Hybrid assembly of ultra-long Nanopore reads augmented with 10x-Genomics contigs: Demonstrated with a human genome.Genomics Dec 2019The 3rd generation of sequencing (3GS) technologies generate ultra-long reads (up to 1 Mb), which makes it possible to eliminate gaps and effectively resolve repeats...
The 3rd generation of sequencing (3GS) technologies generate ultra-long reads (up to 1 Mb), which makes it possible to eliminate gaps and effectively resolve repeats in genome assembly. However, the 3GS technologies suffer from the high base-level error rates (15%-40%) and high sequencing costs. To address these issues, the hybrid assembly strategy, which utilizes both 3GS reads and inexpensive NGS (next generation sequencing) short reads, was invented. Here, we use 10×-Genomics® technology, which integrates a novel bar-coding strategy with Illumina® NGS with an advantage of revealing long-range sequence information, to replace common NGS short reads for hybrid assembly of long erroneous 3GS reads. We demonstrate the feasibility of integrating the 3GS with 10×-Genomics technologies for a new strategy of hybrid de novo genome assembly by utilizing DBG2OLC and Sparc software packages, previously developed by the authors for regular hybrid assembly. Using a human genome as an example, we show that with only 7× coverage of ultra-long Nanopore® reads, augmented with 10× reads, our approach achieved nearly the same level of quality, compared with non-hybrid assembly with 35× coverage of Nanopore reads. Compared with the assembly with 10×-Genomics reads alone, our assembly is gapless with slightly high cost. These results suggest that our new hybrid assembly with ultra-long 3GS reads augmented with 10×-Genomics reads offers a low-cost (less than ¼ the cost of the non-hybrid assembly) and computationally light-weighted (only took 109 calendar hours with peak memory-usage = 61GB on a dual-CPU office workstation) solution for extending the wide applications of the 3GS technologies.
Topics: Contig Mapping; Genome, Human; Genomics; High-Throughput Nucleotide Sequencing; Humans; Software
Genomics Nov 2020Genomic technologies have accelerated research progress in autism spectrum disorder (ASD) genomics and promises to further transform our understanding of the genetic... (Review)
Genomic technologies have accelerated research progress in autism spectrum disorder (ASD) genomics and promises to further transform our understanding of the genetic basis of this neurodevelopmental disorder. Here we review the current evidence for the genetic basis of ASD, present the progress of large-scale studies to date and highlight the potential of genomic technologies. In particular, we discuss evidence for the importance of identifying rare genetic variants in family-based studies. Genomics is a key feature of future healthcare and our review illustrates it's potential to improve our biological understanding of neurodevelopmental disorders, and to ultimately aid ASD diagnosis, inform medical decision making and establish genomics as central to personalised medicine.
Topics: Autism Spectrum Disorder; Gene Dosage; Genetic Variation; Genomics; High-Throughput Nucleotide Sequencing; Humans; Mental Disorders; Whole Exome Sequencing; Whole Genome Sequencing
Genomics approaches to synthesize plant-based biomolecules for therapeutic applications to combat SARS-CoV-2.Genomics Nov 2020COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is devastative to the humankind for which neither vaccines nor precise therapeutic... (Review)
COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is devastative to the humankind for which neither vaccines nor precise therapeutic molecules for treatment are identified. The search for new drugs and repurposing of existing drugs are being performed; however, at the same time, research on plants to identify novel therapeutic compounds or testing the existing ones is progressing at a slower phase. In this context, genomics and biotechnology offer various tools and strategies to manipulate plants for producing those complex biopharmaceutical products. This review enumerates the scope for research on plant-based molecules for their potential application in treating SARS-CoV-2 infection. Strategies to edit gene and genome, overexpression and silencing approaches, and molecular breeding for producing target biomolecules in the plant system are discussed in detail. Altogether, the present review provides a roadmap for expediting research on using plants as a novel source of active biomolecules having therapeutic applications.
Topics: Antiviral Agents; COVID-19; Gene Editing; Genomics; Humans; Plants; Plants, Genetically Modified
Genomics Jul 2019Genome sequencing is commonly used in research laboratories right now thanks to the rise of high-throughput sequencing with higher speed and output-to-cost ratios. Here,... (Review)
Genome sequencing is commonly used in research laboratories right now thanks to the rise of high-throughput sequencing with higher speed and output-to-cost ratios. Here, we summarized the application of genomics in different aspects of plant bacterial pathosystems. Genomics has been used in studying the mechanisms of plant-bacteria interactions, and host specificity. It also helps with taxonomy, study of non-cultured bacteria, identification of causal agent, single cell sequencing, population genetics, and meta-transcriptomic. Overall, genomics has significantly improved our understanding of plant-microbe interaction.
