Dr. Murray Feingold: Animal genetics help scientists understand diseases

Not only have great strides been made in human genetics but also in animal genetics. This is important because such genetic information is not only helpful to the animal, but it frequently can also be applied to humans.

A recent article in the New England Journal of Medicine discussed how genetic research from one type of animal, the dog, has been helpful in better understanding the genetics of certain inherited disorders that are present in both dogs and humans.

It is generally easier to do genetic research on dogs than on people. Dogs reproduce many litters, therefore, more animals are available to study.Compared with dogs who are bred much closer, purebreds, there is more genetic heterogeneity present in humans. This results in a greater number of uncontrolled variables being present in people than in dogs. Such genetic heterogeneity or variables can make it more difficult to interpret the results of genetic studies.

There are many genetic disorders that affect the bones of dogs. Hip dysplasia is frequently found in larger dogs.

Another condition that affects the bones and is also present in both humans and dogs is chondrodysplasia. About 20 breeds of dogs have this condition and as a result they have disproportionately short legs. Examples are dachshunds, corgis and basset hounds.

By studying dogs that are affected with chondrodysplasia, researchers were able to uncover the gene that is responsible for this skeletal abnormality and also the chromosome where it is located.

This information is now being applied to patients with this condition by the geneticists who care for them.

Genetic studies are now underway on dogs who have other human conditions such as cancer, epilepsy, lupus erythematosus and narcolepsy, to name just a few.

But as gene research on humans has been helpful in understanding genetic diseases in people, the same is true of gene research involving animals.

Determining the genetic cause of a disease, be it a human or an animal, brings researchers one big step closer to finding ways to treat and prevent the disorder.

See the article here:

Dr. Murray Feingold: Animal genetics help scientists understand diseases

Feingold: Animal genetics help scientists understand diseases

Not only have great strides been made in human genetics but also in animal genetics. This is important because such genetic information is not only helpful to the animal, but it frequently can also be applied to humans.

A recent article in the New England Journal of Medicine discussed how genetic research from one type of animal, the dog, has been helpful in better understanding the genetics of certain inherited disorders that are present in both dogs and humans.

It is generally easier to do genetic research on dogs than on people. Dogs reproduce many litters, therefore, more animals are available to study. Compared to dogs who are bred much closer, purebreds, there is more genetic heterogeneity present in humans. This results in a greater number of uncontrolled variables being present in people than in dogs. Such genetic heterogeneity or variables can make it more difficult to interpret the results of genetic studies.

There are many genetic disorders that affect the bones of dogs. Hip dysplasia is frequently found in larger dogs.

Another condition that affects the bones and is also present in both humans and dogs is chondrodysplasia. About 20 breeds of dogs have this condition and as a result they have disproportionately short legs. Examples are dachshunds, corgis and basset hounds.

By studying dogs that are affected with chondrodysplasia, researchers were able to uncover the gene that is responsible for this skeletal abnormality and also the chromosome where it is located.

This information is now being applied to patients with this condition by the geneticists who care for them.

Genetic studies are now underway on dogs who have other human conditions such as cancer, epilepsy, lupus erythematosus and narcolepsy, to name just a few.

But as gene research on humans has been helpful in understanding genetic diseases in people, the same is true of gene research involving animals.

Determining the genetic cause of a disease, be it a human or an animal, brings researchers one big step closer to finding ways to treat and prevent the disorder.

Excerpt from:

Feingold: Animal genetics help scientists understand diseases

New insights into why humans are more susceptible to cancer and other diseases

Public release date: 23-Aug-2012 [ | E-mail | Share ]

Contact: Mary Beth O'Leary moleary@cell.com 617-397-2802 Cell Press

Chimpanzees rarely get cancer, or a variety of other diseases that commonly arise in humans, but their genomic DNA sequence is nearly identical to ours. So, what's their secret? Researchers reporting in the September issue of the American Journal of Human Genetics, a Cell Press journal, have found that differences in certain DNA modifications, called methylation, might play a role.

The researchers discovered hundreds of genes that display different patterns of methylation between the two species. These different patterns of methylation lead to different levels of expression, and many of the genes involved are linked to specific human diseases. Given that environmental factors can affect DNA methylation, these results might help researchers to better understand how differences in genetics and environmental exposure contribute to differences, including different disease vulnerabilities, between the two species.

DNA methylation doesn't change a cell's underlying genetic information, but it does affect gene activity and can have a profound impact on processes such as aging and the development of disease. By using new state-of-the-art techniques to look at methylation maps and gene expression in the brains of chimpanzees and humans, the investigators found that changes in DNA methylation at least partially explain the divergence of gene-expression patterns between these species.

In addition, differentially methylated genes showed striking links with specific neurological and psychological disorders and cancers to which modern humans are particularly susceptible, suggesting that changes in DNA methylation might be linked to the evolution of humans' vulnerability to certain diseases.

"Our results hint, but by no means provide proof, that epigenetic divergenceor changes of chemical properties of DNAmay be particularly important for some disease-related phenotypes that are pertinent to modern humans," says senior author Dr. Soojin Yi, from the Georgia Institute of Technology. "Such findings, in the long-term, may contribute to the development of better therapeutic targets for some human diseases," she adds.

