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Journal articles on the topic 'Genomics bioinformatics variant discovery sequence analysis'

Author: Grafiati

Published: 14 March 2023

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1

Ahmed, Zeeshan, Eduard Gibert Renart, and Saman Zeeshan. "Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping." PeerJ 9 (July 26, 2021): e11724. http://dx.doi.org/10.7717/peerj.11724.

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Over the last few decades, genomics is leading toward audacious future, and has been changing our views about conducting biomedical research, studying diseases, and understanding diversity in our society across the human species. The whole genome and exome sequencing (WGS/WES) are two of the most popular next-generation sequencing (NGS) methodologies that are currently being used to detect genetic variations of clinical significance. Investigating WGS/WES data for the variant discovery and genotyping is based on the nexus of different data analytic applications. Although several bioinformatics

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Wiggans, G. R., D. J. Null, J. B. Cole, and H. D. Norman. "256 GENOMIC EVALUATION OF FERTILITY TRAITS AND DISCOVERY OF HAPLOTYPES THAT AFFECT FERTILITY OF US DAIRY CATTLE." Reproduction, Fertility and Development 28, no. 2 (2016): 260. http://dx.doi.org/10.1071/rdv28n2ab256.

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Genomic evaluations of dairy cattle became official in the United States in January 2009 for Holsteins and Jerseys, and later for Brown Swiss, Ayrshires, and Guernseys. Up to 33 yield, fitness, calving, and conformation traits are evaluated, and the fertility traits included daughter pregnancy rate and heifer and cow conception rates. Additional fertility traits, such as age at first calving and days from calving to first insemination, also are being studied. Male fertility (sire conception rate) is evaluated phenotypically rather than through genomics. Over 1 million animals have genotypes in

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Smith, Frances, David Brawand, Laura Steedman, et al. "A Comprehensive Next Generation Sequencing Gene Panel Focused on Unexplained Anemia." Blood 126, no. 23 (2015): 946. http://dx.doi.org/10.1182/blood.v126.23.946.946.

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Abstract Congenital anemia is difficult to diagnose once common causes have been excluded; for example 80% cases of congenital non-spherocytic hemolytic anemia are undiagnosed once pyruvate kinase and G6PD deficiencies have been excluded using phenotypic analysis. We describe a next generation sequencing strategy, targeting 147 genes, to facilitate the diagnosis of these conditions. The coding regions, splice sites and 200 bp into the untranslated regions were examined in each gene. All clinically significant variants were confirmed by Sanger sequencing, including confirmation in any appropria

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Bao, Riyue, Lei Huang, Jorge Andrade, et al. "Review of Current Methods, Applications, and Data Management for the Bioinformatics Analysis of Whole Exome Sequencing." Cancer Informatics 13s2 (January 2014): CIN.S13779. http://dx.doi.org/10.4137/cin.s13779.

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The advent of next-generation sequencing technologies has greatly promoted advances in the study of human diseases at the genomic, transcriptomic, and epigenetic levels. Exome sequencing, where the coding region of the genome is captured and sequenced at a deep level, has proven to be a cost-effective method to detect disease-causing variants and discover gene targets. In this review, we outline the general framework of whole exome sequence data analysis. We focus on established bioinformatics tools and applications that support five analytical steps: raw data quality assessment, preprocessing

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Yang, Junmeng, Anna Liu, Isabella He, and Yongsheng Bai. "Bioinformatics Analysis Revealed Novel 3′UTR Variants Associated with Intellectual Disability." Genes 11, no. 9 (2020): 998. http://dx.doi.org/10.3390/genes11090998.

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MicroRNAs (or miRNAs) are short nucleotide sequences (~17–22 bp long) that play important roles in gene regulation through targeting genes in the 3′untranslated regions (UTRs). Variants located in genomic regions might have different biological consequences in changing gene expression. Exonic variants (e.g., coding variant and 3′UTR variant) are often causative of diseases due to their influence on gene product. Variants harbored in the 3′UTR region where miRNAs perform their targeting function could potentially alter the binding relationships for target pairs, which could relate to disease ca

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Tremblay, Olivier, Zachary Thow, and A. Rod Merrill. "Several New Putative Bacterial ADP-Ribosyltransferase Toxins Are Revealed from In Silico Data Mining, Including the Novel Toxin Vorin, Encoded by the Fire Blight Pathogen Erwinia amylovora." Toxins 12, no. 12 (2020): 792. http://dx.doi.org/10.3390/toxins12120792.

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Mono-ADP-ribosyltransferase (mART) toxins are secreted by several pathogenic bacteria that disrupt vital host cell processes in deadly diseases like cholera and whooping cough. In the last two decades, the discovery of mART toxins has helped uncover the mechanisms of disease employed by pathogens impacting agriculture, aquaculture, and human health. Due to the current abundance of mARTs in bacterial genomes, and an unprecedented availability of genomic sequence data, mART toxins are amenable to discovery using an in silico strategy involving a series of sequence pattern filters and structural

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Alsamman, Alsamman M., Shafik D. Ibrahim, and Aladdin Hamwieh. "KASPspoon: an in vitro and in silico PCR analysis tool for high-throughput SNP genotyping." Bioinformatics 35, no. 17 (2019): 3187–90. http://dx.doi.org/10.1093/bioinformatics/btz004.

