From the 2 March 2012 article at Science News Daily
Washington State University researcher has demonstrated that a variety of environmental toxicants can have negative effects on not just an exposed animal but the next three generations of its offspring.
The animal’s DNA sequence remains unchanged, but the compounds change the way genes turn on and off — the epigenetic effect studied at length by WSU molecular biologist Michael Skinner and expanded on in the current issue of the online journalPLoS ONE.
While Skinner’s earlier research has shown similar effects from a pesticide and fungicide, this is the first to show a greater variety of toxicants — including jet fuel, dioxin, plastics and the pesticides DEET and permethrin — promoting epigenetic disease across generations…
The field opens new ground in the study of how diseases develop. While toxicologists generally focus on animals exposed to a compound, Skinner’s work further demonstrates that diseases can also stem from older, ancestral exposures that are then mediated through epigenetic changes in sperm.
The study was funded by the U.S. Army to study pollutants that troops might be exposed to. Skinner and his colleagues exposed pregnant female rats to relatively high but non-lethal amounts of the compounds and tracked changes in three generations of offspring.
The researchers saw females reaching puberty earlier, increased rates in the decay and death of sperm cells and lower numbers of ovarian follicles that later become eggs. Future studies can use the molecular tools for risk assessment analysis
- Effects of environmental toxicants reach down through generations (eurekalert.org)
- Epigenetics research continues: Variety of toxicants can harm subsequent generations (wsunews.wsu.edu)
- You Might Be Infertile Because Your Grandparents Were Mucking Around in Harmful Chemicals [Science] (gizmodo.com)
- Pollutants long gone, but disease carries on (sciencenews.org)
- Epigenetics and Drug Addiction (epigenomics.wordpress.com)
- Epigenetics: A Turning Point in our Understanding of Heredity (blogs.scientificamerican.com)
- Linking everyday chemicals to disease: New science keeps on intensifying the writing on the wall (blogs.edf.org)
- EPA Supports Environmental Justice for New Jersey Farm Workers (treehugger.com)
- The US Environmental Remediation Services Industry to Reach US$8.29 Billion by 2015, According to New Report by Global Industry Analysts, Inc. (prweb.com)
- Mobile App Helps Public Keep an Eye on Toxic Neighbors (prweb.com)
New Computational Tool For Rapid Identification Of Disease-Causing Variations In The Human Genome & Guides to Genomics Resources
Scientists from the University of Utah and Omicia, Inc., a privately held company developing tools to interpret personal genome sequences, have announced the publication in Genome Research of a new software tool called VAAST, the Variant Annotation, Analysis and Selection Tool, a probabilistic disease-causing mutation finder for individual human genomes.
The dramatic decline in DNA sequencing costs is making personal genome sequencing a reality. Already, significant progress has been made in applying whole genome sequencing to cancerprognosis and early childhood disease. Examples include the 2010 publications on Miller Syndrome in Nature Genetics and Science, and similar studies aimed at identifying the unknown genetic defects responsible for some early childhood diseases…
…However, a data interpretation bottleneck has limited the utility of personal genome information for medical diagnosis and preventive care. VAAST is a new algorithm to assist in overcoming this bottleneck. VAAST is the product of a collaboration between Mark Yandell, Ph.D., Associate Professor of Human Genetics at the University of Utah School of Medicine, and colleagues, and the Omicia scientific team under the leadership of Martin Reese, Ph.D., the company’s CEO and Chief Scientific Officer.
In the Genome Research paper, Yandell and colleagues show that VAAST provides a highly accurate, statistically robust means to rapidly search personal genomes for genes with disease-causing mutations. The authors demonstrate that as few as three genomes from unrelated children, or those of the parents and their two children, are sufficient to identify disease causing mutations.
“The big challenge in genomic medicine today is how to sift through the millions of variants in a personal genome sequence to identify the disease-relevant variations,” said Dr. Reese. “It’s a classic needle in a haystack problem, and VAAST goes a long way toward solving it. We look forward to integrating VAAST into the Omicia Genome Analysis System currently under development for clinical applications.”
Dr. Yandell added: “VAAST solves many of the practical and theoretical problems that currently plague mutation hunts using personal genome sequences. Our results demonstrate that this tool substantially improves upon existing methods with regard to statistical power, flexibility, and scope of use. Further, VAAST is automated, fast, works across all variant population frequencies and is sequencing platform independent.”
