Cargando…
Comprehensive Development and Implementation of Good Laboratory Practice for NGS Based Targeted Panel on Solid Tumor FFPE Tissues in Diagnostics
The speed, accuracy, and increasing affordability of next-generation sequencing (NGS) have revolutionized the advent of precision medicine. To date, standardized validation criteria for diagnostic accreditation do not exist due to variability across the multitude of NGS platforms and within NGS proc...
Autores principales: | , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9141409/ https://www.ncbi.nlm.nih.gov/pubmed/35626446 http://dx.doi.org/10.3390/diagnostics12051291 |
_version_ | 1784715339247910912 |
---|---|
author | Chougule, Anuradha Jagtap, Vinita Nikam, Ankita Kale, Shrutikaa Nambiar, Kavya Bagayatkar, Priyanka Chandrani, Pratik Kaushal, Rajiv Noronha, Vanita Patil, Vijay Banavali, Shripad Prabhash, Kumar |
author_facet | Chougule, Anuradha Jagtap, Vinita Nikam, Ankita Kale, Shrutikaa Nambiar, Kavya Bagayatkar, Priyanka Chandrani, Pratik Kaushal, Rajiv Noronha, Vanita Patil, Vijay Banavali, Shripad Prabhash, Kumar |
author_sort | Chougule, Anuradha |
collection | PubMed |
description | The speed, accuracy, and increasing affordability of next-generation sequencing (NGS) have revolutionized the advent of precision medicine. To date, standardized validation criteria for diagnostic accreditation do not exist due to variability across the multitude of NGS platforms and within NGS processes. In molecular diagnostics, it is necessary to ensure that the primary material of the FFPE sample has good quality and optimum quantity for the analysis, otherwise the laborious and expensive NGS test may result in unreliable information. Therefore, stringent quality control of DNA and RNA before, during, and after library preparation is an essential parameter. Considering the various challenges with the FFPE samples, we aimed to set a benchmark in QC metrics that can be utilized by molecular diagnostic laboratories for successful library preparation and high-quality NGS data output. In total, 144 DNA and 103 RNA samples of various cancer types with a maximum storage of 2 years were processed for 52 gene focus panels. During the making of DNA and RNA libraries, extensive QC check parameters were imposed at different checkpoints. The decision tree approach can be set as a benchmark for FFPE samples and as a guide to establishing a good clinical laboratory practice for targeted NGS panels. |
format | Online Article Text |
id | pubmed-9141409 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-91414092022-05-28 Comprehensive Development and Implementation of Good Laboratory Practice for NGS Based Targeted Panel on Solid Tumor FFPE Tissues in Diagnostics Chougule, Anuradha Jagtap, Vinita Nikam, Ankita Kale, Shrutikaa Nambiar, Kavya Bagayatkar, Priyanka Chandrani, Pratik Kaushal, Rajiv Noronha, Vanita Patil, Vijay Banavali, Shripad Prabhash, Kumar Diagnostics (Basel) Article The speed, accuracy, and increasing affordability of next-generation sequencing (NGS) have revolutionized the advent of precision medicine. To date, standardized validation criteria for diagnostic accreditation do not exist due to variability across the multitude of NGS platforms and within NGS processes. In molecular diagnostics, it is necessary to ensure that the primary material of the FFPE sample has good quality and optimum quantity for the analysis, otherwise the laborious and expensive NGS test may result in unreliable information. Therefore, stringent quality control of DNA and RNA before, during, and after library preparation is an essential parameter. Considering the various challenges with the FFPE samples, we aimed to set a benchmark in QC metrics that can be utilized by molecular diagnostic laboratories for successful library