Genome Sequencing Technologies Research Articles

Genomic and transcriptomic analyses reveal genetic adaptation to cold conditions in the chickens

Under the pressure of natural and artificial selection, domestic animals, including chickens, have evolved unique mechanisms of genetic adaptations such as high-altitude adaptation, hot and arid climate adaptation, and desert adaptation. Here, we investigated the genetic basis of cold tolerance in chicken by integrating whole-genome and transcriptome sequencing technologies. Genome-wide comparative analyses of 118 chickens living in different latitudes showed 46 genes and several pathways that may be involved in cold adaptation. The results of the functional enrichment analysis of differentially expressed genes proved the important role of metabolic pathways and immune-related pathways in cold tolerance in chickens. The subsequent integration of whole genome and transcriptome sequencing technology further identified six genes — dnah5 (dynein axonemal heavy chain 5), ptgs2 (prostaglandin-endoperoxide synthase 2), inhba (inhibin beta A subunit), irx2 (iroquois homeobox 2), ensgalg00000054917, and ensgalg00000046652 — requiring more detailed studies. In addition, we also discovered different allele frequency distributions of five SNPs (single nucleotide polymorphisms) within ptgs2 and nine SNPs within dnah5 in chickens in different latitudes, suggesting strong selective pressure of these two genes in chickens. We provide a novel insight into the genetic adaptation in chickens to cold environments, and provide a reference for evaluating and developing adaptive chicken breeds in cold environments.

Causal Discovery in High-dimensional, Multicollinear Datasets.

As the cost of high-throughput genomic sequencing technology declines, its application in clinical research becomes increasingly popular. The collected datasets often contain tens or hundreds of thousands of biological features that need to be mined to extract meaningful information. One area of particular interest is discovering underlying causal mechanisms of disease outcomes. Over the past few decades, causal discovery algorithms have been developed and expanded to infer such relationships. However, these algorithms suffer from the curse of dimensionality and multicollinearity. A recently introduced, non-orthogonal, general empirical Bayes approach to matrix factorization has been demonstrated to successfully infer latent factors with interpretable structures from observed variables. We hypothesize that applying this strategy to causal discovery algorithms can solve both the high dimensionality and collinearity problems, inherent to most biomedical datasets. We evaluate this strategy on simulated data and apply it to two real-world datasets. In a breast cancer dataset, we identified important survival-associated latent factors and biologically meaningful enriched pathways within factors related to important clinical features. In a SARS-CoV-2 dataset, we were able to predict whether a patient (1) had Covid-19 and (2) would enter the ICU. Furthermore, we were able to associate factors with known Covid-19 related biological pathways.

How plants conquered land: evolution of terrestrial adaptation.

The transition of plants from water to land is considered one of the most significant events in the evolution of life on Earth. The colonization of land by plants, accompanied by their morphological, physiological and developmental changes, resulted in plant biodiversity. Besides significantly influencing oxygen levels in the air and on land, plants manufacture organic matter from CO2 and water with the help of sunlight, paving the way for the diversification of nonplant lineages ranging from microscopic organisms to animals. Land plants regulate the climate by adjusting total biomass and energy flow. At the genetic level, these innovations are achieved through the rearrangement of pre-existing genetic information. Advances in genome sequencing technology are revamping our understanding of plant evolution. This study highlights the morphological and genomic innovations that allow plants to integrate life on Earth.

1337P Implementation of precision oncology in clinical practice: A nationwide survey in Italy

