Introduction

Eukaryotic genomes are full of repeated DNA sequences.

They are designated by the length of the core repeat unit
and the overall length of the repeat region.
These regions are often called satellite DNA and may be
found surrounding the chromosomal centromere.
A core repeat unit for a medium length repeat, is referred
to as a minisatellite or VNTR and ranges in the length of 10
– 100 bps.
First defined as a class of tendem repeats in the 1980s.
DNA regions with a repeat units that are 2-10 bps in length
are called microsatellites/ simple sequence repeats (SSRs)/
short tandem repeats(STRs).
 Tandem repeats
Two important categories of tandem repeat have been used
widely in forensic genetics:
minisatellites, also referred to as variable number tandem
repeats (VNTRs); and
microsatellites, also referred to as short tandem repeats
(STRs).

The general structure of VNTRs and STRs is the same.

Variation between different alleles is caused by a difference

in the number of repeat units that results in alleles that are of
different lengths and it is for this reason that tandem repeat
polymorphisms are known as length polymorphisms
Variable Number Tandem Repeat
(VNTR’s)
A Variable Number Tandem Repeat (VNTR) is a location in a
genome where a short nucleotide sequence is organized as a
tandem repeat .
These can be found on many chromosomes , and often show
variations in length between individuals. Each variant acts as an
inherited allele , allowing them to be used for personal or
parental identification.
Their analysis is useful in genetics and biology research,
forensics , and DNA fingerprinting .
A tandem repeat is a short sequence of DNA that is repeated in a
head-to-tail fashion at a specific chromosomal locus.
Tandem repeats are interspersed throughout the human
genome. Some sequences are found at only one site -- a single
locus -- in the human genome.
For many tandem repeats, the number of repeated units vary
between individuals. Such loci are termed VNTRs.
VNTR structure and allelic variation

In the schematic above, the rectangular blocks

represent each of the repeated DNA sequences at a
particular VNTR location. The repeats are tandem -
they are clustered together and oriented in the same
direction.
 USES
VNTRs have become essential to forensic crime investigations, via DNA
fingerprinting and the CODIS database.
When removed from surrounding DNA by the PCR or RFLP methods, and their
size determined by gel electrophoresis or Southern blotting, they produce a
pattern of bands unique to each individual.
When tested with a group of independent VNTR markers, the likelihood of two
unrelated individuals having the same allelic pattern is extremely improbable.

In analyzing VNTR data, two basic genetic principles can be used:
Identity Matching- both VNTR alleles from a specific location must match. If
two samples are from the same individual, they must show the same allele pattern.
Inheritance Matching- the VNTR alleles must follow the rules of inheritance. In
matching an individual with his parents or children, a person must have an allele
that matches one from each parent. If the relationship is more distant, such as a
grandparent or sibling, then matches must be consistent with the degree of
relatedness.
 RFLP
When DNA tests were first introduced in the late 1980’s,

most laboratories employed a method called RFLP analysis

(restriction fragment length polymorphism analysis).

RFLP uses enzymes to break the long strands of DNA into

shorter fragments (restriction fragments)

and separates these by length (using a process called

electrophoresis).
In a typical case, four to six different loci (each
containing a different length polymorphism) are
examined in this manner.
The full set of alleles identified in a sample is called its
DNA profile.
Because the probability of a "matching" pattern at any
locus is on the order of one in hundreds to one in
thousands,
and the probabilities of a match at the various loci are
assumed to be statistically independent,
the probability of a match at four or more loci is
generally put at one in many millions or even billions.
Forensic RFLP tests examine loci that contain highly
variable numbers of tandem repeats, or VNTRs.
A tandem repeat is an end-to-end duplication of a short
sequence of the genetic code.
Example:
If the DNA strand were a phonograph record, this would
be an area where the record skipped and repeated a
number of times before playing the rest of the tune.
The number of repetitions tends to vary from person to
person.
Consequently, when the DNA strands are broken into
fragments, and the fragments containing VNTRs are
measured, their length tends to vary from person to
person.
This variation is known as a length polymorphism.
RFLP – Restriction fragment length polymorphism
A restriction fragment whose length is variable because of the
presence of polymorphic restriction sites

Steps-

1. Isolation of DNA
2. Digestion of DNA with a restriction enzyme (micro-scissors)
3. Separation of DNA fragments on agarose gel
4. Transfer of DNA fragements from agarose gel to nitrocellulose
membrane
5. Hybridiation with radiolabelled probe
6. Visualisation of hybridised DNA with autoradiography
 RFLP
The DNA is broken into fragments by cutting it with one of
several restriction enzymes.
These enzymes act as "molecular scissors," cutting the DNA
strand at specific, known sites, and producing shorter fragments
known as restriction fragments.
For example, the restriction enzyme HaeI cuts only at the
sequence "AGGCCA" (which occurs randomly about once every
4,000 base-pairs).
The restriction enzymes chosen for forensic RFLP tests cut in
areas that flank the VNTRs.
The goal of the test is to measure the length of these VNTR-
containing restriction fragments,
hence the overall procedure is called restriction fragment length
polymorphism analysis.
Restriction Endonucleases
Also called restriction enzymes

1962: “molecular scissors” discovered in bacteria

3,000 enzymes have been identified,

around 200 have unique properties,
many are purified and available commercially
Nomenclature
Smith and Nathans (1973) proposed enzyme
naming scheme
three-letter acronym for each enzyme derived from the
source organism
First letter from genus
Next two letters represent species
Additional letter or number represent the strain or
serotypes
For example. the enzyme HindII was isolated from
Haemophilus influenzae serotype d.
Restriction Endonucleases
Named for bacterial genus, species, strain, and type

