scholarly journals DIVIS: Integrated and Customizable Pipeline for Cancer Genome Sequencing Analysis and Interpretation

2021 ◽  
Vol 11 ◽  
Author(s):  
Xiaoyu He ◽  
Yu Zhang ◽  
Danyang Yuan ◽  
Xinyin Han ◽  
Jiayin He ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Human Cancer ◽  
Cancer Genome ◽  
Sequencing Analysis ◽  
Cancer Genome Sequencing ◽  
Whole Exome ◽  
Variant Detection ◽  
Next Generation Sequencing Ngs ◽  
Gene Panel Sequencing ◽  
Generation Sequencing

Next-generation sequencing (NGS) has drastically enhanced human cancer research, but diverse sequencing strategies, complicated open-source software, and the identification of massive numbers of mutations have limited the clinical application of NGS. Here, we first presented GPyFlow, a lightweight tool that flexibly customizes, executes, and shares workflows. We then introduced DIVIS, a customizable pipeline based on GPyFlow that integrates read preprocessing, alignment, variant detection, and annotation of whole-genome sequencing, whole-exome sequencing, and gene-panel sequencing. By default, DIVIS screens variants from multiple callers and generates a standard variant-detection format list containing caller evidence for each sample, which is compatible with advanced analyses. Lastly, DIVIS generates a statistical report, including command lines, parameters, quality-control indicators, and mutation summary. DIVIS substantially facilitates complex cancer genome sequencing analyses by means of a single powerful and easy-to-use command. The DIVIS code is freely available at https://github.com/niu-lab/DIVIS, and the docker image can be downloaded from https://hub.docker.com/repository/docker/sunshinerain/divis.

Comprehensive fundamental somatic variant calling and quality management strategies for human cancer genomes

2020 ◽  
Author(s):  
Xiaoyu He ◽  
Shanyu Chen ◽  
Ruilin Li ◽  
Xinyin Han ◽  
Zhipeng He ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
High Throughput Sequencing ◽  
Cancer Genomics ◽  
Sequence Data ◽  
Human Cancer ◽  
Management Strategies ◽  
Variant Calling ◽  
Cancer Genome ◽  
Sequencing Data ◽  
Cancer Genome Sequencing

Abstract Next-generation sequencing (NGS) technology has revolutionised human cancer research, particularly via detection of genomic variants with its ultra-high-throughput sequencing and increasing affordability. However, the inundation of rich cancer genomics data has resulted in significant challenges in its exploration and translation into biological insights. One of the difficulties in cancer genome sequencing is software selection. Currently, multiple tools are widely used to process NGS data in four stages: raw sequence data pre-processing and quality control (QC), sequence alignment, variant calling and annotation and visualisation. However, the differences between these NGS tools, including their installation, merits, drawbacks and application, have not been fully appreciated. Therefore, a systematic review of the functionality and performance of NGS tools is required to provide cancer researchers with guidance on software and strategy selection. Another challenge is the multidimensional QC of sequencing data because QC can not only report varied sequence data characteristics but also reveal deviations in diverse features and is essential for a meaningful and successful study. However, monitoring of QC metrics in specific steps including alignment and variant calling is neglected in certain pipelines such as the ‘Best Practices Workflows’ in GATK. In this review, we investigated the most widely used software for the fundamental analysis and QC of cancer genome sequencing data and provided instructions for selecting the most appropriate software and pipelines to ensure precise and efficient conclusions. We further discussed the prospects and new research directions for cancer genomics.

scholarly journals Sequencing Using a Two-Step Strategy Reveals High Genetic Diversity in the S Gene of SARS-CoV-2 after a High-Transmission Period in Tunis, Tunisia

2021 ◽  
Author(s):  
Wasfi Fares ◽  
Kais Ghedira ◽  
Mariem Gdoura ◽  
Anissa Chouikha ◽  
Sondes Haddad-Boubaker ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
High Genetic Diversity ◽  
Middle Income ◽  
Middle Income Countries ◽  
Transmission Period ◽  
Variant Detection ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

The method of choice for SARS-CoV-2 variant detection is whole-genome sequencing using next-generation sequencing (NGS) technologies. Resources for this technology remain limited in many low- and middle-income countries, where it is not possible to perform whole-genome sequencing for representative numbers of SARS-CoV-2-positive cases.

Next Generation Sequencing in der medizinischen Versorgung – Stellen Zusatzbefunde und ihre potentiellen ökonomischen Implikationen eine Adoptionshürde dar?

