  
Author(s):  
Yun Sung Cho ◽  
Hyunho Kim ◽  
Hak-Min Kim ◽  
Sungwoong Jho ◽  
JeHoon Jun ◽  
...  
Keyword(s):  
Large Scale ◽  
New Technologies ◽  
Reference Genome ◽  
Genomic Structure ◽  
Personal Genomic ◽  
Personal Reference ◽  
Human Genomes ◽  
Scale Population ◽  
Genome Assemblies ◽  
Universal Reference

AbstractHuman genomes are routinely compared against a universal reference. However, this strategy could miss population-specific or personal genomic variations, which may be detected more efficiently using an ethnically-relevant and/or a personal reference. Here we report a hybrid assembly of Korean reference (KOREF) as a pilot case for constructing personal and ethnic references by combining sequencing and mapping methods. KOREF is also the first consensus variome reference, providing information on millions of variants from additional ethnically homogeneous personal genomes. We found that this ethnically-relevant consensus reference was beneficial for efficiently detecting variants. Systematic comparison of KOREF with previously established human assemblies showed the importance of assembly quality, suggesting the necessity of using new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity.

scholarly journals Network integration of data and analysis of oncology interest

2006 ◽  
Vol 3 (1) ◽  
pp. 45-55
Author(s):  
P. Romano ◽  
G. Bertolini ◽  
F. De Paoli ◽  
M. Fattore ◽  
D. Marra ◽  
...  
Keyword(s):  
Web Services ◽  
Large Scale ◽  
New Technologies ◽  
Workflow Management ◽  
Genome Project ◽  
Management Systems ◽  
Workflow Management Systems ◽  
The Creation ◽  
The Human Genome Project ◽  
Integrate Data

Summary The Human Genome Project has deeply transformed biology and the field has since then expanded to the management, processing, analysis and visualization of large quantities of data from genomics, proteomics, medicinal chemistry and drug screening. This huge amount of data and the heterogeneity of software tools that are used implies the adoption on a very large scale of new, flexible tools that can enable researchers to integrate data and analysis on the network. ICT technology standards and tools, like Web Services and related languages, and workflow management systems, can support the creation and deployment of such systems. While a number of Web Services are appearing and personal workflow management systems are also being more and more offered to researchers, a reference portal enabling the vast majority of unskilled researchers to take profit from these new technologies is still lacking. In this paper, we introduce the rationale for the creation of such a portal and present the architecture and some preliminary results for the development of a portal for the enactment of workflows of interest in oncology.

scholarly journals rmvPFBAM: Removing Primers from BAM Files Based on Amplicon-Based Next-Generation Sequencing and Cloud Computing When Analyzing Personal Genome Data

2021 ◽  
Vol 2021 ◽  
pp. 1-6
Author(s):  
Yanjun Ma
Keyword(s):  
Next Generation Sequencing ◽  
False Positive ◽  
Large Scale ◽  
Genomic Data ◽  
Next Generation Sequencing Data ◽  
Personal Genome ◽  
Next Generation ◽  
Sequencing Data ◽  
Personal Genomic ◽  
Generation Sequencing

Personal genomic data constitute one important part of personal health data. However, due to the large amount of personal genomic data obtained by the next-generation sequencing technology, special tools are needed to analyze these data. In this article, we will explore a tool analyzing cloud-based large-scale genome sequencing data. Analyzing and identifying genomic variations from amplicon-based next-generation sequencing data are necessary for the clinical diagnosis and treatment of cancer patients. When processing the amplicon-based next-generation sequencing data, one essential step is removing primer sequences from the reads to avoid detecting false-positive mutations introduced by nonspecific primer binding and primer extension reactions. At present, the removing primer tools usually discard primer sequences from the FASTQ file instead of BAM file, but this method could cause some downstream analysis problems. Only one tool (BAMClipper) removes primer sequences from BAM files, but it only modified the CIGAR value of the BAM file, and false-positive mutations falling in the primer region could still be detected based on its processed BAM file. So, we developed one cutting primer tool (rmvPFBAM) removing primer sequences from the BAM file, and the mutations detected based on the processed BAM file by rmvPFBAM are highly credible. Besides that, rmvPFBAM runs faster than other tools, such as cutPrimers and BAMClipper.

