NCBI has a fairly well developed database of SNPs. Point your browser at http://www.ncbi.nlm.nih.gov/SNP/ In the upper search bar, we'll look for SNP entries for COMT (high and low activity allele), BRCA (cancer gene), and the CCR5 allele that effectively imparts immunity to HIV.
Please note that as of August 2005, these three examples are a work in progress, but they should help you in your exploration of NCBI.
Each of these examples involves a larger question, of biological problem posing. Additionally, each of these examples represents a problem of extreme interest and significance. Some background information is shown below, possibly as motivation to interest you in each example.
COMT - The COMT gene has two forms, soluble (S) and membrane bound (M) . More importantly, there are two alleles for COMT, a high activity allele, and a low activity allele. The alleles are distinguished by a Val / Met substitution at position 158. See the text file marked [V or M]. COMT catalyses the deactivation of catechol neurotransmitters in the brain, and several research papers have linked variations of the COMT enzyme with schizophrenia, heroin addiction, major depression, and other syndromes. You'll really get to know rs4680 in this exercise!
COMT in high activity is associated with a propensity to feel pain more acutely, and the low activity allele with a high tolerance for pain. It's role in depression and schizophrenia is still not certain, as both these 'syndromes' are multigenic, and likely have further environmental influences.
SNP Data Formats:
An overview of data fields used in SNP can be found from this link. Take some time to review the material before proceeding to the exercises.
COMT SNP exercise:
From http://www.ncbi.nlm.nih.gov/SNP/ type COMT into the search field. The display defaults to graphic presentation of SNP entries, which isn't particularly easy to navigate. You can follow a link to protein structure. From that page, scroll down to amino acid position 108. That's the Val - Met substitution (108 and 158). Take a look at all the other information on this page, and consider how many different forms of COMT might exist. Follow the link to the Val - Met substitution (rs4680). There is a lot of information on that page, take your time and sift through it.
BRCA SNP exercise:
Certain forms of breast cancer occur from a single nucleotide change in an intergenic region. You can find detailed information about BRCA1 from a few links within NCBI, including the publication genes and disease, cancer. We'll look for that SNP by searching dbSNP, and using the gene name BRCA1. The information from this page is complicated. Look carefully at the related links to SNP500CANCER, and follow that link. The link to rs1060915 (reference SNP for SNP500CANCER above) is complex, and shows a full SNP entry. Take some time to study it. You should also look at the GeneCards link for BRCA1, which will link you to several other key databases.
Read Single Nucleotide Polymorphisms and Linkage Disequilibrium Mapping for more information on SNPs which has a section on the BRCA1 and BRCA2 mutation, and other good SNP explainations.
Questions:
Can you find the SNP associated with the fatal form of BRCA1? Follow this link to an article on assessing BRCA1 and BRCA2 screening. You can download the PDF version of this article by right-clicking on this link. You can also input SNP rs1060915 in Perlegen's Genotype browser which will return this page http://genome.perlegen.com/cgi-bin/gbrowse/build34?name=rs1060915 Go back to GeneCards and look at the entries for BRCA1 and BRCA2 and scroll down to the bottom of each page to where the SNPs are listed. Try accessing these records.
HIV resistance CCR5-delta 32 exercise:
Several hundred years ago, as the black plague ravages Europe, a mutation in the CCR5 chemokine receptor afforded some individuals a greater chance of survival. Several hundred years later, the same mutation, present in roughly 11% of alleles, affords homozygous individuals (1.2%) with virtual HIV immunity. To explore this mutation, point your browser at NCBI PubMed, and search using the terms 'HIV resistance CCR5-delta 32' . The top link return is 'Evaluating plague and smallpox as historical selective pressures for the CCR5-Delta 32 HIV-resistance allele' can be accessed from this link. Note the link to the free full text publication.
From the full-text article in PubMed Central:
The CCR5 chemokine receptor is fundamental to establishing HIV-1 infection. The receptor is exploited by HIV strains that predominate during the primary phase of infection to gain entry into immune system cells, including macrophages and CD4+ T cells (1-3). The CCR5-?32 deletion confers resistance to HIV-1 by preventing expression of the receptor on the cell surface (4-11). This allele provides almost complete resistance to HIV-1 in the homozygous state (4, 7, 12) and partial resistance with slower disease progression in the heterozygous state (4, 5, 8, 12). Interference with the expression of the CCR5 receptor also appears to have promise in the treatment of HIV (13).
Questions?
Double-stranded RNAs ˜21 nucleotides long [small interfering
RNA (siRNA)] are recognized as powerful reagents to reduce the expression of
specific genes. To use them as reagents to protect cells against viral infection,
effective methods for introducing siRNAs into primary cells are required. Here,
we describe success in constructing a lentivirus-based vector to introduce siRNAs
against the HIV-1 coreceptor, CCR5, into human peripheral blood T lymphocytes.
With high-titer vector stocks, >40% of the peripheral blood T lymphocytes
could be transduced, and the expression of a potent CCR5-siRNA resulted in up
to 10-fold inhibition of CCR5 expression on the cell surface over a period of
2 weeks in the absence of selection. In contrast, the expression of another
major HIV-1 coreceptor, CXCR4, was not affected. Importantly, blocking CCR5
expression by siRNAs provided a substantial protection for the lymphocyte populations
from CCR5-tropic HIV-1 virus infection, dropping infected cells by 3- to 7-fold;
only a minimal effect on infection by a CXCR4-tropic virus was observed. Thus,
our studies demonstrate the feasibility and potential of lentiviral vector-mediated
delivery of siRNAs as a general means of intracellular immunization for the
treatment of HIV-1 and other viral diseases.
White papers from above:
I have downloaded the two papers above. You can access them as follows:
Evaluating plague and smallpox as historical selective pressures for the CCR5-Delta 32 HIV-resistance allele (right click here).
Inhibiting HIV-1 infection in human T cells by lentiviral-mediated delivery of small interfering RNA against CCR5 (right click here).
This lesson is copyrighted using an Educational Common License, and may be used freely without restriction for academic purposes.
Robert D. Cormia