Baylor's Human Genome Sequencing Center looks to bring adult whole genome sequencing to clinical space with unprecedented NHLBI grant - (Wednesday, March 1, 2017)
The National Heart Lung and Blood Institute’s (NHLBI) Trans-Omics for Precision Medicine (TOPMed) program has named the Human Genome Sequencing Center (HGSC) at Baylor College of Medicine as a participant in a groundbreaking half-billion dollar program to bring whole genome sequencing and other –omic technologies that monitor the expression of the genome in response to the environment, to the forefront of clinical research.
Through its TOPMed program, NHLBI is expanding its dedication to advancing the understanding of the underpinnings of complex diseases and how they develop. Previously, the HGSC was awarded funding by NHLBI to sequence whole genomes for TOPMed studies such as sickle cell disease, and venous thromboembolism and will continue to expand this effort in the next phase of the program. The new contract will span five years. In addition to the whole genome sequencing component, the TOPMed program will also provide analysis of other datatypes over the course of the contract period, including RNA transcription sequencing, DNA methylation, metabolomics profiles, and other –omics, including analysis of the microbiome. The initial award from NHLBI supports the whole genome sequencing of 20,000 samples at the HGSC in the first year of the program.
“There is a significant need for large sample sizes; a need that goes beyond the research setting and into the clinic,” said Dr. Richard Gibbs, director of the HGSC and professor of molecular and human genetics at Baylor. “We are grateful to be a part of the TOPMed program which will allow us to access this large sample number and obtain valuable insights into adult heart disease, sickle cell disease, atrial fibrillation and other heart, lung and hematologic disorders.”
Bench to Bedside Podcast: Gene Sequencing Enables Rare Diagnosis in Twins - (Tuesday, February 28, 2017)
The Association of American Medical Colleges' "Bench to Bedside" podcast focuses on the story of Alexis and Noah Beery. For years a degenerative condition kept the twins from living a typical childhood. That changed when thanks to their mother's persistence and breakthrough genomic sequencing and analysis at the Baylor College of Medicine's Human Genome Sequencing Center, researchers were able to zero in on the genetic disorder and restore the siblings to healthy and active lives.
Fighting sickle cell disease using a type 2 diabetes medication - (Tuesday, January 10, 2017)
Researchers at Baylor College of Medicine and Texas Children’s Cancer and Hematology Centers have discovered a gene, FOXO3, involved in controlling fetal hemoglobin production and were able to target the gene and “turn on” fetal hemoglobin levels in patient samples in the lab using the diabetes drug metformin. This offers promising new treatments – the first new drug treatment for sickle cell disease in 30 years and the first ever for beta thalassemia.
Starting with 171 patient blood samples and later expanding to 400 more, Dr. Vivien Sheehan, assistant professor of pediatrics at Baylor and Texas Children’s Cancer and Hematology Centers, and her research colleagues were looking for genetic differences in sickle cell patients who make a lot of fetal hemoglobin versus those who do not. Collaborating with Baylor’s Human Genome Sequencing Center, they used whole exome sequencing and discovered that the FOXO3 gene seemed to control fetal hemoglobin. They found that patients with mutations in the FOXO3 gene made less fetal hemoglobin. Researchers proved this association in the lab by knocking out FOXO3 in human bone marrow cells, which resulted in less fetal hemoglobin, and then overexpressing the gene, which increased it.
With funding from Pfizer, a clinical trial has launched to further study the effectiveness of metformin in patients with sickle cell disease and beta thalassemia.
Newly discovered beetle genome helps to explain woodland destruction - (Friday, November 11, 2016)
The Asian longhorned beetle, or Anoplophora gladbripennis, is an invasive species impacting wooded areas across the globe. In a paper published in Genome Biology, researchers from Baylor College of Medicine and the University of Memphis detail new findings in the beetle’s genome that allow it to thrive on tree bark and other wooded plant material, causing widespread destruction in the process.
In order to understand how the beetle has evolved to be able to digest and receive nutrients from wooded plants and trees, the research team sequenced and annotated its genome, studied the degrading enzymes in the cell walls of plants and compared the genomes of 14 other types of insects with the ability to digest woody plant material.
“In this case, when we fed beetle larvae on wood material from sugar maple trees, we found that the activity of the glycoside hydrolase genes was increased, something not seen in larvae fed on an artificial diet,” said Dr. Stephen Richards, co-lead author on the paper and associate professor in the Human Genome Sequencing Center at Baylor. “This experiment, along with our complementary analysis of the beetle genome, also revealed the specific set of genes, called CYP450 genes, which are involved in the detoxification of compounds encountered by the beetle when feeding on plant tissues.”