preparation and high-quality NGS data output. In total, 144 DNA and 103 RNA samples of various cancer types with a maximum storage of 2 years were processed for 52 gene focus panels. During the making of DNA and RNA libraries, extensive QC check parameters were imposed at different checkpoints. The decision tree approach can be set as a benchmark for FFPE samples and as a guide to establishing a good clinical laboratory practice for targeted NGS panels. MDPI 2022-05-23 /pmc/articles/PMC9141409/ /pubmed/35626446 http://dx.doi.org/10.3390/diagnostics12051291 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Chougule, Anuradha Jagtap, Vinita Nikam, Ankita Kale, Shrutikaa Nambiar, Kavya Bagayatkar, Priyanka Chandrani, Pratik Kaushal, Rajiv Noronha, Vanita Patil, Vijay Banavali, Shripad Prabhash, Kumar Comprehensive Development and Implementation of Good Laboratory Practice for NGS Based Targeted Panel on Solid Tumor FFPE Tissues in Diagnostics |
title | Comprehensive Development and Implementation of Good Laboratory Practice for NGS Based Targeted Panel on Solid Tumor FFPE Tissues in Diagnostics |
title_full | Comprehensive Development and Implementation of Good Laboratory Practice for NGS Based Targeted Panel on Solid Tumor FFPE Tissues in Diagnostics |
title_fullStr | Comprehensive Development and Implementation of Good Laboratory Practice for NGS Based Targeted Panel on Solid Tumor FFPE Tissues in Diagnostics |
title_full_unstemmed | Comprehensive Development and Implementation of Good Laboratory Practice for NGS Based Targeted Panel on Solid Tumor FFPE Tissues in Diagnostics |
title_short | Comprehensive Development and Implementation of Good Laboratory Practice for NGS Based Targeted Panel on Solid Tumor FFPE Tissues in Diagnostics |
title_sort | comprehensive development and implementation of good laboratory practice for ngs based targeted panel on solid tumor ffpe tissues in diagnostics |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9141409/ https://www.ncbi.nlm.nih.gov/pubmed/35626446 http://dx.doi.org/10.3390/diagnostics12051291 |
work_keys_str_mv | AT chouguleanuradha comprehensivedevelopmentandimplementationofgoodlaboratorypracticeforngsbasedtargetedpanelonsolidtumorffpetissuesindiagnostics AT jagtapvinita comprehensivedevelopmentandimplementationofgoodlaboratorypracticeforngsbasedtargetedpanelonsolidtumorffpetissuesindiagnostics AT nikamankita comprehensivedevelopmentandimplementationofgoodlaboratorypracticeforngsbasedtargetedpanelonsolidtumorffpetissuesindiagnostics AT kaleshrutikaa comprehensivedevelopmentandimplementationofgoodlaboratorypracticeforngsbasedtargetedpanelonsolidtumorffpetissuesindiagnostics AT nambiarkavya comprehensivedevelopmentandimplementationofgoodlaboratorypracticeforngsbasedtargetedpanelonsolidtumorffpetissuesindiagnostics AT bagayatkarpriyanka comprehensivedevelopmentandimplementationofgoodlaboratorypracticeforngsbasedtargetedpanelonsolidtumorffpetissuesindiagnostics AT chandranipratik comprehensivedevelopmentandimplementationofgoodlaboratorypracticeforngsbasedtargetedpanelonsolidtumorffpetissuesindiagnostics AT kaushalrajiv comprehensivedevelopmentandimplementationofgoodlaboratorypracticeforngsbasedtargetedpanelonsolidtumorffpetissuesindiagnostics AT noronhavanita comprehensivedevelopmentandimplementationofgoodlaboratorypracticeforngsbasedtargetedpanelonsolidtumorffpetissuesindiagnostics AT patilvijay comprehensivedevelopmentandimplementationofgoodlaboratorypracticeforngsbasedtargetedpanelonsolidtumorffpetissuesindiagnostics AT banavalishripad comprehensivedevelopmentandimplementationofgoodlaboratorypracticeforngsbasedtargetedpanelonsolidtumorffpetissuesindiagnostics AT prabhashkumar comprehensivedevelopmentandimplementationofgoodlaboratorypracticeforngsbasedtargetedpanelonsolidtumorffpetissuesindiagnostics |