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Abstract Motivation Fine mapping becomes a routine trial following quantitative trait loci (QTL) mapping studies to shrink the size of genomic segments underlying causal variants. The availability of whole genome sequences can facilitate the development of high marker density and predict gene content in genomic segments of interest. Correlations between genetic and physical positions of these loci require handling of different experimental genetic data types, and ultimately converting them into positioning markers using a routine and efficient tool. Results To convert classical QTL markers int

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BLAXTER, M., M. ASLETT, D. GUILIANO, J. DAUB, and THE FILARIAL GENOME PROJECT. "Parasitic helminth genomics." Parasitology 118, no. 7 (1999): 39–51. http://dx.doi.org/10.1017/s0031182099004060.

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The initiation of genome projects on helminths of medical importance promises to yield new drug targets and vaccine candidates in unprecedented numbers. In order to exploit this emerging data it is essential that the user community is aware of the scope and quality of data available, and that the genome projects provide analyses of the raw data to highlight potential genes of interest. Core bioinformatics support for the parasite genome projects has promoted these approaches. In the Brugia genome project, a combination of expressed sequence tag sequencing from multiple cDNA libraries represent

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Karabayev, Daniyar, Askhat Molkenov, Kaiyrgali Yerulanuly, et al. "re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files." PeerJ 9 (May 3, 2021): e11333. http://dx.doi.org/10.7717/peerj.11333.

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Background High-throughput sequencing platforms generate a massive amount of high-dimensional genomic datasets that are available for analysis. Modern and user-friendly bioinformatics tools for analysis and interpretation of genomics data becomes essential during the analysis of sequencing data. Different standard data types and file formats have been developed to store and analyze sequence and genomics data. Variant Call Format (VCF) is the most widespread genomics file type and standard format containing genomic information and variants of sequenced samples. Results Existing tools for proces

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Knight, Samantha JL, Ruth Clifford, Pauline Robbe, et al. "The Identification of Further Minimal Regions of Overlap in Chronic Lymphocytic Leukemia Using High-Resolution SNP Arrays." Blood 124, no. 21 (2014): 3315. http://dx.doi.org/10.1182/blood.v124.21.3315.3315.

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Abstract Background:Historically, the identification of minimal deleted regions (MDRs) has been a useful approach for pinpointing genes involved in the pathogenesis of human malignancies and constitutional disorders. Microarray technology has offered increased capability for newly identifying or refining existing MDRs and minimal overlapping regions (MORs) in cancer. Despite this, in chronic lymphocytic leukemia (CLL), published MORs that pinpoint only a few candidate genes have been limited and with the advent of NGS, the utility of high resolution array work as a discovery tool has become un

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Sun, Yawei, Hongxing Ding, Feifan Zhao, et al. "Genomic Characteristics and E Protein Bioinformatics Analysis of JEV Isolates from South China from 2011 to 2018." Vaccines 10, no. 8 (2022): 1303. http://dx.doi.org/10.3390/vaccines10081303.

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Japanese encephalitis is a mosquito-borne zoonotic epidemic caused by the Japanese encephalitis virus (JEV). JEV is not only the leading cause of Asian viral encephalitis, but also one of the leading causes of viral encephalitis worldwide. To understand the genetic evolution and E protein characteristics of JEV, 263 suspected porcine JE samples collected from South China from 2011 to 2018 were inspected. It was found that 78 aborted porcine fetuses were JEV-nucleic-acid-positive, with a positive rate of 29.7%. Furthermore, four JEV variants were isolated from JEV-nucleic-acid-positive material

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Gobalan K and Ahamed John. "Applications of Bioinformatics in Genomics and Proteomics." JOURNAL OF ADVANCED APPLIED SCIENTIFIC RESEARCH 1, no. 3 (2021): 29–42. http://dx.doi.org/10.46947/joaasr13201616.

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Bioinformatics is the application of statistics and computer science to the field of molecular biology. The term bioinformatics was coined by Paulien Hogeweg in 1979 for the study of bioinformatics processes in biotic systems. Its primary use since at least the late 1980s has been in genomics and proteomics, particularly in those areas of genomics involving in large-scale DNA sequencing and proteomics in protein structure prediction. Bioinformatics now entitle the creation and advancement of data bases, algorithms, computational and statistical techniques and theory to solve formal and practic

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Dourmishev, Lyubomir A., Assen L. Dourmishev, Diana Palmeri, Robert A. Schwartz, and David M. Lukac. "Molecular Genetics of Kaposi's Sarcoma-Associated Herpesvirus (Human Herpesvirus 8) Epidemiology and Pathogenesis." Microbiology and Molecular Biology Reviews 67, no. 2 (2003): 175–212. http://dx.doi.org/10.1128/mmbr.67.2.175-212.2003.

