A scalable solution for tumor mutational burden from formalin-fixed, paraffin-embedded samples using the Oncomine
Ruchi Chaudhary1, Luca Quagliata2, Jermann Philip Martin2
1Thermo Fisher Scientific, Waltham, Massachusetts, USA.
Translational Lung Cancer Research
|December 4, 2018
Summary
The Oncomine Tumor Mutation Load (TML) assay accurately estimates tumor mutational burden (TMB) from low-input DNA, correlating well with whole exome sequencing. This method is valuable for immuno-oncology research, especially with limited samples.
Area of Science:
- Genomics
- Cancer Research
- Biomarker Discovery
Background:
- Tumor mutational burden (TMB) is a key biomarker for predicting response to immune checkpoint inhibitors.
- High TMB is associated with improved outcomes in various cancer types.
- Current TMB estimation methods often require substantial DNA input, limiting their use.
Purpose of the Study:
- To develop and validate a TMB estimation method using the Oncomine Tumor Mutation Load (TML) Assay with minimal DNA input (20 ng).
- To assess the performance of the TML assay on formalin-fixed, paraffin-embedded (FFPE) samples across multiple cancer types.
- To compare TML assay results with whole exome sequencing (WES) and evaluate its utility in stratifying patient response to immunotherapy.
Main Methods:
- Development of a TMB estimation method utilizing the Oncomine TML Assay with 20 ng of DNA.
- Analytical validation using control samples and comparison with an orthogonal germline filtering method.
- Comparative analysis with whole exome sequencing (WES) on FFPE samples.
- In-silico analysis of genomic coverage and predictive performance using WES data.
Main Results:
- In-silico analysis showed strong correlation (r²=0.986) between TML panel and WES for somatic mutation estimation.
- The TML assay accurately stratified responders and non-responders to immunotherapy.
- TML assay performance on cell lines and control samples matched known truth.
- High correlation (r²=0.83) observed between TML assay and WES TMB estimates on FFPE samples.
- Biologically relevant tumor mutational burden signatures were identified in colorectal cancer, lung, and melanoma FFPE samples.
Conclusions:
- The TML assay accurately predicts TMB values comparable to WES, utilizing a 1.7-Mb genomic footprint.
- The assay enables TMB estimation from low-input DNA in FFPE samples using a streamlined workflow.
- This TMB assay supports scalable and robust immuno-oncology biomarker research, particularly for scarce samples.
Keywords:
Cancer genomicsOncomine Tumor Mutation Load (TML) Assaycheckpoint inhibitorsimmuno-oncologytumor mutational burden (TMB)More Related Videos
Related Concept Videos
01:39Mutations
94.5K
Overview
94.5K
01:35Mutations
44.5K
Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...
44.5K
00:36Viral Mutations
39.9K
A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
39.9K
01:09Mutation, Gene Flow, and Genetic Drift
64.3K
In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
64.3K
01:18Mutations in Microorganisms
726
Mutations are heritable changes in an organism’s genome involving alterations in the base sequence of DNA or RNA. These changes can influence cellular processes and phenotypic traits, potentially transforming the unaltered wild type into a mutant form. Such changes, termed forward mutations, are pivotal in shaping the genetic diversity of organisms.RNA viruses exhibit the highest mutation rates due to the absence of robust proofreading mechanisms during genome replication. In contrast,...
726
01:30Point and Frameshift Mutations
1.2K
Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
1.2K