Topics: Bacteria; Genome, Bacterial; Genomics; Host-Pathogen Interactions; Plants
Screening and identification of female-specific DNA sequences in octaploid sturgeon using comparative genomics with high-throughput sequencing.Genomics Nov 2021In this study, six candidate female-specific DNA sequences of octaploid Amur sturgeon (Acipenser schrenckii) were identified using comparative genomic approaches with...
In this study, six candidate female-specific DNA sequences of octaploid Amur sturgeon (Acipenser schrenckii) were identified using comparative genomic approaches with high-throughput sequencing data. Their specificity was confirmed by traditional PCR. Two of these sex-specific sequences were also validated as female-specific in other eight sturgeon species and two hybrid sturgeons. The identified female-specific DNA fragments suggest that the family Acipenseridae has a ZZ/ZW sex-determining system. However, one of the two DNA sequences has been deleted in some sturgeons such as Sterlet sturgeon (Acipenser ruthenus), Beluga (Huso huso) and Kaluga (H. dauricus). The difference of sex-specific sequences among sturgeons indicates that there are different sex-specific regions among species of sturgeon. This study not only provided the sex-specific DNA sequences for management, conservation and studies of sex-determination mechanisms in sturgeons, but also confirmed the capability of the workflow to identify sex-specific DNA sequences in the polyploid species with complex genomes.
Topics: Animals; Base Sequence; Female; Fishes; Genome; Genomics; High-Throughput Nucleotide Sequencing
The National Academies' Roundtable on Genomics and Precision Health: Where we have been and where we are heading.American Journal of Human Genetics Oct 2021The clinical application of genetics and genomics to advance precision health is one of the most dynamic and promising areas of medicine. In 2020, building on nearly 15... (Review)
The clinical application of genetics and genomics to advance precision health is one of the most dynamic and promising areas of medicine. In 2020, building on nearly 15 years of work, the Roundtable on Genomics and Precision Health of the National Academies of Sciences, Engineering, and Medicine undertook a strategic planning process to assess its strengths, consider the current challenges facing the field, and set out new goals for its future work. As a result, the Roundtable has updated its vision and mission and prioritized four major areas of inquiry-innovation, dialogue, equity, and adoption-while keeping true to its founding goal of providing a neutral convening space for the diversity of stakeholders in genomics and precision health. The Roundtable is unique for its breadth of membership and is committed to fostering a new era for precision health built on decades of expanding knowledge and the emergence of new technologies. To achieve its goals, the Roundtable seeks to broaden its membership's diversity and to engage with new audiences. Roundtable members explore how evidence-based discoveries in genomics could be adopted and used in innovative ways to better serve human health, how equitable access to genomic and precision health technologies can be ensured, and how the Roundtable and broader genomics and precision health community can communicate more effectively to inform the public regarding genomics and precision health. As a first principle, the Roundtable is working to support the overall goal that all people benefit from genomics for precision health.
Topics: Genomics; Humans; National Academy of Sciences, U.S.; Precision Medicine; Translational Research, Biomedical; United States
Public Health Genomics 2021Despite growing awareness about the potential for genomic information to improve population health, lingering communication challenges remain in describing the role of...
Despite growing awareness about the potential for genomic information to improve population health, lingering communication challenges remain in describing the role of genomics in public health programs. Identifying and addressing these challenges provide an important opportunity for appropriate communication to ensure the translation of genomic discoveries for public health benefits. In this commentary, we describe 5 common communication challenges encountered by the Centers for Disease Control and Prevention's Office of Genomics and Precision Public Health based on over 20 years of experience in the field. These include (1) communicating that using genomics to assess rare diseases can have an impact on public health; (2) providing evidence that genetic factors can add important information to environmental, behavioral, and social determinants of health; (3) communicating that although genetic factors are nonmodifiable, they can increase the impact of public health programs and communication strategies; (4) addressing the concern that genomics is not ready for clinical practice; and (5) communicating that genomics is valuable beyond the domain of health care and can be integrated as part of public health programs. We discuss opportunities for addressing these communication challenges and provide examples of ongoing approaches to communication about the role of genomics in public health to the public, researchers, and practitioners.