Two main aspects are leading precision oncology implementation into clinical practice: the adoption of extended genome sequencing technologies and the institutions and activity of Molecular Tumor Boards (MTBs). On behalf of CIPOMO (Italian association of Oncology Departments directors) we promoted a national survey to obtain a picture of the adoption of precision medicine into clinical oncology in Italy, considering the provisions of the National Recovery and Resilience Plan. We report the results of the survey. 20 questions were sent via Survey Monkey platform (Individual Advantage version) to 169 heads of medical oncology departments, and their answers were collected from the 10th to 28th of February 2022. 129 directors participated; 113 sets of answers were analyzed. 19 regions out of 21 participated, as a representative sample of the Italian healthcare system. 67.3% of participants are aware of ESMO recommendations on Next-generation sequencing (NGS) use for advanced cancer. NGS is currently used by 52.2% of the Departments at cancer diagnosis; 47.8% base molecular diagnostic on single gene analysis. Among the ones using NGS, 49.2% adopt tumor specific panels, 30.5% a unique pan-tumor panel, 20.3% didn’t answer. 72.3% of respondents find appropriate to limit molecular analysis on biomarkers indicated by scientific guidelines at diagnosis; 27.7% would use a more extended sequencing upfront. MTBs are present in 13 out of Regions but overall 33.6% of Departments has not access to them. Among the Centers with an active MTB, 23.9% routinely refer cases for consultation, 43.7% haven’t done it yet, 32.4% report that the nowadays organization does not fit their needs. NGS technologies and MTBs are not homogeneously implemented in Italy. These results could be a starting point for clinicians, scientific societies and health care institutions to outline the best practices, achieve consensus and formulate recommendations for precision oncology implementation in our current clinical practice.

A Review of Genetics in Chronic Pain

Chronic pain impacts up to 50 million Americans yearly, where hundreds of billions of dollars are spent annually treating pain. The burden on health care systems and patients emphasizes our need to further investigate chronic pain. In recent years, the advent of advanced genome sequencing technologies has enabled us to identify variations in genomic regions which might contribute to susceptibility to pain as well as individuals’ response to treatment. The purpose of this review is to better understand the complex and multifactorial pathophysiology of chronic pain. A deeper understanding of the genetics of chronic pain could have wide implications in the diagnosis of pain pathologies as well as pain management therapy. Methods: This review conducted a literature analysis on the genetics of chronic pain. The PubMed® search engine was used to research key words “chronic pain”, “pain management”, “pharmacogenomics”, “gene therapy”, and “individualized medicine”. This paper’s research focused on investigating studies that conducted hypothesis-free genetic studies and genome-wide association studies (GWAS). Data from our literature search was compiled into this review and analyzed to discuss strengths and weaknesses of the current literature, and to discuss future avenues of research. Results: Many gene loci and mutations were identified as being associated with chronic pain pathologies. Results from pertinent genetic studies as well as online gene databases were compared to one another to isolate significant associations between genetics, pharmacogenomics, and pain management therapy. Discussion: When reviewing the literature searches, we found that although individual studies found significant associations between specific genes and chronic pain pathologies, the results from these studies were unable to be replicated on a larger scale. The genetic data associated with chronic pain has yet to be replicated consistently in different studies on subjects of different ethnicities, geographical distributions, and socioeconomic statuses. Further research into the genetics of chronic pain is needed to make generalizable conclusions and implement them in clinical practice.

Current Status and Future Perspectives of Genomics Research in the Rust Fungi.

Rust fungi in Pucciniales have caused destructive plant epidemics, have become more aggressive with new virulence, rapidly adapt to new environments, and continually threaten global agriculture. With the rapid advancement of genome sequencing technologies and data analysis tools, genomics research on many of the devastating rust fungi has generated unprecedented insights into various aspects of rust biology. In this review, we first present a summary of the main findings in the genomics of rust fungi related to variations in genome size and gene composition between and within species. Then we show how the genomics of rust fungi has promoted our understanding of the pathogen virulence and population dynamics. Even with great progress, many questions still need to be answered. Therefore, we introduce important perspectives with emphasis on the genome evolution and host adaptation of rust fungi. We believe that the comparative genomics and population genomics of rust fungi will provide a further understanding of the rapid evolution of virulence and will contribute to monitoring the population dynamics for disease management.

Genome-Wide Associative Study of Phenotypic Parameters of the 3D Body Model of Aberdeen Angus Cattle with Multiple Depth Cameras.

