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Top-10 List of the Most Studied Genes of All Time Includes Several Used in Clinical Laboratory Testing for Cancers, Other Diseases

Harvard School of Medicine researcher discovers only a fraction of all known human genes are ever included in research studies

It seems every day that diagnostic test developers are announcing new genetic tests for everything from researching bloodlines to predicting vulnerability to specific chronic diseases. However, as most pathologists know, there are more than 20,000 protein-coding genes in the human genome. Thus, an overwhelming majority of genes are not being researched or studied.

That’s according to Peter Kerpedjiev, PhD, a Postdoctoral Fellow at Harvard Medical School in Boston. Kerpedjiev analyzed US National Library of Medicine (NLM) data from its PubMed database. He found that roughly 25% of the articles tagged by the NLM only featured 100 of the 20,000 human genes.

Kerpedjiev studied approximately 40,000 NLM articles that were tagged as describing the structure, function, or location of a particular gene. He then created a list of the top-10 most-studied genes of all time, which contained interesting and unforeseen disclosures.

“The list was surprising,” Kerpedjiev told Nature. “Some genes were predictable; others were completely unexpected.”

Guardian of the Genome

According Kerpedjiev, the top-10 most-studied genes are:

  1. TP53;
  2. TNF;
  3. EGFR;
  4. VEGFA;
  5. APOE;
  6. IL6;
  7. TGFBI;
  8. MTHFR;
  9. ESR1; and,
  10. AKT1.

Kerpedjiev discovered that the top gene on the list—Tumor protein p53 (TP53)—was mentioned in about 8,500 articles to date, and that it is typically included in about two PubMed papers per day. When he began his research three years ago, TP53 was referenced in about 6,600 articles.

Peter Kerpedjiev, PhD (above), is a Postdoctoral Fellow in the lab of Nils Gehlenborg at Harvard Medical School. Previously, he was a PhD student working on modelling the tertiary structure of RNA molecules at the Theoretical Biochemistry Group at the University of Vienna. (Photo and caption copyright: Gehlenborg Lab.)

The National Library of Medicine describes the TP53 gene as a tumor suppressor that regulates cell division by preventing cells from growing and proliferating too quickly or uncontrolled. It is mutated in approximately half of all human cancers and is often referred to as the “guardian of the genome.”

“That explains its staying power,” Bert Vogelstein, MD, Professor of Oncology and Pathology at Johns Hopkins School of Medicine in Baltimore, Md., told Nature. “In cancer, there’s no gene more important.”

Critical Roles in Prevention/Treatment of Chronic Disease

The remaining genes on the list also have crucial roles in the functioning of the human body and disease prevention and treatment. Below is a brief summary of genes two through 10 on the list:

TNF encodes a proinflammatory cytokine that is part of the tumor necrosis factor superfamily. This family of proteins was originally distinguished by their ability to cause the necrosis of neoplasms. The TNF gene has been a drug target for cancer and inflammatory diseases, such as:

EGFR makes a protein known as the epidermal growth factor receptor, which positions the cell membrane to bind to other proteins outside the cell to help it receive signals to trigger cell growth, division, and survival. At least eight known mutations of the EGFR gene have been associated with lung cancer and often appear in drug-resistant cases of the disease.

Vascular Endothelial Growth Factor A (VEGFA) contains a heparin-binding protein that promotes the growth of blood vessels and is critical for physiological and pathological angiogenesis. Variants of the VEGFA gene have been affiliated with microvascular complications of diabetes mellitus and atherosclerosis.

ApoE produces a protein named Apolipoprotein E, which combines with lipids in the body to form lipoproteins that carry cholesterol and other fats through the bloodstream. ApoE-e3 is the most common allele (a variant of the gene) and is found in more than 50% of the general population. In addition to its role in cholesterol and lipoprotein metabolism, ApoE is also associated with:

  • Alzheimer’s disease;
  • Age-related hearing loss; and,
  • Macular degeneration.