###

Zeng et al.: "Divergent Whole-Genome Methylation Maps of Human and Chimpanzee Brains Reveal Epigenetic Basis of Human Regulatory Evolution."

Excerpt from:

New insights into why humans are more susceptible to cancer and other diseases

More Clues About Why Chimps and Humans Are Genetically Different

Newswise Ninety-six percent of a chimpanzees genome is the same as a humans. Its the other 4 percent, and the vast differences, that pique the interest of Georgia Techs Soojin Yi. For instance, why do humans have a high risk of cancer, even though chimps rarely develop the disease?

In research published in Septembers American Journal of Human Genetics, Yi looked at brain samples of each species. She found that differences in certain DNA modifications, called methylation, may contribute to phenotypic changes. The results also hint that DNA methylation plays an important role for some disease-related phenotypes in humans, including cancer and autism.

Our study indicates that certain human diseases may have evolutionary epigenetic origins, says Yi, a faculty member in the School of Biology. Such findings, in the long term, may help to develop better therapeutic targets or means for some human diseases.

DNA methylation modifies gene expression but doesnt change a cells genetic information. To understand how it differs between the two species, Yi and her research team generated genome-wide methylation maps of the prefrontal cortex of multiple humans and chimps. They found hundreds of genes that exhibit significantly lower levels of methylation in the human brain than in the chimpanzee brain. Most of them were promoters involved with protein binding and cellular metabolic processes.

This list of genes includes disproportionately high numbers of those related to diseases, said Yi. They are linked to autism, neural-tube defects and alcohol and other chemical dependencies. This suggests that methylation differences between the species might have significant functional consequences. They also might be linked to the evolution of our vulnerability to certain diseases, including cancer.

Yi, graduate student Jia Zeng and postdoctoral researcher Brendan Hunt worked with a team of researchers from Emory University and UCLA. The Yerkes National Primate Research Center provided the animal samples used in the study. It was also funded by the Georgia Tech Fund for Innovation in Research and Education (GT-FIRE) and National Science Foundation grants (MCB-0950896 and BCS-0751481). The content is solely the responsibility of the principal investigators and does not necessarily represent the official views of the NSF.

Here is the original post:

More Clues About Why Chimps and Humans Are Genetically Different

Hidden Meanings in Our Genomes And What To Do With Mendel

Gregor Mendel in textbooks: should he stay or should he go now? (Credit: Natl Library of Medicine)

Summer reading for most people means magazines, novels, and similar escapist fare, but for me, its the American Journal of Human Genetics (AJHG). Perusing the table of contents of the current issue tells me whats dominating this post-genomic era: information beyond the obvious, a subtext hidden within the sequences of A, C, T and G.

In the decades following the cracking of the genetic code in the 1960s the correspondence between DNA (actually RNA) triplets and the 20 types of amino acids in biological proteins the one gene-one protein mindset guided genetic research. Investigators used indirect methods to map genes to chromosomes, then painstakingly made the gene-protein assignments, describing rare, single-gene diseases one at a time.

I looked at past issues of the AJHG at decade intervals from this time of year, to place the current issue into perspective. The September 1982 journal had crude linkage maps of 4 human chromosomes, the idea of a human genome project not yet uttered. Within the next decade, a flurry of genes behind the more familiar single-gene diseases began to reveal themselves: myotonic dystrophy, cystic fibrosis, Duchenne muscular dystrophy, the first type of osteogenesis imperfecta, and the elusive Huntington disease among them.

The functioning of the human genome is much more than the protein-encoding sequences. (DOE - Genomes to Life)

The 2002 AJHG held the first inklings of moving beyond the single gene approach, with genomewide and associations entering the lingo, soon to be wed into the GWAS genomewide association studies that dominated until the recent takeover by whole exome sequencing. Articles dealt with SNPs and susceptibilities, described mutations in non-amino-acid-coding parts of genes, and included more environmentally-influenced traits and conditions, such height and bipolar disorder.

And now, the tone and content of the August 2012 issue highlight how the information in DNA goes far beyond one-gene-one-protein. Here are some such hidden meanings:

A mutant gene behind a form of amyotrophic lateral sclerosis (ALS) also causes essential tremor. In ALS, a missense mutation, which alters an amino acid, hangs around in motor neurons and does something we still dont know what that shuts down the cells. But in essential tremor, the mutation is nonsense, which halts production of the protein and activates a cellular garbage disposal pathway that removes the incomplete proteins, with less dire consequences. (The gene, FUS, accounts for only 4% of the 10% of ALS cases that are inherited).

A fifth form of osteogenesis imperfecta (brittle bone disease) stems from a mutation in the control DNA sequence that lies before the protein-encoding sequence. So instead of spelling get ready to start, the mutation tacks five amino acids onto the 132-amino-acid protein. The gene had eluded classic linkage studies and even the Sanger sequencing of the human genome project.

A potential biomarker for susceptibility to and prognosis for lung cancer lies in having 4 copies of a particular repeated sequence, compared to having 2 or 3 copies, in the promoter control region of a gene called MAPKAPK2.

