Unravelling arthropod genomic diversity over 500 million years of evolution - (Thursday, January 23, 2020)
An international team of scientists report in the journal Genome Biology results from a pilot project to kick-start the global sequencing initiative of thousands of arthropods. Comparative analyses across 76 species spanning 500 million years of evolution reveal dynamic genomic changes that point to key factors behind their success and open up many new areas of research. Dr. Stephen Richards launched the i5k pilot project at the Baylor College of Medicine Human Genome Sequencing Center to sequence, assemble, and annotate the genomes of 28 diverse arthropod species carefully selected from 787 community nominations.
Connecting gene mutations, rare genetic diseases - (Thursday, October 24, 2019)
Clinical exome sequencing has revolutionized genetic testing for children with inherited disorders, and Baylor College of Medicine researchers have led efforts to apply these DNA methods in the clinic. Nevertheless, in more than two-thirds of cases, the underlying genetic changes in children who undergo sequencing are unknown. Researchers everywhere are looking to new methods to analyze exome sequencing data to look for new associations between specific genes and those rare genetic diseases – called Mendelian disorders. Investigators at the Human Genome Sequencing Center have developed new approaches for large-scale analysis of Mendelian disorders, published today in the American Journal of Human Genetics.
The investigators used an Apache Hadoop data lake, a data management platform, to aggregate the exome sequencing data from approximately 19,000 individuals from different sources. Using information from previously solved disease cases, they established methods to rapidly select candidates for Mendelian disease. They found 154 candidate disease-associating genes, which previously had no known association between mutation and rare genetic disease, according to Adam Hansen, lead author of the study and graduate student in molecular and human genetics at Baylor.
“We found at least five people for each of these 154 genes that have very rare genetic mutations that we suspect might be causing disease,” Hansen said. “This shows the power of big data approaches toward accelerating the rate of discovery of associations between genes and rare diseases.”
“These computational methods solve the dual problems of large-scale data management and careful management of data access permission.” said Dr. Richard Gibbs, study author and professor of molecular and human genetics and director of the Human Genome Sequencing Center at Baylor. “They are perfect for outward display of data from the Baylor College of Medicine programs.”
Study builds roadmap for collecting, sequencing genetic data - (Thursday, August 22, 2019)
Precision medicine aims to deliver personalized treatment based on an individual’s genetics, environment and lifestyle. This approach depends on researchers’ ability to study DNA from people with and without clinical conditions. Often, clinical visits provide the perfect opportunity to collect those genetic samples. The National Institutes of Health has conducted a four-year study to harmonize and standardize clinical genetic reporting. The results are published online in the American Journal of Human Genetics.
The work of the NIH’s Electronic Medical Records and Genomics (eMERGE III) program coordinated activities at 11 clinical participant enrollment sites with two sequencing centers and a coordinating center to analyze the DNA of more than 25,000 participants enrolled through biobank programs. The Baylor College of Medicine Human Genome Sequencing Center was one of two Centralized Sequencing and Genotyping (CSG) Facilities, and performed the data generation, analysis and clinical data reporting for more than 14,500 of the 25,000 participants, in this phase of the program.
“Together with our colleagues in the eMERGE III Network we have built a roadmap for coordination of future efforts in precision medicine,” said Dr. Richard Gibbs, study author and director of the Human Genome Sequencing Center and professor of molecular and human genetics at Baylor College of Medicine. “All of the steps, from consenting individual participants, extracting DNA, sequencing, interpreting and returning clinical data, were coordinated and finessed.”
Celebrating National DNA Day - (Thursday, April 25, 2019)
In 1998, the Human Genome Sequencing Center at Baylor College of Medicine was chosen as one of three centers to finish the sequencing of the human genome.
April 25 marks National DNA Day, which recognizes the completion of the Human Genome Project. Learn more about Baylor’s role in the Human Genome Project and see historical photos.
Grant funds mucosal infection research at Baylor - (Thursday, April 18, 2019)
Baylor College of Medicine will receive a grant of up to $19.5 million over five years from the National Institutes of Health and its Genomic Centers of Infectious Diseases Program. This grant will fund Baylor research to study mucosal infection (bacteria, viruses and parasites) through the use of genomics and organoid model systems – cell-derived, in vitro 3D organ models that enable the study of biological processes.