Interleukin 6 (IL6) is a cytokine that is mainly produced at locations of acute and chronic inflammation. Once there, it is secreted into the serum where it incites an anti-inflammatory response. The IL6 gene is connected with inflammation-associated diseases such as:

Transforming Growth Factor Beta 1 (TGFB1) initiates chemical signals that regulate various cell activities including the proliferation, maturation, differentiation, motility, and apoptosis of cells throughout the body. The protein created by TGFB1 is abundant in skeletal tissues and regulates the formation and growth of bones and cartilage. Mutations in the TGFB1 gene have been associated with breast, colorectal, lung, liver, and prostate cancers. At least 12 mutations of this gene are known to cause Camurati-Engelmann disease, which is distinguished by hyperostosis (abnormally thick bones) in the arms, legs, and skull.

MTHFR makes methylenetetrahydrofolate reductase, an enzyme that performs a crucial role in processing amino acids. Polymorphisms of this gene have been linked to risk factors for a variety of conditions including:

  • Cardiovascular disease;
  • Stroke;
  • Hypertension;
  • Pre-eclampsia;
  • Glaucoma;
  • Psychiatric disorders; and,
  • Various cancers.

Estrogen Receptor 1 (ESR1) is a ligand-activated transcription factor that is significant for hormone and DNA binding. Estrogen and its receptors are crucial for sexual development and reproductive functions. They also can affect pathological processes including breast and endometrial cancers and osteoporosis.

AKT1 provides instructions for producing a protein known as AKT1 kinase that is located in many cell types throughout the body and is essential for the development and function of the nervous system. This gene belongs to a classification of genes known as oncogenes, which when mutated have the potential to cause normal cells to turn cancerous.

We Don’t Know What We Don’t Know

“It’s revealing how much we don’t know about because we just don’t bother to research it,” noted Dr. Helen Anne Curry, Senior Lecturer and Historian of Modern Science and Technology at the University of Cambridge, UK, in the Nature article. As far back as 2010, Dark Daily reported on university researchers predicting massive growth in anatomic pathology and clinical laboratory diagnostic testing based on the human genome.

How Kerpedjiev’s discovery might impact future genetic diagnostic test development remains to be seen. It will, however, be fascinating to see how this top-10 list of the most studied genes will change over time and how medical laboratory genetic testing may be affected.

—JP Schlingman

Related Information:

The Most Popular Gene in the Human Genome

Top 10 Genes in the Human Genome (by Number of Citations)

Explore the Normal Functions of Human Genes and the Health Implications of Genetic Changes

Stanford Study Shows How Pathologists May Eventually Use the Whole Human Genome for Diagnostic Purposes

Former Hershey Medical Technologist Floyd Benko Sentenced to 15 Months in Prison for Failing to Follow Procedures when Performing Clinical Laboratory Tests

The indicted medical laboratory technician will also be required to pay back more than $69,000 to Hershey Medical Center

It what may be a unique first for the clinical laboratory industry, a medical technologist in Pennsylvania has been found guilty of a criminal felony for failing to perform certain cancer genetic tests according to approved protocols. The judge has sentenced the medical technologist to 15 months in prison and repayment of almost $70,000 in restitution.

Dark Daily reported on earlier developments in this case in 2017. Medical technologist Floyd Benko was indicted in 2015 after pleading guilty to false statement charges stemming from his work with genetic testing at Hershey Medical Center (HMC) between November 2014 and April 2015. Now, Benko has been sentenced to nearly 15 months in prison after pleading guilty to false statement charges.

US Middle District Judge Yvette Kane sentenced Benko to 15 months in prison with three years of supervised release following his prison term. He must also make restitution to HMC in the amount of $69,742 related to retesting of the gene mutation tests he previously performed in which the results were found to be inaccurate.

The sentence required Benko to report to the Pennsylvania Bureau of Prisons on January 22, 2018.

Failure to Follow Protocols Leads to Faulty Results and Eventual Sentencing

The charges levied against Benko relate to DNA gene mutation tests performed by him on behalf of HMC for 124 advanced-stage cancer patients. According to a Department of Justice press release, the genetic testing included:

“Benko failed to perform the assays in the manner called for by Hershey’s standard operating procedures,” the press release states. “Subsequent retesting of the patients during summer 2014, revealed that 60 of the 124 patients had assay results discordant with results obtained by two outside medical laboratories.”