scholarly journals Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Malte Petersen ◽  
Sven Winter ◽  
Raphael Coimbra ◽  
Menno J. de Jong ◽  
Vladimir V. Kapitonov ◽  
...  
Keyword(s):  
Large Scale ◽  
Population Analysis ◽  
Model Organism ◽  
Population Level ◽  
Data Sets ◽  
Ltr Retrotransposons ◽  
Scale Population ◽  
Mammalian Genomes ◽  
Genome Assemblies ◽  
First Time

Abstract Background The majority of structural variation in genomes is caused by insertions of transposable elements (TEs). In mammalian genomes, the main TE fraction is made up of autonomous and non-autonomous non-LTR retrotransposons commonly known as LINEs and SINEs (Long and Short Interspersed Nuclear Elements). Here we present one of the first population-level analysis of TE insertions in a non-model organism, the giraffe. Giraffes are ruminant artiodactyls, one of the few mammalian groups with genomes that are colonized by putatively active LINEs of two different clades of non-LTR retrotransposons, namely the LINE1 and RTE/BovB LINEs as well as their associated SINEs. We analyzed TE insertions of both types, and their associated SINEs in three giraffe genome assemblies, as well as across a population level sampling of 48 individuals covering all extant giraffe species. Results The comparative genome screen identified 139,525 recent LINE1 and RTE insertions in the sampled giraffe population. The analysis revealed a drastically reduced RTE activity in giraffes, whereas LINE1 is still actively propagating in the genomes of extant (sub)-species. In concert with the extremely low activity of the giraffe RTE, we also found that RTE-dependent SINEs, namely Bov-tA and Bov-A2, have been virtually immobile in the last 2 million years. Despite the high current activity of the giraffe LINE1, we did not find evidence for the presence of currently active LINE1-dependent SINEs. TE insertion heterozygosity rates differ among the different (sub)-species, likely due to divergent population histories. Conclusions The horizontally transferred RTE/BovB and its derived SINEs appear to be close to inactivation and subsequent extinction in the genomes of extant giraffe species. This is the first time that the decline of a TE family has been meticulously analyzed from a population genetics perspective. Our study shows how detailed information about past and present TE activity can be obtained by analyzing large-scale population-level genomic data sets.

scholarly journals A robust benchmark for germline structural variant detection

2019 ◽  
Author(s):  
Justin M. Zook ◽  
Nancy F. Hansen ◽  
Nathan D. Olson ◽  
Lesley M. Chapman ◽  
James C. Mullikin ◽  
...  
Keyword(s):  
New Technologies ◽  
De Novo ◽  
Sequence Data ◽  
False Negative ◽  
Strong Support ◽  
False Positives ◽  
Genome Project ◽  
Personal Genome ◽  
Tier 1 ◽  
Long Read

AbstractNew technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution, and comprehensiveness. Translating these methods to routine research and clinical practice requires robust benchmark sets. We developed the first benchmark set for identification of both false negative and false positive germline SVs, which complements recent efforts emphasizing increasingly comprehensive characterization of SVs. To create this benchmark for a broadly consented son in a Personal Genome Project trio with broadly available cells and DNA, the Genome in a Bottle (GIAB) Consortium integrated 19 sequence-resolved variant calling methods, both alignment- and de novo assembly-based, from short-, linked-, and long-read sequencing, as well as optical and electronic mapping. The final benchmark set contains 12745 isolated, sequence-resolved insertion and deletion calls ≥50 base pairs (bp) discovered by at least 2 technologies or 5 callsets, genotyped as heterozygous or homozygous variants by long reads. The Tier 1 benchmark regions, for which any extra calls are putative false positives, cover 2.66 Gbp and 9641 SVs supported by at least one diploid assembly. Support for SVs was assessed using svviz with short-, linked-, and long-read sequence data. In general, there was strong support from multiple technologies for the benchmark SVs, with 90 % of the Tier 1 SVs having support in reads from more than one technology. The Mendelian genotype error rate was 0.3 %, and genotype concordance with manual curation was >98.7 %. We demonstrate the utility of the benchmark set by showing it reliably identifies both false negatives and false positives in high-quality SV callsets from short-, linked-, and long-read sequencing and optical mapping.

