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indels</title> <meta name="description" content="Search results for: indels"> <meta name="keywords" content="indels"> <meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1, maximum-scale=1, user-scalable=no"> <meta charset="utf-8"> <link href="https://cdn.waset.org/favicon.ico" type="image/x-icon" rel="shortcut icon"> <link href="https://cdn.waset.org/static/plugins/bootstrap-4.2.1/css/bootstrap.min.css" rel="stylesheet"> <link href="https://cdn.waset.org/static/plugins/fontawesome/css/all.min.css" rel="stylesheet"> <link href="https://cdn.waset.org/static/css/site.css?v=150220211555" rel="stylesheet"> </head> <body> <header> <div class="container"> <nav class="navbar navbar-expand-lg navbar-light"> <a class="navbar-brand" href="https://waset.org"> <img src="https://cdn.waset.org/static/images/wasetc.png" alt="Open Science Research Excellence" title="Open Science Research Excellence" /> </a> <button class="d-block d-lg-none navbar-toggler ml-auto" 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class="input-group"> <i class="fas fa-search"></i> <input type="text" class="search-query" name="q" placeholder="Author, Title, Abstract, Keywords" value="indels"> <input type="submit" class="btn_search" value="Search"> </div> </div> </form> </div> </div> <div class="row mt-3"> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Commenced</strong> in January 2007</div> </div> </div> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Frequency:</strong> Monthly</div> </div> </div> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Edition:</strong> International</div> </div> </div> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Paper Count:</strong> 10</div> </div> </div> </div> <h1 class="mt-3 mb-3 text-center" style="font-size:1.6rem;">Search results for: indels</h1> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">10</span> Genetic Identification of Crop Cultivars Using Barcode System</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Kesavan%20Markkandan">Kesavan Markkandan</a>, <a href="https://publications.waset.org/abstracts/search?q=Ha%20Young%20Park"> Ha Young Park</a>, <a href="https://publications.waset.org/abstracts/search?q=Seung-Il%20Yoo"> Seung-Il Yoo</a>, <a href="https://publications.waset.org/abstracts/search?q=Sin-Gi%20Park"> Sin-Gi Park</a>, <a href="https://publications.waset.org/abstracts/search?q=Junhyung%20Park"> Junhyung Park</a> </p> <p class="card-text"><strong>Abstract:</strong></p> For genetic identification of crop cultivars, insertions/deletions (InDel) markers have been preferred currently because they are easy to use, PCR based, co-dominant and relatively abundant. However, new InDels need to be developed for genetic studies of new varieties due to the difference of allele frequencies in InDels among the population groups. These new varieties are evolved with low levels of genetic diversity in specific genome loci with high recombination rate. In this study, we described soybean barcode system approach based on InDel makers, each of which is specific to a variation block (VB), where the genomes split by all assumed recombination sites. Firstly, VBs in crop cultivars were mined for transferability to VB-specific InDel markers. Secondly, putative InDels in the VB regions were identified for the development of barcode system by analyzing particular cultivar’s whole genome data. Thirdly, common VB-specific InDels from all cultivars were selected by gel electrophoresis, which were converted as 2D barcode types according to comparing amplicon polymorphisms in the five cultivars to the reference cultivar. Finally, the polymorphism of the selected markers was assessed with other cultivars, and the barcode system that allows a clear distinction among those cultivars is described. The same approach can be applicable for other commercial crops. Hence, VB-based genetic identification not only minimize the molecular markers but also useful for assessing cultivars and for marker-assisted breeding in other crop species. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=variation%20block" title="variation block">variation block</a>, <a href="https://publications.waset.org/abstracts/search?q=polymorphism" title=" polymorphism"> polymorphism</a>, <a href="https://publications.waset.org/abstracts/search?q=InDel%20marker" title=" InDel marker"> InDel marker</a>, <a href="https://publications.waset.org/abstracts/search?q=genetic%20identification" title=" genetic identification"> genetic identification</a> </p> <a href="https://publications.waset.org/abstracts/67342/genetic-identification-of-crop-cultivars-using-barcode-system" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/67342.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">380</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">9</span> Functional Variants Detection by RNAseq</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Raffaele%20A.