Unusual Application of Federal Fraud Statute

Dark Daily’s previous coverage provides a detailed timeline of events leading up to Benko’s guilty plea.

Court filings state that in late 2013, a treating physician at HMC noted discordant results for tests when compared to a patient’s clinical profile. The physician resubmitted the test to an outside lab and received results that differed from those of Benko’s test.

This led to a request from HMC supervisors for Benko to repeat the test. Again, results differed from the outside laboratory. When supervisors asked for access to the tissue samples used for the test, Benko could not provide them.

Penn State Milton S. Hershey Medical Center (above) where in 2013 to 2014 Floyd Benko, a 60-year-old research technologist, improperly conducted 124 gene mutation clinical laboratory tests and then lied about it to cover up his lack of following standard operating procedures. (Photo copyright: PennLive/Paul Chaplin.)

Standard operating procedures (SOPs) for the tests in question—procedures Benko himself helped to create in conjunction with HMC—required preservation of all tissue samples. They also required the use of a Thermo Scientific NanoDrop 2000 spectrophotometer—a piece of equipment that Benko did not acknowledge using.

With Benko unable to provide samples, HMC triggered an FBI investigation into testing practices by Benko. The investigation yielded 125 tests for which samples were not preserved. Repeat testing by two outside medical laboratories—at HMC’s expense—resulted in 60 assay results returned that were discordant with Benko’s original findings.

Benko eventually resigned from HMC. He later attempted to explain the discordant results in two separate letters to HMC supervisors. However, in July 2015, a federal grand jury returned an indictment: one count of healthcare fraud and two counts of making false statements in healthcare matters to HMC.

Copies of court filings available at Leagle show that Benko initially disputed the charges using four primary arguments and requested case dismissal. These arguments were eventually denied by Kane. “In refusing to dismiss the charges against Benko, Kane rejected his arguments that his alleged actions don’t constitute a crime, especially since he didn’t profit financially,” noted PennLive. “The judge did, however, characterize the Benko case as an ‘unusual application of the federal healthcare fraud statute.’”

After denial of his dismissal, Benko entered a guilty plea to false statement charges in July 2017. Follow-up coverage from PennLive explained that Benko’s plea agreement included a stipulation that advised a sentence of up to 18 months—of which he received 15 months. At the time of sentencing, the final charge appears to be one count of making false statements.

Establishing Protocols and Ensuring Accuracy in Medical Laboratory Testing

Anatomic pathology and medical laboratory testing is an increasingly important part of the modern healthcare system. Both value-based care models and personalized medicine rely on lab results to help improve outcomes and tailor treatments to the individual patient profile.

By failing to follow SOPs when performing these clinical laboratory tests, Benko potentially jeopardized the treatment outcomes and health of more than 100 patients and also created liability concerns for the laboratory in which he was employed.

As highlighted by Benko’s sentence, the impact from this case was not limited to the lives of more than 100 patients. It also affected both the reputation of HMC and their financials—requiring nearly $70,000 in additional spending for the flawed assays—and to confirm the results of suspect tests performed by Benko. And, this does not account for the time and monetary costs related to the investigation and prosecution of the case, or public relations work surrounding the case.

As test volumes continue to increase and lab liability continues to take the spotlight, it is essential that clinical laboratories, anatomical pathology groups, and other diagnostic service providers maintain effective protocols and procedures to ensure the accuracy of test results. And they must establish comprehensive documentation and compliance programs that create accountability and highlight concerns quickly to ensure both patient and laboratory safety.

