Exploring Human Genetic Variation – Scientific and Ethical Challenges

2018 ◽  
Author(s):  
Paula Dobosz ◽  
Jakub Zawiła-Niedźwiecki
Keyword(s):  
Genetic Variation ◽  
High Throughput Sequencing ◽  
Current Knowledge ◽  
Human Genetic Variation ◽  
Ethical Challenges ◽  
New Techniques ◽  
Public And Private ◽  
Sequencing Technologies ◽  
Health And Disease ◽  
And Storage

Since the genomic era is a reality nowadays, we need deeper understanding and consideration upon the benefits and challenges it brings. Apart from all the enthusiasm, there are also concerns related to genomics, specifically to the use and storage of personal genetic information as well as concerns regarding, for instance, so-called incidental findings, and right not to know. It started with Mendel’s simple experiments, but led to high-throughput sequencing technologies, resulting complex genomic data is constantly poured into public and private databases, inevitably changing our current knowledge. With the advent of new techniques and methods, like CRISPR/Cas9 engineering, researchers are provided with improved and expanded repertoire of research tools to analyse an organism in health and disease. This paper is aimed at providing examples of the applications and challenges, both practical and theoretical, in exploring human genetic variation.

scholarly journals The Dark Matter of Human Microbiota: Virobiota and Virome

2021 ◽  
Author(s):  
Gülendam Bozdayı ◽  
Işıl Fidan
Keyword(s):  
High Throughput Sequencing ◽  
Inflammatory Diseases ◽  
Human Microbiome ◽  
Endogenous Retroviruses ◽  
Therapeutic Approaches ◽  
Sequencing Technologies ◽  
Health And Disease ◽  
New Generation Sequencing ◽  
New Generation ◽  
Generation Sequencing

The viral component of the human microbiome is referred as ‘virobiota’. The virobiota is the sum of all viruses found in or on humans. The set of all genes of virobiota is referred as ‘virome’. The human virome consists of virus-derived genetic elements found in human genome constituted of viruses that infect eukaryotic cells, bacteriophages, prokaryotic cells, and, endogenous retroviruses. The development of new sequencing technologies, such as high-throughput sequencing techniques allowed the analysis of the human virome. Many new viruses have been discovered lately, using new generation sequencing technology. In recent years, there has been an increase in the studies of the human virome as changes in virome have been observed in diseases. The alterations in the human virome may be associated with infectious, inflammatory diseases, cancer and autoimmunity. The understanding of how the virome affects human health and disease can provide the development of potential therapeutic approaches that target the members of the virome.

Bats, bacteria and their role in health and disease

2017 ◽  
Vol 38 (1) ◽  
pp. 28 ◽  
Author(s):  
Kristin Mühldorfer
Keyword(s):  
High Throughput Sequencing ◽  
Habitat Preferences ◽  
Data Sets ◽  
Infectious Agents ◽  
Emerging Pathogens ◽  
Microbial Detection ◽  
White Nose Syndrome ◽  
Sequencing Technologies ◽  
Health And Disease ◽  
Reservoir Hosts

Bats are ancient and among the most diverse mammals in terms of species richness, diet and habitat preferences, characteristics that may contribute to a high diversity of infectious agents. During the past two decades, the interest in bats and their microorganisms largely increased because of their role as reservoir hosts or carriers of important pathogens. Rapid advances in microbial detection and characterisation by high-throughput sequencing technologies have led to large genetic data sets but also improved our possibilities and speed of identifying unknown infectious agents. Assessing the risk of infectious diseases in bats and their pathological manifestation, however, is still challenging because of limited access to appropriate material and field data, and continuing limitations in wildlife diagnostics and the interpretation of genetic results. As a consequence, emerging pathogens can suddenly appear with devastating effects as happened for the white nose syndrome. To date, much research on bats and infectious agents still focusses on viruses, whilst the knowledge on bacteria and their role in disease is comparatively low.

scholarly journals Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

Quaternary ◽  
2021 ◽  
Vol 4 (1) ◽  
pp. 6
Author(s):  
Eric Capo ◽  
Charline Giguet-Covex ◽  
Alexandra Rouillard ◽  
Kevin Nota ◽  
Peter D. Heintzman ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Recent Literature ◽  
State Of The Art ◽  
Current Knowledge ◽  
Aquatic Biota ◽  
Aquatic Biodiversity ◽  
Sequencing Technologies ◽  
Long Term Changes ◽  
Original Case

The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.

scholarly journals Massively parallel sequencing: the new frontier of hematologic genomics

Blood ◽  
2013 ◽  
Vol 122 (19) ◽  
pp. 3268-3275 ◽  
Author(s):  
Jill M. Johnsen ◽  
Deborah A. Nickerson ◽  
Alex P. Reiner
Keyword(s):  
Genetic Variation ◽  
Dna Sequencing ◽  
Massively Parallel Sequencing ◽  
Genomic Medicine ◽  
Human Genetic Variation ◽  
Dna Variation ◽  
Sequencing Technologies ◽  
Genomic Technologies ◽  
New Frontier ◽  
Different Types

Abstract Genomic technologies are becoming a routine part of human genetic analysis. The exponential growth in DNA sequencing capability has brought an unprecedented understanding of human genetic variation and the identification of thousands of variants that impact human health. In this review, we describe the different types of DNA variation and provide an overview of existing DNA sequencing technologies and their applications. As genomic technologies and knowledge continue to advance, they will become integral in clinical practice. To accomplish the goal of personalized genomic medicine for patients, close collaborations between researchers and clinicians will be essential to develop and curate deep databases of genetic variation and their associated phenotypes.