%20Calogero">Raffaele A. Calogero</a> </p> <p class="card-text"><strong>Abstract:</strong></p> RNAseq represents an attractive methodology for the detection of functional genomic variants. RNAseq results obtained from polyA+ RNA selection protocol (POLYA) and from exonic regions capturing protocol (ACCESS) indicate that ACCESS detects 10% more coding SNV/INDELs with respect to POLYA. ACCESS requires less reads for coding SNV detection with respect to POLYA. However, if the analysis aims at identifying SNV/INDELs also in the 5’ and 3’ UTRs, POLYA is definitively the preferred method. No particular advantage comes from ACCESS or POLYA in the detection of fusion transcripts. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=fusion%20transcripts" title="fusion transcripts">fusion transcripts</a>, <a href="https://publications.waset.org/abstracts/search?q=INDEL" title=" INDEL"> INDEL</a>, <a href="https://publications.waset.org/abstracts/search?q=RNA-seq" title=" RNA-seq"> RNA-seq</a>, <a href="https://publications.waset.org/abstracts/search?q=WES" title=" WES"> WES</a>, <a href="https://publications.waset.org/abstracts/search?q=SNV" title=" SNV"> SNV</a> </p> <a href="https://publications.waset.org/abstracts/57993/functional-variants-detection-by-rnaseq" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/57993.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">288</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">8</span> Sequence Polymorphism and Haplogroup Distribution of Mitochondrial DNA Control Regions HVS1 and HVS2 in a Southwestern Nigerian Population</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Ogbonnaya%20O.%20Iroanya">Ogbonnaya O. Iroanya</a>, <a href="https://publications.waset.org/abstracts/search?q=Samson%20T.%20Fakorede"> Samson T. Fakorede</a>, <a href="https://publications.waset.org/abstracts/search?q=Osamudiamen%20J.%20Edosa"> Osamudiamen J. Edosa</a>, <a href="https://publications.waset.org/abstracts/search?q=Hadiat%20A.%20Azeez"> Hadiat A. Azeez</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The human mitochondrial DNA (mtDNA) is about 17 kbp circular DNA fragments found within the mitochondria together with smaller fragments of 1200 bp known as the control region. Knowledge of variation within populations has been employed in forensic and molecular anthropology studies. The study was aimed at investigating the polymorphic nature of the two hypervariable segments (HVS) of the mtDNA, i.e., HVS1 and HVS2, and to determine the haplogroup distribution among individuals resident in Lagos, Southwestern Nigeria. Peripheral blood samples were obtained from sixty individuals who are not related maternally, followed by DNA extraction and amplification of the extracted DNA using primers specific for the regions under investigation. DNA amplicons were sequenced, and sequenced data were aligned and compared to the revised Cambridge Reference Sequence (rCRS) GenBank Accession number: NC_012920.1) using BioEdit software. Results obtained showed 61 and 52 polymorphic nucleotide positions for HVS1 and HVS2, respectively. While a total of three indels mutation were recorded for HVS1, there were seven for HVS2. Also, transition mutations predominate nucleotide change observed in the study. Genetic diversity (GD) values for HVS1 and HVS2 were estimated to be 84.21 and 90.4%, respectively, while random match probability was 0.17% for HVS1 and 0.89% for HVS2. The study also revealed mixed haplogroups specific to the African (L1-L3) and the Eurasians (U and H) lineages. New polymorphic sites obtained from the study are promising for human identification purposes. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=hypervariable%20region" title="hypervariable region">hypervariable region</a>, <a href="https://publications.waset.org/abstracts/search?q=indels" title=" indels"> indels</a>, <a href="https://publications.waset.org/abstracts/search?q=mitochondrial%20DNA" title=" mitochondrial DNA"> mitochondrial DNA</a>, <a href="https://publications.waset.org/abstracts/search?q=polymorphism" title=" polymorphism"> polymorphism</a>, <a href="https://publications.waset.org/abstracts/search?q=random%20match%20probability" title=" random match probability"> random match probability</a> </p> <a href="https://publications.waset.org/abstracts/125506/sequence-polymorphism-and-haplogroup-distribution-of-mitochondrial-dna-control-regions-hvs1-and-hvs2-in-a-southwestern-nigerian-population" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/125506.