Skip to Main Content

genomics

  • sam patrick posted an article
    Genetic Center a key initiative at Clemson University see more

    Compliments of Scribble

    The sequencing of the human genome in 2000 gave rise to the vision of personalized medicine. Realizing the importance of this landmark achievement, Clemson University established Human Genetics as a major pillar of its long-term strategic ScienceForward plan. This vision was realized in 2016 with philanthropic support of Self Regional Healthcare and the Self Family Foundation, leading to the construction of Self Regional Hall on the Partnership Innovation campus of the Greenwood Genetic Center (GGC). 

    Self Regional Hall is a 17,000 sq. ft. state-of-the-art facility designed to provide a collaborative environment that is conducive to spontaneous interactions among students and faculty. The Clemson Center for Human Genetics was formally inaugurated in the facility on August 8, 2018.

    In the short period of three years, the Center for Human Genetics has flourished under the leadership of its inaugural director, Dr. Trudy Mackay.

    The Center started with two faculty — Dr. Mackay and spouse and long-term collaborator, Dr. Robert Anholt — two staff scientists, and two doctoral students. With strong support from Clemson University, the Center recruited four assistant professors from Yale University, Stanford University, the University of Chicago, and the University of North Carolina at Chapel Hill. This enabled the Center to expand rapidly to six faculty and a cohort of 16 graduate students on the Greenwood campus and eight affiliated members on the main campus of Clemson University. 

    In 2021, the Clemson University Center for Human Genetics, in collaboration with the GGC, received a grant from the National Institutes of Health for over $13.5 million total cost to establish a Center of Biomedical Research Excellence (COBRE) in Human Genetics to promote the professional development of young investigators. 

    The Center’s Goals for Genetic Research

    The goals of the Clemson Center are two-fold:

    1. to leverage comprehensive systems genetic approaches and comparative genomics to elucidate fundamental principles of the genetic underpinnings of human complex traits, including disease risk.

    2. to promote precision medicine by developing advanced mathematical models to predict disease risk and assess therapeutic benefits based on genetic and environmental factors.

    To enable these activities, the Center has established the most advanced genomics facility in South Carolina with capabilities for short- and long-read DNA sequencing as well as analyses of gene expression networks in single cells. The Center also contains a microscopy facility, a bioinformatics facility, and its own high performance computing cluster for analyses of large datasets.   

    Faculty in the Center use comparative genomics approaches to gain insights in human disorders. Such approaches include studies on the fruitfly (Drosophila) model, which enables sophisticated genetic experimentation, zebrafish (in collaboration with the GGC), which is a powerful model for developmental genetics, and human cell lines. These systems have complementary advantages, so combined insights from studies on these systems can be applied to patients and human populations. 

    Studies in the Center focus on substance use disorders — including cocaine, methamphetamine, and alcohol — cardiovascular disease, cancer, and neurodegenerative disorders. Most genetic studies to date have focused on genes that code for proteins, structural components of our cells and enzymes that catalyze reactions that sustain intermediary metabolism and the formation of macromolecules, such as our DNA. 

    However, protein coding genes comprise only ~2% of the human genome and there is a growing realization that non-protein coding elements of the genome play an important role in gene regulation in health and disease. Thus, a major focus of the Center’s studies is dedicated to elucidating the contributions of noncoding elements of the genome to disease manifestation. Another major focus of faculty in the Center is to develop computational methods to predict disease susceptibility based on genetic and environmental information, a critical prerequisite for personalized medicine. The Center also interacts closely with the GGC to obtain insights in the pathology of rare pediatric diseases.

    The Clemson Center for Human Genetics seeks to develop local, regional, national, and international collaborations to advance human genetics and is currently part of a large international consortium funded by the European Commission to study the genetics of susceptibility to environmental toxins. As part of a major research university, the Center is also strongly committed to educating the next generation of human geneticists by providing educational opportunities for high school students, their teachers, undergraduate and graduate students, postdoctoral fellows and visiting scientists, and to promote public understanding of human genetics through community outreach.

     September 08, 2021
  • sam patrick posted an article
    PMLS launches one of the nation’s largest variant surveillance initiatives see more

    The Biden Administration announced Friday a $1.7 billion investment to monitor new and emerging COVID-19 variants which could induce another pandemic wave. Concurrently, to combat these mutated strains, advanced molecular diagnostics laboratory, Premier Medical Laboratory Services announces their launch of one of the nation’s largest variant surveillance initiatives. Now conducting genomic sequencing of 6,000 specimens per day, PMLS plans to increase that number to 12,000 by May. The large amounts of data gathered by this initiative will help protect the population from a future surge and cases with increased severity of symptoms.  

