Gene Databases

Gene databases:

Entrez Gene is a searchable database of genes, from RefSeq genomes, and defined by sequence

Molecule Pages: A comprehensive signaling database
The Molecule Pages is a database of keys facts about proteins involved in cellular signaling. It currently covers over 3,700 proteins.

OMIM, Online Mendelian Inheritance in Man
This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere.

UniProt (Universal Protein Resource)
UniProt (Universal Protein Resource) is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.


New Gene-Hunting Tricks

Researchers in the United States and France announced a surprising discovery: a single genetic variation is responsible for 18 to 37 percent of Parkinson's disease cases in Ashkenazi Jews and North African Arabs.
The discovery of the gene variation, which researchers think originated in a single person in the Middle East approximately 2,000 years ago, is important in understanding the causes of Parkinson's. It also reflects a growing tactic used by those hunting for the causes of diseases.

More and more scientists are studying populations of specific ancestry in order to hunt down genes linked to complex diseases.
Population geneticists are particularly enthusiastic about studying the genetic signatures of two types of communities: so-called "founder" populations, such as Ashkenazi Jews and French Canadians, in which only a few ancestors contributed to the population.
Says David Reich, a geneticist at Harvard Medical School in Boston. "In these populations, the genome comes in big chunks of shared ancestry."
That makes genetic studies more efficient, because scientists have to sift through fewer chunks of DNA.

While gene testing for diseases that have no known cure, such as Parkinson's, is controversial, Laurie J. Ozelius, a molecular geneticist at Albert Einstein College of Medicine of Yeshiva University in the Bronx, who was involved in the research, says testing still could have some advantages. "People who come to the doctor [with symptoms of Parkinson's] already have a lot of degeneration. Now we can look at [earlier] stages of the disease," she says. "If we find treatments that slow the disease, it's better to identify a gene carrier so we can start the treatment earlier."

The Impact of Emerging Technologies: New Gene-Hunting Tricks - Technology Review

Intensive Efforts To Determine Genetic, Environmental Roots Of Diseases

The Department of Health and Human Services (HHS) recently announced the creation of two new, closely related initiatives to speed up research on the causes of common diseases such as asthma, arthritis and Alzheimer's disease.

The Genes and Environment Initiative (GEI), a research effort at NIH to combine a type of genetic analysis and environmental technology development to understand the causes of common diseases.
GEI will have two main components: a laboratory procedure for efficiently analyzing genetic variation in groups of patients with specific illnesses and a technology development program to devise new ways of monitoring personal environmental exposures that interact with genetic variations and result in human diseases.

The proposed federal funding level will enable GEI to perform genetic analysis - or genotyping - studies for several dozen common diseases.

At the same time, a public-private partnership between NIH, FNIH, which is a non-profit foundation established by Congress to support the mission of the NIH; Pfizer and Affymetrix is being created to further accelerate this important research on the genetic association studies.
The new partnership, called the Genetic Association Information Network (GAIN), is being launched with a $5 million donation from Pfizer to set up the management structure and $15 million worth of laboratory studies to determine the genetic contributions to five common diseases.

The genetic analysis of both GAIN and GEI will focus on the alternative spellings - called single nucleotide polymorphisms or SNPs - that normally occur in the order of the 3 billion DNA base pairs or letters that make up a person's genome. SNPs are like single-letter misspellings of a word. Most of these genetic variations are biologically meaningless. But a small fraction of these SNPs alter the function of a gene - often only slightly. The combination of many slightly altered genes may significantly increase the risk of a specific disease, but identifying such a complex set of genetics changes is challenging. Finding these disease-causing variants is one of the highest priorities of current biomedical research.

"Virtually all diseases have a hereditary component, transmitted from parent to child through the three billion DNA letters that make up the human genome," said Francis S. Collins, M.D., Ph.D., Director of the National Human Genome Research Institute at NIH and chairman of the GAIN Steering Committee and co-chairman of the NIH Coordinating Committee for GEI.

ScienceDaily: Intensive Efforts Launched To Determine Genetic And Environmental Roots Of Common Diseases

National Institute of Environmental Health Sciences


Atmericans Prefer to Leave Child's Sex to Chance, Survey Finds

Most people would not choose the sex of their child if given the option, according to a new nationwide survey. The study is the first to examine the demand and preferences for sex selection among the U.S. general population.

"We found that only 8 percent of people would use pre-implantation sex selection for non-medical reasons," said Dr. Tarun Jain, assistant professor of reproductive endocrinology and infertility at University of Illinois at Chicago and senior author of the report.

Pre-conception sex selection using sperm-separation technology is currently available in the United States as part of an FDA-approved clinical trial. The technique is not without controversy, but is expected to become more readily available to consumers at the completion of that trial.

Only 12 percent would use sex selection technology if it were available in any doctor's office, if it required only a single cycle of intrauterine insemination, and if it were covered by health insurance.

Even if it were possible to choose the sex of a child simply by taking a "blue pill" for a boy or a "pink pill" for a girl, only 18 percent of respondents indicated they would do so. The rest were opposed or undecided.

Jain cautioned that the results of this survey do not apply to other countries, where there may be legitimate concerns about sex selection leading to an imbalance of the sexes.

University of Illinois Medical Center:Americans Prefer to Leave Child's Sex to Chance, Survey Finds


Backwards DNA Associated with Lukemia

When otherwise normal DNA adopts an unusual shape called Z-DNA, it can lead to the kind of genetic instability associated with cancers such as leukemia and lymphoma, according to a study by researchers at The University of Texas M. D. Anderson Cancer Center.

Interestingly, these sequences prone to forming Z-DNA are often found in genetic “hot spots,” areas of DNA known to be prone to the genetic rearrangements associated with cancer. About 90 percent of patients with Burkitt’s lymphoma, for example, have DNA breaks that map to regions with the potential to form these odd DNA structures.

Imagine untwisting the DNA ladder and then winding it up the other way. The result is a twisted mess with segments jutting out left and right, and the all important base pairs that hold the DNA code zigzagging in a jagged zipper shape. Scientists call this left-hand twist Z-DNA. This is a far cry from the graceful right-hand twisted helix that has become an iconic symbol of biology.

Analysis of the genome reveals that DNA sequences prone to forming the Z-DNA structure occur in 0.25 percent of the genome.

Since formation of Z-DNA is naturally occurring and can exist in the genome, the scientists next want to understand why cells can sometimes process the structure without creating double-stranded breaks. They also want to know why certain places in the genome become “hot spots” for these breaks, while other seemingly similar areas do not.

M. D. Anderson Cancer Center - News Release - When Good DNA Goes Bad

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