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">115</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">7</span> Analytical Validity Of A Tech Transfer Solution To Internalize Genetic Testing</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Lesley%20Northrop">Lesley Northrop</a>, <a href="https://publications.waset.org/abstracts/search?q=Justin%20DeGrazia"> Justin DeGrazia</a>, <a href="https://publications.waset.org/abstracts/search?q=Jessica%20Greenwood"> Jessica Greenwood</a> </p> <p class="card-text"><strong>Abstract:</strong></p> ASPIRA Labs now offers an en-suit and ready-to-implement technology transfer solution to enable labs and hospitals that lack the resources to build it themselves to offer in-house genetic testing. This unique platform employs a patented Molecular Inversion Probe (MIP) technology that combines the specificity of a hybrid capture protocol with the ease of an amplicon-based protocol and utilizes an advanced bioinformatics analysis pipeline based on machine learning. To demonstrate its efficacy, two independent genetic tests were validated on this technology transfer platform: expanded carrier screening (ECS) and hereditary cancer testing (HC). The analytical performance of ECS and HC was validated separately in a blinded manner for calling three different types of variants: SNVs, short indels (typically, <50 bp), and large indels/CNVs defined as multi-exonic del/dup events. The reference set was constructed using samples from Coriell Institute, an external clinical genetic testing laboratory, Maine Molecular Quality Controls Inc. (MMQCI), SeraCare and GIAB Consortium. Overall, the analytical performance showed a sensitivity and specificity of >99.4% for both ECS and HC in detecting SNVs. For indels, both tests reported specificity of 100%, and ECS demonstrated a sensitivity of 100%, whereas HC exhibited a sensitivity of 96.5%. The bioinformatics pipeline also correctly called all reference CNV events resulting in a sensitivity of 100% for both tests. No additional calls were made in the HC panel, leading to a perfect performance (specificity and F-measure of 100%). In the carrier panel, however, three additional positive calls were made outside the reference set. Two of these calls were confirmed using an orthogonal method and were re-classified as true positives leaving only one false positive. The pipeline also correctly identified all challenging carrier statuses, such as positive cases for spinal muscular atrophy and alpha-thalassemia, resulting in 100% sensitivity. After confirmation of additional positive calls via long-range PCR and MLPA, specificity for such cases was estimated at 99%. These performance metrics demonstrate that this tech-transfer solution can be confidently internalized by clinical labs and hospitals to offer mainstream ECS and HC as part of their test catalog, substantially increasing access to quality germline genetic testing for labs of all sizes and resources levels. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=clinical%20genetics" title="clinical genetics">clinical genetics</a>, <a href="https://publications.waset.org/abstracts/search?q=genetic%20testing" title=" genetic testing"> genetic testing</a>, <a href="https://publications.waset.org/abstracts/search?q=molecular%20genetics" title=" molecular genetics"> molecular genetics</a>, <a href="https://publications.waset.org/abstracts/search?q=technology%20transfer" title=" technology transfer"> technology transfer</a> </p> <a href="https://publications.waset.org/abstracts/139070/analytical-validity-of-a-tech-transfer-solution-to-internalize-genetic-testing" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/139070.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">178</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">6</span> Complete Chloroplast DNA Sequences of Georgian Endemic Polyploid Wheats</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=M.%20Gogniashvili">M. Gogniashvili</a>, <a href="https://publications.waset.org/abstracts/search?q=I.%20Maisaia"> I. Maisaia</a>, <a href="https://publications.waset.org/abstracts/search?q=A.%20Kotorashvili"> A. Kotorashvili</a>, <a href="https://publications.waset.org/abstracts/search?q=N.%20Kotaria"> N. Kotaria</a>, <a href="https://publications.waset.org/abstracts/search?q=T.%20Beridze"> T. Beridze</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Three types of plasmon (A, B and G) is typical for genus Triticum. In polyploid species - Triticum turgidum L. and Triticum aestivum L. plasmon B is detected. In the forthcoming paper, complete nucleotide sequence of chloroplast DNA of 11 representatives of Georgian wheat polyploid species, carrying plasmon B was determined. Sequencing of chloroplast DNA was performed on an Illumina MiSeq platform. Chloroplast DNA molecules were assembled using the SOAPdenovo computer program. All contigs were aligned to the reference chloroplast genome sequence using BLASTN. For detection of SNPs and Indels and phylogeny tree construction computer programs Mafft and Blast were used. Using Triticum aestivum L. subsp. macha (Dekapr. & Menabde) Mackey var. paleocolchicum Dekapr. et Menabde as a reference, 5 SNPs can be identified in chloroplast DNA of Georgian endemic polyploid wheat. The number of noncoding substitutions is 2, coding substitutions - 3. In comparison with reference DNA two - 38 bp and 56 bp inversions were observed in paleocolchicum subspecies. There were six 1 bp indels detected in Georgian polyploid wheats, all of them at microsatellite stretches. The phylogeny tree shows that subspecies macha, carthlicum and paleocolchicum occupy different positions. According to the simplified scheme based on SNP and indel data, the ancestral, female parent of the all studied polyploid wheat is unknown X predecesor, from which four lines were formed. 