Simple SummaryThis article aims to develop a new approach to the lifetime evaluation of cattle by 3-D visualization of economic-biological and genetic features. The following indicators were selected as phenotypic features: chest width and chest girth retrieved by 3-D model and meat output on the bones. Correlation analysis showed a reliable positive relationship between chest width and meat output on the bones, which can potentially be used for lifetime evaluation of meat productivity of animals. Genome-wide associations analysis revealed the following potential loci of quantitative traits on cattle chromosomes for chest width, chest girth, and meat output on bones.In beef cattle breeding, genome-wide association studies (GWAS) using single nucleotide polymorphisms (SNPs) arrays can reveal many loci of various production traits, such as growth, productivity, and meat quality. With the development of genome sequencing technologies, new opportunities are opening up for more accurate identification of areas associated with these traits. This article aims to develop a novel approach to the lifetime evaluation of cattle by 3-D visualization of economic-biological and genetic features. The purpose of this study was to identify significant variants underlying differences in the qualitative characteristics of meat, using imputed data on the sequence of the entire genome. Samples of biomaterial of young Aberdeen-Angus breed cattle (n = 96) were the material for carrying out genome-wide SNP genotyping. Genotyping was performed using a high-density DNA chip Bovine GPU HD BeadChip (Illumina Inc., San Diego, CA, USA), containing ~150 thousand SNPs. The following indicators were selected as phenotypic features: chest width and chest girth retrieved by 3-D model and meat output on the bones. Correlation analysis showed a reliable positive relationship between chest width and meat output on the bones, which can potentially be used for lifetime evaluation of meat productivity of animals.

Using Genomics to Understand the Epidemiology of Infectious Diseases in the Northern Territory of Australia.

The Northern Territory (NT) is a geographically remote region of northern and central Australia. Approximately a third of the population are First Nations Australians, many of whom live in remote regions. Due to the physical environment and climate, and scale of social inequity, the rates of many infectious diseases are the highest nationally. Molecular typing and genomic sequencing in research and public health have provided considerable new knowledge on the epidemiology of infectious diseases in the NT. We review the applications of genomic sequencing technology for molecular typing, identification of transmission clusters, phylogenomics, antimicrobial resistance prediction, and pathogen detection. We provide examples where these methodologies have been applied to infectious diseases in the NT and discuss the next steps in public health implementation of this technology.

The retroelement Lx9 puts a brake on the immune response to virus infection.

The notion that mobile units of nucleic acid known as transposable elements can operate as genomic controlling elements was put forward over six decades ago1,2. However, it was not until the advancement of genomic sequencing technologies that the abundance and repertoire of transposable elements were revealed, and they are now known to constitute up to two-thirds of mammalian genomes3,4. The presence of DNA regulatory regions including promoters, enhancers and transcription-factor-binding sites within transposable elements5-8 has led to the hypothesis that transposable elements have been co-opted to regulate mammalian gene expression and cell phenotype8-14. Mammalian transposable elements include recent acquisitions and ancient transposable elements that have been maintained in the genome over evolutionary time. The presence of ancient conserved transposable elements correlates positively with the likelihood of a regulatory function, but functional validation remains an essential step to identify transposable element insertions that have a positive effect on fitness. Here we show that CRISPR-Cas9-mediated deletion of a transposable element-namely the LINE-1 retrotransposon Lx9c11-in mice results in an exaggerated and lethal immune response to virus infection. Lx9c11 is critical for the neogenesis of a non-coding RNA (Lx9c11-RegoS) that regulates genes of the Schlafen family, reduces the hyperinflammatory phenotype and rescues lethality in virus-infected Lx9c11-/- mice. These findings provide evidence that a transposable element can control the immune system to favour host survival during virus infection.

Machine Learning Approaches to TCR Repertoire Analysis.

Sparked by the development of genome sequencing technology, the quantity and quality of data handled in immunological research have been changing dramatically. Various data and database platforms are now driving the rapid progress of machine learning for immunological data analysis. Of various topics in immunology, T cell receptor repertoire analysis is one of the most important targets of machine learning for assessing the state and abnormalities of immune systems. In this paper, we review recent repertoire analysis methods based on machine learning and deep learning and discuss their prospects.

