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Str

Short Tandem Repeats (STRs) are polymorphic microsatellites found in eukaryotic genomes, particularly in humans, where they make up about 3% of the genome. They are classified by length (e.g., dinucleotides, trinucleotides) and pattern (simple, compound, complex) and are crucial in forensic DNA analysis, especially for distinguishing male DNA in mixed samples. STRs offer advantages over traditional VNTRs, including better sensitivity for degraded samples and applications in paternity testing, contamination detection, and cancer research.

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Str

Short Tandem Repeats (STRs) are polymorphic microsatellites found in eukaryotic genomes, particularly in humans, where they make up about 3% of the genome. They are classified by length (e.g., dinucleotides, trinucleotides) and pattern (simple, compound, complex) and are crucial in forensic DNA analysis, especially for distinguishing male DNA in mixed samples. STRs offer advantages over traditional VNTRs, including better sensitivity for degraded samples and applications in paternity testing, contamination detection, and cancer research.

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prvnkumar112233
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STR (Short Tandem Repeats)

Genomes of eukaryotes are full of repeated DNA sequences. These sequences are present in
various sizes. They are usually named according to the length of the core repeat unit and the
number of adjacent repeat units or complete length of the repeat region. There might be
several hundred to thousand bases in core repeats of long repeat units. Those regions of
DNA which have short repeats (2-6 bps in length) are known as Short Tandem Repeats
(STRs). These are highly polymorphic microsatellites. The center of the chromosome is
surrounded by STRs.

Thousands of polymorphic microsatellites have been discovered in human DNA. Only 3% of


human genome comprises of Short Tandem Repeats. These are dispersed throughout
the genome and are present after every 1000 nucleotides on the average.

Figure 1: 13 CODIS core STR loci with chromosomal position

Figure 2: Comparison of crime scene and suspect DNA


Types of Short Tandem Repeats
Types of short tandem repeats on the basis of length:

i. Dinucleotides: They have two nucleotides which are repeated next to each other
again and again.
ii. Trinucleotides: They have three nucleotides which are repeated next to each other
again and again.
iii. Tetranucleotides: They have four nucleotides which are repeated next to each other
again and again.
iv. Pentanucleotides: They have five nucleotides which are repeated next to each other
again and again.
v. Hexanucleotides: They have six nucleotides which are repeated next to each other
again and again.

Types of short tandem repeats on the basis of pattern:

i. Simple repeats: Identical length and sequence are present in simple repeats.
ii. Compound repeats: Two or more adjacent simple repeats are present in compound
repeats.
iii. Complex repeats: Several repeat blocks of variable unit length and variable
intervening sequences are present in complex sequences. Complex repeats are not
commonly used in forensic DNA typing because of the difficulties with measurement
variability between laboratories and allele nomenclature.

Y-STR

These are Short Tandem Repeats present on male specific Y chromosome. Short arm of Y
chromosome comprises of coding genes which are responsible for spermatogenesis and other
male related functions and in determination of male sex. Among unrelated males, these Short
Tandem Repeats are polymorphic. They are inherited from father (paternal line) and show
little change through generations. They are mainly used to examine sexual assault evidence in
forensic laboratories. In such cases female as well as male DNA will be present in vaginal
swabs. To separate female components from male components differential extraction is used.
However, sometimes separation of male and female components of DNA is not complete as a
result male component also contains female component. In such cases during amplification of
male DNA, female DNA also undergoes amplification and can even mask the male DNA
which in turn makes the autosomal STR analysis difficult. This masking does not occur while
examining Y-STRs. Due to absence of Y STR in female sample and presence of Y-STR in
male sample, the culprit in case of sexual assault can be linked to the crime. Y-STRs are also
useful in non-sexual assault cases where the evidence materials contain mixed samples of
several males. Identification of all males can be done through Y-STR testing.
Mini-STR

Short tandem repeat testing is not successful in case of highly degraded DNA samples or
which are limited in quality or quantity. In such situations only partial STR profile may be
obtained due to drop out of STR alleles. Such partial DNA profiles do not provide enough
information in forensic cases.

