Hybrid computational strategy for scalable whole genome data analysis
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 known as The Cohorts for Heart and Aging Research in Genomic Epidemiology, or CHARGE.
An Open Access Pilot Freely Sharing Cancer Genomic Data From Participants in Texas
In a pilot Open Access (OA) project from the CPRIT-funded Texas Cancer Research Biobank (TCRB), many Texas cancer patients were willing to openly share genomic data from tumor and normal matched pair specimens. For the first time, genetic data from seven human cancer cases with matched normal are freely available without requirement for data use agreements nor any major restriction except that end users cannot attempt to re-identify the participants.
The TCRB was created to bridge the gap between doctors and scientific researchers to improve the prevention, diagnosis and treatment of cancer.
› Access data
› Read data descriptor in Scientific Data journal
Assessing structural variation in a personal genome—towards a human reference diploid genome
In a paper published in BMC Genomics, a team led by scientists from Baylor College of Medicine’s Human Genome Sequencing Center present Parliament, a structural variant (SV) calling pipeline that brings together multiple data types and SV detection methods to improve the characterization of these larger variants.
Whole Genome Sequencing
The development and clinical implementation of the Whole Exome Sequencing test derives from a joint effort by Baylor's Human Genome Sequencing Center and Baylor Genetics to establish a clinical laboratory dedicated to state-of-the-art next generation sequencing.
BCM-HGSC in the News
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.
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.
With Illumina set to start shipping its newest sequencers as early as March, Dr. Richard Gibbs talks with Sharon Begley of STAT and weighs in on the potential for decreasing costs.
“Just getting that genomic data is half the work,” Gibbs remarked. “So if [the new sequencers] can speed that up by a factor of two or three, that’s a big deal.”
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.
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 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.
