Studies Conducted in Single Nucleotide Polymorphism in B GalT-I

Single Nucleotide PolymorphismDNA sequence variations that occur when a single nucleotide (A, T, C, or G) in the genome sequence is altered. Each individual has many single nucleotide polymorphisms that together create a unique DNA pattern for that person. SNPs promise to significantly advance our ability to understand and treat human disease.

Within a population, SNPs can be assigned a minor allele frequency - the ratio of chromosomes in the population carrying the less common variant to those with the more common variant. Usually one will want to refer to SNPs with a minor allele frequency of ≥ 1% (or 0.5% etc.), rather than to "all SNPs" (a set so large as to be unwieldy). It is important to note that there are variations between human populations, so a SNP that is common enough for inclusion in one geographical or ethnic group may be much rarer in another.

SNPs may fall within coding sequences of genes, noncoding regions of genes, or in the intergenic regions between genes.

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European population substructure

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SNPs within a coding sequence will not necessarily change the amino acid sequence of the protein that is produced, due to redundancy in the genetic code. A SNP in which both forms lead to the same protein sequence is termed synonymous - if different proteins are produced they are non-synonymous. SNPs that are not in protein coding regions may still have consequences for gene splicing, transcription factor binding, or the sequence of non-coding RNA.

SNPs make up 90% of all human genetic variations, and SNPs with a minor allele frequency of ≥ 1% occur every 100 to 300 bases along the human genome, on average, where two of every three SNPs substitute cytosine with thymine.

Variations in the DNA sequences of humans can affect how humans develop diseases, respond to pathogens, chemicals, drugs, etc. As a consequence SNPs are of great value to biomedical research and in developing pharmacy products. Because SNPs are inherited and do not change much from generation to generation, following them during population studies is straightforward. They are also used in some forms of genealogical DNA testing.

Detection of SNPA convenient method for detecting SNPs is restriction fragment length polymorphism (SNP-RFLP). If one allele contains a recognition site for a restriction enzyme while the other does not, digestion of the two alleles will give rise to fragments of different length. Currently, the study of existing SNPs is most easily studied using microarrays. Microarrays allow the simultaneous testing of over a thousand separate SNPs and are quickly screened by computer.

Uses of SNPHelps in identifying disease genesSNPs will catapult into the era of personalized medicine, when pharmacogenetics will enable physicians to prescribe drugs based on detailed knowledge of our genotypes.

SNPs are used as genetic marker-the equivalent of landmarks in the human genome. They help in keeping record of the "recombination segments" -blocks of 3000-30,000 base pairs in which SNPs tend to be associated with one another. These blocks are mixed and matched by the process of recombination.

These markers provide:1.Information about a patient's risk for disease2.Insight into the disease process3.Protein targets for novel drug therapiesBenefits of Using SNPs1.A person's SNP pattern is highly unlikely to change over time or as a result of disease.

2.SNP data can be collected from any tissue in the body (not just from diseased tissue).This allows a larger number of samples to be obtained (especially controls) since faster and less invasive procedures are used.

Challenges of Using SNPs1.There are now over one million SNPs known but measuring them all is typically cost-prohibitive. SNP data contain measurements for only a small fraction of known SNPs (typically a few thousand). If prior knowledge is available, focus the SNPs collected to particular region(s) of the genome. Otherwise, choose SNPs to give good overall coverage of the genome.

2.SNP data commonly contain missing values. This can adversely affect many algorithms used for classification tasks. When choosing an algorithm to use, this must be taken into consideration in order to choose an appropriate one.

3.Proper and accurate mining of the SNP data requires instrumentations with super computing facility. Hence, the cost factor takes center stage.

ß (1,4) galactosyltransferaseß (1,4) galactosyltransferase (b4GalT-I) is a constitutively expressed, trans-Golgi resident, type II membrane-bound glycoprotein that catalyzes the transfer of galactose to N-acetylglucosamine residues, forming the b4-N-acetyllactosamine (Galb4-GlcNAc) or poly-b4-N-acetyllactosamine structures found in glycoconjugates (15, 16).

ß4-Galactosyltransferase enzymatic activity is widely distributed in the vertebrate kingdom, in both mammals and nonmammals, including avians (17) and amphibians (unpublished observations) (15).

ß4GalT-I functions in lactose biosynthesis. In mammals β4GalT-I has been recruited for a second biosynthetic function, the tissue-specific production of lactose which takes place only in the lactating mammary gland. The synthesis of lactose is carried out by the protein heterodimer assembled from b4GalT-I and the mammalian protein a-lactalbumin (15). The notion that the β4GalT-I gene has been recruited from the nonmammalian vertebrate pool of constitutively expressed genes for lactose biosynthesis is supported by the observation that the β4GalT-I ortholog from chicken (15) can also functionally interact with a-lactalbumin in vitro.

The presence of five additional β4GalT-I related sequence groups (genes) in the human genome, or a total of six genes when β4GalT-I is included. The family members are designated as β4GalT-I, -II, -III, -IV, -V and -VI, where β4GalT-I represents the previously well-characterized β4GalT recognized to function in lactose biosynthesis (15).

The following diagram indicates the chromosome number and location of each of the gene family members.

FIG 4: Schematic representation of the human 4GalT family members. The transcript representing the gene located on human chromosome 9p13 (4GalT-I) is shown at the top. The five additional family members (4GalT-II through -VI) are shown with their chromosomal location and mRNA size (from Northern blot analysis) noted. The open box indicates coding sequence; the first three numbers indicate the number of amino acids in the stem region, catalytic domain and full-length coding region, respectively. The total number of nucleotides in the coding region is also shown. Since the full-length 5'-untranslated region of each homolog has not been determined, this region is depicted by a dashed line with the number of nucleotides obtained from the most 5'-clone indicated. The thin line at the right indicates the 3'-untranslated region with the number of nucleotides, available from the EST clones shown. As three of the homologs (4GalT-II,-V, and -VI) do not contain a consensus polyadenylation signal sequence (An), the predicted length of the 3'-untranslated region is given in italics. The sequence of 4GalT-II and -VI that was obtained by RACE, is 5'of the solid arrowhead. Superimposed on each mRNA is the position of the transmembrane domain (solid box) and the position of each Cys residue. The position, in 4GalT-I of the only intramolecular disulfide bond, Cys130 and Cys243 is indicated. Cys338 in the 4GalT-I sequence is replaced by a Tyr in each family member.

Identification of large family of ß (1,4) galactosyltransferaseSeveral groups independently used the emerging EST database information in 1997 to identify a group of human cDNA sequences with similarities to the classical ß4Gal-T (designated ß4Gal-T1) (18, 19). Within 1 year, five novel human ß4Gal- T genes designated ß4Gal-T2 to -T6 were identified cloned, and enzymatic functions of their recombinant proteins demonstrated (18, 19).The two genes, ß4Gal-T5 and -T6, were identified by traditional cloning strategies as well as computer cloning (18). Recently, a seventh homologous gene designated ß4Gal-T7 was identified by the computer cloning strategy (18, 20). Its homology has not been established yet.

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Figure 3

Haplotypes from comparison of SNPs in a part of th...

Figure legend in source article (CC-by-2.0): "Geno...