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