1 SNP and two inversions (38 bp and 56 bp) caused the formation of subsp. paleocolchicum. Three other lines are macha, durum and carthlicum lines. Macha line is further divided into two sublines (M_1 and M_4). Carthlicum line includes subsp.carthlicum and T.aestivum - C_1 - C_2 - A_1. One of the central question of wheat domestication is which people(s) participated in wheat domestication? It is proposed that the predecessors of Georgian peoples (Proto-Kartvelians) must be placed, on the evidence of archaic lexical and toponymic data, in the mountainous regions of the western and central part of the Little Caucasus (the Transcaucasian foothills) at least 4,000 years ago. One of the possibility to explain the ‘wheat puzzle’ is that Kartvelian speakers brought domesticated wheat species and subspecis from Fertile Crescent further north to South Caucasus. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=chloroplast%20DNA" title="chloroplast DNA">chloroplast DNA</a>, <a href="https://publications.waset.org/abstracts/search?q=sequencing" title=" sequencing"> sequencing</a>, <a href="https://publications.waset.org/abstracts/search?q=SNP" title=" SNP"> SNP</a>, <a href="https://publications.waset.org/abstracts/search?q=triticum" title=" triticum"> triticum</a> </p> <a href="https://publications.waset.org/abstracts/95115/complete-chloroplast-dna-sequences-of-georgian-endemic-polyploid-wheats" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/95115.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">153</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">5</span> Postmortem Genetic Testing to Sudden and Unexpected Deaths Using the Next Generation Sequencing</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Eriko%20Ochiai">Eriko Ochiai</a>, <a href="https://publications.waset.org/abstracts/search?q=Fumiko%20Satoh"> Fumiko Satoh</a>, <a href="https://publications.waset.org/abstracts/search?q=Keiko%20Miyashita"> Keiko Miyashita</a>, <a href="https://publications.waset.org/abstracts/search?q=Yu%20Kakimoto"> Yu Kakimoto</a>, <a href="https://publications.waset.org/abstracts/search?q=Motoki%20Osawa"> Motoki Osawa</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Sudden and unexpected deaths from unknown causes occur in infants and youths. Recently, molecular links between a part of these deaths and several genetic diseases are examined in the postmortem. For instance, hereditary long QT syndrome and Burgada syndrome are occasionally fatal through critical ventricular tachyarrhythmia. There are a large number of target genes responsible for such diseases, the conventional analysis using the Sanger’s method has been laborious. In this report, we attempted to analyze sudden deaths comprehensively using the next generation sequencing (NGS) technique. Multiplex PCR to subject’s DNA was performed using Ion AmpliSeq Library Kits 2.0 and Ion AmpliSeq Inherited Disease Panel (Life Technologies). After the library was constructed by emulsion PCR, the amplicons were sequenced 500 flows on Ion Personal Genome Machine System (Life Technologies) according to the manufacture instruction. SNPs and indels were analyzed to the sequence reads that were mapped on hg19 of reference sequences. This project has been approved by the ethical committee of Tokai University School of Medicine. As a representative case, the molecular analysis to a 40 years old male who received a diagnosis of Brugada syndrome demonstrated a total of 584 SNPs or indels. Non-synonymous and frameshift nucleotide substitutions were selected in the coding region of heart disease related genes of ANK2, AKAP9, CACNA1C, DSC2, KCNQ1, MYLK, SCN1B, and STARD3. In particular, c.629T-C transition in exon 3 of the SCN1B gene, resulting in a leu210-to-pro (L210P) substitution is predicted “damaging” by the SIFT program. Because the mutation has not been reported, it was unclear if the substitution was pathogenic. Sudden death that failed in determining the cause of death constitutes one of the most important unsolved subjects in forensic pathology. The Ion AmpliSeq Inherited Disease Panel can amplify the exons of 328 genes at one time. We realized the difficulty in selection of the true source from a number of candidates, but postmortem genetic testing using NGS analysis deserves of a diagnostic to date. We now extend this analysis to SIDS suspected subjects and young sudden death victims. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=postmortem%20genetic%20testing" title="postmortem genetic testing">postmortem genetic testing</a>, <a href="https://publications.waset.org/abstracts/search?q=sudden%20death" title=" sudden death"> sudden death</a>, <a href="https://publications.waset.org/abstracts/search?q=SIDS" title=" SIDS"> SIDS</a>, <a href="https://publications.waset.org/abstracts/search?q=next%20generation%20sequencing" title=" next generation sequencing"> next generation sequencing</a> </p> <a href="https://publications.waset.org/abstracts/17129/postmortem-genetic-testing-to-sudden-and-unexpected-deaths-using-the-next-generation-sequencing" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/17129.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">359</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">4</span> Genomic Analysis of Whole Genome Sequencing of Leishmania Major</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Fatimazahrae%20Elbakri">Fatimazahrae Elbakri</a>, <a href="https://publications.waset.org/abstracts/search?q=Azeddine%20Ibrahimi"> Azeddine Ibrahimi</a>, <a href="https://publications.waset.org/abstracts/search?q=Meryem%20Lemrani"> Meryem Lemrani</a>, <a href="https://publications.waset.org/abstracts/search?q=Dris%20Belghyti"> Dris Belghyti</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Leishmaniasis represents a major public health problem because of the number of cases recorded each year and the wide distribution of the disease. It is a parasitic disease of flagellated protozoa transmitted by the bite of certain species of sandfly, causing a spectrum of clinical pathology in humans ranging from disfiguring skin lesions to fatal visceral leishmaniasis. Cutaneous leishmaniasis due to Leishmania major is a polymorphic disease; in fact, the infection can be asymptomatic, localized, or disseminated. The objective of this work is to determine the genomic diversity that contributes to clinical variability by trying to identify the variation in chromosome number and to extract SNPs and SNPs and InDels; it is based on four sequences (WGS) of Leishmania major available on NCBI in Fastq form, from three countries: Tunisia, Algeria, and Israel, the analysis is set up from a pipeline to facilitate the discovery of genetic diversity, in particular SNP and chromosomal somy. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=Leshmania%20major" title="Leshmania major">Leshmania major</a>, <a href="https://publications.waset.org/abstracts/search?q=cutaneous%20Leishmania" title=" cutaneous Leishmania"> cutaneous Leishmania</a>, <a href="https://publications.waset.org/abstracts/search?q=NGS" title=" NGS"> NGS</a>, <a href="https://publications.waset.org/abstracts/search?q=genomic" title=" genomic"> genomic</a>, <a href="https://publications.waset.org/abstracts/search?q=somy" title=" somy"> somy</a>, <a href="https://publications.waset.org/abstracts/search?q=variant%20calling" title=" variant calling"> variant calling</a> </p> <a href="https://publications.waset.org/abstracts/170783/genomic-analysis-of-whole-genome-sequencing-of-leishmania-major" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/170783.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">79</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3</span> Resequencing and Genomic Study of Wild Coffea Arabica Unveils Genetic Groups at Its Origin and Their Geographic Distribution</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Zate%20Zewdneh%20Zana">Zate Zewdneh Zana</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Coffea arabica (Arabica coffee), a cornerstone of the global beverage industry, necessitates rigorous genetic conservation due to its economic significance and genetic complexity. In this study, we performed whole-genome resequencing of wild species collected from its birthplace, Ethiopia. Advanced Illumina sequencing technology facilitated the mapping of a high percentage of clean reads to the C. arabica reference genome, revealing a substantial number of genetic variants, predominantly SNPs. Our comprehensive analysis not only uncovered a notable distribution of genomic variants across the coffee genome but also identified distinct genetic groups through phylogenetic and population structure analyses. This genomic study provides invaluable insights into the genetic diversity of C. arabica, highlighting the potential of identified SNPs and InDels in enhancing our understanding of key agronomic traits. The findings contribute significantly to genetic studies and support strategic breeding and conservation efforts essential for sustaining the global coffee industry. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=population%20genetics" title="population genetics">population genetics</a>, <a href="https://publications.waset.org/abstracts/search?q=wild%20species" title=" wild species"> wild species</a>, <a href="https://publications.waset.org/abstracts/search?q=evolutionary%20study" title=" evolutionary study"> evolutionary study</a>, <a href="https://publications.waset.org/abstracts/search?q=coffee%20plant" title=" coffee plant"> coffee plant</a> </p> <a href="https://publications.waset.org/abstracts/187447/resequencing-and-genomic-study-of-wild-coffea-arabica-unveils-genetic-groups-at-its-origin-and-their-geographic-distribution" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/187447.