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SUMMARY Kaposi's sarcoma had been recognized as unique human cancer for a century before it manifested as an AIDS-defining illness with a suspected infectious etiology. The discovery of Kaposi's sarcoma-associated herpesvirus (KSHV), also known as human herpesvirus-8, in 1994 by using representational difference analysis, a subtractive method previously employed for cloning differences in human genomic DNA, was a fitting harbinger for the powerful bioinformatic approaches since employed to understand its pathogenesis in KS. Indeed, the discovery of KSHV was rapidly followed by publication of i

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Bug, Dmitrii S., Ildar M. Barkhatov, Yana V. Gudozhnikova, Artem V. Tishkov, Igor B. Zhulin, and Natalia V. Petukhova. "Identification and Characterization of a Novel CLCN7 Variant Associated with Osteopetrosis." Genes 11, no. 11 (2020): 1242. http://dx.doi.org/10.3390/genes11111242.

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Osteopetrosis is a group of rare inheritable disorders of the skeleton characterized by increased bone density. The disease is remarkably heterogeneous in clinical presentation and often misdiagnosed. Therefore, genetic testing and molecular pathogenicity analysis are essential for precise diagnosis and new targets for preventive pharmacotherapy. Mutations in the CLCN7 gene give rise to the complete spectrum of osteopetrosis phenotypes and are responsible for about 75% of cases of autosomal dominant osteopetrosis. In this study, we report the identification of a novel variant in the CLCN7 gene

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Bortoluzzi, Stefania, Andrea Bisognin, Marta Biasiolo, et al. "Characterization and discovery of novel miRNAs and moRNAs in JAK2V617F-mutated SET2 cells." Blood 119, no. 13 (2012): e120-e130. http://dx.doi.org/10.1182/blood-2011-07-368001.

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Abstract To gain insights into a possible role of microRNAs in myeloproliferative neoplasms, we performed short RNA massive sequencing and extensive bioinformatic analysis in the JAK2V617F-mutated SET2 cell line. Overall, 652 known mature miRNAs were detected, of which 21 were highly expressed, thus being responsible of most of miRNA-mediated gene repression. microRNA putative targets were enriched in specific signaling pathways, providing information about cell activities under massive posttranscriptional regulation. The majority of miRNAs were mixtures of sequence variants, called isomiRs, m

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Lin, Bichen, Yang Liu, Lanxin Su, et al. "A Novel CDH1 Variant Identified in a Chinese Family with Blepharocheilodontic Syndrome." Diagnostics 12, no. 12 (2022): 2936. http://dx.doi.org/10.3390/diagnostics12122936.

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The goal of the current study was to identify the pathogenic gene variant in a Chinese family with Blepharocheilodontic (BCD) syndrome. Whole-exome sequencing (WES) and Sanger sequencing were used to identify the pathogenic gene variant. The harmfulness of the variant was predicted by bioinformatics. We identified a novel heterozygous missense variant c.1198G>A (p.Asp400Asn) in the CDH1 gene in the proband and his mother with BCD syndrome. The sequencing results of three healthy individuals in this family are wild type. This result is consistent with familial co-segregation. According to Re

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Yang, Andrian, Joshua Y. S. Tang, Michael Troup, and Joshua W. K. Ho. "Scavenger: A pipeline for recovery of unaligned reads utilising similarity with aligned reads." F1000Research 8 (October 13, 2022): 1587. http://dx.doi.org/10.12688/f1000research.19426.2.

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Read alignment is an important step in RNA-seq analysis as the result of alignment forms the basis for downstream analyses. However, recent studies have shown that published alignment tools have variable mapping sensitivity and do not necessarily align all the reads which should have been aligned, a problem we termed as the false-negative non-alignment problem. Here we present Scavenger, a python-based bioinformatics pipeline for recovering unaligned reads using a novel mechanism in which a putative alignment location is discovered based on sequence similarity between aligned and unaligned rea

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Yang, Andrian, Joshua Y. S. Tang, Michael Troup, and Joshua W. K. Ho. "Scavenger: A pipeline for recovery of unaligned reads utilising similarity with aligned reads." F1000Research 8 (September 4, 2019): 1587. http://dx.doi.org/10.12688/f1000research.19426.1.

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Read alignment is an important step in RNA-seq analysis as the result of alignment forms the basis for downstream analyses. However, recent studies have shown that published alignment tools have variable mapping sensitivity and do not necessarily align all the reads which should have been aligned, a problem we termed as the false-negative non-alignment problem. Here we present Scavenger, a python-based bioinformatics pipeline for recovering unaligned reads using a novel mechanism in which a putative alignment location is discovered based on sequence similarity between aligned and unaligned rea

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19

Feau, Nicolas, David L. Joly, and Richard C. Hamelin. "Poplar leaf rusts: model pathogens for a model treeThis minireview is one of a selection of papers published in the Special Issue on Poplar Research in Canada." Canadian Journal of Botany 85, no. 12 (2007): 1127–35. http://dx.doi.org/10.1139/b07-102.