A child with genetic FN1 mutation in the absence of classic glomerulopathy with fibronectin deposits(GFND) findings on biopsy

BackgroundGlomerulopathy with fibronectin deposits (GFND) is a rare autosomal dominant genetic disorder, and proteinuria and hematuria are the most common clinical manifestations. The pathogenesis of this disease is primarily related to mutation of the fibronectin 1 gene. Unfortunately, without specific treatment, the prognosis remains poor. Here we present a case report that investigates the clinical characteristics, renal pathology, and gene testing of childhood GFND.Case presentationA two-year-old child was brought to our hospital for “persistent hematuria for 1 year and 10 months.” The disease onset was at the age of 4 months, with persistent microscopic hematuria accompanied by intermittent gross hematuria, occasionally with proteinuria, and without hypertension or renal failure. The chief complaint was intermittent gross hematuria, without massive proteinuria, hypertension, or renal failure. Family history: The child’s mother had microscopic hematuria, his maternal aunt had nephrotic syndrome due to focal segmental glomerulosclerosis, and his maternal grandmother had end-stage renal disease. No significant pathological changes were found in the renal pathological biopsy of the child under a light microscope. Under the electron microscope, the basement membrane was found to be of uneven thickness, ranging from 150 to 400 nm. The stratum compactum of the basement membrane was thickened, with a small part showing tear-like and cobweb-like morphology. No electron-dense deposits were found. The renal tubular epithelial cells were vacuolated, and there were no unique pathological changes in the renal interstitium. Immunofluorescence showed that IgG, IgM, IgA, C3, and C1q were all negative. Alport syndrome was preliminarily considered. However, exome sequencing revealed a mutated site in the fibronectin 1 gene. The child’s mother was the carrier of the pathogenic gene and the final diagnosis was GFND.ConclusionsFibronectin deposition is a typical pathological change in GFND, and the disease progresses slowly to end-stage renal disease. There is no specific treatment so far, and the prognosis is poor. The early onset of childhood patients may not show typical renal pathological changes, but only changes in the thickness of basement membrane, etc. Genome sequencing technology may helpful for the early diagnosis of GFND.

Genome and Transcriptome Sequence Resources and Effector Repertoire of Pythium myriotylum Drechsler.

Genome and Transcriptome Sequence Resources and Effector Repertoire of Pythium myriotylum Drechsler.

Comparative Analysis of Chloroplast Genome in Saccharum spp. and Related Members of 'Saccharum Complex'.

High ploids of the sugarcane nuclear genome limit its genomic studies, whereas its chloroplast genome is small and conserved, which is suitable for phylogenetic studies and molecular marker development. Here, we applied whole genome sequencing technology to sequence and assemble chloroplast genomes of eight species of the ‘Saccharum Complex’, and elucidated their sequence variations. In total, 19 accessions were sequenced, and 23 chloroplast genomes were assembled, including 6 species of Saccharum (among them, S. robustum, S. sinense, and S. barberi firstly reported in this study) and 2 sugarcane relative species, Tripidium arundinaceum and Narenga porphyrocoma. The plastid phylogenetic signal demonstrated that S. officinarum and S. robustum shared a common ancestor, and that the cytoplasmic origins of S. sinense and S. barberi were much more ancient than the S. offcinarum/S. robustum linage. Overall, 14 markers were developed, including 9 InDel markers for distinguishing Saccharum from its relative species, 4 dCAPS markers for distinguishing S. officinarum from S. robustum, and 1 dCAPS marker for distinguishing S. sinense and S. barberi from other species. The results obtained from our studies will contribute to the understanding of the classification and plastome evolution of Saccharinae, and the molecular markers developed have demonstrated their highly discriminatory power in Saccharum and relative species.

Natural variation of the BRD2 allele affects plant height and grain size in rice.