“Incorporating genomics with novel organoid approaches will facilitate the dissection of host-pathogen-microbiome molecular relationships, potentially revealing novel therapeutic and diagnostic interventions for life-threatening infectious diseases,” said Dr. Joseph Petrosino, director of the Alkek Center for Metagenomics and Microbiome Research and professor and interim chair of molecular virology and microbiology at Baylor College of Medicine.
Petrosino will serve as co-principal investigator for the grant along with Dr. Richard Gibbs, Wofford Cain Chair and Professor and director of the Human Genome Sequencing Center at Baylor.
Baboon genome sequence reveals evolutionary diversification - (Wednesday, January 30, 2019)
Rapidly increasing efforts to generate whole genome sequences for many vertebrate species are providing a significantly improved understanding of the biological differences among animals across the tree of life. In a new study published in Science Advances, an international multi-institutional research team, led by the Human Genome Sequencing Center at Baylor College of Medicine, reports novel results describing the genome sequences and evolutionary history of six Papio baboon species. This work sheds new light on the fundamental biological processes that generate new species and has implications for the origin of our own species, Homo sapiens.
Baboon populations are widespread across sub-Saharan Africa, and various researchers have conducted extensive analyses of the behavior, morphology and ecology of these species, leading to a detailed understanding of how they have thrived in their respective environments. However, far less is known about how each of the six baboon species arose and became distinct from the others.
“Baboons have long attracted scientific attention because they evolved within the same sub-Saharan African habitat in which early human ancestors arose. The behavioral and ecological differences among baboons make them an excellent model for investigating how a socially complex, highly adaptable primate lineage diversifies over time. In this new work, we show that baboon diversification and evolution was a more complex and reticulated process than was previously recognized,” said Dr. Jeffrey Rogers, associate professor in the Human Genome Sequencing Center at Baylor and lead author on the paper.
Distinct stages in infant microbiome development identified - (Wednesday, October 24, 2018)
In the largest clinical microbiome study in infants reported to date, a team led by researchers at Baylor College of Medicine explored the sequence of microbial colonization in the infant gut through age 4 and found distinct stages of development in the microbiome that were associated with early life exposures. Published in the journal Nature, their report and an accompanying report led by the Broad Institute are the result of extensive analysis of data collected from a cohort of participants involved in the TEDDY diabetes study.
The TEDDY study (The Environmental Determinants of Diabetes in the Young) study has been collecting data for 10 years with the goal of understanding what triggers type 1 diabetes in children at increased genetic risk for the disease. Researchers at six clinical centers in the U.S., Sweden, Finland, and Germany, as well as the Data Coordinating Center at the University of South Florida, have gathered monthly stool samples and data from more than 8,600 children who are genetically susceptible to type 1 diabetes. From this cohort, researchers at Baylor College of Medicine sequenced and analyzed 12,005 stool samples that were collected from 903 children between three and 46 months of age to further understand what the microbiome looks like early in life.
“We know that the first few years of life are important for microbiome establishment. You are born with very few microbes, and microbial communities assemble on and in your body through those first years of your life,” said Dr. Joseph Petrosino, director of the Alkek Center for Metagenomics and Microbiome Research and professor and interim chair of molecular virology and microbiology at Baylor. “In this study, we took a closer look in this amazing cohort at the establishment of the microbiome over the first few years of life and the early life exposures associated with that sequence of events.”
In collaboration with the Human Genome Sequencing Center at Baylor, state-of-the-art sequencing of both RNA and DNA was applied to uncover the complete genetic makeup of all microbes. Upon analysis of these data, Petrosino and his team determined that the developing gut microbiome undergoes three distinct phases of microbiome progression:
- Developmental phase (3 to 14 months of age)
- Transitional phase (15 to 30 months of age)
- Stable phase (31 to 46 months of age)
“This information is useful for any future microbiome studies looking at an infant cohort for scientific discovery and potential intervention purposes. The idea that we can stratify the development phases in this manner may give researchers additional resolution to reveal differences that could potentially be disease-associated,” Petrosino said.