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With the availability of the entire genome of the model tree Populus trichocarpa Torr. & A. Gray and the current genome sequencing project of its rust pathogen Melampsora larici-populina Kleb., rust–poplar interaction research has entered the genomic era. Recent genomics research on poplars has attempted to connect the genetic localizations of loci for qualitative and quantitative disease resistance with putative genes encoding resistance or signalling proteins. The interactions between these putative resistance genes and rust effectors remain unknown. Genomic resources developed for Melam

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Li, Juyi, Shan Sun, Xiufang Wang, et al. "A Missense Mutation in IRS1 is Associated with the Development of Early-Onset Type 2 Diabetes." International Journal of Endocrinology 2020 (January 25, 2020): 1–8. http://dx.doi.org/10.1155/2020/9569126.

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There could be an overlap of monogenic diabetes and early-onset type 2 diabetes mellitus. Precise diagnosis of early-onset diabetes has proven valuable for understanding the mechanism of diabetes and selecting optimal therapy. The majority of maturity onset diabetes of the young (MODY) pathogenic genes in China is still unknown. In this study, a family with suspected MODY was enrolled. Whole-exome sequencing (WES) was used to analyze the variants of the proband. Variants were filtered according to their frequency, location, functional consequences, and bioinformatics software. Candidate pathog

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Adawiah, Rabiatul, A. R. Shahril Firdaus, A. Norzihan, and A. B. Umi Kalsom. "Mining of single nucleotide polymorphism (SNP) and simple sequence repeats (SSRs) from EST tropical fruits." Asian Journal of Plant Biology 2, no. 2 (2014): 48–52. http://dx.doi.org/10.54987/ajpb.v2i2.181.

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The advancement in genomics technology has produced vast amount of expressed sequencetags (ESTs) sequence from tropical fruits. These resources have increased the publicavailability of ESTs sequence from year after year. Therefore, this effort permits mining ofsingle nucleotide polymorphism (SNP) and simple sequence repeat (SSR) from EST tropicalfruits. SNP and SSR are types of molecular marker which commonly used in modern geneticanalysis for wide application such as diversity analysis, linkage analysis and association study.In this study, a small scale EST sequences from tropical fruits (pin

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Maison, David P., Sean B. Cleveland, and Vivek R. Nerurkar. "Genomic analysis of SARS-CoV-2 variants of concern circulating in Hawai’i to facilitate public-health policies." PLOS ONE 17, no. 12 (2022): e0278287. http://dx.doi.org/10.1371/journal.pone.0278287.

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Using genomics, bioinformatics and statistics, herein we demonstrate the effect of statewide and nationwide quarantine on the introduction of SARS-CoV-2 variants of concern (VOC) in Hawai’i. To define the origins of introduced VOC, we analyzed 260 VOC sequences from Hawai’i, and 301,646 VOC sequences worldwide, deposited in the GenBank and global initiative on sharing all influenza data (GISAID), and constructed phylogenetic trees. The trees define the most recent common ancestor as the origin. Further, the multiple sequence alignment used to generate the phylogenetic trees identified the cons

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Hasan, Imtiaj, Marco Gerdol, Yuki Fujii, and Yasuhiro Ozeki. "Functional Characterization of OXYL, A SghC1qDC LacNAc-specific Lectin from The Crinoid Feather Star Anneissia Japonica." Marine Drugs 17, no. 2 (2019): 136. http://dx.doi.org/10.3390/md17020136.

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We identified a lectin (carbohydrate-binding protein) belonging to the complement 1q(C1q) family in the feather star Anneissia japonica (a crinoid pertaining to the phylum Echinodermata). The combination of Edman degradation and bioinformatics sequence analysis characterized the primary structure of this novel lectin, named OXYL, as a secreted 158 amino acid-long globular head (sgh)C1q domain containing (C1qDC) protein. Comparative genomics analyses revealed that OXYL pertains to a family of intronless genes found with several paralogous copies in different crinoid species. Immunohistochemistr

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Tenedini, Elena, Isabella Bernardis, Valentina Artusi, et al. "Targeted Cancer Exome Sequencing Discovers Novel Recurrent Mutations In MPN." Blood 122, no. 21 (2013): 4099. http://dx.doi.org/10.1182/blood.v122.21.4099.4099.

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Abstract The discovery of the JAK2V617F mutation in 2005 [Kralovics R, N Engl J Med 2005] represented a major breakthrough in the understanding of the molecular pathogenesis of Philadelphia chromosome negative chronic myeloproliferative neoplasms (MPN). Nevertheless several observations suggest that the JAK2V617F mutation may not be the disease funding mutation, at least in most instances. Therefore, a great deal of effort is ongoing with the aim to identifying novel genetic lesions contributing to the disease pathogenesis. The two major theoretical and technical drawbacks to the identificatio

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Melidis, Damianos P., Christian Landgraf, Gunnar Schmidt, et al. "GenOtoScope: Towards automating ACMG classification of variants associated with congenital hearing loss." PLOS Computational Biology 18, no. 9 (2022): e1009785. http://dx.doi.org/10.1371/journal.pcbi.1009785.

