Bioinformatics Tools for Detection and Clinical Interpretation of Genomic Variations最新文献

Bioinformatics Workflows for Genomic Variant Discovery, Interpretation and Prioritization 基因组变异发现、解释和优先排序的生物信息学工作流程

Bioinformatics Tools for Detection and Clinical Interpretation of Genomic Variations Pub Date : 2019-06-14 DOI: 10.5772/INTECHOPEN.85524

O. U. Sezerman, Ege Ülgen, Nogayhan Seymen, I. M. Durasi

{"title":"Bioinformatics Workflows for Genomic Variant Discovery, Interpretation and Prioritization","authors":"O. U. Sezerman, Ege Ülgen, Nogayhan Seymen, I. M. Durasi","doi":"10.5772/INTECHOPEN.85524","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.85524","url":null,"abstract":"Next-generation sequencing (NGS) techniques allow high-throughput detection of a vast amount of variations in a cost-efficient manner. However, there still are inconsistencies and debates about how to process and analyse this ‘ big data ’ . To accurately extract clinically relevant information from genomics data, choosing appropriate tools, knowing how to best utilize them and interpreting the results correctly is crucial. This chapter reviews state-of-the-art bioinformatics approaches in clinically relevant genomic variant detection. Best practices of reads-to-variant discovery workflows for germline and somatic short genomic variants are presented along with the most commonly utilized tools for each step. Additionally, methods for detecting structural variations are overviewed. Finally, approaches and current guidelines for clinical interpretation of genomic variants are discussed. As emphasized in this chapter, data processing and variant discovery steps are relatively well-understood. The differences in prioritization algorithms on the other hand can be perplexing, thus creating a bottleneck during interpretation. This review aims to shed light on the pros and cons of these differences to help experts give more informed decisions.","PeriodicalId":301810,"journal":{"name":"Bioinformatics Tools for Detection and Clinical Interpretation of Genomic Variations","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129121829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Orienting Future Trends in Local Ancestry Deconvolution Models to Optimally Decipher Admixed Individual Genome Variations 定位未来趋势的局部祖先反褶积模型，以最佳地破译混合个体基因组变异

Bioinformatics Tools for Detection and Clinical Interpretation of Genomic Variations Pub Date : 2019-05-15 DOI: 10.5772/INTECHOPEN.82764

G. Mazandu, Ephifania Geza, Milaine Seuneu, E. Chimusa

{"title":"Orienting Future Trends in Local Ancestry Deconvolution Models to Optimally Decipher Admixed Individual Genome Variations","authors":"G. Mazandu, Ephifania Geza, Milaine Seuneu, E. Chimusa","doi":"10.5772/INTECHOPEN.82764","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.82764","url":null,"abstract":"Rapid advances in sequencing and genotyping technologies have significantly contributed to shaping the area of medical and population genetics. Several thou-sand genomes are completed with millions of variants identified in the human deoxyribonucleic acid (DNA) sequences. These genomic variations highly influence changes in phenotypic manifestations and physiological functions of different individuals or population groups. Of particular importance are variations introduced by admixture event, contributing significantly to a remarkable phenotypic variability with medical and/or evolutionary implications. In this case, knowledge of local ancestry estimates and date of admixture is of utmost importance for a better understanding of genomic variation patterns throughout modern human evolution and adaptive processes. In this chapter, we survey existing local ancestry deconvolution and dating admixture event models to identify possible gaps that still need to be filled and orient future trends in designing more effective models, which account for current challenges and produce more accurate and biological relevant estimates.","PeriodicalId":301810,"journal":{"name":"Bioinformatics Tools for Detection and Clinical Interpretation of Genomic Variations","volume":"31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125724138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

HCV Genotyping with Concurrent Profiling of Resistance-Associated Variants by NGS Analysis HCV基因分型与耐药相关变异的NGS分析

Bioinformatics Tools for Detection and Clinical Interpretation of Genomic Variations Pub Date : 2019-03-20 DOI: 10.5772/INTECHOPEN.84577