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">41</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">2</span> Identification of Genomic Mutations in Prostate Cancer and Cancer Stem Cells By Single Cell RNAseq Analysis</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Wen-Yang%20Hu">Wen-Yang Hu</a>, <a href="https://publications.waset.org/abstracts/search?q=Ranli%20Lu"> Ranli Lu</a>, <a href="https://publications.waset.org/abstracts/search?q=Mark%20Maienschein-Cline"> Mark Maienschein-Cline</a>, <a href="https://publications.waset.org/abstracts/search?q=Danping%20Hu"> Danping Hu</a>, <a href="https://publications.waset.org/abstracts/search?q=Larisa%20Nonn"> Larisa Nonn</a>, <a href="https://publications.waset.org/abstracts/search?q=Toshi%20Shioda"> Toshi Shioda</a>, <a href="https://publications.waset.org/abstracts/search?q=Gail%20S.%20Prins"> Gail S. Prins</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Background: Genetic mutations are highly associated with increased prostate cancer risk. In addition to whole genome sequencing, somatic mutations can be identified by aligning transcriptome sequences to the human genome. Here we analyzed bulk RNAseq and single cell RNAseq data of human prostate cancer cells and their matched non-cancer cells in benign regions from 4 individual patients. Methods: Sequencing raw reads were aligned to the reference genome hg38 using STAR. Variants were annotated using Annovar with respect to overlap gene annotation information, effect on gene and protein sequence, and SIFT annotation of nonsynonymous variant effect. We determined cancer-specific novel alleles by comparing variant calls in cancer cells to matched benign cells from the same individual by selecting unique alleles that were only detected in the cancer samples. Results: In bulk RNAseq data from 3 patients, the most common variants were the noncoding mutations at UTR3/UTR5, and the major variant types were single-nucleotide polymorphisms (SNP) including frameshift mutations. C>T transversion is the most frequently presented substitution of SNP. A total of 222 genes carrying unique exonic or UTR variants were revealed in cancer cells across 3 patients but not in benign cells. Among them, transcriptome levels of 7 genes (CITED2, YOD1, MCM4, HNRNPA2B1, KIF20B, DPYSL2, NR4A1) were significantly up or down regulated in cancer stem cells. Out of the 222 commonly mutated genes in cancer, 19 have nonsynonymous variants and 11 are damaged genes with variants including SIFT, frameshifts, stop gain/loss, and insertions/deletions (indels). Two damaged genes, activating transcription factor 6 (ATF6) and histone demethylase KDM3A are of particular interest; the former is a survival factor for certain cancer cells while the later positively activates androgen receptor target genes in prostate cancer. Further, single cell RNAseq data of cancer cells and their matched non-cancer benign cells from both primary 2D and 3D tumoroid cultures were analyzed. Similar to the bulk RNAseq data, single cell RNAseq in cancer demonstrated that the exonic mutations are less common than noncoding variants, with SNPs including frameshift mutations the most frequently presented types in cancer. Compared to cancer stem cell enriched-3D tumoroids, 2D cancer cells carried 3-times higher variants, 8-times more coding mutations and 10-times more nonsynonymous SNP. Finally, in both 2D primary and 3D tumoroid cultures, cancer stem cells exhibited fewer coding mutations and noncoding SNP or insertions/deletions than non-stem cancer cells. Summary: Our study demonstrates the usefulness of bulk and single cell RNAseaq data in identifying somatic mutations in prostate cancer, providing an alternative method in screening candidate genes for prostate cancer diagnosis and potential therapeutic targets. Cancer stem cells carry fewer somatic mutations than non-stem cancer cells due to their inherited immortal stand DNA from parental stem cells that explains their long-lived characteristics. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=prostate%20cancer" title="prostate cancer">prostate cancer</a>, <a href="https://publications.waset.org/abstracts/search?q=stem%20cell" title=" stem cell"> stem cell</a>, <a href="https://publications.waset.org/abstracts/search?q=genomic%20mutation" title=" genomic mutation"> genomic mutation</a>, <a href="https://publications.waset.org/abstracts/search?q=RNAseq" title=" RNAseq"> RNAseq</a> </p> <a href="https://publications.waset.org/abstracts/193081/identification-of-genomic-mutations-in-prostate-cancer-and-cancer-stem-cells-by-single-cell-rnaseq-analysis" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/193081.