Scientists Want to Sequence the DNA Of Every Species On Earth - (Wednesday, May 9, 2018)
Dr. Stephen Richards, associate professor at the Baylor Collge of Medicine Human Genome Sequencing Center, joined Craig Cohen on Houston Public Media's "Houston Matters" program to discuss the Earth BioGenome Project, an initative to sequence all 1.5 million eukaryote species on Earth.
"It's a big project; there's going to be a lot of data," said Richards regarding the proposed 10-year international undertaking. "We think now because the cost of sequencing has dropped so much that the overall cost to do this on planet Earth would be about the same or even less than it was to do the human genome the first time."
Xia-Gibbs Syndrome study led to new patient registry - (Friday, May 4, 2018)
Researchers at the Human Genome Sequencing Center at Baylor College of Medicine have conducted a study of 20 individuals with Xia-Gibbs Syndrome, a rare condition that has symptoms of severe developmental delay, sleep apnea, delayed speech and generalized upper body weakness, and have established a registry to collect genetic and other clinical information from patients with the condition.
As discovered in 2014 by a team led by Dr. Richard Gibbs, professor and director of the Human Genome Sequencing Center at Baylor, Xia-Gibbs Syndrome is the result of new changes within the AT-Hook DNA Binding Motif Containing 1 gene (AHDC1). The new study, which appears in the American Journal of Medical Genetics, shows that the gene is more susceptible to mutations than previously known.
The registry, which is private and HIPAA protected, is the next step in identifying and studying the full spectrum of the disorder. The current group of 30 enrollees in the registry learned about the study through their doctors, social media, including a private Facebook page for families affected by Xia-Gibbs Syndrome, or elsewhere on the internet.
“We know of about nearly 70 families worldwide, and roughly half of these are participating in the registry thus far,” said Dr. Yunyun Jiang, postdoctoral associate in the Human Genome Sequencing Center and lead author on the study.
As more patients join the registry, accompanying laboratory work aims to understand the full range of underlying molecular changes that cause the symptoms of Xia-Gibbs Syndrome.
“We recently encountered a patient who is more than 50 years old, which is remarkable because this condition is typically only identifiable in children,” said contributing author Dr. David Murdock, assistant professor of molecular and human genetics at Baylor and assistant director of the clinical lab in the Human Genome Sequencing Center. “When we fully understand how this gene damage causes Xia-Gibbs Syndrome, we can begin the path to a cure.”
Current work in the Human Genome Sequencing Center is focused on whether mild mutations lead to a more mild form of the disorder, as well as the construction of animal models to help study the condition.
“Given the rarity of this disease, scientists and physicians are seldom able to gather all the information about a group like this. It is something that has really been lacking in the field,” said Gibbs, corresponding author on the study and also the Wofford Cain Chair and Professor in Molecular and Human Genetics at Baylor. “With the growth of the registry and future mouse model studies, there is hope that we will get to the bottom of this one.”
Other contributors to this work include Drs. Amy McGuire, James Lupski, Jennifer Posey, Michael Khayat, Fan Xia, Qingchang Meng and Mullai Murugan, all with Baylor, Luis Sanchez-Pulido and Chris Ponting with the University of Edinburgh, and Jill Hunter with Texas Children’s Hospital.
This work was supported by the National Human Genome Research Institute, the Texas Institute for Advanced Studies at Texas A&M, the UK Medical Research Council, and by a private donation.
PacBio Blog Interviews Baylor’s Fritz Sedlazeck on New Long-Read Algorithms - (Monday, April 30, 2018)
A PacBio blogger reached out to Dr. Fritz Sedlazeck of Baylor's Human Genome Sequencing Center to learn more about a newly published article appearing in Nature Methods, "Accurate detection of complex structural variations using single-molecule sequencing." Lead author Sedlazeck discusses two new tools designed for use with long-read sequencing data, the NGMLR aligner and Sniffles structural variant caller.
Scientists seek to sequence genomes of all known species - (Monday, April 23, 2018)
Ever since the completion of the Human Genome Project, scientists have become increasingly interested in sequencing the genomes of more cultures and populations of humans, as well as various species of animals and organisms to better understand evolution, adaptability and disease susceptibility. In what is perhaps the most ambitious biological proposal since the initial Human Genome Project, an international group of researchers, including researchers from Baylor College of Medicine, seek to sequence every known species that calls planet Earth home. The perspective piece on the project, called the Earth BioGenome Project, appears in the journal Proceedings of the National Academy of Sciences.
The unprecedented initiative aims to sequence each of the roughly 1.5 million species of eukaryotes – all living organisms with a clearly defined nucleus – that have been described in modern science, although there are estimated to be upward of 15 million species, most of which have yet to be identified.
“There are several reasons, both philosophical and practical, as to why this global initiative is a crucial one,” said Dr. Stephen Richards, associate professor in the Human Genome Sequencing Center at Baylor. “The Earth BioGenome Project will demonstrate the value of life on earth, provide a comprehensive understanding of the primary genetic data of life, reveal insights into future novel therapies and drug development and connect the large population of urban humans to the ecosystems that exist, and may be in jeopardy, across the world.”