    When speaking on Pfizer’s ability to adjust the vaccine for effective inoculation against the new variants, a Pfizer Executive said Saturday, “You can basically, within a couple of weeks, put a new sequence in.” In order to make these adjustments to vaccines, scientists developing them need genomic sequencing data on a large scale, like that being produced by PMLS.

    Scientific Director of Clinical Genetics for PMLS, Vidhya Narayanan commented, “Sequening information and population studies can give us vital information regarding evolution of the COVID 19 virus and transmission pattern which otherwise can go unnoticed.”

    The COVID-19 virus is structured so that inside each nucleocapsid protein is the viral genome, which over time can mutate for the virus to be more efficient at spreading and to potentially cause more severe illness than the original strain. Genomic sequencing decodes the genomes to learn about the virus and how it is evolving. Standard polymerase chain reaction (PCR) COVID-19 tests, which are most widely used for detection of the COVID-19 virus, are very specific to detecting the pathogens of the original COVID-19 strain. Next generation sequencing is able to detect new pathogens so that epidemiologists can study viral genome mutations to understand how they affect the viral characteristics of COVID-19 and to determine future health implications the novel variants may cause.

    Because library prep instruments and genomic sequencers are in short supply, many laboratories spend hours conducting library prep and sequencing manually. With high throughput genomic sequencers and library prep instruments that automate the library prep and sequencing process, PMLS achieves a much higher capacity for genomic sequencing. By monitoring an exponentially higher amount of specimens, PMLS is better equipped to provide meaningful analysis with larger amounts of data and faster turnaround times for the effective surveillance of SARS-CoV-2.

    “We want to be proactive with these new variants in case any adjustments need to be made within the healthcare industry for patient care or new safety protocols need to be put into place,” said Kevin Murdock, Founder of Premier Medical Laboratory Services. “Data is the most vital piece in beating this pandemic, so we made this a top priority to aquire the most advanced sequencing equipment and top scientists to help monitor them.”

    Of growing concern, among other variants, is the Indian variant (B.1.617), which has spread to the UK and made landfall in California approximately two weeks ago. This variant is potentially the catalyst for a recent surge of cases in India and is believed to have more rapid rates of transmission than the original strain like the UK variant (B.1.1.7) that is estimated 50 percent more than the standard form of SARS-CoV-2 which is also been shown to cause higher mortality rates. (1,2)

    Other current known variants:

    • Brazil (P.1)
    • South Africa (B.1.351)
    • California (B.1.427/B.1.429)
    • New York (B.1.526)

    The high-volume sequencing being conducted at PMLS follows suit with COVID-19 testing solutions they have provided as a laboratory with one of the highest testing capacities in the nation. Their ability to test over 300,000 specimens per day for COVID-19 paired with their rapid turnaround of accurate results is why they are the chosen laboratory to conduct testing for Human Health Services surge sites, large organizations, schools, athletic teams, and state health departments across the US.

    According to the CDC, genomic surveillance can help detect variants with:

    • Ability to spread more quickly in people
    • Ability to cause either milder or more severe disease in people
    • Ability to evade detection by specific diagnostic tests 
    • Decreased susceptibility to therapeutics that employ monoclonal antibodies
    • Ability to evade natural or vaccine-induced immunity (3)

    Sources:

    1. Harvard Magazine https://harvardmagazine.com/2021/01/covid-19-variants
    2. Nature Research Journal: https://www.nature.com/articles/s41586-021-03426-1
    3. CDC: https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance.html?CDC_l.html

    For more information, please visit www.premedinc.com/ngs or call 1.866.800.5470.

     

    ABOUT PREMIER MEDICAL LABORATORY SERVICES

    Premier Medical Laboratory Services (PMLS), based in Greenville, South Carolina, is an advanced molecular diagnostics lab fully certified by top laboratory accrediting organizations, including CLIA and COLA. With the most advanced laboratory information systems (LIS) easy to read one-page test result reports are generated with higher accuracy and a customizable report for each client. PMLS prides itself on having some of the most rapid turnaround times for testing results in the industry. Their expansive testing menu includes Pharmacogenomics, COVID-19 testing, Advanced Cardiovascular Testing, Diabetes, Women’s Wellness panels, Allergen Specific Ige Blood Testing, Toxicology, and a first of its kind predictive genetic test for type II diabetes, DiabetestPredict. For more information, please visit www.PreMedInc.com

  • sam patrick posted an article
    Vikor Scientific and Quantgene announce major advance in precision genomics see more

    Courtesy of GSA Business

    Starting this March, a South Carolina lab will become ground zero for a preventative test that can detect cancer-causing mutations, risks or tumors in advance through a quick blood sample taken at home or a physician’s office.