Long noncoding RNAs: lincs between human health and disease

2017 ◽  
Vol 45 (3) ◽  
pp. 805-812 ◽  
Author(s):  
Zhi Hao Kwok ◽  
Yvonne Tay
Keyword(s):  
Cancer Biology ◽  
High Throughput Sequencing ◽  
Current Knowledge ◽  
Noncoding Rnas ◽  
Clinical Applications ◽  
Long Noncoding Rnas ◽  
Cellular Processes ◽  
Health And Disease ◽  
Underlying Mechanisms ◽  
Sequencing Platforms

Long noncoding RNAs (lncRNAs) represent one of the largest classes of transcripts and are highly diverse in terms of characteristics and functions. Advances in high-throughput sequencing platforms have enabled the rapid discovery and identification of lncRNAs as key regulatory molecules involved in various cellular processes and their dysregulation in various human diseases. Here, we summarize the current knowledge of the functions and underlying mechanisms of lncRNA activity with a particular focus on cancer biology. We also discuss the potential of lncRNAs as diagnostic and therapeutic targets for clinical applications.

scholarly journals Ethical challenges in pathogen sequencing: a systematic scoping review

2020 ◽  
Vol 5 ◽  
pp. 119
Author(s):  
Stephanie Johnson ◽  
Michael Parker
Keyword(s):  
Public Health ◽  
Ethical Issues ◽  
Sequence Data ◽  
Public Health Practice ◽  
Empirical Work ◽  
Outbreak Investigation ◽  
Ethical Challenges ◽  
Public And Private ◽  
Ethical Frameworks ◽  
Sequencing Technologies

Background: Going forward, the routine implementation of genomic surveillance activities and outbreak investigation is to be expected. We sought to systematically identify the emerging ethical challenges; and to systematically assess the gaps in ethical frameworks or thinking and identify where further work is needed to solve practical challenges. Methods: We systematically searched indexed academic literature from PubMed, Google Scholar, and Web of Science from 2000 to April 2019 for peer-reviewed articles that substantively engaged in discussion of ethical issues in the use of pathogen genome sequencing technologies for diagnostic, surveillance and outbreak investigation. Results: 28 articles were identified; nine United States, five United Kingdom, five The Netherlands, three Canada, two Switzerland, one Australia, two South Africa, and one Italy. Eight articles were specifically about the use of sequencing in HIV. Eleven were not specific to a particular disease. Results were organized into four themes: tensions between public and private interests; difficulties with translation from research to clinical and public health practice; the importance of community trust and support; equity and global partnerships; and the importance of context. Conclusion: While pathogen sequencing has the potential to be transformative for public health, there are a number of key ethical issues that must be addressed, particularly around the conditions of use for pathogen sequence data. Ethical standards should be informed by public values, and further empirical work investigating stakeholders’ views are required. Development in the field should also be under-pinned by a strong commitment to values of justice, in particular global health equity.

scholarly journals The genomic landscape of polymorphic human nuclear mitochondrial insertions

2014 ◽  
Author(s):  
Gargi Dayama ◽  
Sarah B Emery ◽  
Jeffrey M Kidd ◽  
Ryan E Mills
Keyword(s):  
High Throughput Sequencing ◽  
Reference Genome ◽  
Current Knowledge ◽  
Genetic Material ◽  
Purifying Selection ◽  
Genomic Variation ◽  
Human Populations ◽  
Sequencing Data ◽  
Sequencing Technologies ◽  
D Loop

The transfer of mitochondrial genetic material into the nuclear genomes of eukaryotes is a well-established phenomenon. Many studies over the past decade have utilized reference genome sequences of numerous species to characterize the prevalence and contribution of nuclear mitochondrial insertions to human diseases. The recent advancement of high throughput sequencing technologies has enabled the interrogation of genomic variation at a much finer scale, and now allows for an exploration into the diversity of polymorphic nuclear mitochondrial insertions (NumtS) in human populations. We have developed an approach to discover and genotype previously undiscovered Numt insertions using whole genome, paired-end sequencing data. We have applied this method to almost a thousand individuals in twenty populations from the 1000 Genomes Project and other data sets and identified 138 novel sites of Numt insertions, extending our current knowledge of existing Numt locations in the human genome by almost 20%. Most of the newly identified NumtS were found in less than 1% of the samples we examined, suggesting that they occur infrequently in nature or have been rapidly removed by purifying selection. We find that recent Numt insertions are derived from throughout the mitochondrial genome, including the D-loop, and have integration biases consistent with previous studies on older, fixed NumtS in the reference genome. We have further determined the complete inserted sequence for a subset of these events to define their age and origin of insertion as well as their potential impact on studies of mitochondrial heteroplasmy.

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