Kok Siong Poon, Julian Wei-Tze Tang, Evelyn Siew- Chuan Koay

{"title":"HCV Genotyping with Concurrent Profiling of Resistance-Associated Variants by NGS Analysis","authors":"Kok Siong Poon, Julian Wei-Tze Tang, Evelyn Siew- Chuan Koay","doi":"10.5772/INTECHOPEN.84577","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.84577","url":null,"abstract":"Determination of viral characteristics including genotype (GT), subtype (ST) and resistance-associated variants (RAVs) profile is important in assigning direct-acting antivirals regimes in HCV patients. To help achieve the best clinical management of HCV patients, a routine diagnostic laboratory should aim at reporting accurate viral GT/ST and RAVs using a reliable diagnostic platform of choice. A laboratory study was conducted to evaluate performance characteristics of a new commercial next-generation sequencing (NGS)-based HCV genotyping assay in comparison to another widely used commercial line probe assay for HCV genotyping. Information on RAVs from deeply sequenced NS3, NS5A and NS5B regions in samples classified as HCV 1a and 1b was harnessed from the fully automated software. Perfect (100%) concordance at HCV genotype level was achieved in GT2 (N = 13), GT3 (N = 55) and GT5 (N = 7). NGS refined the ST assignment in GTs 1, 4 and 6, and resolved previously indeterminate GTs reported by line probe assay. NGS was found to have consistent intra- and inter-run reproducibility in terms of genotyping, subtyping and RAVs identification. Detection of infections with multiple HCV GTs or STs is feasible by NGS. Deep sequencing allows sensitive identification of RAVs in the GT 1a and 1b NS3, NS5A and NS5B regions, but the list of target RAVs is not exhaustive.","PeriodicalId":301810,"journal":{"name":"Bioinformatics Tools for Detection and Clinical Interpretation of Genomic Variations","volume":"123 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126637593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Recognition of Multiomics-Based Molecule-Pattern Biomarker for Precise Prediction, Diagnosis, and Prognostic Assessment in Cancer 识别基于多组学的分子模式生物标志物用于癌症的精确预测、诊断和预后评估

Bioinformatics Tools for Detection and Clinical Interpretation of Genomic Variations Pub Date : 2019-03-07 DOI: 10.5772/INTECHOPEN.84221

Xanquan Zhan, Tian Zhou, Tingting Cheng, Miaolong Lu

引用次数: 4

The Bioinformatics Tools for Discovery of Genetic Diversity by Means of Elastic Net and Hurst Exponent 利用弹性网和赫斯特指数发现遗传多样性的生物信息学工具

Bioinformatics Tools for Detection and Clinical Interpretation of Genomic Variations Pub Date : 2018-12-28 DOI: 10.5772/INTECHOPEN.82755

L. M. Ferreira, T. Sáfadi, T. Setotaw, J. L. Ferreira

{"title":"The Bioinformatics Tools for Discovery of Genetic Diversity by Means of Elastic Net and Hurst Exponent","authors":"L. M. Ferreira, T. Sáfadi, T. Setotaw, J. L. Ferreira","doi":"10.5772/INTECHOPEN.82755","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.82755","url":null,"abstract":"The genome era allowed us to evaluate different aspects on genetic variation, with a precise manner followed by a valuable tip to guide the improvement of knowledge and direct to upgrade to human life. In order to scrutinize these treasured resources, some bioinformatics tools permit us a deep exploration of these data. Among them, we show the importance of the discrete non-decimated wavelet transform (NDWT). The wavelets have a better ability to capture hidden components of biological data and an efficient link between biological systems and the mathematical objects used to describe them. The decomposition of signals/ sequences at different levels of resolution allows obtaining distinct characteristics in each level. The analysis using technique of wavelets has been growing increasingly in the study of genomes. One of the great advantages associated to this method corresponds to the computational gain, that is, the analyses are processed almost in real time. The applicability is in several areas of science, such as physics, mathematics, engineering, and genetics, among others. In this context, we believe that using R software and applied NDWT coupled with elastic net domains and Hurst exponent will be of valuable guideline to researchers of genetics in the investigation of the genetic variability.","PeriodicalId":301810,"journal":{"name":"Bioinformatics Tools for Detection and Clinical Interpretation of Genomic Variations","volume":"25 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132896399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0