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Since next-generation sequencing (NGS) has become widely available, large gene panels containing up to several hundred genes can be sequenced cost-efficiently. However, the interpretation of the often large numbers of sequence variants detected when using NGS is laborious, prone to errors and is often difficult to compare across laboratories. To overcome this challenge, the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) have introduced standards and guidelines for the interpretation of sequencing variants. Additionally, disease-specific

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Tiong, Ing Soo, Clarissa Wilson, Satwica Yerneni, et al. "Mutational and Copy Number Profiling of Circulating Tumor DNA in Acute Myeloid Leukemia Using Targeted Next Generation Sequencing." Blood 136, Supplement 1 (2020): 39–40. http://dx.doi.org/10.1182/blood-2020-138933.

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The assessment of circulating tumor DNA (ctDNA), released by tumor cells undergoing apoptosis or necrosis, has established utility in solid tumors due to the advantage of a non-invasive "liquid biopsy" replacing multiple site-specific biopsies. However, its role in acute myeloid leukemia (AML) is uncertain, where a significant proportion of variants detected in the bone marrow (BM) may not be detected in ctDNA (Short, Blood Adv 2020). We have previously demonstrated the possibility of comprehensive genomic characterization of lymphoid malignancy from ctDNA using a single targeted next generati

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Yang, Yunyun, Song Yang, Xiaolu Jiao, et al. "ANGPTL3 Mutations in Unrelated Chinese Han Patients with Familial Hypercholesterolemia." Current Pharmaceutical Design 25, no. 2 (2019): 190–200. http://dx.doi.org/10.2174/1381612825666190228000932.

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Background and objective: Familial hypercholesterolemia (FH) is a severe genetic hyperlipidemia characterized by increased levels of low-density lipoprotein cholesterol (LDL-C), leading to premature atherosclerosis. Angiopoietin-like protein (ANGPTL3) is a hepatocyte-specific protein that can be used to lower LDL in FH. However, it was unknown whether ANGPTL3 variants are present in FH patients. This study was performed to identify ANGPTL3 variants in unrelated Chinese Han patients with FH. Methods and Results: We screened 80 patients with FH (total cholesterol >7.8mmol/L, LDL-cholesterol &

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König, Simone, Wolfgang M. J. Obermann, and Johannes A. Eble. "The Current State-of-the-Art Identification of Unknown Proteins Using Mass Spectrometry Exemplified on De Novo Sequencing of a Venom Protease from Bothrops moojeni." Molecules 27, no. 15 (2022): 4976. http://dx.doi.org/10.3390/molecules27154976.

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(1) Background: The amino acid sequence elucidation of peptides from the gas phase fragmentation mass spectra, de novo sequencing, is a valuable method for the identification of unknown proteins complementary to Edman sequencing. It is increasingly used in shot-gun mass spectrometry (MS)-based proteomics experiments. We review the current state-of-the-art and use the identification of an unknown snake venom protein targeting the human tissue factor (TF) as an example to describe the analysis process based on manual spectrum interrogation. (2) Methods: The immobilized TF was incubated with a cr

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Malek, Sami N., Denzil Bernard, Zhang Xiao Ying, et al. "Analysis of 54 Follicular Lymphomas By Whole Exome Sequencing Identifies Multiple Novel Recurrently Mutated Pathways." Blood 126, no. 23 (2015): 112. http://dx.doi.org/10.1182/blood.v126.23.112.112.

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Abstract Introduction: Follicular lymphoma (FL) constitutes the second most common non-Hodgkin's lymphoma in the Western world. FL carries multiple recurrently mutated genes that are under active investigation. However, due to the relatively small number of published sequenced cases, knowledge regarding the coding genome in FL is still evolving. Methods: To further our understanding of the genetic basis of FL, we used solution exon capture of sheared and processed genomic DNA isolated from highly purified light chain restricted B-cells and paired CD3+ T-cells from 54 FL cases for paired-end ma

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Takei, Tomomi, Kazuaki Yokoyama, Nozomi Yusa, et al. "Artificial Intelligence Guided Precision Medicine Approach to Hematological Disease." Blood 132, Supplement 1 (2018): 2254. http://dx.doi.org/10.1182/blood-2018-99-117941.

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Abstract Background: Next-generation sequencing (NGS) is an attractive tool for prospective use in the field of precision medicine. Using NGS to guide therapy has provided a large volume of genomic data and therapeutic actionability of somatic NGS results. These data are evolving too rapidly to rely solely on human curation. So the interpretation of the clinical significance of such large amounts of genetic data remains the most severe bottleneck preventing the realization of precision medicine. Watson for Genomics (WfG) is a representative artificial intelligence (AI) software, which analyzes

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Cannon, Matthew, Kori Kuzma, James Stevenson, et al. "Abstract 1177: Introduction of the GA4GH Variation Representation Specification (VRS) and supporting tools for discovery and exchange of clinical genomic and cytogenomic knowledge in cancers." Cancer Research 82, no. 12_Supplement (2022): 1177. http://dx.doi.org/10.1158/1538-7445.am2022-1177.