—Jon Stone

Related Information:

U.S. v. BENKO No. 1:15-cr-00159

Former Hershey Medical Center Worker Pleads Guilty to Lying About Cancer Testing Procedure

Judge Won’t Dismiss Charges That Hershey Med Tech Fudged Genetic Tests for Cancer Patients

Former Hershey Medical Center Research Technologist Sentenced for Making False Statements About Cancer Tests

Penn State University College of Medicine (COM); The Penn State Hershey Medical Center (PSHMC): Standard Operating Procedures (SOPs) Regarding Review and Management of Conflict of Interest

Hershey, Pennsylvania, Clinical Laboratory Technician Indicted in 2015 for Fraudulent Cancer Test Results Pleads Guilty to False Statement Charges

Hershey, Pennsylvania, Clinical Laboratory Technician Indicted in 2015 for Fraudulent Cancer Test Results Pleads Guilty to False Statement Charges

Indicted on charges related to 124 genetic cancer tests performed between 2013 and 2014, former Hershey Medical Center Research Technologist Floyd Benko pleads guilty to charges with a maximum sentence of up to five years in prison

Wake up calls don’t come any clearer. False reporting of clinical laboratory test results will not be tolerated and anyone engaged in it will pay hefty fines and go to jail. Medical laboratories and anatomic pathology groups were put on notice when in July, nearly two years after he was indicted for healthcare fraud, Floyd Benko, of Palmyra, Penn., pled guilty in State District Court to charges of making false statements.

Benko, a 60-year old former research technologist at the Hershey Medical Center (HMC) in Hershey, Penn., surrendered to authorities on July 31, 2015, according a 2015 news release from The United States Attorney’s Office for the Middle District of Pennsylvania. The charges centered on 124 genetic diagnostic tests he performed at HMC between 2013 and 2014. Repeat testing conducted at HMC’s expense resulted in 60 tests results returned from two outside laboratories that differed from Benko’s reported results. No civil charges related to those 60 patients have been filed at the time of writing. And while sentencing is not yet scheduled, part of Benko’s plea requires restitution to HMC in the amount of approximately $70,000.

According to a Department of Justice (DOJ) press release, “The maximum penalty for false statements in healthcare matters is five years’ imprisonment, a term of supervised release following imprisonment, and a fine.” Coverage of the case at PennLive adds, “That agreement also cites a stipulation between the prosecution and defense that the advisory guidelines for Benko’s case call for a prison term of up to one and a half years.”

A Brief History of the Case and Charges

Details in media coverage regarding the case remain scant. However, case filings highlight a few details that help to establish a timeline of the alleged wrongdoing.

According to filings found at Leagle, charges stem around results to a range of genetic diagnostics, including:

·       Epidermal Growth Factor Receptor (EGFR);

·       KRAS gene mutation; and,

·       BRAF gene mutation tests.

Documents show Benko had more than two decades of experience working with HMC. He also helped to define standard operating procedures (SOPs) for the tests in question. This is key to the case as charges stem from failing to follow the SOPs he helped to put in place.

Between April 9, 2013, and November 10, 2014, Benko performed 124 of these procedures for HMC. The SOPs required use of a NanoDrop 2000 spectrophotometer and preservation of tissue samples and specimens involved in all procedures.

Court filings note, “In late 2013, a treating physician observed that a patient’s HMC test results were at odds with the patient’s clinical profile. Defendant had performed the particular test in question. The treating physician ordered the same test from an outside laboratory, which reached a different result than the results reached by Defendant on the same patient’s tissue.”

Penn State Milton S. Hershey Medical Center (above) where in 2013 to 2014 Floyd Benko, a 60-year-old research technologist, improperly conducted 124 gene mutation clinical laboratory tests and then lied about it to cover up his lack of following standard operating procedures. (Photo copyright: PennLive/Paul Chaplin.)

When these results were brought to the attention of HMS supervisors, they requested Benko repeat the test. His results, again, differed from those of outside laboratories. This led to a request to access the tissues used in the test. Benko could not provide them.

Upon further investigation, the samples for 124 tests were missing. Court filings note, “[Benko] had no explanation for the missing DNA and tissue slides at that time.” HMS ordered retests for the tests with outside laboratories at a loss of more than $102,000. The 2015 DOJ press release breaks down these losses further, separating the figure into “$65,000 for outside laboratory testing and $37,406 for assay refunds.”