Topics: Centers for Disease Control and Prevention, U.S.; Communication; Delivery of Health Care; Genomics; Humans; Public Health; Social Determinants of Health; United States
Genomics Nov 2021Fruit tree crops are an essential part of the food production systems and are key to achieve food and nutrition security. Genetic improvement of fruit trees by... (Review)
Fruit tree crops are an essential part of the food production systems and are key to achieve food and nutrition security. Genetic improvement of fruit trees by conventional breeding has been slow due to the long juvenile phase. Advancements in genomics and molecular biology have paved the way for devising novel genetic improvement tools like genome editing, which can accelerate the breeding of these perennial crops to a great extent. In this article, advancements in genomics of fruit trees covering genome sequencing, transcriptome sequencing, genome editing technologies (GET), CRISPR-Cas system based genome editing, potential applications of CRISPR-Cas9 in fruit tree crops improvement, the factors influencing the CRISPR-Cas editing efficiency and the challenges for CRISPR-Cas9 applications in fruit tree crops improvement are reviewed. Besides, base editing, a recently emerging more precise editing system, and the future perspectives of genome editing in the improvement of fruit and nut crops are covered.
Topics: Fruit; Gene Editing; Genome, Plant; Genomics; Nuts; Plant Breeding
Ensuring best practice in genomics education and evaluation: reporting item standards for education and its evaluation in genomics (RISE2 Genomics).Genetics in Medicine : Official Journal... Jul 2021Widespread, quality genomics education for health professionals is required to create a competent genomic workforce. A lack of standards for reporting genomics education...
Widespread, quality genomics education for health professionals is required to create a competent genomic workforce. A lack of standards for reporting genomics education and evaluation limits the evidence base for replication and comparison. We therefore undertook a consensus process to develop a recommended minimum set of information to support consistent reporting of design, development, delivery, and evaluation of genomics education interventions.
Draft standards were derived from literature (25 items from 21 publications). Thirty-six international experts were purposively recruited for three rounds of a modified Delphi process to reach consensus on relevance, clarity, comprehensiveness, utility, and design.
The final standards include 18 items relating to development and delivery of genomics education interventions, 12 relating to evaluation, and 1 on stakeholder engagement.
These Reporting Item Standards for Education and its Evaluation in Genomics (RISE2 Genomics) are intended to be widely applicable across settings and health professions. Their use by those involved in reporting genomics education interventions and evaluation, as well as adoption by journals and policy makers as the expected standard, will support greater transparency, consistency, and comprehensiveness of reporting. Consequently, the genomics education evidence base will be more robust, enabling high-quality education and evaluation across diverse settings.
Topics: Consensus; Delphi Technique; Genomics; Humans; Research Report; Stakeholder Participation
Organizational perspectives on implementing complex health interventions: clinical genomics in Australia.Journal of Health Organization and... Jul 2021Clinical genomics is a complex, innovative medical speciality requiring clinical and organizational engagement to fulfil the clinical reward promised to date. Focus thus...
Clinical genomics is a complex, innovative medical speciality requiring clinical and organizational engagement to fulfil the clinical reward promised to date. Focus thus far has been on gene discovery and clinicians' perspectives. The purpose of this study was to use implementation science theory to identify organizational barriers and enablers to implementation of clinical genomics along an organizations' implementation journey from through to and .
We used a deductive qualitative approach study design drawing on implementation science theory - (1) Translation Science to Population Impact Framework, to inform semi structured interviews with organizational decision-makers collaborating with Australian and Melbourne Genomics, alongside and (2) Theoretical Domains Framework (TDF), to guide data analysis.
We identified evolving organizational barriers across the implementation journey from to . Initially the organizational focus is on understanding the value of clinical genomics (TDF code: belief about consequences) and setting the scene (TDF code: goals) before organizational (TDF codes: knowledge and belief about consequences) and clinician (TDF codes: belief about capability and intentions) willingness to adopt is apparent. Once at the stage of Implementation, leadership and clarity in organizational priorities (TDF codes: intentions, professional identity and emotion) that include clinical genomics are essential prerequisites to implementing clinical genomics in practice. Intuitive enablers were identified (e.g. 'providing multiple opportunities for people to come on board) and mapped hypothetically to barriers.
Attention to date has centred on the barriers facing clinicians when introducing clinical genomics into practice. This paper uses a combination of implementation science theories to begin to unravel the organizational perspectives of implementing this complex health intervention.
Topics: Australia; Genomics; Humans; Implementation Science; Leadership; Qualitative Research