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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

Severe Lack of Volunteers for Clinical Laboratory Studies Has US Alzheimer’s Researchers Employing Innovative Methods to Recruit Participants

Low interest and a lack of diversity among study participants hinders research into one of America’s most fatal and costly chronic diseases

Finding enough people to participate in clinical laboratory trials for Alzheimer’s disease can be a daunting task for researchers. The shortage of participants has compelled scientists to develop innovative ways to locate volunteers for their studies. That includes “Swab-a-Palooza” events to make it easy for individuals to provide samples for this research and get speedy feedback about their ApoE.

“It’s all about recruitment now,” Stephen Salloway, MD, Director of Neurology and the Memory and Aging Program at Butler Hospital in Providence, R.I., and Professor of Clinical Neurosciences and Psychiatry at Brown Medical School, said in an article on the Biomedical Research Forum (BRF) website.

Some researchers are hunting online and offering free genetic testing to interested individuals to ensure they obtain the number of participants needed for their trials. Both the Alzheimer’s Prevention Registry (APR) and the Brain Health Registry (BHR) are using the Internet to compile listings of suitable participants.

The APR is dedicated to uniting Alzheimer’s researchers with individuals interested in participating in clinical trials. The Phoenix-based non-profit organization also educates the public on Alzheimer’s and prevention of the disease. The Brain Health Registry is a web-based research study led by medical researchers at the University of California, San Francisco. Participants complete online questionnaires and tests that provide researchers with information regarding an individual’s health, lifestyle, and cognitive function. The collected data is used to create a listing of potential participants for Alzheimer’s studies.

Using Genetic Testing to Recruit Alzheimer’s Study Participants

GeneMatch is a program led by the Banner Alzheimer’s Institute in the Phoenix area that is part of the APR. The purpose of this national program is to recruit participants for research on Alzheimer’s disease by using genetic testing to match qualified volunteers with research studies. According to their website, 80% of research studies on the disease aren’t completed on time due to a lack of volunteers.

Anyone can register to be part of GeneMatch as long as they live in the United States and are between the ages of 55 and 75. In addition, participants cannot have a diagnosis of cognitive impairment, Alzheimer’s, or dementia.

“We hold local swabbing parties, where the GeneMatch sign-up rate is 95%,” Pierre Tariot, MD, Internal Medicine and Psychiatry, and Director of Banner Alzheimer’s Institute, said in the BRF article. “Jeffrey Cummings calls them Swab-a-Paloozas.”

GeneMatch screens individuals for the Apolipoprotein E (ApoE) and the ApoE-e4 allele which increases the risk for Alzheimer’s disease and is associated with earlier onset of memory loss and other symptoms. At this time, it is not known how this allele is related to the risk of getting the disease, but researchers have discovered the brain tissue of affected individuals have an increased number of protein clumps called amyloid plaques. A buildup of these plaques may lead to the death of neurons and the presence of Alzheimer’s symptoms.

“I spend a lot of time in my community doing outreach. People are very interested and receptive,” said Salloway, who recently hosted a swabbing party for GeneMatch. “At events, I ask everyone to tell five other people about what they learned, and to host swabbing parties themselves.”

The DNA samples obtained by GeneMatch are analyzed by a Clinical Laboratory Improvement Amendments (CLIA) certified laboratory. Over the past two years, GeneMatch has tested over 45,000 individuals for the ApoE-e4 allele and were able to identify 1,000 homozygote and 9,000 heterozygote carriers.

Lack of Diversity Among Study Participants

A paper published in September 2017 by Jeffrey Cummings, MD, Director of the Cleveland Clinic Lou Ruvo Center for Brain Health in Las Vegas, estimated the number of participants currently needed for Alzheimer’s research is over 55,000. Clinical trials for Alzheimer’s need volunteers who have little or no symptoms of the illness and locating such interested individuals can be complicated.


