scholarly journals Clin.iobio: A Collaborative Diagnostic Workflow to Enable Team-Based Precision Genomics

2022 ◽  
Vol 12 (1) ◽  
pp. 73
Author(s):  
Alistair Ward ◽  
Matt Velinder ◽  
Tonya Di Sera ◽  
Aditya Ekawade ◽  
Sabrina Malone Jenkins ◽  
...  
Keyword(s):  
Clinical Practice ◽  
Genomic Analysis ◽  
Knowledge Bases ◽  
Diagnostic Process ◽  
Whole Genome Sequencing Data ◽  
Specific Gene ◽  
Sequencing Data ◽  
Team Members ◽  
Variant Information ◽  
Allele Segregation

The primary goal of precision genomics is the identification of causative genetic variants in targeted or whole-genome sequencing data. The ultimate clinical hope is that these findings lead to an efficacious change in treatment for the patient. In current clinical practice, these findings are typically returned by expert analysts as static, text-based reports. Ideally, these reports summarize the quality of the data obtained, integrate known gene–phenotype associations, follow allele segregation and affected status within the sequenced samples, and weigh computational evidence of pathogenicity. These findings are used to prioritize the variant(s) most likely to cause the given patient’s phenotypes. In most diagnostic settings, a team of experts contribute to these reports, including bioinformaticians, clinicians, and genetic counselors, among others. However, these experts often do not have the necessary tools to review genomic findings, test genetic hypotheses, or query specific gene and variant information. Additionally, team members often rely on different tools and methods based on their given expertise, resulting in further difficulties in communicating and discussing genomic findings. Here, we present clin.iobio—a web-based solution to collaborative genomic analysis that enables diagnostic team members to focus on their area of expertise within the diagnostic process, while allowing them to easily review and contribute to all steps of the diagnostic process. Clin.iobio integrates tools from the popular iobio genomic visualization suite into a comprehensive diagnostic workflow, encompassing (1) genomic data quality review, (2) dynamic phenotype-driven gene prioritization, (3) variant prioritization using a comprehensive set of knowledge bases and annotations, (4) and an exportable findings summary. In conclusion, clin.iobio is a comprehensive solution to team-based precision genomics, the findings of which stand to inform genomic considerations in clinical practice.

scholarly journals Predicting Insect Invasiveness With Whole-genome Sequencing Data

2020 ◽  
Author(s):  
Cong Huang ◽  
Nianwan Yang ◽  
Shuping Wang ◽  
Xiaodan Fan ◽  
Cong Pian ◽  
...  
Keyword(s):  
Insect Pest ◽  
Genomic Analysis ◽  
Gene Families ◽  
Insect Species ◽  
Whole Genome Sequencing Data ◽  
Comparative Genomic ◽  
Nucleic Acid Metabolism ◽  
Sequencing Data ◽  
Invasive Insects ◽  
Invasive Insect

Abstract Background Invasive alien insects threaten agriculture, biodiversity, and human livelihoods globally. Unfortunately, insect invasiveness still cannot be reliably predicted. Empirical policies of insect pest quarantine and inspection are mainly designed against species that are already problematic. Results We conducted a comparative genomic analysis of 37 invasive insect species and six non-invasive insect species, showing that the gene families associated with defense, protein and nucleic acid metabolism, chemosensory function, and transcriptional regulation were significantly expanded in invasive insects, suggesting that enhanced abilities in self-protection, nutrition exploitation, and locating food or mates are intrinsic features conferring invasiveness in insects. By using these intrinsic genome features, we proposed an invasiveness index and estimated the invasiveness of 99 other insect species with genome data, classifying them as highly, moderately, or minimally invasive. Insects possessing all these aforementioned enhanced abilities are predicted to be highly invasive, and vice versa. Next, a logistic-regression classifier was trained to predict insect invasiveness, achieving 93.2% accuracy. Conclusions We present evidence that several traits may confer invasiveness in insects and these features can be used to predict insect invasiveness accurately, and we quantify insect invasiveness with an invasiveness index.

scholarly journals Predicting Insect Invasiveness with Whole-Genome Sequencing Data

2020 ◽  
Author(s):  
Cong Huang ◽  
Nianwan Yang ◽  
Shuping Wang ◽  
Xiaodan Fan ◽  
Cong Pian ◽  
...  
Keyword(s):  
Insect Pest ◽  
Genomic Analysis ◽  
Gene Families ◽  
Insect Species ◽  
Whole Genome Sequencing Data ◽  
Comparative Genomic ◽  
Nucleic Acid Metabolism ◽  
Sequencing Data ◽  
Invasive Insects ◽  
Invasive Insect