The zqdm1 identified from a rice mutant is a novel allele of BRD2 and is responsible for regulating rice plant height, grain size and appearance, which has possibilities on improving rice quality. Plant height is an important agronomic trait related to rice yield, and grain size directly determines grain yield in rice (Oryza sativa L.). With the development of molecular biotechnology and genome sequencing technology, more and more key genes associated with plant height and grain size have been cloned and identified in recent years. This study identified the zqdm1 gene from a mutant with reduced plant height and grain size. The zqdm1 gene was revealed to be a new allele of BRASSINOSTEROID DEFICIENT DWARF 2 (BRD2), encoding a FAD-linked oxidoreductase protein involved in the brassinosteroid (BR) biosynthesis pathway, and regulates plant height by reducing cell number of longitudinal sections of the internode and regulates grain size by altering cell expansion. A 369-bp DNA fragment was found inserted at the first exon, resulting in protein-coding termination. This mutation has not been discovered in previous studies. Complementation tests have confirmed that 369-bp insertion in BRD2 was responsible for the plant height and grain size changing in the zqdm1 mutant. Over-expression of BRD2 driven by different promoters into indica rice variety Jiafuzhan (JFZ) results in slender grains, suggesting its function on regulating grain shape. In summary, the current study has identified a new BRD2 allele, which facilitated the further research on the molecular mechanism of this gene on regulating growth and development.

Omics approaches to discover pathophysiological pathways contributing to human pain.

Omics approaches to discover pathophysiological pathways contributing to human pain.

Overview of Transcriptomic Research on Type 2 Diabetes: Challenges and Perspectives.

Type 2 diabetes (T2D) is a common chronic disease whose etiology is known to have a strong genetic component. Standard genetic approaches, although allowing for the detection of a number of gene variants associated with the disease as well as differentially expressed genes, cannot fully explain the hereditary factor in T2D. The explosive growth in the genomic sequencing technologies over the last decades provided an exceptional impetus for transcriptomic studies and new approaches to gene expression measurement, such as RNA-sequencing (RNA-seq) and single-cell technologies. The transcriptomic analysis has the potential to find new biomarkers to identify risk groups for developing T2D and its microvascular and macrovascular complications, which will significantly affect the strategies for early diagnosis, treatment, and preventing the development of complications. In this article, we focused on transcriptomic studies conducted using expression arrays, RNA-seq, and single-cell sequencing to highlight recent findings related to T2D and challenges associated with transcriptome experiments.

Focused Commentary; About Revision of CLSI Antimicrobial Breakpoints, 2018-2021

In recent years, antimicrobial resistance has been on the rise and infectious disease specialists and other clinicians face several challenges when treating patients with antimicrobial resistant infections. Clinical and Laboratory Standards Institute (CLSI) annually publishes guidelines for antimicrobial resistance tests, including revised antimicrobial breakpoints, because of the rise in antimicrobial resistance and changes to nomenclature owing to advances in whole genome sequencing technology. However, many laboratories use historical guidelines and do not follow the revised breakpoints. Moreover, the current breakpoints have limitations. This study evaluated the changes in antimicrobial breakpoints over the last 4 years, from 2018 to 2021. Here, I describe the microbiological and clinical background of the CLSI breakpoint revision and evaluate the advantages and limitations of new breakpoints with a review of large study data. In addition, I reviewed problems associated with each antimicrobial breakpoint and made suggestions for how they might be improved, for example, increasing or decreasing the minimum inhibitory concentration (MIC) or zone diameter, deleting or adding an S, I, or R category, introducing new concepts (such as susceptible-dose dependent (SDD)), and requesting more evaluation methods. Conclusions; CLSI annually publishes guidelines for antimicrobial resistance tests. I reviewed problems associated with each antimicrobial breakpoint for last 4 years, and made suggestions for how they might be improved.

Commentary: Retinitis pigmentosa in Laurence-Moon-Bardet-Biedl syndrome: Genomic sequencing, gene therapy, and gene editing.