Two General Genomics Resources
- Public Health Genomics (US Centers for Disease Control and Prevention) information includes
- Family Health History with collection tools (as how to create a family health portrait), FAQs, fact sheets, and more
- Genetic Testing with information on the limitations for most genetic tests, FAQs, and more
- Links to Genomics Resources, including Disease and Genetic Information, Educational Materials, Genetic Testing, and Support Groups
- Genetics Home Reference – Your Guide to Understanding Genetic Conditions with information on diseases and conditions, information on specific genes, a handbook presenting basic information about genetics in clear language and links to online resources, and more
- “When People Share their Genome on Facebook” (spittoon.23andme.com)
- Genome editing — a next step in genetic therapy — corrects hemophilia in animals (sciencedaily.com)
- Genome Study Solves Twins’ Mystery Illness (nlm.nih.gov)
- Genomics and social network analysis team up to solve disease outbreaks (eurekalert.org)
- Personal genome map solves Calif. teen’s illness (seattletimes.nwsource.com)
- Further Analysis on Improved Genome Assembly Indicates the Outbreak E. coli has Complex Genetics With Resistance to at Least Eight Antibiotics (prnewswire.com)
- Alzheimer’s may cause global cash crunch: experts (physorg.com)
- iPad App Genome Wowser Lets You Browse the Human Genome (news.dice.com)
- Genome sequence could reveal ‘Achilles’ heels’ of important wheat disease (physorg.com)
- We are all mutants (eurekalert.org)
- Now, browse the human genome with iPad app! (news.bioscholar.com)
- Blog – Human Genome Contaminated With Mycoplasma DNA (technologyreview.com)
- Complete Genomics Makes 29 Genomes Public (xconomy.com)
- Decoding human genes is the goal of a new open-source encyclopedia (eurekalert.org)
- Basques (?) in 1000 Genomes IBS (Iberian Spanish) sample (dienekes.blogspot.com)
- Genomics and social network analysis team up to solve disease outbreaks (medicalxpress.com)
Researchers looking at a rare disease make breakthrough that could benefit everyone
Geneticists unveil workings of 3 genes that control cell development and growth
MONTREAL, March 1, 2011 – By working with Canadians of French ancestry who suffer a rare genetic disease, researchers have discovered how three genes contribute to abnormal growth, making a breakthrough that will improve our understanding of many disorders such as foetal and childhood growth retardation, abnormal development of body parts and cancer. “As a result of the Human Genome Project, we know the basic identity of essentially all the genes in the human body, but we don’t automatically know what they do in detail,” explained lead researcher Dr. Mark Samuels of the University of Montreal’s Department of Medicine and the Sainte-Justine University Hospital Research Centre. “It’s like opening your car and seeing the parts, but not knowing what each one does. When a part breaks however, you learn how it fits with the rest of the machine. Working with people who have specific health or development problems linked to specific genes enables us to see how those genes contribute to our bodies’ development and functioning.”
In this case, the team of researchers characterized the molecular basis in patients who suffer from Meier-Gorlin Syndrome (MGS), a rare disorder that is characterized by short stature, small ears, and absent or underdeveloped knee-caps. The patients were mostly francophonic, coming from the Maritimes, Quebec, British Columbia as well as the Louisiana Cajun community. MGS is a classic “single gene disorder,” meaning it is related to mutations in individual genes, although in the case of MGS different patients surprisingly seem to carry mutations in any of three different genes.
The genes are called ORC1L, ORC4L and CDT1, and are known to play a critical role in correct copying of DNA. Cells reproduce by dividing in two. All the chromosomes must also be duplicated. This process is tightly controlled to prevent having too many or two few copies of large segments of the genome. “This seems to be the first example of any naturally occurring, inherited mutations identified in this set of important regulatory genes in any mammal. Finding the genes is a great example of the value of this type of research,” Samuels said. “We learn the cause of the disease, and discover new things about our cellular function. However we still have a lot to learn about why mutations in these genes lead to the specific consequences in Meier-Gorlin patients.”
There are 20-25,000 genes in the human genetic sequence, and it’s important to note that they don’t necessarily each correspond to a specific function or group of functions, or indeed to a single disease. The same gene can have subtle effects on a number of bodily functions. Moreover, in complex genetic diseases – diabetes, for example – environment and lifestyle have as much or more of an impact on health than a person’s genetic background.
“Understanding rare genetic conditions like MGS is important to the general public for two reasons,” Samuels stressed. “Firstly, they provide insight into how our genes, and therefore our bodies, work. Secondly, although there are few people concerned for each particular disorder, in sum all patients with genetic conditions consume substantial amounts of health resources, and by diagnosing them more quickly, we can improve patient management and reduce the strain on the health care system.” Research suggests that up to 70% of admissions to paediatric hospitals may be related to some kind of genetic disorder. “It’s also important to note that behind the science and the statistics, there are real people suffering. It’s an immense relief for patients and their families to finally have a clear diagnosis,” Samuels added.
In an unusual coincidence, a competing team of researchers obtained similar findings on Meier-Gorlin Syndrome in a different set of patients. These findings were published in the same issue of Nature Genetics. Samuels notes, “Neither team can claim absolute priority in the discovery. However this is the way science works best: when important results are quickly verified by multiple teams independently.”
- The Promise and Payoff of Rare Diseases Research, From NIH Director Dr. Francis S. Collins (NIH MedlinePlus Magazine, May 2011)
- The NIH Undiagnosed Diseases Program (NIH MedlinePlus Magazine May 2011)
- NIH researchers create comprehensive collection of approved drugs to identify new therapies (jflahiff.wordpress.com)