WorkFlow

PGDx processes all samples through the following steps of our validated workflow:

Step 01

Pathologic Review

The pathology of each sample is examined to confirm a diagnosis of the diseased tissue.

Step 02

Sample processing and tumor enrichment

We accept DNA, frozen tissue, biopsy (including liquid biopsy), FFPE blocks or slides, cells, and plasma.

Step 03

Library construction

Next-generation sequencing libraries are constructed and may undergo exome or targeted gene capture.

Step 04

Sequencing

We use high-throughput NGS at extremely high coverage to identify point mutations, copy number changes, rearrangements, insertions, and deletions.

Step 05

Bioinformatic analyses

All samples are analyzed using our patented approaches for novel genetic analyses and proprietary data analysis algorithms.

Step 06

Report generation

The results of all analyses are captured in a final report that links data to biological information.

Analysis

PGDx provides access to a variety of patented approaches for novel genetic analyses and proprietary data analysis algorithms:

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Analyze sequence mutations

VariantDx analysis for identification of single-base, insertion, and deletion mutations with high sensitivity and specificity.*

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Analyze Copy number alterations

Proprietary Digital Karyotyping analysis for high resolution annotation of copy number alterations.

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Analyze structural changes

PARE (Personalized Analysis of Rearranged Ends) technology to identify structural changes in tumor-specific DNA.

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Separate Artifacts

Proprietary analysis algorithms to identify bona fide sequence changes and to exclude sequence artifacts.

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Inspection and Curation

Detailed inspection and curation of tumor-specific mutations by world-class cancer bioinformatic experts.

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Identify Important mutations

Identification of mutated genes with biologic or clinical implications in human cancer.

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Analyze genes enriched for alterations

Proprietary analysis algorithms to evaluate genes and pathways enriched for alterations.

*PGDx is the only company to validate these methods against whole-exome PCR and Sanger sequencing of cancer.

Report

Services result in a comprehensive report with the following information:

Individual mutations in each tumor specimen
Incidence of gene mutations in previous cancer genome analyses
Alteration frequency among samples analyzed

Tumor specific sequence mutations, copy-number alterations, and specific translocations

Functional impact of mutations

Mutated genes/pathways with biologic or clinical implications

In depth COSMIC analysis for recurrent mutations

Proprietary CHASM analysis for identification of driver mutations

Integrated analysis report

Data summary statistics

Incidence of gene mutations across study

Database of sequence and copy number alterations

Gene and sample matrix for mutations identified