See original here:

Hidden Meanings in Our Genomes And What To Do With Mendel

MARC travel awards announced for the 2012 American Society of Human Genetics Annual Meeting

Public release date: 8-Aug-2012 [ | E-mail | Share ]

Contact: Fran Yates fyates@faseb.org 301-634-7109 Federation of American Societies for Experimental Biology

Bethesda, MD FASEB MARC (Maximizing Access to Research Careers) Program has announced the travel award recipients for the 2012 American Society of Human Genetics (ASHG) Annual Meeting in San Francisco, CA from November 6-10, 2012. These awards are meant to promote the entry of underrepresented minority students, postdoctorates and scientists into the mainstream of the basic science community and to encourage the participation of young scientists at the 2012 ASHG Annual Meeting.

Awards are given to poster/platform presenters and faculty mentors paired with the students/trainees they mentor. This year MARC conferred 21 awards totaling $38,850.

The FASEB MARC Program is funded by a grant from the National Institute of General Medical Sciences, National Institutes of Health. A primary goal of the MARC Program is to increase the number and competitiveness of underrepresented minorities engaged in biomedical and behavioral research.

FASEB is composed of 26 societies with more than 100,000 members, making it the largest coalition of biomedical research associations in the United States. Celebrating 100 Years of Advancing the Life Sciences in 2012, FASEB is rededicating its efforts to advance health and well-being by promoting progress and education in biological and biomedical sciences through service to our member societies and collaborative advocacy.

The following ASHG members have been selected to receive FASB MARC Travel Awards for their poster/platform presentations:

The following faculty/mentors and students/trainees have been selected to receive FASEB MARC Travel Awards:

Dr. Nadeem Fazal, Chicago State University [ASHG member]

###

Read the original here:

MARC travel awards announced for the 2012 American Society of Human Genetics Annual Meeting

Body Tremors Have A Genetic Cause

Editor's Choice Main Category: Genetics Also Included In: Neurology / Neuroscience Article Date: 03 Aug 2012 - 15:00 PDT

Current ratings for: Body Tremors Have A Genetic Cause

5 (1 votes)

Researchers and clinicians have investigated for years as to why this shaking occurs, but have so far remained unsuccessful. Even though scientists know that the problem is related to parts of the brain that control certain muscles, they have been unable to identify the exact cause for this malfunction in the nervous system of those affected by ET. Strong evidence of years of research suggested that the disease is due to genetics but until now researchers have been unable to identify the actual genetic link.

The fact that mutations in a gene called FUS (Fused in Sarcoma) cause amyotrophic lateral sclerosis (ALS), a nerve cell disease in the brain and spinal cord that controls voluntary muscle movement, is already known amongst scientists. However, the new study was able to successfully identify mutations that cause ET in FUS, and also managed to provide evidence that the disease mechanisms for ET and ALS FUS mutations are different.

Leading author Dr. Nancy Merner, explained:

Her clinical focus is shared by her other team members. Dr. Guy Rouleau declared:

Dr. Patrick Dion, another key researcher on this project, added: "There is currently a lack of consensus on the diagnostic criteria of ET thus a genetic diagnosis can be beneficial, especially for familial cases. Transitioning to a genetic diagnosis would cut down on ET misdiagnosis."

37-50% of individual cases are misdiagnosed.

Affected individuals usually feel embarrassed or annoyed at the tremors that impact their everyday tasks like eating, writing, working, or drinking as these tremors most often affect the hands and make it difficult for those affected to hold or use small objects.

More:

Body Tremors Have A Genetic Cause

Genetic copy-number variants and cancer risk

Public release date: 2-Aug-2012 [ | E-mail | Share ]

Contact: Elisabeth Lyons elyons@cell.com 617-386-2121 Cell Press

Genetics clearly plays a role in cancer development and progression, but the reason that a certain mutation leads to one cancer and not another is less clear. Furthermore, no links have been found between any cancer and a type of genetic change called "copy-number variants," or CNVs. Now, a new study published by Cell Press in The American Journal of Human Genetics on August 2 identifies CNVs associated with testicular cancer risk, but not with the risk of breast or colon cancer.

Some cancers, including breast and colon cancer, are caused by mutations that are passed from one generation to the next. However, most cancers, including testicular cancer, are sporadicthey arise without a family history of cancer. Many of these sporadic cancers result from genetic mutations in germ cellsthe cells involved in reproductioneven though neither parent has the mutation. Scientists call these "de novo" mutations.

In order to identify rare de novo mutations associated with cancer risk, Dr. Kenneth Offit and colleagues searched for CNVs, which are duplications or deletions of one or more sections of DNA, in cancer patients and their cancer-free relatives. They found a significant increase in the number of rare de novo CNVs in individuals with testicular cancer as opposed to breast or colon cancer. Although such CNVs have been associated with autism and other neurocognitive and cardiovascular disorders, they were not previously known to be associated with cancer.

The authors propose that de novo changes (as opposed to those inherited from parents) might be indicative of conditions that have traditionally resulted in reduced fertility. Although modern treatment regimens allow more than 90% of men with testicular cancer to live long and reproductive lives, the condition traditionally left affected men childless. "We speculate that the paradigm of a de novo germline disease etiology may be less applicable to late-onset cancers," says Offit, "in part explaining the lower frequency of de novo events we found in adult-onset breast and colon cancer cases." Pinpointing the specific genetic changes that lead to cancer development will improve the understanding of the origins of cancer, leading to new treatment strategies and ultimately easing the burden on those afflicted with these diseases.