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Abstract Precision oncology is the practice of interpreting the clinical significance of observed molecular changes in patient neoplasms, potentially impacting medical decision making and care. This process is labor-intensive and (among other challenges) involves accurately translating between variation representation conventions from one resource to the next. For example, differences in representations of Copy Number Variation (CNV) from genomic regions, cytogenomic bands, or gene features create challenges in knowledge matching due to lack of standards covering all of these modalities of obs

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Wohler, Elizabeth, Renan Martin, Sean Griffith, et al. "PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data." Orphanet Journal of Rare Diseases 16, no. 1 (2021). http://dx.doi.org/10.1186/s13023-021-01916-z.

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Abstract Background With the advent of whole exome (ES) and genome sequencing (GS) as tools for disease gene discovery, rare variant filtering, prioritization and data sharing have become essential components of the search for disease genes and variants potentially contributing to disease phenotypes. The computational storage, data manipulation, and bioinformatic interpretation of thousands to millions of variants identified in ES and GS, respectively, is a challenging task. To aid in that endeavor, we constructed PhenoDB, GeneMatcher and VariantMatcher. Results PhenoDB is an accessible, freel

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Choi, Hyejin, Kwanghwan Lee, Donghyo Kim, Sanguk Kim, and Jae Hoon Lee. "The implication of holocytochrome c synthase mutation in Korean familial hypoplastic amelogenesis imperfecta." Clinical Oral Investigations, March 3, 2022. http://dx.doi.org/10.1007/s00784-022-04413-0.

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Abstract Objectives This study aimed to comprehensively characterise genetic variants of amelogenesis imperfecta in a single Korean family through whole-exome sequencing and bioinformatics analysis. Material and methods Thirty-one individuals of a Korean family, 9 of whom were affected and 22 unaffected by amelogenesis imperfecta, were enrolled. Whole-exome sequencing was performed on 12 saliva samples, including samples from 8 affected and 4 unaffected individuals. The possible candidate genes associated with the disease were screened by segregation analysis and variant filtering. In silico m

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Su, Zhiguang, Allison Cox, Yuan Shen, Ioannis Stylianou, and Beverly Paigen. "Abstract 1388: Hdlq14 Gene, A New Gene Regulating HDL Levels." Circulation 116, suppl_16 (2007). http://dx.doi.org/10.1161/circ.116.suppl_16.ii_285-a.

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Background . The discovery of new genes responsible for regulation of high-density lipoprotein cholesterol (HDL) has great clinical relevance since increases in HDL can reduce cardiovascular disease risk. Quantitative trait locus (QTL) analysis is a means of finding novel genes that regulate complex traits, such as atherosclerosis and HDL. Hdlq14 and Hdlq15 , two closely linked QTLs for HDL on mouse Chr 1, have been detected by using an intercross between strains C57BL/6 (B6) and 129S1/SvImJ (129). Apoa2 is the gene for Hdlq15 locus, but the gene for Hdlq14 is unknown. Methods: To confirm the

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Yun, Taedong, Helen Li, Pi-Chuan Chang, Michael F. Lin, Andrew Carroll, and Cory Y. McLean. "Accurate, scalable cohort variant calls using DeepVariant and GLnexus." Bioinformatics, January 5, 2021. http://dx.doi.org/10.1093/bioinformatics/btaa1081.

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Abstract Motivation Population-scale sequenced cohorts are foundational resources for genetic analyses, but processing raw reads into analysis-ready cohort-level variants remains challenging. Results We introduce an open-source cohort-calling method that uses the highly-accurate caller DeepVariant and scalable merging tool GLnexus. Using callset quality metrics based on variant recall and precision in benchmark samples and Mendelian consistency in father-mother-child trios, we optimized the method across a range of cohort sizes, sequencing methods, and sequencing depths. The resulting callsets

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Khorsand, Parsoa, Luca Denti, Paola Bonizzoni, Rayan Chikhi, and Fereydoun Hormozdiari. "Comparative genome analysis using sample-specific string detection in accurate long reads." Bioinformatics Advances 1, no. 1 (2021). http://dx.doi.org/10.1093/bioadv/vbab005.

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Abstract Motivation Comparative genome analysis of two or more whole-genome sequenced (WGS) samples is at the core of most applications in genomics. These include the discovery of genomic differences segregating in populations, case-control analysis in common diseases and diagnosing rare disorders. With the current progress of accurate long-read sequencing technologies (e.g. circular consensus sequencing from PacBio sequencers), we can dive into studying repeat regions of the genome (e.g. segmental duplications) and hard-to-detect variants (e.g. complex structural variants). Results We propose

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Farkas, Carlos, Andy Mella, Maxime Turgeon, and Jody J. Haigh. "A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3′ Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity." Frontiers in Microbiology 12 (June 21, 2021). http://dx.doi.org/10.3389/fmicb.2021.665041.

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An unprecedented amount of SARS-CoV-2 sequencing has been performed, however, novel bioinformatic tools to cope with and process these large datasets is needed. Here, we have devised a bioinformatic pipeline that inputs SARS-CoV-2 genome sequencing in FASTA/FASTQ format and outputs a single Variant Calling Format file that can be processed to obtain variant annotations and perform downstream population genetic testing. As proof of concept, we have analyzed over 229,000 SARS-CoV-2 viral sequences up until November 30, 2020. We have identified over 39,000 variants worldwide with increased polymo

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Srivastava, Himangi, Drew Ferrell, and George V. Popescu. "NetSeekR: a network analysis pipeline for RNA-Seq time series data." BMC Bioinformatics 23, no. 1 (2022). http://dx.doi.org/10.1186/s12859-021-04554-1.

