US NIH creates registry for genetic testing

The United States National Institutes of Health is creating a public database that researchers, consumers, health care providers, and others can search for information submitted voluntarily by genetic test providers. The Genetic Testing Registry (GTR) aims to enhance access to information about the availability, validity, and usefulness of genetic tests.

Currently, more than 1,600 genetic tests are available to patients and consumers, but there is no single public resource that provides detailed information about them. GTR is intended to fill that gap.

The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease. As such, the registry will have several key functions: • Encourage providers of genetic tests to enhance transparency by publicly sharing information about the availability and utility of their tests

• Provide an information resource for the public, including researchers, health care providers and patients, to locate laboratories that offer particular tests

• Facilitate genomic data-sharing for research and new scientific discoveries

“The need for this database reflects how far we have come in the last 10 years,” said Francis S. Collins, MD, PhD, NIH director. “The registry will help consumers and health care providers determine the best options for genetic testing, which is becoming more and more common and accessible. Our combined expertise in biomedical research and managing such large databases makes NIH the ideal home for the registry.”

The registry is expected to be available in 2011. GTR genetic test data will be integrated with information in other NIH/NCBI genetic, scientific, and medical databases to facilitate the research process. This integration will allow scientists to make, more easily and effectively, the kinds of connections that ultimately lead to discoveries and scientific advances.

Visit the Genetic Testing Registry:

Geneticists use new sequencing strategy to uncover rare inherited disorders

A team of researchers from the US National Human Genome Research Institute (NHGRI) has demonstrated a new technical strategy that promises to rapidly determine the genetic cause for very rare inherited illnesses. Relying on inexpensive, high-speed sequencing and a newly developed ability to capture pieces of the genome that encode genes, the team diagnosed an extremely rare X chromosome-linked cleft palate syndrome known to affect just two families.

The disorder, called TARP (talipes equinovarus, atrial septal defect, robin sequence, persistent left superior vena cava), is caused by a mutation in a gene called RBM10.

This is the first example of uncovering a gene defect on the X chromosome by analyzing DNA samples from unaffected carriers. In this case, the DNA came from the mothers of the two affected families. DNA was unavailable from any of the affected male infants because they died before, or soon after, birth. TARP syndrome is 100 percent lethal in males. The findings were published in the 14 May issue of the American Journal of Human Genetics.

“This study demonstrates the feasibility of using new sequencing technologies to uncover causative genes for thousands of rare diseases, an effort that historically has been costly and arduous,” said the paper’s senior author Leslie G. Biesecker, MD, chief of NHGRI’s Genetic Disease Research Branch. “It is also gratifying to know that the two families known to be affected by TARP syndrome finally have answers about what causes the devastating disorder that has afflicted their families for decades.

“There are about 2,500 of these rare, inherited disorders, and the cause of the great majority of them is unknown,” said Dr Biesecker. “With the help of these new technologies, biomedical researchers can potentially start making major inroads into finding the genes that cause such diseases.”

Human Microbiome Project adds new level of health knowledge

The Human Microbiome Project (HMP) has published an analysis of 178 genomes from microbes that live in or on the human body.

The researchers discovered novel genes and proteins that serve functions in human health and disease, adding a new level of understanding to what is known about the complexity and diversity of these organisms.

The human microbiome consists of all the microorganisms that reside in or on the human body. Outnumbering cells in the human body by 10 to 1, some of the microorganisms cause illnesses, but many are necessary for good health.

Currently, researchers can grow only some of the bacteria, fungi and viruses in a laboratory setting. However, new genomic techniques can identify minute amounts of microbial DNA in an individual and determine its identity by comparing the genetic signature to known sequences in the project's data base. The paper is published in the 21 May issue of the journal Science.

“This initial work lays the foundation for this ambitious project and is critical for understanding the role that the microbiome plays in human health and disease,” said National Institutes of Health Director Francis S. Collins, MD, PhD. “We are only at the very beginning of a fascinating voyage that will transform how we diagnose, treat and ultimately, prevent many health conditions.”

Launched in 2008, the HMP is a US$157 million, five-year effort that will implement a series of increasingly complicated studies that reveal the interactive role of the microbiome in human health.

The 178 microbial genomes in this report launch the HMP reference collection that eventually will total approximately 900 microbial genomes of bacteria, viruses and fungi.

These data will then be used by HMP researchers to characterise the microbial communities found in samples taken from healthy human volunteers and, later, those with specific illnesses. Samples are currently being collected for HMP from five areas of the body: the digestive tract, the mouth, the skin, the nose and the vagina.

“Although this is only the first step in making HMP medically useful, we already have learned surprising things about the diversity and complexity of the microorganisms that live in and on our body,” said Jane Peterson, Ph.D., associate director of the NHGRI Division of Extramural Researcher and a leader of the HMP effort. “The next stages of this coordinated study will begin to associate the presence or absence of specific micro-organisms with various states of health and illness.”

One of the primary goals of the HMP reference collection is to expand researchers' ability to interpret data from metagenomic studies. Metagenomics is the study of a collection of genetic material (genomes) from a mixed community of organisms. Comparing metagenomic sequence data with genomes in the reference collection can help researchers determine whether they are novel or already existing sequences.

The initial stage of the HMP, which includes the current study, focused on bacteria, but future genome sequencing and human microbiome studies also will capture information about more complex microbes and viruses.

The effort so far also has allowed researchers to create a framework for data resources and standards. In addition, the project is supporting the development of innovative technologies and computational tools, coordination of data analysis, and an examination of some of the ethical, legal and social implications of human microbiome research.

• The Human Microbiome Project can be accessed at:

Researchers develop first genetic parts list of mouse hypothalamus

A Johns Hopkins and Japanese research team has generated the first comprehensive genetic “parts” list of a mouse hypothalamus, an enigmatic region of the brain – roughly cherry-sized, in humans – that controls hunger, thirst, fatigue, body temperature, wake-sleep cycles and links the central nervous system to control of hormone levels.

Flaws in hypothalamus development may underlie both inborn and acquired metabolic balance problems that can lead to obesity, diabetes, mood disorders and high blood pressure, according to a report on the study published 2 May in the advance online publication of Nature Neuroscience.

“Knowing how cells develop in this part of the brain will help us understand how they regulate behaviour, mood and metabolism,” says Seth Blackshaw, PhD, an assistant professor in the Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine.

The hypothalamus is one of the most diverse and complex parts of the brain, and having an index of the genes involved in producing its many cell types is a toolbox that researchers can use to manipulate the activity of brain cells by turning them on and off, or tracing their connections. This may ultimately lead to better diagnostic and treatment options for a variety of disorders.

“The study of hypothalamic development, particularly of cell specification, will help us to understand how hypothalamic neurons function to regulate behaviour and physiology,” says Blackshaw. “Because of when and where we saw certain genes turn on, we now have identified a set of candidate players that guide the assembly of the different parts of the hypothalamus and that specify the many individual cell types within it.

“We were able to use this data to find genes whose expression matched every individual hypothalamic nucleus and essentially assemble a jigsaw puzzle of gene expression patterns that completely covered the developing hypothalamus,” Blackshaw says. “Now that we have a complete set of molecular landmarks, along with an extensive molecular parts list, we can begin to learn how all these parts fit together to create this essential and highly complex brain region.” 

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