###

Stadler et al.: "Rare De Novo Germline Copy-Number Variation in Testicular Cancer."

ABOUT THE AMERICAN JOURNAL OF HUMAN GENETICS

The American Journal of Human Genetics (AJHG) is ASHG's official scientific journal, published by Cell Press. AJHG is the most highly regarded peer-reviewed journal dedicated to studies in human genetics and earned an impact factor of 11.680 in 2011. AJHG provides cutting-edge research and review articles related to genetics and genomics and the application of genetic principles in health, disease, medicine, population studies, evolution, and societal impacts. For more information about AJHG, visit: http://www.ajhg.org.

Visit link:

Genetic copy-number variants and cancer risk

The "Harry Potter" magic

Scientists have theorized that magical traits described in the Harry Potter series have a realistic connection to recessive genes in human genetics. University of Oxford geneticists Sreeram Ramagopalan, Marian Knight, George Ebers, and Julian Knight published a paper that analyzes the heritability of the described magical abilities in many of the characters.

In describing magical family lineages, they wrote:

We estimated familial aggregation to detect whether a characteristic has a genetic component. The final Harry Potter book Harry Potter and the Deathly Hallows goes into great detail about magical families, notable examples being the Black and Gaunt lineages. Although shared environmental influences can also lead to familial clustering of a trait, the presence of magical abilities in seven generations of the Black family and at least three generations in others strongly suggests the influence of genetic factors in determining magical ability.

The geneticists also said magic, similar to athletic ability, is not a dichotomous trait, but rather carries a wide range of capacities, ranging from the power of Albus Dumbledore to the unimpressive abilities of Crabbe and Goyle.

Magical ability is likely to be affected by the environment, with experience and emotional state being important factors, the scientists said.

The flying broomstick

Bernoullis principle states that as air flow speeds up, air pressure must decrease.

In the case of an airplane, air flows more quickly at the top of the planes surface than the bottom, reducing pressure on the bottom of the plane. The planes ability to fly relies mostly on its wings, which are shaped to allow the air to deflect downward, giving the aircraft its lift.

This concept doesnt work for a broomstick without wings. Instead, flying broomsticks would have to use a completely different approach: antigravity. Just as magnets have the ability to repel each other, they also apparently have the ability to repel other objects that have their own natural magnetic fields. In 1997, a group of British and Dutch scientists successfully levitated a frog with super magnets, which repelled the frog 2 meters into the air.

In 1999, scientists at the Rensselaer Polytechnic Institute in New York made a saucer fly on a 10-kilowatt beam of light. The super magnet developed for this experiment is powerful and large enough to lift a human and his broomstick.

More:

The "Harry Potter" magic

Gene mutations linked to most cases of rare disorder — Alternating Hemoplegia of Childhood

Public release date: 30-Jul-2012 [ | E-mail | Share ]

Contact: Phil Sahm phil.sahm@hsc.utah.edu 801-581-2517 University of Utah Health Sciences

(SALT LAKE CITY)Alternating hemiplegia of childhood (AHC) is a rare disorder that usually begins in infancy, with intermittent episodes of paralysis and stiffness, first affecting one side of the body, then the other. Symptoms mysteriously appear and disappear, again and again, and affected children often experience dozens of episodes per week. As they get older, children fall progressively behind their peers in both intellectual abilities and motor skills, and more than half develop epilepsy. Unfortunately, medications that work for epilepsy have been unsuccessful in controlling the recurrent attacks of paralysis, leaving parents and physicians with few options, and significantly disabling those affected.

Researchers at the University of Utah Departments of Neurology and Human Genetics, in collaboration with researchers at Duke University Medical Center, have discovered that mutations in the ATP1A3 gene cause the disease in the majority of patients with a diagnosis of AHC. The study was published online on Sunday, July 29, 2012, in Nature Genetics.

In a collaborative effort with the AHC Foundation, Kathryn J. Swoboda, M.D., co-first author on the study, associate professor of neurology and pediatrics, and director of the Pediatric Motor Disorders Research Program at the University of Utah, established an international database of patients with AHC from around the world, starting with a single family nearly 14 years ago. This database now includes 200 affected individuals from more than a dozen countries. Access to clinical information and DNA samples from this database were critical to the success of the international collaboration that helped to identify the first gene causing AHC in a significant percentage of patients.

"AHC is almost always a sporadic disease, which means that there is no family history of the disorder," says Tara Newcomb, genetic counselor, University of Utah Department of Neurology, and a co-author of the study. "The rarity of the disease and the almost exclusively sporadic inheritance made AHC an ideal candidate for next-generation sequencing."

The mysterious and intermittent nature of the neurologic symptoms, which range from unusual eye movements to seizure-like episodes, to partial and/or full body paralysis often results in a prolonged diagnostic odyssey for parents and children, according to Matthew Sweney, M.D., an instructor in the U of U Departments of Neurology and Pediatrics and an epilepsy specialist at Primary Children's Medical Center. "Families often present again and again to the emergency room, and children may undergo dozens of tests and invasive procedures," says Sweney, also a study co-author. "Often, it is only after the spells fail to respond to antiepileptic medications that the diagnosis is considered."

