Validating Next-Generation Sequencing Bioinformatics Pipelines

Publication Date: January 1, 2018
Last Updated: March 14, 2022

Consensus Recommendation Statements for NGS Bioinformatics Pipeline Validation

Consensus Recommendation Statements for NGS Bioinformatics Pipeline Validation

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1 Clinical laboratories offering NGS-based testing should perform their own validation of the bioinformatics pipeline
2 A qualified medical professional with appropriate training in NGS interpretation and certification must oversee and be involved in the validation process
3 Validation must be performed only after completion of design, development, optimization, and familiarization of the bioinformatics pipeline and its components
4 Bioinformatics pipeline validation should closely emulate the real-world environment of the laboratory in which the test is performed
5 Validation should include all individual components of the bioinformatics pipeline used in the analysis, and each component must be reviewed and approved by an appropriately qualified medical molecular professional and the laboratory director
6 The design and implementation of the bioinformatics pipeline must ensure the security of identifiable patient information and be compliant with all applicable laws at the local, state, and national levels
7 Validation of the NGS bioinformatics pipeline must be appropriate and applicable for the intended clinical use, specimen, and variant types detected of the NGS test
8 Laboratories must ensure that the design, implementation, and validation of the bioinformatics pipeline are compliant with applicable laboratory accreditation standards and regulations
9 The bioinformatics pipeline is part of the test procedure, and its components and processes must be documented according to laboratory accreditation standards and regulations
10 The identity of the sample must be preserved throughout each step of the NGS bioinformatics pipeline with a minimum of four unique identifiers, including a unique location identifier within the content of each data file read and/or generated by the pipeline
11 Specific quality control and quality assurance parameters must be evaluated during validation and used to determine satisfactory performance of the bioinformatics pipeline
12 The methods used to alter or filter sequence reads at any point in the bioinformatics pipeline before interpretation must be validated to ensure that the data presented for interpretation accurately and reproducibly represent the sequence in the specimen, and full documentation of these methods must be kept as part of the test documentation according to laboratory accreditation standards and regulations
13 Laboratories must include specific measures to ensure that each data file generated in the bioinformatics pipeline maintains its integrity and provides alerts for or prevents the use of data files that have been altered in an unauthorized or unintended manner
14 In silico validation can be used to supplement the validation of the bioinformatics pipeline but shall not be used in lieu of end-to-end validation of the bioinformatics pipelines using human samples
15 Validation of the bioinformatics pipeline must include confirmation of a representative set of variants with high-quality independent data; appropriate validation metrics by variant type should be reported
16 Clinical laboratories must ensure the accuracy of software-generated HGVS variant nomenclature and annotations and have an alert in place to indicate when the software-generated nomenclature and annotations need to be manually reviewed and/or corrected, and documentation of any corrections must be maintained
17 Supplemental validation is required whenever a significant change is made to any component of the bioinformatics pipeline

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Overview

Title

Validating Next-Generation Sequencing Bioinformatics Pipelines

Authoring Organization

Endorsing Organization

Publication Month/Year

January 1, 2018

Last Updated Month/Year

June 7, 2023

Supplemental Implementation Tools

Document Type

Guideline

External Publication Status

Published

Country of Publication

US

Inclusion Criteria

Adolescent, Adult, Older adult

Health Care Settings

Ambulatory, Hospital

Intended Users

Clinical researcher, nurse, nurse practitioner, physician, physician assistant

Scope

Assessment and screening, Diagnosis, Prevention, Management, Treatment

Keywords

NGS, Next-Generation Sequencing, Bioinformatics Pipelines, Sequence Alignment, variant annotation, variant filtering, variant calling, variant prioritization