Jeffrey Cummings, MD (above), is Medical Director at Lou Ruvo Center for Brain Health in Las Vegas. In an interview with Drug Discovery and Development, Cummings said, “There is a huge problem of recruitment for many diseases throughout the nation. The problem goes beyond Alzheimer’s disease; there is a general lack of awareness by the public of either the availability or the importance of clinical trials.” (Photo copyright: Jerry Henkel/Las Vegas Review-Journal.)

Additional obstacles that face Alzheimer’s researchers are the lack of diversity among volunteers for their studies. The participants in GeneMatch are 78% female and there is little representation of African-American and Latino minorities.

“It’s not easy to get healthy individuals to join, and those who do are predominantly highly educated, white, and female,” Jessica Langbaum, PhD, Principal Scientist at Banner Alzheimer’s Institute, said in the BRF article. “That’s okay if the women are the health-info gatherers and send their men for trials, but it will be a problem if we cannot get men into studies.”

Delivering ApoE Genotype Results at Events

Technology that could help locate participants for Alzheimer’s research at open “Swab-a-Palooza” events include a small ApoE analyzer called the Spartan Cube. The small molecular diagnostic device, manufactured by Ottawa-based Spartan Bioscience, Inc., can deliver an ApoE genotype result in less than an hour. The gadget is perfect for outreach gatherings, as people can learn their ApoE genotype while at an event. At this time, the Spartan Cube is used only for research purposes and is not CLIA approved.

The paper by Cummings was a topic of discussion at the Clinical Trials on Alzheimer’s Disease (CTAD), which was held in November in Boston. The CTAD is an annual conference for Alzheimer’s disease researchers to meet and share information about the disease with each other. The 11th CTAD conference will take place in Barcelona, Spain, in October of this year.

More than five million people are living with Alzheimer’s disease in the United States and this number could reach 16 million by 2050, according to the Alzheimer’s Association. It is the sixth leading cause of death in the US and cost the nation $259 billion in 2017. It’s estimated that the costs associated with the disease could reach $1.1 trillion by 2050, which makes finding volunteers for research studies an important endeavor.

—JP Schlingman


Related Information:

Don’t Be an Enrollment Loser: Throw Your Own Swab-a-Palooza!

Alzheimer’s Disease Drug Development Pipeline: 2017

A Cure for Alzheimer’s by 2025? An Interview with Jeff Cummings, MD

Two Different Research Teams Announce Tests for Alzheimer’s Disease That Could Be Useful for Clinical Laboratories after Clearance by the FDA

A university research team and a global diagnostics company simultaneously but independently unveil two new tests that accurately identify people predisposed to Alzheimer’s at earlier stages in the disease

Medical laboratory scientists and clinical pathologists have long awaited an accurate and clinically-useful test for the predisposition and early diagnosis of Alzheimer’s disease. Now comes pioneering efforts from two organizations that suggest real progress is being made.

One organization is an academic center and the other is an in vitro company. It was a research team at Rowan University School of Osteopathic Medicine (RowanSOM) that announced development of the first blood test to use the body’s own immune system to detect mild cognitive impairment (MCI), an early stage of Alzheimer’s disease.

Similarly, research scientists for Randox Laboratories unveiled to pathologists, clinical laboratory leaders, and others attending the American Association for Clinical Chemistry (AACC) Annual Scientific Meeting, how their biochip-based technology also could be used to detect elevated risk for Alzheimer’s disease. (more…)

Geneticist at University of California Davis Sequences His Unborn Baby’s DNA in a Global First for Whole Genome Sequencing

Prenatal genome sequencing raises ethical issues for gene sequencing labs and clinical labs, since a baby’s genetic information may present lifelong consequences for that individual

Pathologists and clinical laboratory managers will be interested to learn that another milestone in genetic testing was reached earlier this year. A geneticist at the University of California at Davis, has sequenced the whole human genome of his unborn baby, the first time this feat has been accomplished.

Notably, it was geneticist and graduate student Razib Khan of the UC Davis School of Veterinary Medicine who sequenced his unborn son’s genome during the third trimester of pregnancy using a sample of the fetus’ placenta. This is the first healthy person born in the United States with his entire genetic makeup deciphered prior to birth, noted a recent story published by the MIT Technology Review(more…)