The ATP1A3 gene encodes one piece of a key transporter molecule that normally would move sodium and potassium ions across a channel between neurons (nerve cells) to regulate brain activity. Mutations in this gene are already known to cause another rare movement disorder, rapid onset dystonia parkinsonism, and clinical testing for mutations in this gene is readily available through a blood test. "Having a means to confirm a diagnosis more quickly, using a simple blood test, will allow us to better care for our patients and provide them opportunities for early enrollment in clinical trials," Swoboda says. "The identification of the gene provides scientists with the opportunity to identify specifically targeted and truly effective therapies."

In a broad international collaborative effort, the initial collaboration between the University of Utah and Duke investigators expanded to involve more than three dozen researchers from 13 countries. "This discovery is a testament to the power of the next-generation sequencing technologies, which are becoming increasingly available as a result of the Human Genome Project," says co-author Lynn Jorde, Ph.D., professor and chair of the U of U Department of Human Genetics. "These technologies are rapidly revolutionizing our ability to diagnose rare disorders, and provide hope for hundreds of families of children with rare disorders about which little is known and no targeted treatments currently exist."

###

Continue reading here:

Gene mutations linked to most cases of rare disorder -- Alternating Hemoplegia of Childhood

Gene Mutations Identified as Cause of Most Cases of Rare Disorder–AHC

Newswise (SALT LAKE CITY)Alternating hemiplegia of childhood (AHC) is a rare disorder that usually begins in infancy, with intermittent episodes of paralysis and stiffness, first affecting one side of the body, then the other. Symptoms mysteriously appear and disappear, again and again, and affected children often experience dozens of episodes per week. As they get older, children fall progressively behind their peers in both intellectual abilities and motor skills, and more than half develop epilepsy. Unfortunately, medications that work for epilepsy have been unsuccessful in controlling the recurrent attacks of paralysis, leaving parents and physicians with few options, and significantly disabling those affected.

Researchers at the University of Utah Departments of Neurology and Human Genetics, in collaboration with researchers at Duke University Medical Center, have discovered that mutations in the ATP1A3 gene cause the disease in the majority of patients with a diagnosis of AHC. The study was published online on Sunday, July 29, 2012, in Nature Genetics.

In a collaborative effort with the AHC Foundation, Kathryn J. Swoboda, M.D., co-first author on the study, associate professor of neurology and pediatrics, and director of the Pediatric Motor Disorders Research Program at the University of Utah, established an international database of patients with AHC from around the world, starting with a single family nearly 14 years ago. This database now includes 200 affected individuals from more than a dozen countries. Access to clinical information and DNA samples from this database were critical to the success of the international collaboration that helped to identify the first gene causing AHC in a significant percentage of patients.

AHC is almost always a sporadic disease, which means that there is no family history of the disorder, says Tara Newcomb, genetic counselor, University of Utah Department of Neurology, and a co-author of the study. The rarity of the disease and the almost exclusively sporadic inheritance made AHC an ideal candidate for next-generation sequencing.

The mysterious and intermittent nature of the neurologic symptoms, which range from unusual eye movements to seizure-like episodes, to partial and/or full body paralysis often results in a prolonged diagnostic odyssey for parents and children, according to Matthew Sweney, M.D., an instructor in the U of U Departments of Neurology and Pediatrics and an epilepsy specialist at Primary Childrens Medical Center. Families often present again and again to the emergency room, and children may undergo dozens of tests and invasive procedures, says Sweney, also a study co-author. Often, it is only after the spells fail to respond to antiepileptic medications that the diagnosis is considered.

The ATP1A3 gene encodes one piece of a key transporter molecule that normally would move sodium and potassium ions across a channel between neurons (nerve cells) to regulate brain activity. Mutations in this gene are already known to cause another rare movement disorder, rapid onset dystonia parkinsonism, and clinical testing for mutations in this gene is readily available through a blood test. Having a means to confirm a diagnosis more quickly, using a simple blood test, will allow us to better care for our patients and provide them opportunities for early enrollment in clinical trials, Swoboda says. The identification of the gene provides scientists with the opportunity to identify specifically targeted and truly effective therapies.

In a broad international collaborative effort, the initial collaboration between the University of Utah and Duke investigators expanded to involve more than three dozen researchers from 13 countries. This discovery is a testament to the power of the next-generation sequencing technologies, which are becoming increasingly available as a result of the Human Genome Project, says co-author Lynn Jorde, Ph.D., professor and chair of the U of U Department of Human Genetics. These technologies are rapidly revolutionizing our ability to diagnose rare disorders, and provide hope for hundreds of families of children with rare disorders about which little is known and no targeted treatments currently exist.

Funding for the work at the University of Utah was provided by a grant from the Alternating Hemiplegia of Childhood Foundation (AHCkids.org). The Utah team also included former postdoctoral fellow Chad Huff, Ph.D., from the Department of Human Genetics, and Louis Viollet, M.D., Ph.D., and Sandra Reyna, M.D., from the Department of Neurology Pediatric Motor Disorders Research Program (https://medicine.utah.edu/neurology/research/swoboda).

Whole genome sequencing was performed in collaboration with the Institute for Systems Biology.

