April 15, 2016 (Vol. 36, No. 8)

GenPro’s Platform Can Derive Both Genetic and Epigenetic Insights from One Sequencing Run

Molecular clinical genetics has focused on identifying mutations that affect patient health and how those variations can be used to increase the accuracy of diagnoses and prognoses while improving the selection of medications.

“Now we’re realizing the importance of epigenetics in those determinations,” says Adam Marsh, Ph.D., chief science officer and co-founder of Genome Profiling (GenPro). Although scientists don’t yet fully understand the range of epigenetic effects, quantitative technology to assess and measure the epigenetic process is emerging.

GenPro asserts that it can transform next-generation sequencing (NGS) data into epigenetic markers, which the company refers to as EpiMarkers. The company indicates that it accomplishes this feat by means of a genome-wide methylation profiling platform, which is called, appropriately enough, the EpiMarker Discovery Platform.

“The platform integrates technologies to enable samples to be processed by NGS to concurrently provide both gene variant and epigenetic analysis, cutting analysis time and cost by half,” declares Jeb Connor, GenPro’s CEO. “That’s unique.”

According to GenPro, the EpiMarker Discovery Platform generates methylation profiles without using bisulfite oxidation. The company adds that the platform is designed to transform methylation profiles into actionable clinical and biological information.

“In traditional genome sequencing using bisulfite oxidation, the mutation of ‘C’ to ‘T’ removes almost 85% of the sequence information in a read,” Dr. Marsh explains. “Aligning those mutated reads back to a reference genome takes lots of computational time and is error-prone.”

By using a sequencing method that eschews bisulfite oxidation, the GenPro platform avoids inducing mutations. Instead, it scores quantitative differential changes in 5-methylcytosine (5-mC) between two samples.

The platform, suggests Dr. Marsh, is extremely sensitive, specific, and accurate. “For every CpG site [where a cytosine nucleotide is followed by a guanine nucleotide], we derive two lines of evidence in the NGS read,” he states. “They serve as replicates to assign a methylation value. They’re self-correcting, which gives us high repeatability and a very high discrimination between sample groups.”

Separating important epigenetic changes from genomic noise is possible with comparative statistics. “The normal noise that is present in a control set will be the same as that present in the disease sets,” Dr. Marsh explains. “Our analytics engine filters out those noise similarities” so only differentiating epigenetic signals remain.

Comparing quantitative cytosine-phosphate-guanine (CpG) methylation profiles between responders and nonresponders reveals a significant pretreatment epigenetic signal separating these patients into two subpopulations. For the prediction ellipses shown, the confidence intervals are 90%, and P

Clinical Study Results

GenPro began a novel EpiMarker discovery leukemia study during the summer 2015, collaborating with a large cancer center in the southeastern United States. Patients received an azacitidine derivative drug, a first-line treatment for acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS).

“The response rate for this drug is 15–20%,” informs Dr. Marsh. “Our study analyzed bone marrow biopsies that were taken from five responders and five nonresponders before their treatment began. The epigenetic profiles of responders and nonresponders were dramatically different, showing greater than 95% stratification certainty, whereas their gene variant analyses provided no stratification evidence.”

The next phase of the study will expand the cohort to 25 responders and 25 nonresponders, as well as blind unknowns, to validate the findings and determine whether they are predictive. Novel EpiMarker pilot studies also have been conducted for Parkinson’s disease and triple-negative breast cancer. These studies showed distinct epigenetic differences between healthy and diseased patients from tissue and liquid (blood) biopsies.

Such epigenetic data can be gained without disrupting the normal sequencing workflow, says GenPro, which adds that the feat can be achieved by means of the gDNA prep kit the company provides. The restriction enzymes in the kit are matched to GenPro Analytics methylation-profiling and EpiMarker discovery algorithms, enabling both epigenetics and genetic variants to be identified and analyzed with one sequencing run.

Analytics are hosted in an Amazon secure private cloud computing environment that enables GenPro to accomplish two key tasks: receiving NGS data from certified NGS partners, and producing epigenetic analyses for biopharma, diagnostic, and clinical research clients. “Through milestone-based collaboration agreements,” Connor notes, “we operate as an extension of our clients’ teams from feasibility through commercialization.”

Epigenetic Phenotypic Variation

It is often said that we are 99.9% the same genetically, the implication being that our phenotypic differences arise from variability in just 0.1% of the genome. No doubt our phenotypic differences reflect our genome-level differences. But our epigenome-level differences matter, too. Epigenome-level differences of interest to Dr. Marsh include those related to cytosine methylation.

“There are approximately 13.3 million sites within a genome that may carry cytosine methylation marks,” Dr. Marsh says. “These sites affect genes expression, the timing of that expression, how RNA is spliced to make variants, and the broad range of cellular impacts that translate to phenotypic differences in people.”

“The largest portion of what makes us different is the epigenetic layer of chemical modifications on DNA,” Dr. Marsh stresses. “Understanding the role of epigenetics is critical for precision medicine.”

Correlating epigenetic biomarkers to disease will help explain different patient sensitivities to drug therapies; identify risk factors affecting remission and recovery; and reveal individual disease triggers. This information will be of use to drug developers, particularly those trying to improve the stratification of patients in clinical trials.

Formed in 2015, GenPro has milestone-based collaborative agreements with cancer research institutes and biopharma and diagnostic companies. Connor is continuing to build the GenPro team of experts and investors, and is discussing collaborations with biopharma companies. “We’re interested,” he says, “in talking with potential collaborators to advance this work.”

This year likely will see epigenetic biomarkers playing a greater role in patient segmentation for drug developers. “We also will continue to advance our platform and expand its capabilities,” Connor tells GEN.

“It’s a wide-open frontier,” Dr. Marsh proclaims. “A lot of information can be derived from NGS sequence data. We’re working on refining those metrics and pushing toward functional analysis.”

Genome Profiling

Location: 4701 Ogletown-Stanton Rd, Newark, DE 19713

Phone: (610) 389-1726

Website: www.genprollc.com

Principal: Jeb Connor, Chairman, CEO, and Co-founder

Number of Employees: 5

Focus: Genome Profiling (GenPro) is an epigenetic biomarker discovery and analytics company. Its genome methylation profiling and analysis technology enables concurrent analysis of epigenetic and genomic variant data.


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