Dr. Duane McKenna, co-lead author from the University of Memphis, added, "Our detailed genomic analysis reveals that the Asian longhorned beetle has more than 1,000 genes that aren’t present in any other arthropod. We identified a total of 86 genes for enzymes called glycoside hydrolases – more than have been found in any other insect. These enzymes enable the beetle to digest woody plant material and detoxify plant chemicals and indicate a genetic reason for their apparent success in feeding on trees worldwide.”
The study has allowed the researchers to establish a genomic basis for the evolutionary techniques and tools to manage the presence and damage of the Asian longhorned beetle and other wood-boring pests.
“This publically available genome is part of a larger group as a pilot for the i5K initiative to sequence thousands of insects. We hope that, in the long term, this foundational information about how any species works can be made available to anyone interested in biology, from researchers addressing specific questions to high school students and hobbyist entomologists at home,” Richards said.
International team discovers novel Alzheimer’s disease risk gene among Icelanders - (Thursday, October 20, 2016)
Scientists at Baylor College of Medicine and the Jan and Dan Duncan Neurological Research Institute (NRI) at Texas Children’s Hospital are part of a multicenter collaborative study that has identified a novel genetic risk factor for late-onset Alzheimer’s disease. The study appears in the journal PLoS Genetics.
Alzheimer’s disease is the most common cause of dementia among older adults, and the presence of certain genetic variants increases an individual’s risk for developing this disease.
Baylor researchers Dr. Shinya Yamamoto, assistant professor of molecular and human genetics; Dr. Joshua M. Shulman, assistant professor of neurology, neuroscience, and molecular and human genetics; Dr Eric Boerwinkle, associate director of the Human Genome Sequencing Center; and Dr. Hugo J. Bellen, professor and director of the program in developmental biology and also an investigator at the Howard Hughes Medical Institute, were part of an international team that analyzed samples from 1,393 subjects with late-onset Alzheimer’s disease and compared the results with those of 8,141 neurologically healthy individuals.
The consortium found a variant in TM2D3, a gene that has never been studied in human or other vertebrate species. Interestingly, while the probability of this variant was very rare among people of European ancestry, it was significantly enriched among Icelanders (but still less than 1 percent frequency). The researchers estimated that carriers of this variant would have an approximately six-fold increased risk of developing Alzheimer’s disease.
Mapping life took a turn through Houston - (Monday, October 3, 2016)
Dr. Richard Gibbs, director of Baylor College of Medicine's Human Genome Sequencing Center, talks with the Houston Chronicle about the legacy of the Human Genome Project (HGP). With the BCM-HGSC as one of the key sequencing centers, the HGP encouraged mass collaboration and openness in the science community, allowing research results to spur new genomic discoveries around the globe.
"The world, as we know, it doesn't change in predictable ways," Gibbs said in the interview with the Chronicle's Dug Begley. "It changes in these quantum leaps."
Baylor researchers receive grant to study canine cancer, test new therapies for translation to human cancers - (Thursday, September 29, 2016)
Researchers at Baylor College of Medicine have been awarded a $500,000 grant from the National Institutes of Health that will increase our understanding about the interactions between cancer and the immune system in dogs with naturally occurring tumors. The project will study dogs that have been diagnosed with cancer at the collaborating veterinary hospitals and apply that knowledge to the understanding of human cancer.
Dr. Jonathan Levitt, associate professor of pathology & immunology at Baylor leads the project, which involves a large group of investigators, including Drs. David Wheeler and Linghua Wang in the Human Genome Sequencing Center at Baylor.
The researchers will determine whether spontaneously arising canine organ-site tumors are sufficiently similar to those of humans to employ canine cancer as a model for trials of experimental combination therapies for human use. Another major goal of this study is to characterize the immune cells that infiltrate canine tumors and compare them with those in the respective human cancers.
Baylor researchers develop hybrid computational strategy for scalable whole genome data analysis - (Monday, September 12, 2016)
In a study published in BMC Bioinformatics, researchers from Baylor College of Medicine’s Human Genome Sequencing Center, along with Oak Ridge National Laboratory, DNAnexus and the Human Genetics Center at the University of Texas Health Science Center, have developed a novel hybrid computational strategy to address the growing need for scalable, cost effective and real time variant calling of whole genome sequencing data.
This new strategy has proven successful in analyzing an unprecedented set of 5,000 samples, which constitute a critical part for the international consortia efforts called CHARGE (The Cohorts for Heart and Aging Research in Genomic Epidemiology), aiming to identify genetic culprits for a number of common chronic diseases.
“The demand for and the sheer size of sequencing is advancing more quickly than the downstream analytical technologies can adapt.” said Dr. Zhuoyi Huang, the leading author and a postdoctoral fellow with Baylor’s Human Genome Sequencing Center.
“We have created a strategy that is highly scalable for increasingly larger samples, and have developed an understanding of best practices for the process, which can be replicated by other research institutions,” said Dr. Navin Rustagi, the other leading author on the paper, also a postdoctoral fellow with the Human Genome Sequencing Center at Baylor.