Of the 124 results, 60 returned discordant with Benko’s findings. This led to Benko sending two letters to HMS supervisors—one in April 2014 and another in October 2014, following his termination—attempting to explain the discordant results. Neither mentioned the NanoDrop 2000 spectrophotometer or provided reasons for failing to preserve tissue samples.

In July 2015, a federal grand jury returned an indictment on three counts related to the questioned testing. The court filing lists charges as follows:

“In Count I, the indictment charges Defendant with healthcare fraud in violation of 18 U.S.C. § 1347. According to the indictment, Defendant defrauded HMC in connection with the delivery of healthcare services by:

1.     Failing to use the NanoDrop 2000 spectrophotometer in conducting the assays;

2.     Failing to preserve the leftover patient tissue samples;

3.     Failing to disclose his actions to his supervising physician or HMC management; and,

4.     By providing false statements about the manner in which he performed the tests.

Counts II and III charge Defendant with making false statements to HMC. Counts II and III are predicated on the letters Defendant wrote to HMC in April and October of 2014.”

Critical Considerations for Medical Laboratories

The criminal charges levied at Benko directly result from his work in a clinical laboratory. And while the guilty plea does not include the healthcare fraud charge, it highlights the potential criminal liability risks pathology and medical laboratory workers face when tests prove inaccurate due to user error.

Because of discordant test results, an individual worker of a clinical laboratory was held liable for damages. Ensuring protocol adherence and accuracy of test results—particularly as new genetic assays and diagnostics reach laboratory test menus—can help to identify potential problems before they become a legal concern.

Maintaining rigorous records and following protocols for required samples and specimens also can help to establish evidence and resolve concerns should they arise.

—Jon Stone

Related Information:

Former Hershey Medical Center Research Technologist Charged with Healthcare Fraud

Former Hershey Medical Center Research Technologist Pleads Guilty to Making False Statements About Cancer Tests

Former Hershey Med Center Research Technologist Indicted for Fraud

Former Hershey Medical Center Worker Pleads Guilty to Lying About Cancer Testing Procedure

Hospital Staffer Admits to Lying About Genetic Cancer Tests

Former Hershey Med Tech Pleads Guilty to Lying About Fudging Cancer Testing

U.S. v. Benko No. 1:15-cr-00159

United States of America v. Floyd A. Benko, Defendant

Medical Scientists Call for Standard Method for Validating Antibodies Used in Research and Clinical Laboratory Diagnostics

Antibody validation standards would help ensure reproducibility of research studies and improve the consistency medical laboratory test results

As science and industry gets better at measuring things and assessing quality, the acceptable standard often comes into question. This seems to be happening with antibodies, the most common reagents used in diagnostics, clinical laboratory diagnostic tests, and medical research. In many cases, the end result is that companies and their suppliers must use new technologies and quality methods to revise the “old way” and create products that have measurable better quality.

The techniques currently used to validate antibodies is the topic of a recently-published scientific paper. The authors of a paper published in the March, 2010, issue of Biotechniques pointed out, antibody validation and standardization ensure study reproducibility, which is critical to accuracy. And yet, no standard guidelines define how these important biological tools should be validated prior to use.

Thus, researchers participating in a recent webinar, presented by The Scientist expressed concern that—without improved antibody validation and standardization—the accuracy of published research is in question and diagnostic test results, such as those produced by medical laboratories, will continue to be inconsistent. (more…)

Pathology Testing for Molecular Genetics “Not Ready for Prime Time”

Experts at National Comprehensive Cancer Network conference voice opinions

It may surprise many pathologists and clinical laboratory managers to learn that a number of prominent healthcare leaders recently voiced significant reservations about the current status of molecular genetics testing. In their view, clinical pathology laboratory testing that incorporates genetic and molecular technologies needs further refinement, improved billing codes, and additional regulation before it can fulfill its potential to be a precise diagnostic tool.

That was the conclusion reached by a panel of distinguished physicians representing healthcare organizations, pharmaceutical giants, insurance companies, and the government at this year’s annual National Comprehensive Cancer Network (NCCN) conference.