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">23</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">1</span> South African Breast Cancer Mutation Spectrum: Pitfalls to Copy Number Variation Detection Using Internationally Designed Multiplex Ligation-Dependent Probe Amplification and Next Generation Sequencing Panels </h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Jaco%20Oosthuizen">Jaco Oosthuizen</a>, <a href="https://publications.waset.org/abstracts/search?q=Nerina%20C.%20Van%20Der%20Merwe"> Nerina C. Van Der Merwe</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The National Health Laboratory Services in Bloemfontien has been the diagnostic testing facility for 1830 patients for familial breast cancer since 1997. From the cohort, 540 were comprehensively screened using High-Resolution Melting Analysis or Next Generation Sequencing for the presence of point mutations and/or indels. Approximately 90% of these patients stil remain undiagnosed as they are BRCA1/2 negative. Multiplex ligation-dependent probe amplification was initially added to screen for copy number variation detection, but with the introduction of next generation sequencing in 2017, was substituted and is currently used as a confirmation assay. The aim was to investigate the viability of utilizing internationally designed copy number variation detection assays based on mostly European/Caucasian genomic data for use within a South African context. The multiplex ligation-dependent probe amplification technique is based on the hybridization and subsequent ligation of multiple probes to a targeted exon. The ligated probes are amplified using conventional polymerase chain reaction, followed by fragment analysis by means of capillary electrophoresis. The experimental design of the assay was performed according to the guidelines of MRC-Holland. For BRCA1 (P002-D1) and BRCA2 (P045-B3), both multiplex assays were validated, and results were confirmed using a secondary probe set for each gene. The next generation sequencing technique is based on target amplification via multiplex polymerase chain reaction, where after the amplicons are sequenced parallel on a semiconductor chip. Amplified read counts are visualized as relative copy numbers to determine the median of the absolute values of all pairwise differences. Various experimental parameters such as DNA quality, quantity, and signal intensity or read depth were verified using positive and negative patients previously tested internationally. DNA quality and quantity proved to be the critical factors during the verification of both assays. The quantity influenced the relative copy number frequency directly whereas the quality of the DNA and its salt concentration influenced denaturation consistency in both assays. Multiplex ligation-dependent probe amplification produced false positives due to ligation failure when ligation was inhibited due to a variant present within the ligation site. Next generation sequencing produced false positives due to read dropout when primer sequences did not meet optimal multiplex binding kinetics due to population variants in the primer binding site. The analytical sensitivity and specificity for the South African population have been proven. Verification resulted in repeatable reactions with regards to the detection of relative copy number differences. Both multiplex ligation-dependent probe amplification and next generation sequencing multiplex panels need to be optimized to accommodate South African polymorphisms present within the genetically diverse ethnic groups to reduce the false copy number variation positive rate and increase performance efficiency. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=familial%20breast%20cancer" title="familial breast cancer">familial breast cancer</a>, <a href="https://publications.waset.org/abstracts/search?q=multiplex%20ligation-dependent%20probe%20amplification" title=" multiplex ligation-dependent probe amplification"> multiplex ligation-dependent probe amplification</a>, <a href="https://publications.waset.org/abstracts/search?q=next%20generation%20sequencing" title=" next generation sequencing"> next generation sequencing</a>, <a href="https://publications.waset.org/abstracts/search?q=South%20Africa" title=" South Africa"> South Africa</a> </p> <a href="https://publications.waset.org/abstracts/79169/south-african-breast-cancer-mutation-spectrum-pitfalls-to-copy-number-variation-detection-using-internationally-designed-multiplex-ligation-dependent-probe-amplification-and-next-generation-sequencing-panels" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/79169.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">231</span> </span> </div> </div> </div> </main> <footer> <div id="infolinks" class="pt-3 pb-2"> <div class="container"> <div style="background-color:#f5f5f5;" class="p-3"> <div class="row"> <div class="col-md-2"> <ul class="list-unstyled"> About <li><a href="https://waset.org/page/support">About Us</a></li> <li><a href="https://waset.org/page/support#legal-information">Legal</a></li> <li><a target="_blank" rel="nofollow" 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