Abstract Background: Invasive alien insects threaten agriculture, biodiversity, and human livelihoods globally. Unfortunately, insect invasiveness still cannot be reliably predicted. Empirical policies of insect pest quarantine and inspection are mainly designed against species that are already problematic.Results: We conducted a comparative genomic analysis of 37 invasive insect species and six non-invasive insect species, showing that the gene families associated with defense, protein and nucleic acid metabolism, chemosensory function, and transcriptional regulation were significantly expanded in invasive insects, suggesting that enhanced abilities in self-protection, nutrition exploitation, and locating food or mates are intrinsic features conferring invasiveness in insects. By using these intrinsic genome features, we proposed an invasiveness index and estimated the invasiveness of 99 other insect species with genome data, classifying them as highly, moderately, or minimally invasive. Insects possessing all these aforementioned enhanced abilities are predicted to be highly invasive, and vice versa. Next, a logistic-regression classifier was trained to predict insect invasiveness, achieving 93.2% accuracy. Conclusions: We present evidence that several traits may confer invasiveness in insects and these features can be used to predict insect invasiveness accurately, and we quantify insect invasiveness with an invasiveness index.

scholarly journals lncRNAKB: A comprehensive knowledgebase of long non-coding RNAs

2019 ◽  
Author(s):  
Fayaz Seifuddin ◽  
Komudi Singh ◽  
Abhilash Suresh ◽  
Yun-Ching Chen ◽  
Vijender Chaitankar ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Functional Characterization ◽  
Gene Expression Profiles ◽  
Tissue Expression ◽  
Whole Genome Sequencing Data ◽  
Specific Gene ◽  
Solid Organ ◽  
Sequencing Data ◽  
Additional Information ◽  
Gene Modules

ABSTRACTWe have assembled a comprehensivelongnon-codingRNAknowledgebase (lncRNAKB) of 77,199 annotated human lncRNAs (224,286 transcripts) by methodically integrating widely used lncRNAs resources. To facilitate functional characterization of lncRNAs, we employed Genotype-Tissue Expression (GTEx) project to provide tissue-specific gene expression profiles of lncRNAs in 31 solid organ tissues. Additional information includes network analysis to identify co-expressed gene modules to potentially delineate lncRNA function. Tissue-specificity, phylogenetic conservation scores and coding potential for lncRNAs are included. Finally, using whole genome sequencing data from GTEx, expression quantitative trait loci (cis-eQTL) regulated lncRNAs were calculated in all tissues. lncRNAKB is available athttp://www.lncrnakb.org.

scholarly journals 1046. Clinical and Microbiological Characteristics of Patients With Septicemia Caused by IMP-1-Producing Enterobacteriaceae in a Tertiary Hospital in Japan

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S312-S313
Author(s):  
Nobuaki Mori ◽  
Narito Kagawa ◽  
Kotaro Aoki ◽  
Yoshikazu Ishii ◽  
Kazuhiro Tateda ◽  
...  
Keyword(s):  
Severe Disease ◽  
Previous History ◽  
Genomic Analysis ◽  
Underlying Disease ◽  
Tertiary Hospital ◽  
Mercaptoacetic Acid ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Microbiological Characteristics

Abstract Background Carbapenemase-producing Enterobacteriaceae (CPE) infection has become a great threat to public health worldwide. Although KPC and OXA-48 infections have mostly described, IMP-1 producing Enterobacteriaceae (IMP1-E) are not well studied. We investigated the clinical and microbiological characteristics of septicemia due to the IMP1-E. Methods This observational study of inpatients who developed IMP-1E septicemia was conducted in a Japanese tertiary hospital from April 2013 to March 2017. IMP1-E was defined as a decreased susceptibility to meropenem (minimum inhibitory concentration, ≥2 mg/L), as well as a positive sodium mercaptoacetic acid test, and polymerase chain reaction for blaIMP genes. Clinical data were collected from medical charts. Antimicrobial susceptibilitly was determined by the MicroScan Walkway. We performed total genomic analysis, plasmid analysis, and multilocus sequence typing (MLST) using whole genome sequencing data. Results In total, six patients were identified (median age: 55 years). All had severe underlying disease on admission, and five were admitted to the intensive care unit. The sources of IMP1-E septicemia were as follows: two catheter-related BSI, one pyelonephritis, one cholangitis, one bacterial peritonitis, and one unknown focus. Four isolates were Enterobacter cloacae and two were Klebsiella pneumoniae. All patients had a previous history of antibiotic treatment and long-term hospitalization. All patients were treated with either levofloxacin (LVFX) only or LVFX and aminoglycoside (AG). Follow-up blood culture was negative for all patients. All-cause 30-day mortality rate was 50%. Although no isolates were resistant to LVFX and AG, they harbored aac(6’)-Ⅱc, sul1, and tet(B) genes.Two isolates harbored the qnrB6 gene. There was a high probability that blaIMP-1 was carried by IncHI2 plasmids. MLST sequence type of E. cloacae isolates comprised three ST78, and one ST997; K. pneumonia isolates comprised ST134, and ST252. Conclusion This study showed that IMP1-E septicemia was isolated in patients with severe disease and long-term hospitalization. Selection of antibiotics therapy based on antimicrobial susceptibility induced microbiological cure, but clinical response was dependent on the underlying diseases. Disclosures All authors: No reported disclosures.