2018 ◽  
Vol 24 (04) ◽  
pp. 197-208
Author(s):  
Susan Raths ◽  
Heiko Paland ◽  
Marit Buschke ◽  
Steffen Fleßa
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequencing ◽  
Next Generation ◽  
Whole Exome ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Zusammenfassung Ziel der Arbeit Ziel ist es, die Bedeutung des Next Generation Sequencing (NGS) und die Relevanz von Zusatzbefunden im derzeitigen klinischen Alltag zu bewerten. Dies soll eine Beurteilung erlauben, ob die ökonomischen Konsequenzen von Zusatzbefunden in der klinischen Routine einer Adoption von modernen Genanalysen entgegenstehen. Methodik Hierzu wurde eine Literaturrecherche sowie eine Online-Befragung unter Humangenetikern (n = 53) zur Relevanz von NGS-Methoden und Zusatzbefunden durchgeführt. Ergebnisse Whole Exome und Genome Sequencing (WES/WGS) werden bislang nur für ausgewählte Patientengruppen angewandt. Die Auftrittswahrscheinlichkeit von Zusatzbefunden wird nur von wenigen Publikationen thematisiert und hängt von der Filterstrategie der Rohdaten ab. Soweit keine ausdrückliche Suche nach Zusatzbefunden erfolgt, scheinen sie nicht gehäuft aufzutreten. Dies deckt sich mit den Angaben der deutschen Humangenetiker, wobei die Befragten zukünftig eine deutliche Zunahme von genetischen Analysen und Zusatzbefunden erwarten. Schlussfolgerung Umfassende Genanalysen sind bisher kein Massenphänomen in der Versorgung, sondern stellen eine frühe Mikroinnovation des Gesundheitswesens dar. Zusatzbefunde können durch fokussierte Auswertungsstrategien minimiert werden. Derzeit behindern (noch) vielfältige Herausforderungen und die teilweise fehlende Evidenz des Patientennutzens eine Übernahme als Standardlösung. Zusatzbefunde und ihre potentiellen Kosten spielen hingegen (noch) keine bedeutende Rolle im Adoptionsprozess dieser Versorgungsinnovation.

Kindler's Syndrome with Recurrent Neutropenia: Report of Two Cases from Saudi Arabia

2020 ◽  
Author(s):  
Yousef Binamer ◽  
Muzamil A. Chisti
Keyword(s):  
Autosomal Recessive ◽  
Common Mechanism ◽  
Sequencing Analysis ◽  
Loss Of Function ◽  
Skin Atrophy ◽  
Whole Exome ◽  
Infancy And Childhood ◽  
Genetics And Genomics ◽  
New Feature ◽  
Generation Sequencing

AbstractKindler syndrome (KS) is a rare photosensitivity disorder with autosomal recessive mode of inheritance. It is characterized by acral blistering in infancy and childhood, progressive poikiloderma, skin atrophy, abnormal photosensitivity, and gingival fragility. Besides these major features, many minor presentations have also been reported in the literature. We are reporting two cases with atypical features of the syndrome and a new feature of recurrent neutropenia. Whole exome sequencing analysis was done using next-generation sequencing which detected a homozygous loss-of-function (LOF) variant of FERMT1 in both patients. The variant is classified as a pathogenic variant as per the American College of Medical Genetics and Genomics guidelines. Homozygous LOF variants of FERMT1 are a common mechanism of KS and as such confirm the diagnosis of KS in our patients even though the presentation was atypical.

scholarly journals Evaluation of Ion Torrent next-generation sequencing for thalassemia diagnosis

2020 ◽  
Vol 48 (12) ◽  
pp. 030006052096777
Author(s):  
Peisong Chen ◽  
Xuegao Yu ◽  
Hao Huang ◽  
Wentao Zeng ◽  
Xiaohong He ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Ion Torrent ◽  
Next Generation ◽  
Large Deletions ◽  
Different Types ◽  
Variant Detection ◽  
Polymerase Chain ◽  
Next Generation Sequencing Ngs ◽  
Accuracy And Repeatability ◽  
Generation Sequencing

Introduction To evaluate a next-generation sequencing (NGS) workflow in the screening and diagnosis of thalassemia. Methods In this prospective study, blood samples were obtained from people undergoing genetic screening for thalassemia at our centre in Guangzhou, China. Genomic DNA was polymerase chain reaction (PCR)-amplified and sequenced using the Ion Torrent system and results compared with traditional genetic analyses. Results Of the 359 subjects, 148 (41%) were confirmed to have thalassemia. Variant detection identified 35 different types including the most common. Identification of the mutational sites by NGS were consistent with those identified by Sanger sequencing and Gap-PCR. The sensitivity and specificities of the Ion Torrent NGS were 100%. In a separate test of 16 samples, results were consistent when repeated ten times. Conclusion Our NGS workflow based on the Ion Torrent sequencer was successful in the detection of large deletions and non-deletional defects in thalassemia with high accuracy and repeatability.

scholarly journals FaSD-somatic: a fast and accurate somatic SNV detection algorithm for cancer genome sequencing data

2014 ◽  
Vol 30 (17) ◽  
pp. 2498-2500 ◽  
Author(s):  
Weixin Wang ◽  
Panwen Wang ◽  
Feng Xu ◽  
Ruibang Luo ◽  
Maria Pik Wong ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Detection Algorithm ◽  
Cancer Genome ◽  
Sequencing Data ◽  
Cancer Genome Sequencing
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