Post on 11-May-2015
transcript
SHORT TANDEM REPEATS
The heritable unit that may influence a
trait is called gene.
A gene is a strand of DNA that is a part of vary long and compacted string of DNA called a
Chromosome.
An important reference
point along this compacted
string(Chromosome) is called Centromere.
The distance from a gene to the
centromere is referred to as the gene’s locus
or map location.
Allele
is one of a series of different forms of a gene.
“Polymorphisms are DNA sequences that differ from the sequences of a
majority of a population but are still shared by a certain percentage”.
Polymorphic DNA in humans is great due to the relatively large size of our
genome. 98% of which does not code for
genes.
It is estimated that genome sequences
differ by one nucleotide every 1000–1500 bases.
These single nucleotide differences, or single nucleotide polymorphisms (SNPs), may occur in gene-coding regions as well as intergenic sequences.
Polymorphisms are inherited in a mendelian fashion, and locations
of many polymorphisms in the genome are known. Therefore, polymorphisms can be used as landmarks, or markers, in
the genome to determine the location of other
genes.
PolymorphisPolymorphismm
Structure Detection Detection MethodMethod
RFLPRFLP One or more One or more nucleotidenucleotidechanges that changes that affectaffectthe size of the size of restrictionrestrictionenzyme enzyme productsproducts
Southern blotSouthern blot
VNTRVNTR Repeats of 10–Repeats of 10–50 base50 basesequences in sequences in tandemtandem
Southern blot,Southern blot,PCRPCR
STR Repeats of 1–10 basesequences in tandem
PCR
SNPSNP Alterations of a Alterations of a singlesinglenucleotidenucleotide
Sequencing, Sequencing, otherother
Repeats of 1–10 base sequences in tandem. AGCT. Occasionally, STRs contain repeat units with altered sequences. Microvariants repeat units missing
one or more bases of the repeat. In contrast to VNTRs, the smaller
STRs are efficiently amplified by PCR.
The amount of specimen required for STR analysis by PCR is reduced from
1 μg to 10 ng, a key factor for forensic analysis.
STRs within genes are designated according to the gene name.
for example, TH01 is in intron 1 of the human tyrosine hydroxylase gene on chromosome 11, and TPOX is in
intron 10 of the human thyroid peroxidase gene on chromosome 2.
STR alleles are identified by PCR
product size. Primers are designed to produce amplicons 100–400 bp in which
the STRs are embedded. The sizes of the PCR products
influenced by the number of embedded repeats.
If one of each primer pair is labeled with a fluorescent marker, the PCR
product can be analyzed in fluorescent detection systems. Silver-stained gels may also be used; however, capillary electrophoresis with fluorescent dyes is the preferable method, especially for high throughput requirements.
TEST RESULTS
DNA testing results in peak or band patterns that must be converted to genotype (allele identification) for the comparison of result between laboratories
STR locus genotype is defined by number of repeats in the alleles.
Microvariants alleles containing partial repeats units are indicated by the number of complete repeats followed by decimal points and then the number of bases in the partial repeats.
Y-STR
Y-STR are represented only once per genome and only in the male.
A set of Y-STR alleles comprises a haplotype.
because the Y chromosome cannot change the information (recombine) with another Y chromosome.
Thus ,marker alleles on the Y chromosome are inherited from generation to generation in a single block.
Significance
Provide marker loci for Y chromosome, or surname, tests to determine ancestry.
Linkage analysis
Because the location of many STRs in the genome are known, these structure can be used to map gene. especially those genes associated with disease.
Three basic approaches are used to map genes,
1. Family history. 2. Population studies.3. Sibling analysis.
Quality assurance for surgical section using STR.
Proper identification and assurance of uncontamination.
Confirmation of the tissue origin by multiplex PCR