scholarly journals Genomic medicine: genetic variation and its impact on the future of health care

2005 ◽  
Vol 360 (1460) ◽  
pp. 1543-1550 ◽  
Author(s):  
Huntington F Willard ◽  
Misha Angrist ◽  
Geoffrey S Ginsburg
Keyword(s):  
Health Care ◽  
Large Scale ◽  
New Technologies ◽  
Clinical Medicine ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Genomic Medicine ◽  
Genome Project ◽  
Breast Cancer Patients ◽  
Individualized Care

Advances in genome technology and other fruits of the Human Genome Project are playing a growing role in the delivery of health care. With the development of new technologies and opportunities for large-scale analysis of the genome, transcriptome, proteome and metabolome, the genome sciences are poised to have a profound impact on clinical medicine. Cancer prognostics will be among the first major test cases for a genomic medicine paradigm, given that all cancer is caused by genomic instability, and microarrays allow assessment of patients' entire expressed genomes. Analysis of breast cancer patients' expression patterns can already be highly correlated with recurrence risks. By integrating clinical data with gene expression profiles, imaging, metabolomic profiles and proteomic data, the prospect for developing truly individualized care becomes ever more real. Notwithstanding these promises, daunting challenges remain for genomic medicine. Success will require planning robust prospective trials, analysing health care economic and outcome data, assuaging insurance and privacy concerns, developing health delivery models that are commercially viable and scaling up to meet the needs of the whole population.

scholarly journals General Attitudes Towards Robots Scale (GAToRS): A New Versatile Instrument for Social Surveys

2021 ◽  
Author(s):  
Mika Koverola ◽  
Anton Kunnari ◽  
Jukka Reima Ilmari Sundvall ◽  
Michael Laakasuo
Keyword(s):  
Large Scale ◽  
New Technologies ◽  
Population Based ◽  
Context Dependency ◽  
Equal Weight ◽  
Human Society ◽  
Social Scientists ◽  
New Instrument ◽  
Scale Population ◽  
People’S Attitudes

Psychometric scales are useful tools in understanding people’s attitudes towards different aspects of life. As societies develop and new technologies arise, new validated scales are needed. Robots and artificial intelligences of various kinds are about to occupy just about every niche in human society. Several tools to measure fears and anxieties about robots do exist, but there is a definite lack of tools to measure hopes and expectations for these new technologies. Here, we cre-ate and validate a novel multi-dimensional scale which measures people’s attitudes towards ro-bots, giving equal weight to positive and negative attitudes. Our scale reliably differentiated a) comfort and enjoyment around robots, b) discomfort and anxiety around robots, c) rational hopes about robots in general and d) rational worries about robots in general. In addition to its psycho-metric qualities our scale is compact (only 20 items), aesthetically pleasing (5 items in each of the four sub-scales) and produces reliably the same factor structure in different samples. In contrast to previous tools our new instrument also allows large-scale population based and intercultural re-search without context dependency. Due to its easy-to-use nature, we hope our scale will be a use-ful instrument for social scientists who wish to study human-technology relations with a validated scale in efficient and generalizable ways.

scholarly journals Genomic Medicine

2016 ◽  
Vol 23 (1) ◽  
pp. 21
Author(s):  
Kremema Star ◽  
Barbara Birshtein
Keyword(s):  
Human Genome ◽  
Human Disease ◽  
Human Genome Project ◽  
Large Scale ◽  
New Technologies ◽  
Genomic Medicine ◽  
Genetic Material ◽  
Genome Project ◽  
The Human Genome Project