Use of mini-STRs is an alternative approach to such cases. For mini STR analysis, specially
designed primers are used which target the mini - STR for amplification. Mini-STR typing
helps in obtaining DNA profile even from highly degraded samples.

Characteristics of STRs selected for Human Identification


It is important to have DNA markers which show maximum variation so that they can be
used for human identification. A large number of tetra-nucleotide short tandem repeats have
been discovered which can be used for human identification. Y chromosome STRs are used
for analyzing male-female mixtures from sexual crimes and in cases where more than one
male are involved in the crime.

Following characteristics have been considered for selection of short tandem repeat loci
which have been validated for identification:

i. High discriminating power, usually >0.9, with observed heterozygosity >70%.


ii. The chromosomal locations chosen should be separate to make sure that closely
linked loci are not chosen.
iii. The results should be reproducible and robust when multiplexed with other markers.
iv. Formation of stutter products (small peaks formed that are several bases smaller than
STR peaks resulting from PCR process when short tandem repeat loci are copied by a
DNA polymerase) should be low.
v. Mutation rate should be low.
vi. For analysis of degraded samples alleles with length in range of 90-500 bps should be
preferred.
vii. The short tandem repeat markers should be chosen from separate chromosome for
forensic DNA typing to avoid any problem with linkage between markers.
Figure 3: Human identification using STR

Advantages of STRs over conventional VNTRs

There are several advantages of PCR- based STRs over conventional RFLP technique of
VNTRs (Variable Number of Tandem Repeats):

i. Multiplexing is possible with a narrow allele size range.


ii. Allelic dropouts from preferential amplification of smaller alleles are reduced due to
narrow allele size.
iii. STR can generate small PCR products which help in recovering the information from
degraded DNA samples.
iv. The stutter product formation is reduced as compared to dinucleotide repeats which
help in interpretation of sample mixtures.

Applications of STRs

Short tandem repeats (STRs) are small regions in DNA which are analyzed for various
purposes. These are used in forensic testing in crime cases, in missing person cases and
paternity disputes. Besides, STRs are used for following purposes also:

a) Detection of contamination of tissue samples

To understand various normal or abnormal physiological or cellular functions, tissues are


dissected and analyzed. In cases where sample’s identity is disputed, comparison of STR
profile of tissues can be done with reference sample to determine sample’s identity. This
analysis is used to detect sample contamination. The profile of contaminated sample appears
as mixed STR profile. Due to sensitivity of STR analysis, it can create full profiles from less
than 100 pg of DNA. This sensitivity allows detection of very little quantities of
contaminating cells or tissues.

b) Detecting Maternal Cell Contamination and Fetal Aneuploidy


Prenatal samples are contaminated with maternal cells. Before assaying prenatal fetal sample
short tandem repeat analysis is performed to make sure prenatal fetal sample is not
contaminated with maternal cells. This is an important consideration where maternal DNA
can interfere with results. This analysis is also used to detect fetal blood in maternal blood.
STR analysis is used to detect fetal chromosomal abnormalities like trisomy or aneuploidies.
Fetal gender can be determined using dimorphic Amelogenin locus which distinguishes XX
(female) and XY (male) individuals.

c) Cancer Research
Genetic mutations result in unregulated growth of abnormal cells. This unregulated growth of
cells is known as cancer. Genetic mutations generally occur in tumor suppressor genes or
other proto-oncogenes. To understand all the details of development and progression of
cancer it is necessary to study the associated genetic changes. The genetic changes can be
determined using short tandem repeat loci.

d) Determining Twin Zygosity


To analyze whether the twins are monozygotic or dizygotic, short tandem repeat analysis is
used. STRs are also used for examining the rate of monozygotic twin or triple births as a
result of artificial techniques.

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