A Universal Analysis Pipeline of Hybrid Capture-Based Targeted Sequencing Data with Unique Molecular Indexes (UMIs).

07:00 EST 1st December 2018 | BioPortfolio

Summary of "A Universal Analysis Pipeline of Hybrid Capture-Based Targeted Sequencing Data with Unique Molecular Indexes (UMIs)."

Hybrid capture-based targeted sequencing is increasingly used for genomic variants profiling in tumor patients. Unique molecular index (UMI) technology has recently been developed and helps to increase the accuracy of variant calling by minimizing PCR biases and sequencing errors. However, UMI-adopted targeted sequencing data analysis is slightly different from the methods for other types of omics data, and its pipeline for variant calling is still being optimized in various studying groups for their own purpose. Due to this provincial usage range of tools, our group built an analysis pipeline for global application to many studies of targeted sequencing generated with different methods. First, we generated hybrid capture-based data using genomic DNA extracted from tumor tissues of colorectal cancer patients. Sequencing libraries were prepared, pooled together and an 8-plexed capture library was processed to the enrichment step before 150bp paired-end (PE) sequencing with Illumina Hiseq series. For the analysis, we evaluated several different tools published. We mainly focused on the compatibility of input and output of each tool. Finally, our laboratory built an analysis pipeline specialized for UMI-adopted data. Through this pipeline, we were able to estimate the even on-target rates and filtered consensus reads for more accurate variant calling. These results suggest the potential of our analysis pipeline in the precise examination of quality and efficiency of conducted experiments.


Journal Details

This article was published in the following journal.

Name: Genomics & informatics
ISSN: 1598-866X
Pages: e29


DeepDyve research library

PubMed Articles [35653 Associated PubMed Articles listed on BioPortfolio]

Information and Statistical Analysis Pipeline for High-Throughput RNA Sequencing Data.

Applications of RNA sequencing have been wide-spreading in various subfields of life science. Construction of information and statistical analysis pipeline is indispensable to process raw RNA sequenci...

Rapid and highly-specific generation of targeted DNA sequencing libraries enabled by linking capture probes with universal primers.

Targeted Next Generation Sequencing (NGS) is being adopted increasingly broadly in many research, commercial and clinical settings. Currently used target capture methods, however, typically require co...

Evaluation of analytical factors associated with targeted MEFV gene sequencing using long-range PCR/massively parallel sequencing of whole blood DNA for molecular diagnosis of Familial Mediterranean fever.

Long-range PCR (LR-PCR) is used to enrich the target regions of the genome. This study aimed to establish the pipeline of targeted gene sequencing using LR-PCR and massively parallel sequencing (MPS).

Amplicon-Based Targeted Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue.

Next-generation sequencing (NGS) is rapidly becoming the method of choice for mutation analysis in both research and diagnostics. The benefit of targeted NGS compared to whole-genome and whole-exome s...

Comprehensive elaboration of database resources utilized in next-generation sequencing-based tumor somatic mutation detection.

The rapid evolution of next-generation sequencing (NGS)-based tumor genomic profile detection and the emergence of molecularly targeted therapies have enabled precision oncology. In NGS-based analysis...

Clinical Trials [8338 Associated Clinical Trials listed on BioPortfolio]

Interest of High-throughput Sequencing of RNAs for the Diagnosis of Heterogeneous Genetic Diseases

The advent of high throughput genomic DNA sequencing has led to major advances in the diagnosis of genetic diseases of heterogeneous origin. Thus, our hospital laboratory has developed in ...

Universal Endometrial Cancer DNA Sequencing for Detection of Lynch Syndrome and Personalized Care

This clinical trial studies universal screening for deoxyribonucleic acid (DNA) mismatch repair deficiency in patients with endometrial cancer, mutations in the genes responsible for Lynch...

Universal vs. Targeted School Screening for Adolescent Major Depressive Disorder

The primary goal of the proposed study is to compare the effectiveness of universal school based screening for adolescent major depressive disorder to the current school process of targete...

Integrative Sequencing In Germline and Hereditary Tumours

This study will investigate the utility of integrative sequencing of individuals and families at risk of hereditary cancer syndromes and will uncover novel contributors to tumourigenesis. ...

What Benefit of a Full Analysis of Exome? Routine Care Study in Patients With Solid Tumors

The management of cancers and their therapeutic guidance was until shortly mostly based on histopathological considerations of the tumor. the development of targeted therapies is a turning...

Medical and Biotech [MESH] Definitions

Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.

Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.

A multistage process that includes RNA cloning, physical mapping, subcloning, sequencing, and information analysis.

A multistage process that includes DNA cloning, physical mapping, subcloning, sequencing, and information analysis.

A method of chemical analysis based on the detection of characteristic radionuclides following a nuclear bombardment. It is also known as radioactivity analysis. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

Quick Search

DeepDyve research library

Relevant Topics

DNA sequencing
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. During DNA sequencing, the bases of a small fragment of DNA are sequentially identified from signals emitted as each fragment is re-synthesized from a ...

Polymerase Chain Reaction (PCR)
PCR (Polymerase Chain Reaction) uses the ability of DNA polymerase (enzymes that create DNA molecules by assembling nucleotides, the building blocks of DNA. These enzymes are essential to DNA replication and usually work in pairs to create two ident...

Searches Linking to this Article