Being a rare inherited retinal dystrophy, retinitis pigmentosa (RP) in Laurence–Moon–Bardet–Biedl syndrome (LMBBS) is typically described in case series and reports. In the current study,[1] the authors describe a detailed big data analysis of patients with RP which helps document the degree and progeression of vision loss in affected patients. It also helps depict in detail, associated systemic and ocular co-morbidities. Genetic testing in such patients helps significantly. The advantages are threefold. First, we are able to share the likely course and progression of vision loss to patients by comparing them with people reported to have similar mutations. Second, the inheritance pattern can be informed and discussed with patients, which helps in family planning. Last but not the least, knowing the mutation helps us discuss potential ongoing gene therapy clinical trials and therapies in development, if available, for the same mutation. That said, in a busy retina practice, often explaining the advantages of the same and discussing the nuances around it may not always be possible. Further, the genomic sequencing technology is financially formidable for most patients, restricting its applicability at present. LMBBS is caused by mutations in the BBS gene (BBS1–BBS21), which account for 80% of cases with a clinical diagnosis of Bardet Biedl Syndrome (BBS).[2] The BBS1 gene, which is the most commonly affected, is responsible for cilia formation in photoreceptors. The impact of BBS gene mutations is seen in ciliated cells. Therefore, photoreceptor changes accompany hearing loss and renal, gonadal, and intellectual dysfunction. Advances in gene therapy have received US Food and Drug Administration (FDA) approval for retinal dystrophy caused by RPE65 gene mutations (voretigene neparvovec), and clinical trials are in progress for various other mutations causing RP. However, targeting the BBS gene mutations via gene therapy has been found to be complex due to the structural stoichiometry of the BBSome protein.[3] Gene editing using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) received the Nobel Prize in 2020. This promising new technique allows for editing the mutation. The CRISPR effector molecules consist of a guide RNA and Cas9 protein. The guide RNA identifies the target DNA to be edited, and the Cas9 protein cleaves the DNA, following which DNA repair mechanisms take place, which can insert the desired DNA bases, thereby correcting the mutation.[4] The technique can, however, cause DNA editing at other areas of the genome, called off-target effects. To mitigate this, CRISPR base editing and prime editing have been developed.[5] The technology holds promise and is currently in clinical trials for mutations in the CEP290 gene causing RP, the Brilliance Trial.[6] The role of CRISPR is yet to be explored in BBS gene mutations and perhaps could form a prudent area to explore in the future. To conclude, LMBBS is an important syndrome affecting multiple organs and tissues, the retina being one of them. Such descriptive studies driven by big data analytics help elucidate clinical characteristics of rare inherited retinal dystrophies. In future, an associated relevant genetic analysis of the causative mutations will help describe the mutational landscape in our country and plan therapies for the same.

Better and faster is cheaper.

The rapid pace of advancement in genomic sequencing technology has recently reached a new milestone, with a record-setting time to molecular diagnosis of a mere 8 h. The catalyst behind this achievement is the accumulation of evidence indicating that quicker results more often make an impact on patient care and lead to healthcare cost savings. Herein, we review the diagnostic and clinical utility of rapid whole genome and rapid whole exome sequencing, the associated reduction in healthcare costs, and the relationship between these outcome measures and time-to-diagnosis.

The Genomics of Auditory Function and Disease.

Current estimates suggest that nearly half a billion people worldwide are affected by hearing loss. Because of the major psychological, social, economic, and health ramifications, considerable efforts have been invested in identifying the genes and molecular pathways involved in hearing loss, whether genetic or environmental, to promote prevention, improve rehabilitation, and develop therapeutics. Genomic sequencing technologies have led to the discovery of genes associated with hearing loss. Studies of the transcriptome and epigenome of the inner ear have characterized key regulators and pathways involved in the development of the inner ear and have paved the way for their use in regenerative medicine. In parallel, the immense preclinical success of using viral vectors for gene delivery in animal models of hearing loss has motivated the industry to work on translating such approaches into the clinic. Here, we review the recent advances in the genomics of auditory function and dysfunction, from patient diagnostics to epigenetics and gene therapy.