    S.C. life science organization SCBio and the Charleston Regional Development Alliance linked together Charleston’s Vikor Scientific and California’s Quantgene Inc. when the West Coast company was on the hunt for a lab that could commercialize its AI and genomic-powered preventative care program, Serenity.

    Serenity puts to task a deep genomic sequence process that covers 20,000 genes in combination with the disease, medication and lifestyle risks that could contribute to multiple variations of cancer. Along with the blood test, or “liquid biopsy,” it can detect cancerous mutations in the blood, according to Vikor Scientific co-founder Shea Harrelson.

    “What this means is that we can detect cancer early enough so that patients don’t have to resort to chemotherapy,” she said during SCBio’s Virtual Meeting Wednesday morning. “They may have options for immunotherapy or aggressive preventative strategies or even excisional therapy.”

    Patient-specific health profiles covering personal and family history, as well as lifestyle choices, will brief analysts on how additional risks may contribute to a patient’s likelihood of developing early-stage cancer, thus prompting preventative care.

    “With Serenity, we are first-to-market in combining liquid biopsy cancer detection with whole exome sequencing and advanced medical intelligence,” Johannes Bhakdi, founder and CEO of Quantgene, said in a news release. “We hope to unlock a new era in medicine in which trained physicians can detect multiple cancers at early stages in the blood with single molecule precision. Serenity brings genomic technologies to patients within an innovative system of preventative care that we believe will set a new standard in patient-centered personalized medicine. We are excited to take this important step with our partners at Vikor Scientific.”

    Vikor Scientific, a hub for medical testing, will process test results in collaboration with Serenity’s proprietary cloud for both individual end-users and health care professionals.

    The South Carolina company will launch its public awareness and physician education campaigns alongside the concierge-product release on March 1, according to Scotty Branch, co-founder of Vikor Scientific, and will soon build out its current location in Charleston.

    “Our number one goal is to educate physicians throughout the country, which is what we do best,” Branch told GSA Business Report, adding that the team is working to get insurance companies on board with the treatment program now.

    “Until then, the liquid biopsy, or the early detection portion, will be on a concierge or cash-paid basis,” he said.

    Vikor Scientific will conduct whole exome sequencing and send that information to the Serenity cloud for both physicians and individual consumers, potentially for a variety of uses.

    While existing genetic tests on the market like those sold by 23 and Me may be able to offer a surface level detection of certain cancer-causing genetic variations in a patient, Serenity takes genomic testing to the next step of preventative treatment, the company said.

    “Genetic mutations only play a role in about 5% to 10% of cancer,” Harrelson said. “So, there’s about 90-95% of cancers that don’t have genetic mutations, and without that, you still have a lot of familial cancers. And most people die from cancer than heart disease or automobile accidents, so this liquid biopsy test will be very important, because if patients have put stress on their body or smoke or other risk factors that can increase their chance for cancer, this liquid biopsy test is pretty painless and a great screening tool for this and other cancers that … like pancreatic cancer. We often don’t find out about pancreatic cancer until stage three or four.”

    Taking into account detected at-risk genetic variations, the Vikor-Quantgene team will analyze additional risks for early stages of cancer through the liquid biopsy test, in lieu of more invasive measures, which can detect whether nascent tumors are forming in the body.

    “It’s a great continuum of care,” he added. The test analysis could then be used, in tandem with additional data, to launch preventative treatment and care.

    “We need to use liquid biopsy as part of an annual or bi-annual screening,” Branch said.

    After a Monday Vikor Scientific Board meeting, Branch said 99% of the plans for the facility buildout have been nailed down. The full announcement will come when the company approves the final portion of its development strategy.

    “This is an amazing announcement for South Carolina and for economic development, where we are going to build out at our location at 22 West Edge, where Vikor’s location is currently,” he said. The company will start small with 10 to 20 new employees and scale up from there. “That is exciting news that a corporate hub would be located here in Charleston’s West Edge Medical Innovation District."