Correction: Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing

Duez, Marc; Giraud, Mathieu; Herbert, Ryan; Rocher, Tatiana; Salson, Mikaël; Thonier, Florian

doi:10.1371/journal.pone.0172249

Cited by 4 publications

(3 citation statements)

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“…Vidjil is an open source platform for the analysis of highthroughput V(D)J immune repertoire sequencing data (Duez et al, 2017). The algorithm is intended to work on ampliconbased sequencing as well as hybrid capture-based sequencing.…”

Section: Read Alignmentmentioning

confidence: 99%

Evaluation of Somatic Hypermutation Status in Chronic Lymphocytic Leukemia (CLL) in the Era of Next Generation Sequencing

Gupta

Viswanatha

Patel

2020

Front. Cell Dev. Biol.

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Somatic hypermutation (SHM) status provides an important prognostic indicator for chronic lymphocytic leukemia (CLL), a very common type of mature B-cell leukemia. Owing to the adverse prognosis associated with an unmutated immunoglobulin heavy chain variable (IGHV) status, SHM testing is performed as a standard of care in CLL. Conventionally, SHM testing has been performed using labor intensive and primarily analog Sanger sequencing method following PCR amplification of the clonal immunoglobulin heavy chain gene rearrangements in CLL cells. In comparison, recent availability of next generation sequencing (NGS) allows more versatile detection and direct identification of clonal immunoglobulin gene rearrangements in neoplastic B-cell populations. The ability to identify specific clonal IGHV signature(s) in both baseline (diagnostic) and post-treatment settings enables unique clinical applications of NGS such as determination of SHM status, minimal residual disease (MRD) monitoring, clonal heterogeneity and B cell receptor IG stereotypy. We provide a review of current practices and recommendations for SHM determination using NGS including examples of difficult cases.

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Section: Read Alignmentmentioning

confidence: 99%

Evaluation of Somatic Hypermutation Status in Chronic Lymphocytic Leukemia (CLL) in the Era of Next Generation Sequencing

Gupta

Viswanatha

Patel

2020

Front. Cell Dev. Biol.

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“…In recent years, new analytical tools (i.e. VDJtools, VDJdb 77 , Vidjil 78 , and VDJServer 79 ) have been applied to the analysis of immune repertoire sequencing data. These tools are accessible online, require no installation, and are suitable for researchers and biologists without the knowledge of computers or bioinformatics.…”

Section: Methodology On Adaptive Immune Repertoire Sequencingmentioning

confidence: 99%

The methods and advances of adaptive immune receptors repertoire sequencing

Pan

Tang

et al. 2021

Theranostics

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The adaptive immune response is a powerful tool, capable of recognizing, binding to, and neutralizing a vast number of internal and external threats via T or B lymphatic receptors with widespread sets of antigen specificities. The emergence of high-throughput sequencing technology and bioinformatics provides opportunities for research in the fields of life sciences and medicine. The analysis and annotation for immune repertoire data can reveal biologically meaningful information, including immune prediction, target antigens, and effective evaluation. Continuous improvements of the immunological repertoire sequencing methods and analysis tools will help to minimize the experimental and calculation errors and realize the immunological information to meet the clinical requirements. That said, the clinical application of adaptive immune repertoire sequencing requires appropriate experimental methods and standard analytical tools. At the population cell level, we can acquire the overview of cell groups, but the information about a single cell is not obtained accurately. The information that is ignored may be crucial for understanding the heterogeneity of each cell, gene expression and drug response. The combination of high-throughput sequencing and single-cell technology allows us to obtain single-cell information with low-cost and high-throughput. In this review, we summarized the current methods and progress in this area.

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“…In our study, diagnostic and follow‐up BM samples were obtained from patients for routine standard‐of‐care testing by molecular MRD. Methods for HTS have been previously described, and Vidjil was used for analysis . Patients had MRD RT‐qPCR measured on day +29 post diagnosis, day+35 post relapse, and other time points as clinically necessary.…”

Section: Methodsmentioning

confidence: 99%

Clinical benefit of a high‐throughput sequencing approach for minimal residual disease in acute lymphoblastic leukemia

Wright

Watt

Inglott

et al. 2019

Pediatric Blood & Cancer

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The molecular detection of minimal residual disease (MRD) is standard of care in acute lymphoblastic leukemia to personalize the stratification of patients to appropriate intensity chemotherapy regimens. High‐throughput sequencing (HTS) techniques are driving changes to MRD methodologies. Our study demonstrates HTS can identify suitable diagnostic markers, even in cases where traditional screening has been unsuccessful. Markers identified by HTS were used to track MRD using standard real‐time quantitative PCR. We show, with six patient examples, clinical benefits of utilizing HTS to screen diagnostic samples and its necessity when traditional screening techniques fail. This is practical evidence that current MRD diagnostic marker screening should be replaced by an HTS approach.

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Correction: Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing

Cited by 4 publications

References 1 publication

Evaluation of Somatic Hypermutation Status in Chronic Lymphocytic Leukemia (CLL) in the Era of Next Generation Sequencing

Evaluation of Somatic Hypermutation Status in Chronic Lymphocytic Leukemia (CLL) in the Era of Next Generation Sequencing

The methods and advances of adaptive immune receptors repertoire sequencing

Clinical benefit of a high‐throughput sequencing approach for minimal residual disease in acute lymphoblastic leukemia

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