See the article here:

Gene Mutations Identified as Cause of Most Cases of Rare Disorder--AHC

American Society of Human Genetics to hold 2012 annual meeting, Nov. 6 to 10, in San Francisco

Public release date: 28-Jul-2012 [ | E-mail | Share ]

Contact: Cathy Yarbrough press@ashg.org sciencematter@yahoo.com 858-243-1814 American Society of Human Genetics

The American Society of Human Genetics will hold its 62nd annual meeting, Tuesday to Saturday, Nov. 6 to 10, at San Francisco's Moscone Center.

Over 6,000 scientists, medical geneticists and genetic counselors are expected to attend the ASHG annual meeting, the world's largest scientific conference on human genetics.

"The ASHG annual meeting provides a forum for presenting the highest quality basic and translational science and the latest clinical information in human genetics, as well as nurturing scientific collaborations through networking" said ASHG Executive Vice President Joann Boughman, Ph.D.

Mary-Claire King, Ph.D., ASHG president and professor of genome sciences and medicine at University of Washington, Seattle, will kick-off the conference, Tuesday, Nov. 6, by speaking on the topic, "The Scientist as a Citizen of the World."

The meeting's closing symposium, Saturday, Nov. 10, will address, "Present and Future Directions for Human Genetics."

Topics of the ASHG meeting's invited scientific sessions, platform presentations and posters will include:

Speaking at the presidential symposium, "Gene Discovery and Patent Law: Present Experience in the U.S. and in Europe," will be: Lori B. Andrews, J.D., ITT Chicago-Kent College of Law, Hank Greely, J.D., Mark Lemley, J.D., Stanford Law School, and Gert Matthijs, Ph.D., Catholic University of Leuven, Belgium.

The annual meeting also will feature presentations of ASHG's annual awards and the Gruber Genetics Prize.

Follow this link:

American Society of Human Genetics to hold 2012 annual meeting, Nov. 6 to 10, in San Francisco

Running: Salt Lake City’s Nathan Krah wins San Francisco Marathon

Running University of Utah student Krah finishes in 2:26.45.

Salt Lake City runner Nathan Krah won the San Francisco Marathon on Sunday, according to unofficial results.

Krah, a 26-year-old Ph.D. student in human genetics at the University of Utah, was the mens winner, finishing the hilly 26.2-mile course that wound through the city and across the Golden Gate Bridge in 2 hours 26 minutes and 45 seconds, according to preliminary results.

"Even coming from a mountainous area, this was still really hard," Krah said in a statement after winning. "It was just an endless assault of hills."

Devon Crosby-Helms, 30, of San Anselmo, Calif., finished first among the women with a time of 2 hours 44 minutes 5 seconds, according to results.

"That was extremely satisfying," Crosby-Helms said in a statement. "This was my third time racing here, and I really felt I had a good chance to win."

More than 7,000 runners took part in this years marathon, alongside 18,000 people who participated in two separate half-marathons, a 5K run and a Munchkins Kids Fun Run, organizers said.

Copyright 2012 The Salt Lake Tribune. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.

See more here:

Running: Salt Lake City’s Nathan Krah wins San Francisco Marathon

Research Validates BioNano Genomics’ Mapping Platform for Complex Human Genome Analysis

SAN DIEGO--(BUSINESS WIRE)--

In a paper published today in Nature Biotechnology, researchers at the University of California San Francisco (UCSF) Institute for Human Genetics and Cardiovascular Research Institute demonstrated the utility of the Irys platform from BioNano Genomics for structural variation analysis and de novo assembly of next generation sequencing (NGS) data. Using Irys, the authors were able to accurately map and comprehensively analyze structural variation in the human major histocompatibility complex (MHC) region, which is associated with autoimmune and infectious diseases.

While the idea of using physical genome maps has been around for some time, the methods available have not been able to accurately address complex regions in humans, said Pui-Yan Kwok, MD, PhD, senior author and Henry Bachrach Distinguished Professor at the UCSF School of Medicine. BioNanos approach brings us one step closer to fully understanding the relevance of genetic variation in studies of new pathogens, complex metagenomics, and cancer genomes, where copy number variation and structural variation are abundant.

Complex genomes contain highly repetitive sequences and prove challenging for whole genome assembly. The MHC region is notoriously difficult to study owing to its large number of genes, repetitive sequences, extreme variation and pseudogenes. While advances have been made to short read sequencing methods attempting to address complex genomes, such methods have not performed well in repetitive regions and do not readily resolve haplotypes or localize structural variants precisely.

Irys is a multiplex-capable, scalable platform that uses a proprietary chip to uncoil and confine long DNA molecules in nanochannels, causing them to spontaneously and uniformly linearize for high-resolution, single-molecule imaging. Irys eliminates the DNA fragmentation and amplification steps typical with NGS, resulting in read lengths of hundreds of kilobases to megabases. These extremely long read lengths preserve the valuable structural information inherent in the sample, making it possible to directly observe structural variants including translocations and inversions. The system automates sample processing and imaging to provide a simple technique for genome mapping by labs of any size or level of expertise.

The BioNano approach to genome mapping achieves uniform DNA stretching in a high throughput format, allowing researchers to directly view genome variation in the full biological context, said Dr. Erik Holmlin, CEO of BioNano Genomics. This paper demonstrates how the Irys system provides a completely new data type that opens the door to more accurate and comprehensive structural variation discovery studies and improves our ability to achieve higher quality sequence assemblies.