The human genome project created the field of genomics – understanding genetic material on a large scale. Scientists are deciphering the information held within the sequence of our genome. By building upon this knowledge, physicians and scientists will create fundamental new technologies to understand the contribution of genetics to diagnosis, prognosis, monitoring, and treatment of human disease. The science of genomic medicine has only begun to affect our understanding of health.

scholarly journals Welfare Genome Project: A Participatory Korean Personal Genome Project With Free Health Check-Up and Genetic Report Followed by Counseling

2021 ◽  
Vol 12 ◽  
Author(s):  
Yeonsu Jeon ◽  
Sungwon Jeon ◽  
Asta Blazyte ◽  
Yeo Jin Kim ◽  
Jasmin Junseo Lee ◽  
...  
Keyword(s):  
Large Scale ◽  
Genome Project ◽  
Health Check ◽  
Personal Genome ◽  
Lifestyle Management ◽  
Healthcare Data ◽  
Sequencing Technologies ◽  
The Social ◽  
Genotype Information ◽  
Medical Infrastructure

The Welfare Genome Project (WGP) provided 1,000 healthy Korean volunteers with detailed genetic and health reports to test the social perception of integrating personal genetic and healthcare data at a large-scale. WGP was launched in 2016 in the Ulsan Metropolitan City as the first large-scale genome project with public participation in Korea. The project produced a set of genetic materials, genotype information, clinical data, and lifestyle survey answers from participants aged 20–96. As compensation, the participants received a free general health check-up on 110 clinical traits, accompanied by a genetic report of their genotypes followed by genetic counseling. In a follow-up survey, 91.0% of the participants indicated that their genetic reports motivated them to improve their health. Overall, WGP expanded not only the general awareness of genomics, DNA sequencing technologies, bioinformatics, and bioethics regulations among all the parties involved, but also the general public’s understanding of how genome projects can indirectly benefit their health and lifestyle management. WGP established a data construction framework for not only scientific research but also the welfare of participants. In the future, the WGP framework can help lay the groundwork for a new personalized healthcare system that is seamlessly integrated with existing public medical infrastructure.

Financial and Economic Support of Innovation Processes in the Russian Fuel and Energy Complex

2019 ◽  
Vol 12 (3) ◽  
pp. 77-85
Author(s):  
L. D. Kapranova ◽  
T. V. Pogodina
Keyword(s):  
Oil Recovery ◽  
Large Scale ◽  
Oil And Gas ◽  
New Technologies ◽  
Innovative Development ◽  
Oil Reserves ◽  
Energy Complex ◽  
Innovation Activities ◽  
Substantial Investment ◽  
The Government

The subject of the research is the current state of the fuel and energy complex (FEC) that ensures generation of a significant part of the budget and the innovative development of the economy.The purpose of the research was to establish priority directions for the development of the FEC sectors based on a comprehensive analysis of their innovative and investment activities. The dynamics of investment in the fuel and energy sector are considered. It is noted that large-scale modernization of the fuel and energy complex requires substantial investment and support from the government. The results of the government programs of corporate innovative development are analyzed. The results of the research identified innovative development priorities in the power, oil, gas and coal sectors of the fuel and energy complex. The most promising areas of innovative development in the oil and gas sector are the technologies of enhanced oil recovery; the development of hard-to-recover oil reserves; the production of liquefied natural gas and its transportation. In the power sector, the prospective areas are activities aimed at improving the performance reliability of the national energy systems and the introduction of digital technologies. Based on the research findings, it is concluded that the innovation activities in the fuel and energy complex primarily include the development of new technologies, modernization of the FEC technical base; adoption of state-of-the-art methods of coal mining and oil recovery; creating favorable economic conditions for industrial extraction of hard-to-recover reserves; transition to carbon-free fuel sources and energy carriers that can reduce energy consumption and cost as well as reducing the negative FEC impact on the environment.

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