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Abstract Background Recent development of bioinformatics tools for Next Generation Sequencing data has facilitated complex analyses and prompted large scale experimental designs for comparative genomics. When combined with the advances in network inference tools, this can lead to powerful methodologies for mining genomics data, allowing development of pipelines that stretch from sequence reads mapping to network inference. However, integrating various methods and tools available over different platforms requires a programmatic framework to fully exploit their analytic capabilities. Integrating

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Lo, Chien-Chi, Migun Shakya, Ryan Connor, et al. "EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts." Bioinformatics, March 24, 2022. http://dx.doi.org/10.1093/bioinformatics/btac176.

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Abstract Summary Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A range of technologies and strategies for pathogen genome enrichment and sequencing are being used by laboratories worldwide, together with different and sometimes ad hoc, analytical procedures for generating genome sequences. A fully integrated analytical process for raw sequence to consensus genome determination, suited to outbreaks such as the ongoing COVID-19 pandemic, is critical to provide a solid genomic basis for epidemiological analyses and well-informed decision making

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Sserwadda, Ivan, and Gerald Mboowa. "rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data." Microbial Genomics 7, no. 6 (2021). http://dx.doi.org/10.1099/mgen.0.000583.

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The recent re-emergence of multidrug-resistant pathogens has exacerbated their threat to worldwide public health. The evolution of the genomics era has led to the generation of huge volumes of sequencing data at an unprecedented rate due to the ever-reducing costs of whole-genome sequencing (WGS). We have developed the Rapid Microbial Analysis Pipeline (rMAP), a user-friendly pipeline capable of profiling the resistomes of ESKAPE pathogens ( Enterococcus faecium , Staphylococcus aureus , Klebsiella pneumoniae , Acinetobacter baumannii , Pseudomonas aeruginosa and Enterobacter species) using WG

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Camiolo, Salvatore, Nicolás M. Suárez, Antonia Chalka, Cristina Venturini, Judith Breuer, and Andrew J. Davison. "GRACY: a tool for analysing human cytomegalovirus sequence data." Virus Evolution, December 30, 2020. http://dx.doi.org/10.1093/ve/veaa099.

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Abstract Modern DNA sequencing has instituted a new era in human cytomegalovirus (HCMV) genomics. A key development has been the ability to determine the genome sequences of HCMV strains directly from clinical material. This involves the application of complex and often non-standardized bioinformatics approaches to analysing data of variable quality in a process that requires substantial manual intervention. To relieve this bottleneck, we have developed GRACy (Genome Reconstruction and Annotation of Cytomegalovirus), an easy-to-use tookit for analysing HCMV sequence data. GRACy automates and i

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Rana, Shashank, Preeti P, Vartika Singh, and Nikunj Bhardwaj. "Bioinformatics in Microbial Biotechnology: A Genomics and Proteomics Perspective." Innovations in Information and Communication Technology Series, February 28, 2021, 54–69. http://dx.doi.org/10.46532/978-81-950008-7-6_005.

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Biological data is a new era with new growth in numerical and memory retention capacity, many microbial and eukaryotic genomes encapsulate the human genome's pure structure, followed by raising the prospect of higher viral control. The goal is as high as the development of drug development based on the study of the structures and functions of target molecules (rational drug) and antimicrobial agents, the growth is simple to manage drugs, protein biomarkers that develop different bacterial infections and healthier considerate of protein(host)-protein(bacteria) interactions to avert bacterial di

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Bradbury, P. J., T. Casstevens, S. E. Jensen, et al. "The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation." Bioinformatics, June 24, 2022. http://dx.doi.org/10.1093/bioinformatics/btac410.

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Abstract Motivation Pangenomes provide novel insights for population and quantitative genetics, genomics, and breeding not available from studying a single reference genome. Instead, a species is better represented by a pangenome or collection of genomes. Unfortunately, managing and using pangenomes for genomically diverse species is computationally and practically challenging. We developed a trellis graph representation anchored to the reference genome that represents most pangenomes well and can be used to impute complete genomes from low density sequence or variant data. Results The Practic

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Bersell, Kevin, Tao Yang, and Dan Roden. "Abstract 96: A Unique Jervell Lange-Nielsen Syndrome Mutation Modeled in Induced Pluripotent Stem Cell Derived Cardiomyocytes." Circulation Research 117, suppl_1 (2015). http://dx.doi.org/10.1161/res.117.suppl_1.96.

