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Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

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Development and Validation of StrataNGS, a Multiplex PCR, Semiconductor Sequencing-Based Comprehensive Genomic

Scott A Tomlins¹, Daniel H Hovelson¹, Paul Harms²

¹Strata Oncology, Ann Arbor, Michigan.

The Journal of Molecular Diagnostics : JMD

|August 28, 2021

Summary

StrataNGS, a novel multiplex PCR/semiconductor sequencing test, enables comprehensive genomic profiling (CGP) of tumor DNA and RNA. This validated assay accurately detects multiple variant classes, including tumor mutational burden (TMB), for clinical use.

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Area of Science:

Oncology
Genomics
Molecular Diagnostics

Background:

Multiplex PCR/semiconductor sequencing for comprehensive genomic profiling (CGP) has faced limitations.
Targeted tumor testing is crucial for personalized cancer treatment.

Purpose of the Study:

To develop and validate StrataNGS, a multiplex PCR/semiconductor sequencing assay for CGP.
To assess the accuracy and reproducibility of StrataNGS across various variant classes.

Main Methods:

Development of a 429-gene multiplex PCR/semiconductor sequencing test (StrataNGS).
Co-isolation of DNA and RNA from formalin-fixed, paraffin-embedded tumor specimens.
Validation using 1986 clinical samples and an optimized bioinformatics pipeline.

Main Results:

StrataNGS demonstrated high accuracy (>0.999 for mutations/fusions, 0.945 for TMB status).
Positive predictive values ranged from 0.915 (TMB) to 1.00 (gene fusions).
Reproducibility was high across all variant classes (0.998-1.00).

Conclusions:

StrataNGS is a feasible and validated multiplex PCR/semiconductor sequencing assay for tumor tissue CGP.
Optimized bioinformatic approaches are key to successful implementation.
The assay provides reliable detection of multiple variant classes for clinical decision-making.