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The sleep/circadian rhythm SNP gene array initiative
Video recording of DAM 'sleep' bout
Penn Center for Sleep and Respiratory Neurobiology
The Sleep/Circadian Rhythm SNP Gene Array Initiative

In a joint initiative on the “feasibility of a sleep/circadian rhythms gene chip” at the NIH workshop held in Bethesda, MD on April 10-12, 2008 (see Workshop flyer), the group strongly endorsed the development of a sleep/circadian rhythm SNP gene array chip.

An SNP array is a type of DNA microarray which is used to detect polymorphisms within a population. A single nucleotide polymorphism (SNP), a variation at a single site in DNA, is the most frequent type of variation in the genome. There are around 10 million SNPs that have been identified in the human genome. As SNPs are highly conserved throughout evolution and within a population, the map of SNPs serves as an excellent genotypic marker for research.

The most important application of an SNP array is in determining disease susceptibility or resistance. In sleep research, for example, the sleep/circadian rhythm SNP gene array chip could be used to indentify gene variants conferring risk for circadian rhythm disorders or in differential susceptibility to sleep deprivation.

To spearhead the process of developing of a sleep/circadian rhythm SNP gene array chip, the SRS Presidential Task Force on Genetics and Sleep was established. The members of the Task Force are:

1. Joseph Bass, Northwestern University
2. Mary Carskadon, Brown University
3. Chiara Cirelli, University of Wisconsin-Madison
4. Thomas Kilduff, SRI International
5. Mirek Mackiewicz, University of Pennsylvania
6. Emanuel Mignot, Stanford University
7. Allan Pack, University of Pennsylvania (Chair of the Task Force)
8. Susan Redline, Case Western Reserve University
9. David Rye, Emory University
10. Clifford Saper, Harvard University
11. Joseph Takahashi, Northwestern University
12. Fred Turek, Northwestern University
13. Phyllis Zee, Northwestern University

The Task Force is charged with four tasks:

1. Determination of whether there should be a specific gene chip identified with SNPs from a selection of genes that are likely to be involved in sleep and circadian disorders, which can be used to screen well characterized clinical populations for specific gene mutations. If so, how many genes should be represented on the chip, how many SNPs, and what should those be? Should the NIH be encouraged to assist the sleep community with the development and distribution of these Sleep Gene Chips for the use by a broad range of clinical researchers?

2. Determination of the current status of research definitions for all sleep disorders. If applicable, propose a methodology that could be used to develop phenotypic definitions that would be used internationally in studies of genetics of sleep.

3. Determination of whether the NIH should be encouraged to establish a nationwide system of Sleep Centers that would agree on standardized ways to phenotype patients with sleep and circadian disorders. If so, what types of clinical information (history, physical exam, basic laboratory tests) should be collected in a standardized way? What types of specialized sleep studies should be done to establish the diagnoses, and are there standardized ways in which this could be collected for comparison across centers?

4. Determination of the best method, going forward, to provide the underpinnings for a nationwide Genetics and Sleep Initiative. What would be the best structure for such and initiative? Can this be done with private funds, or will it require public funding? If this becomes so large it could only be funded by the NIH, what should our strategies be in encouraging and solidifying that support? Should there be an international component and if so how would that work if the US component were NIH sponsored?

The written recommendations of the Task Force will be presented to the President of the Sleep Research Society no later than February 14, 2009.

Based on the recommendations provided by the participants of the NIH workshop, the initial working group that formed thereafter and the current Task Force members, a list of potential candidate genes for the SNP sleep/circadian rhythms gene chip was developed (see attached file).

The following classes of genes are currently included on the list:
a. Genes identified in human studies where polymorphisms are associated with different sleep/circadian phenotypes.
b. Genes identified in studies in model systems (rat, mice, fruit flies etc.) where variants affect sleep/wake circadian phenotypes and response to sleep deprivation.
c. Other genes in signaling pathways involving genes in (a) and (b).
d. Clock genes.
e. Genes for neuronal circuitry—neurotransmitters, neurotransmitter receptors, relevant enzymes, relevant transporters.
f. Selected genes identified in microarray studies as being differentially expressed in sleep wakefulness or after sleep deprivation. Priority should be given to genes found in more than one microarray study (in the same species or different species).
g. Selected genes for relevant metabolic pathways.

You can comment on the sleep/circadian rhythms gene chip, propose additional genes or suggest a gene be removed from the list by sending e-mail message to: mirekmm@mail.med.upenn.edu.

To learn more about a similar initiative in the cardiovascular field (i.e., IBC chip) follow this link: bmic.upenn.edu/cvdsnp/index.php