scholarly journals Genomic analysis reveals selection signatures of Yucatan miniature pig on its X chromosome during domestication

2019 ◽  
Author(s):  
Wei Zhang ◽  
Yuanlang Wang ◽  
Min Yang ◽  
Xudong Wu ◽  
Xiaodong Zhang ◽  
...  
Keyword(s):  
X Chromosome ◽  
Genetic Relationships ◽  
Genomic Analysis ◽  
Fixation Index ◽  
Sweat Glands ◽  
Whole Genome Sequencing Data ◽  
Miniature Pig ◽  
Sequencing Data ◽  
Selection Signatures ◽  
Long Time

AbstractYucatan miniature pig (YMP), a naturally small breed, has been domesticated in the hot and arid Yucatan Peninsula for a long time. However, its selection signatures on the X chromosome remain poorly understood. In this study, we focused on elucidating the selection signatures of YMP on the X chromosome during its domestication and breeding, using the whole-genome sequencing data. We performed population admixture analyses to determine its genetic relationships with other domesticated breeds and wild boars. Subsequently, we used two approaches, the fixation index (Fst) and π ratios, to identify the selection signatures with 100 kb windows sliding in 10 kb steps. As a result, we found that the ectodysplasin A (EDA) gene was related with hypoplasia or absence of hair and sweat glands. This could uncover the relative lack of odor in YMP and the presence of hypoplasia or absence of hair in pigs. Furthermore, we found several genes under selection in other animals. A bioinformatics analysis of the genes in selection regions showed that they were associated with growth, lipid metabolism, reproduction, and immune system. Our findings will lead to a better understanding of the unique genetic and phenotypic characteristics of YMP and offer a plausible method for their utilization as an animal model for hair and odor disease research.

scholarly journals Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes

2021 ◽  
Author(s):  
Eric S Tvedte ◽  
Mark Gasser ◽  
Benjamin C Sparklin ◽  
Jane Michalski ◽  
Carl E Hjelmen ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
Hybrid Approach ◽  
Cost Effective ◽  
Fruit Fly ◽  
Drosophila Ananassae ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
E Coli ◽  
Hybrid Approaches ◽  
Long Read

Abstract The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.

scholarly journals A 127 kb truncating deletion of PGRMC1 is a novel cause of X-linked isolated paediatric cataract

2021 ◽  
Author(s):  
Johanna L. Jones ◽  
Mark A. Corbett ◽  
Elise Yeaman ◽  
Duran Zhao ◽  
Jozef Gecz ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Protein Interactions ◽  
Cholesterol Biosynthesis ◽  
Crystalline Lens ◽  
Whole Genome Sequencing Data ◽  
Mendelian Disease ◽  
Cataract Formation ◽  
Sequencing Data ◽  
Zebrafish Model ◽  
Paediatric Cataract

AbstractInherited paediatric cataract is a rare Mendelian disease that results in visual impairment or blindness due to a clouding of the eye’s crystalline lens. Here we report an Australian family with isolated paediatric cataract, which we had previously mapped to Xq24. Linkage at Xq24–25 (LOD = 2.53) was confirmed, and the region refined with a denser marker map. In addition, two autosomal regions with suggestive evidence of linkage were observed. A segregating 127 kb deletion (chrX:g.118373226_118500408del) in the Xq24–25 linkage region was identified from whole-genome sequencing data. This deletion completely removed a commonly deleted long non-coding RNA gene LOC101928336 and truncated the protein coding progesterone receptor membrane component 1 (PGRMC1) gene following exon 1. A literature search revealed a report of two unrelated males with non-syndromic intellectual disability, as well as congenital cataract, who had contiguous gene deletions that accounted for their intellectual disability but also disrupted the PGRMC1 gene. A morpholino-induced pgrmc1 knockdown in a zebrafish model produced significant cataract formation, supporting a role for PGRMC1 in lens development and cataract formation. We hypothesise that the loss of PGRMC1 causes cataract through disrupted PGRMC1-CYP51A1 protein–protein interactions and altered cholesterol biosynthesis. The cause of paediatric cataract in this family is the truncating deletion of PGRMC1, which we report as a novel cataract gene.

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