# Analysis of Pre-Analytic Factors Affecting the Success of Clinical Next-Generation Sequencing of Solid Organ Malignancies

## TL;DR

This paper reviews how pre-analytic factors influence the success of next-generation sequencing in solid tumors, focusing on clinical practices and sample requirements.

## Contribution

The paper provides a detailed review of pre-analytic factors affecting NGS success, specifically for AmpliSeq PCR-based sequencing on the Ion Torrent PGM platform.

## Key findings

- NGS success depends on factors like DNA quantity, quality, and tumor cellularity.
- Formalin-fixed paraffin-embedded tissue requires specific handling for optimal sequencing results.
- Proper tissue selection and preparation are critical for accurate mutational analysis in clinical settings.

## Abstract

Application of next-generation sequencing (NGS) technology to routine clinical practice has enabled characterization of personalized cancer genomes to identify patients likely to have a response to targeted therapy. The proper selection of tumor sample for downstream NGS based mutational analysis is critical to generate accurate results and to guide therapeutic intervention. However, multiple pre-analytic factors come into play in determining the success of NGS testing. In this review, we discuss pre-analytic requirements for AmpliSeq PCR-based sequencing using Ion Torrent Personal Genome Machine (PGM) (Life Technologies), a NGS sequencing platform that is often used by clinical laboratories for sequencing solid tumors because of its low input DNA requirement from formalin fixed and paraffin embedded tissue. The success of NGS mutational analysis is affected not only by the input DNA quantity but also by several other factors, including the specimen type, the DNA quality, and the tumor cellularity. Here, we review tissue requirements for solid tumor NGS based mutational analysis, including procedure types, tissue types, tumor volume and fraction, decalcification, and treatment effects.