Researchers impact final round in The Cancer Genome Atlas - (Friday, April 6, 2018)
When The Cancer Genome Atlas (TCGA) was initiated in 2006, it brought together broad and talented research teams from around the country. By the time it ended in 2017, it had involved faculty from numerous departments across Baylor College of Medicine, the Dan L Duncan Comprehensive Cancer Center and the Human Genome Sequencing Center.
This week, a collection of 27 papers is being published reporting on the integrated project to analyze all 33 cancer types and to classify mutations and specific pathways. The release of 29 papers, many of them with significant contributions from Baylor researchers, and findings from the 11,000 patient cohort data appear in the current editions of Cell publications. The project has produced game changers for translational research and clinical trials.
“The TCGA project allowed us to apply team science to biology, and the things we learn from the TCGA have the potential to impact clinical practice, drug development and the way we diagnose and treat a wide range of cancers,” said Dr. David Wheeler, professor of molecular and human genetics in the Human Genome Sequencing Center at Baylor.
The papers are grouped into three key themes that explore Cancer Pathways, Cell of Origin and Oncogenic Processes. Wheeler co-organized and co-led the Oncogenic Processes theme.
Primate genomics study reveals clues into AIDS resistance - (Wednesday, January 3, 2018)
Simian immunodeficiency virus (SIV) infection in macaques behaves in a similar way as infection by human immunodeficiency virus (HIV) in humans, progressing into acquired immunodeficiency syndrome (AIDS) over time. However, in sooty mangabeys, a primate species native to West Africa, SIV infection is non-pathogenic. Researchers from an international group of institutions, organized and led by Baylor College of Medicine and Emory University, set out to sequence and analyze the genomes of two nonhuman primates to investigate the mechanisms that drive disease progression, and thus to develop new insights into the behavior of the HIV virus in humans. The research appears in Nature.
“Primates are natural hosts for certain diseases, and sooty mangabeys in particular are natural hosts for SIV, meaning they can be naturally infected with the virus and sustain long-term infection without ever progressing to disease. However, macaques rapidly progress into AIDS-like disease and succumb to SIV when infected,” said Dr. Jeffrey Rogers, associate professor in the Human Genome Sequencing Center (HGSC) and Department of Molecular and Human Genetics at Baylor.
Researchers at the Yerkes National Primate Research Center, Emory University, led by Dr. Guido Silvestri, shared sooty mangabey samples with Rogers and his team at the HGSC to be sequenced and assembled. Once sequenced, the mangabey genome results were sent back to Emory for analysis, including direct comparison with the rhesus macaque and human genomes.
Rare Whole Genome Duplication Gave Rise To Arizona Bark Scorpion - (Wednesday, August 23, 2017)
Dr. Kim Worley of the Baylor College of Medicine Human Genome Sequencing Center spoke with science journalist Nicholas Gerbis of KJZZ in Phoenix about the genome study of the common house spider and the Arizona bark scorpion appearing in BMC Biology.
Analysis of these genomes indicates that spiders and scorpions share an ancestor that made new copies of all the genes in its genome over 400 million years ago. This process, known as whole genome duplication, is one of the largest evolutionary changes that can happen to a genome and is relatively rare during animal evolution.
"One copy can continue to provide the functions that it was used for originally," remarked Worley, "and the new copy is not constrained to provide those functions because the original copy's already providing it."
Researchers sequence megapest genome, aim to stop spread - (Tuesday, August 8, 2017)
The Human Genome Sequencing Center at Baylor College of Medicine, in collaboration with the Australian Commonwealth Scientific and Industrial Research Organisation (CSIRO) and an international team of renowned researchers, has sequenced the genomes of the world’s most destructive caterpillar pests of broad-acre crops. The research appears in BCM Biology.
Helicoverpa armigera and Helicoverpa zea, commonly known as the Cotton Bollworm and Corn Earworm, respectively, cause in excess of $5 billion in control costs and damage each year across Asia, Europe, Africa, the Americas and Australia. The old-world bollworm, which is dominant in Australia, attacks more crops and develops much more resistance to pesticides than its new-world earworm counterpart.
“The bollworm is the single most important pest of agriculture in the world, making it humanity’s greatest competitor for food and fiber," said CSIRO scientist Dr. John Oakeshott. "Its genomic arsenal has allowed it to outgun all our known insecticides through the development of resistance, reflecting its name armigera, which means armed and warlike.’
In Brazil, the recently arrived bollworm H. armigera has been spreading rapidly, and cases of it hybridizing with the earworm have been found, posing a real threat that this new “superbug” could spread into the United States.
Because they are good fliers, populations of the old-world bollworm range across Europe to China and as far as Australia, with the oceans separating them from the new-world Corn Earworm known in the Americas.
“There has been good control of the Cotton Bollworm with Bt Cotton, a plant that expresses a toxic bacterial insecticide, which enabled far less use of chemical pesticides. But the species is adept at overcoming both plant resistance and pesticides as evidenced by the many genes encoding detoxifying enzymes found in its genome – a major reason for its megapest status,” said Dr. Stephen Richards, assistant professor in the Human Genome Sequencing Center at Baylor.
Identifying pest origins will enable resistance profiling that reflects countries of origin when developing a resistance management strategy, while identifying incursion pathways will improve biosecurity protocols and risk analysis at biosecurity hotspots, including national ports. These genome sequences also allow the application of new genetic tools such as RNA interference and CRISPR to be used in an attempt to control these pests.