Study Findings

Results showed that sequence motif maps generated by the Irys system provide useful scaffolds for de novo assembly of sequencing data generated from structurally complex regions for identifying misassemblies, characterization of structural variants and retention of haplotype phasing.

To demonstrate the utility of this approach, the authors constructed sequence motif maps of 95 bacterial artificial chromosome (BAC) clones covering the 4.7 Mb MHC region from two individuals (PDF and COX libraries used by the MHC Haplotype Consortium). Subsequently, they performed de novo sequence assembly using NGS reads. The maps and NGS contigs were then compared to the reference sequences reported by the MHC Haplotype Consortium as confirmation and to uncover potential differences.

Employing this method, the study found and confirmed a number of interesting genomic features, including a 4kb error in one reference sequence, anchoring and gap sizing of four NGS contigs, identification of misassembled NGS contigs, differentiation of the two HLA-DRB1 variants, and definition of numerous structural variants, such as a 5kb insertion and 30kb tandem duplication. The authors further concluded that the Irys is scalable to a variety of genome analyses including large-scale, whole genomes based on throughputs achieved in the study of >300 Mb per scan.

Continued here:

Research Validates BioNano Genomics’ Mapping Platform for Complex Human Genome Analysis

Gene Discovered By Scientists Linked To Facial Abnormalities

Editor's Choice Main Category: Genetics Article Date: 09 Jul 2012 - 12:00 PDT

Current ratings for: Gene Discovered By Scientists Linked To Facial Abnormalities

The finding was published in The American Journal of Human Genetics and was conducted by Dr. Hyung-Goo Kim, molecular geneticist at the Medical College of Georgia at Georgia Health Sciences University and his team.

The researchers discovered the PHG21A mutated gene in patients with Potocki-Shaffer syndrome, a rare disorder that can result in significant abnormalities, like a small head and chin as well as intellectual disability.

The researchers conducted experiments in zebrafish, which developed similar head and brain abnormalities to those found in humans and discovered that their findings were confirmed when they suppressed the PHF21A gene in zebrafish.

Dr. Kim explained:"With less PHF21A, brain cells died, so this gene must play a big role in neuron survival."

To reconfirm their finding, the team inserted the gene back into the malformed fish, which subsequently became normal. The gene was also found in the craniofacial area of normal mice. Even though it is impossible to cure humans just by re-inserting the normal gene as is possible in zebrafish, the researchers believe that their finding will, in the future, allow genetic screening and possibly early intervention during fetal development, as well as treatments to increase PHF21A levels. In addition, the finding provides more insight into a better understanding of face, skull and brain formation.

The team focused on the gene when they used a distinctive chromosomal break found in patients with Potocki-Shaffer syndrome as a starting point. Chromosomes, i.e. packages of DNA and protein, are not supposed to break. However, when they do, they can damage nearby genes. Co-author of the study, Dr. Lawrence C. Layman, who is Chief of the MCG Section of Reproductive Endocrinology, Infertility and Genetics, explained: "We call this breakpoint mapping and the breakpoint is where the trouble is."

Damaged genes can no longer retain their optimum function. In PHF21A's case for instance the functionality is reduced to about half of the norm.

Layman continues: "When you see the chromosome translocation, you don't know which gene is disrupted. You use the break as a focus then use a bunch of molecular techniques to zoom in on the gene."

Here is the original post:

Gene Discovered By Scientists Linked To Facial Abnormalities

Fish provide proof of genetic defect that leads to brain, skull malformations

In a study published today in the American Journal of Human Genetics, an international team of researchers looked at blood samples from two patients with a rare disorder called Potocki-Shaffer syndrome, said Hyung-Goo Kim, lead author and a research fellow in Dr. Lawrence Layman's OB/GYN genetics lab at GHSU.

Read the original post:

Fish provide proof of genetic defect that leads to brain, skull malformations

Genetics and Graphite Provide Scribe Fodder

When last we met, the subject was athletic performance enhancement. I spoke of modalities for raising one's game, including surgery, lucky genetics and, of course, eau de Canseco, also known as anabolic steroids. That column contended that many world-class athletes are freaksof nature, yes, but freaks nonetheless. In effect, they make use of performance-enhancing substances that happen to be produced by their own bodies rather than by a friend of a friend who knows a really good pharmaceutical chemist.

I'll continue to pull on that thread briefly here because within days of that column going to press, news broke that is directly related to the topic. After being lobbied by the union representing its players, the National Football League has agreed to do a study. The investigation will try to determine if football players, who represent the last remnants of a once thriving pre-Clovis North American population of megafauna, naturally have crazy high amounts of compounds that can make one large.

As the New York Times put it on April 21, the union has said that football players, because of their size, might have a higher level of naturally occurring human growth hormone [HGH] and could be at risk of having false positives. At which point, league officials would presumably stand on a chair to raise the level of HGH that counts as a positive test result in pigskin land.

All of which brings me back to the question I asked last time: If users of performance-enhancing drugs are disqualified, should holders of performance-enhancing mutations be barred, too? In other wordsand I do not know the right answer to this questionwhy is it okay for a guy to have a body that makes a lot of hormone but not a buddy who makes a lot of hormone to inject?

