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Pharmacogenomics (PGx)

Streamline Your Patient Stratification

Empire Genomics offers a variety of pharmacogenomic (PGx) services to help streamline your drug development process and optimize your clinical trial design. Our PGx testing can indicate how a drug may be metabolized, which can aid in determining dosage, efficacy, and potential side effects. Having this genetic data available in your clinical trials can allow for patient stratification, ultimately reducing trial time and costs. Our standard PGx panel is outlined below, however we are also able to develop custom panels that target the specific genes or hotspots you are interested in.

Genes Included in Standard PGx Panel
ABCB1 COMT CYP2C9 DPYD GABRA6 ITGB3 OPRM1 UGT2B7
ABCG2 CYP1A2 CYP2D6 DRD1 GABRP KIF6 SLCO1B1 VKORC1
ADRA2A CYP2B6 CYP3A4 DRD4 GRIK4 MTHFR TPMT HLA-A*3101
ANKK1 CYP2C19 CYP3A5 F2 HTR2A OPRD1 UGT1A1 HLA-B*5701
APOE CYP2C8 DBH F5 HTR2C OPRK1 UGT2B15 HLA-B*1502
PGx Panel Specifications
PGx Amplicons 119
Number of Pools 1
Sample ID Amplicons 9
Genes Covered 40
Total Alleles 138
SNV/INDEL Targets 136
CYP2D6 Events 2*
Specimen Types DNA, blood, saliva

Data Analysis & Reporting

Basic targeted PGx Panel reports include project summary information along with genotypes of all targeted SNVs/INDELs. Secondary and tertiary analysis can include more comprehensive genetic data including drug bank, gene model, clinical variant, OMIM, dbSNP, and many more. Custom data exports may include information such as locus, gene, mutation, classifications, and percent frequency.

Technologies


Single base mutations can be as clinically relevant as large scale genomic aberrations. Analyzing a gene down to this level can uncover changes that implicate its role in changing how an individual metabolizes a drug. Below is an overview of each of our molecular technologies and when they are most applicable.  

Next Generation Sequencing (NGS)

NGS is a platform that allows us to design targeted panels and run multiple reactions simultaneously. The biggest advantage to NGS is its throughput, which allows for the analysis of a number of genes and alleles at the same time. Although we have a pre-designed panel, we are able to customize the genes and alleles within the panel or create a novel custom panel. 

Variants per Test: 138 SNPs and INDELs
Minimum DNA Requirement: 10 ng/reaction
Average TAT (50 samples): 2 Weeks
Genes in Standard Panel:

ABCB1
ABCG2
ADRA2A
ANKK1
APOE
COMT
CYP1A2
CYP2B6
CYP2C19
CYP2C8
CYP2C9
CYP2D6
CYP3A4
CYP3A5
DBH
DPYD
DRD1
DRD4
F2
F5
GABRA6
GABRP
GRIK4
HLA-A*3101
HLA-B*1502
HLA-B*5701
HTR2A
HTR2C
ITGB3
KIF6
MTHFR
OPRD1
OPRK1
OPRM1
SLCO1B1
TPMT
UGT1A1
UGT2B15
UGT2B7
VKORC1
Sanger Sequencing

Sanger sequencing was the original sequencing standard and remains a useful tool. An advantage of Sanger sequencing is its flexibility. Though the throughput is not as high as an NGS platform is, Sanger sequencing can be more useful in the sequencing of novel genes. 

Variants per Test: Variable based on distribution
Minimum DNA Requirement: 25 ng/reaction
Average TAT (50 samples): 1 Week

Real-Time PCR (rtPCR)

Real-time PCR  (rtPCR) has an advantage in its rapid reporting of results. This process takes advantage of standard PCR protocols, with modifications made that eliminate the need for a secondary step such as gel electrophoresis. This technology is most useful when used as a rapid reporting or confirmatory tool. 

Variants per Test:  1 - 4 SNPs
Minimum DNA Requirement: 25 ng/reaction
Average TAT (50 samples): 1 Week

Fragment Analysis

Fragment analysis is useful in determining mutations that are larger than a single nucleotide such as insertions and deletions, often referred to as INDELs. These INDELs can cause large areas of damage including frameshift mutations...

Variants per Test: 1 INDEL at least 4bp in size
Minimum DNA Requirement: 25 ng/reaction
Average TAT (50 samples): 1 Week