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Introduction: Current screening for mutations in human disease is turning increasingly to next-generation methods that map short reads to a reference sequence. We report here an unusual variant that was undetected by next generation sequencing in a patient diagnosed with Jervell Lange-Nielsen syndrome (JLNS) and initial results in an induced pluripotent stem cell-derived cardiomyocyte (iPSC-CM) model. Methods and Results: A diagnosis of JLNS was made in a middle-aged woman with congenital deafness and QT intervals as long as 800 msec. However, next-generation sequencing found only a heterozygo

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Peng, Qi, Wenyan Qin, Siping Li, Meihua Huang, Chunbao Rao, and Xiaomei Lu. "A Novel IRF6 Frameshift Mutation in a Large Chinese Pedigree With Van der Woude syndrome." Cleft Palate-Craniofacial Journal, April 28, 2021, 105566562110109. http://dx.doi.org/10.1177/10556656211010909.

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Aims: Van der Woude syndrome (VWS) is one of the most common craniofacial anomalies, causing significant functional and psychological burden to the patients. This study aimed to identify the genetic cause of VWS in a Chinese family. Methods: Whole genome sequencing (WGS) was performed to screen for pathogenic mutations. Various Bioinformatics tools were used to assess the pathogenicity of the variants. Cosegregation analysis of the candidate variant was carried out. Interpretation of variants was performed according to the American College of Medical Genetics and Genomics guidelines. Results:

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Chen, Jia, Yuting Ma, Hong Li, et al. "Rare and potential pathogenic mutations of LMNA and LAMA4 associated with familial arrhythmogenic right ventricular cardiomyopathy/dysplasia with right ventricular heart failure, cerebral thromboembolism and hereditary electrocardiogram abnormality." Orphanet Journal of Rare Diseases 17, no. 1 (2022). http://dx.doi.org/10.1186/s13023-022-02348-z.

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Abstract Background Arrhythmogenic right ventricular cardiomyopathy/dysplasia (ARVC/D) is associated with ventricular arrhythmia, heart failure (HF), and sudden death. Thromboembolism is also an important and serious complication of ARVC/D. However, the etiology of ARVC/D and thromboembolism and their association with genetic mutations are unclear. Methods Genomic DNA samples of peripheral blood were conducted for whole-exome sequencing (WES) and Sanger sequencing in the ARVC/D family. Then, we performed bioinformatics analysis for genes susceptible to cardiomyopathies and arrhythmias. Further

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Reid, Thomas, and Jordyn Bergsveinson. "How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes." Frontiers in Molecular Biosciences 8 (May 7, 2021). http://dx.doi.org/10.3389/fmolb.2021.662888.

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Culture-independent and meta-omics sequencing methods have shed considerable light on the so-called “microbial dark matter” of Earth’s environmental microbiome, improving our understanding of phylogeny, the tree of life, and the vast functional diversity of microorganisms. This influx of sequence data has led to refined and reimagined hypotheses about the role and importance of microbial biomass, that paradoxically, sequencing approaches alone are unable to effectively test. Post-genomic approaches such as metabolomics are providing more sensitive and insightful data to unravel the fundamental

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Chu, Chunfang, Lin Li, Shenghui Li, et al. "Variants in genes related to development of the urinary system are associated with Mayer–Rokitansky–Küster–Hauser syndrome." Human Genomics 16, no. 1 (2022). http://dx.doi.org/10.1186/s40246-022-00385-0.

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AbstractMayer–Rokitansky–Küster–Hauser (MRKH) syndrome, also known as Müllerian agenesis, is characterized by uterovaginal aplasia in an otherwise phenotypically normal female with a normal 46,XX karyotype. Previous studies have associated sequence variants of PAX8, TBX6, GEN1, WNT4, WNT9B, BMP4, BMP7, HOXA10, EMX2, LHX1, GREB1L, LAMC1, and other genes with MRKH syndrome. The purpose of this study was to identify the novel genetic causes of MRKH syndrome. Ten patients with MRKH syndrome were recruited at Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China. Wh

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Samaha, Georgina, Claire M. Wade, Hamutal Mazrier, Catherine E. Grueber, and Bianca Haase. "Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management." BMC Genomics 22, no. 1 (2021). http://dx.doi.org/10.1186/s12864-021-07899-2.

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Abstract Background While recent advances in genomics has enabled vast improvements in the quantification of genome-wide diversity and the identification of adaptive and deleterious alleles in model species, wildlife and non-model species have largely not reaped the same benefits. This has been attributed to the resources and infrastructure required to develop essential genomic datasets such as reference genomes. In the absence of a high-quality reference genome, cross-species alignments can provide reliable, cost-effective methods for single nucleotide variant (SNV) discovery. Here, we demons

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Vasconcelos, Ana M., Maria Beatriz Carmo, Beatriz Ferreira, et al. "IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner." BMC Bioinformatics 22, no. 1 (2021). http://dx.doi.org/10.1186/s12859-021-03955-6.

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Abstract Background IsomiRs are miRNA variants that vary in length and/or sequence when compared to their canonical forms. These variants display differences in length and/or sequence, including additions or deletions of one or more nucleotides (nts) at the 5′ and/or 3′ end, internal editings or untemplated 3′ end additions. Most available tools for small RNA-seq data analysis do not allow the identification of isomiRs and often require advanced knowledge of bioinformatics. To overcome this, we have developed IsomiR Window, a platform that supports the systematic identification, quantification

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