Speaking of hormones and injections, have you seen Museum of Copulatory Organs? Part of the 18th Sydney Biennale in Australia, this collection of 3-D models of insect genitalia was the Ph.D. project of Colombian-born artist Maria Fernanda Cardoso.

Her previous claim to fame was a recreation of a 19th-century-style flea circus, which is paradoxically no small task. A blog post at the Australian Broadcasting Corporation (ABC) Web site quotes Cardoso as saying, It's one of the hardest things in life to train fleas, it took six years and it requires a lot of patience, no one knew how to train fleas anymore. Actually the New York City subway system still trains fleas on a daily basis, judging by the number of passengers carrying tiny dogs around with them for some reason probably related to the effect of Paris Hilton on our culture.

According to the ABC article, Cardoso was inspired to pursue the copulatory organ project when she found within the flea literature this quote about the insects' penises: It's not size that matters, it is shape. Indeed, some insect penises come equipped with hooks that enable the ensconced male to grab a previous suitor's sperm packet and remove it from the female. I suggest that these hooks be called cuckholders.

Speaking of shaft-shaped devices used to convey information, have you visited the Cumberland Pencil Museum in England lately? It bills itself as a great all weather attraction for the whole family, although I would submit that a pencil museum is best appreciated when rain necessitates the cancellation of outdoor festivities. Fortunately for pencil aficionados, this is England.

The museum's Web site speculates that Cumberland locals first struck graphite some five centuries ago, when a violent storm uprooted trees and unearthed vast stores of the carbon allotrope. Shepherds soon used the material to mark their sheep. Meanwhile aspiring scribes wrapped sticks of graphite in sheep hides to make rudimentary pencils. This animal-implement relationship was clearly the source of the old adage He was as write as a sheep.

Pencils reached their pinnacle in the U.S. in the second half of the 20th century, when millions of high school students clutched No. 2 versions in their clammy hands to mark the answers on their SATs. Some who may not have done well still managed to earn sheepskins by carrying pigskins.

Continued here:

Genetics and Graphite Provide Scribe Fodder

Following the Genomic Pathways to Stop the Spread of Cancer

Newswise BETHESDA, MD July 3, 2012 As the Genetics Society of Americas Model Organism to Human Biology (MOHB): Cancer Genetics Meeting in Washington, D.C. drew to a close, it was clear that the mantra for drug discovery to treat cancers in the post-genomic era is pathways.

Pathways are ordered series of actions that occur as cells move from one state, through a series of intermediate states, to a final action. Because model organisms fruit flies, roundworms, yeast, zebrafish and others are related to humans, they share many of the same pathways, but in systems that are much easier to study. Focusing on pathways in model organisms can therefore reveal new drug targets that may be useful in treating human disease.

By reading evolutions notes, we can discover what really matters in the genome, keynote speaker Eric Lander, Ph.D., founding director of the Broad Institute of Harvard and MIT and professor of biology at MIT, told a packed crowd at the MOHB: Cancer Genetics Meeting on June 19.

What matters the most in the genome of a cancer cell may be the seeds of drug resistance, the genetic changes that enable cells to evade our best drugs. Bert Vogelstein, M.D., director of the Ludwig Center at Johns Hopkins University and an investigator with the Howard Hughes Medical Institute and a keynote speaker on June 17, told participants. He called drug resistance to single agents a fait accompli, or a done deal as a side effect of the evolution of cancer.

About 3,000 resistant cells are present in every visible metastasis, said Dr. Vogelstein. Thats why we see resistance with all therapeutics, even when they work. And we cant get around it with single agents. Cancer treatment requires combinations of agents.

Presentations throughout the meeting offered specific examples of events in pathways involved in the progression of cancer in model organisms that shed light on how human cancer may metastasize.

To identify the genes behind a breast cancers spread to the lungs, Joan Massagu, Ph.D., chair of the Cancer Biology & Genetics Program at Memorial Sloan-Kettering Cancer Center and colleagues, placed cells from the lung fluid of patients into mice, deducing a breast cancer lung metastasis signature and identifying several mediators of metastasis that are clinically relevant and potential drug targets.

Denise Montell, Ph.D., from Johns Hopkins University School of Medicine, traced the signaling pathways that developing egg cells in the Drosophila (fruit fly) ovary use to migrate as using some of the same genes that are expressed as ovarian cancer spreads.

David Botstein, Ph.D., and his group at Princeton University use yeast to model the evolution of cancer through serial mutations, revealing that only a few destinations for a particular type of cancer are possible. Breast cancers cant turn into leukemias, There are limited subtypes, not just anything can happen, he explained.

David Q. Matus, Ph.D., a postdoctoral researcher at Duke University, discussed an in vivo model of cell invasion, a key component of cancer metastasis that occurs during the larval development of the roundworm, Caenorhabditis elegans. He showed that the invasive gonadal anchor cell needs to exit the cell cycle, (be non-dividing), in order to invade. Proliferative anchor cells fail to form "invadopodia" -- invasive feet or protrusions in the basement membrane -- suggesting that cell division and cell invasion are disparate states.

See more here:

Following the Genomic Pathways to Stop the Spread of Cancer