Example: EcoR1
Genus: Escherichia
Species: coli
Strain: R
Order discovered: 1
Few Restriction Enzymes
Target sequence
Enzyme Organism from which derived (cut at *)
5' -->3'
Bam HI Bacillus amyloliquefaciens G* G A T C C
Eco RI Escherichia coli RY 13 G* A A T T C
Hind III Haemophilus inflenzae Rd A* A G C T T
Mbo I Moraxella bovis *G A T C
Pst I Providencia stuartii CTGCA*G
Sma I Serratia marcescens CCC*GGG
Taq I Thermophilus aquaticus T*CGA
Xma I Xanthamonas malvacearum C*CCGGG
Restriction Endonucleases
Recognition sites have symmetry (palindromic)

“Able was I, ere, I saw Elba”

5’-GGATCC-3’
Bam H1 site:
3’-CCTAGG-5’
Restriction Endonucleases
Enzymes recognize specific 4-8 bp sequences

Some enzymes cut in a staggered fashion - “sticky ends”

EcoRI 5’…GAATTC…3’
3’…CTTAAG…5’

Some enzymes cut in a direct fashion – “blunt ends”

PvuII 5’…CAGCTG…3’
3’…GTCGAC…5’
Recognition Sequences

Each restriction enzyme always cuts at the same recognition

sequence.

Produce the same gel banding pattern (fingerprint)

Many restriction sequences are palindromic. For example,

5’ GAATTC 3’
3’ CTTAAG 5’
(Read the same in the opposite direction (eg. madam, race car…)
Sticky End Cutters
Most restriction enzymes make staggered cuts
Staggered cuts produce single stranded “sticky-
ends”
DNA from different sources can be spliced easily
because of sticky-end overhangs.
5’ P
- OH -
3’
HindIII ’
5
-P
H-
3’ O

EcoRI
Blunt End Cutters
Some restriction enzymes cut DNA at opposite base
They leave blunt ended DNA fragments
These are called blunt end cutters

AluI

HaeIII
Advantages
Highly polymorphic and reproducible

Present throughout the genome

The RFLP method of creating DNA profiles-
Extraction of DNA
The first step in DNA profiling is to extract the DNA from
nucleated cells of the evidence sample obtained during the
course of an investigation as well as from a reference sample
of tissue or blood from the person in question.
In order to obtain the DNA sample from the evidence, there
must be a blood sample, tissue, bone or commonly a semen
sample.
The DNA is extracted from the cell in a fairly simple series of
steps and the sample is chemically purified for use.
After extraction, laboratories typically estimate the
quantity of DNA in each sample.
The amount of DNA required for typing varies for different
procedures.
RFLP analysis requires the most DNA, typically 50-100 ng
(nanograms).
RFLP analysis requires DNA of high molecular weight.
If the DNA is too degraded, however, no test can type it.
The RFLP method of creating DNA profiles-
Fragmentation by restriction enzymes

Once DNA is extracted, proteins called "restriction enzymes" are

use to break long DNA molecules into shorter fragments by
cutting them at specific sequences of nucleotides.
When a tandemly repeated sequence occurs between two
restriction enzyme sites on a DNA molecule the length of the
resulting fragment will be determined in part by the number of
times that the sequence is tandemly repeated.
If the number of repeats differs from one person to the next (is
polymorphic) those differences in the length of the resulting
fragments can be used as identifying features in the following
steps of the procedure.
Generally speaking, restriction enzymes either cut DNA to yield
fragments of specific length (they generate a result) or they do not
(they generate no result) - it is not possible for one DNA profile to
be converted to another.
The RFLP method of creating DNA
profiles-Gel electrophoresis
Separating DNA fragments on the basis of their size was and
remains to be a very common practice for molecular biologists.
The basis of virtually all DNA size fractionation is gel
electrophoresis. In this process, DNA fragments are loaded onto
small indentations called "wells" at one end of a at gelatin surface
containing agarose gel.
One end of the gel is attached to a positively charged electrode
and at the other to a negatively charged electrode. Because DNA
is an intrinsically negatively charged molecule, it moves away
from the negative electrode and travels toward the positive
electrode.
Larger fragments of DNA have more difficulty traveling through
the gel's "matrix" (essentially a long series of sieves at a molecular
level) than smaller fragments which move more quickly.
Fragment sizes for RFLP analyses were typically in the range
of between 200 bp and 7,000 bp. One of the problems with
agarose gel electrophoresis is its ability to resolve fragments
that do not differ in size by at least 20 to 100 bp since such
fragments (especially fragments at the larger end of the
typical size range) move so similarly and because of
sometimes subtle differences in how quickly DNA moves in
one lane of a gel relative to another.
As a result, most sizing of fragments for forensic purposes
was done by "binning" - essentially saying that a fragment
could be said to fall within a certain size range and other
fragments that fell within the same size range were said "to
match."
This "match" would be declared even though the fragments
might actually have different numbers of tandem repeats and
could not have come from the same individual.
 Denaturation

Transfer
The RFLP method of creating DNA profiles-
Southern hybridization and visualization
After their trip through the gel, the double stranded DNA
fragments are chemically split into two strands,
separating their paired nitrogenous bases from each other
(A from T and C from G).
These fragments are then directly transferred from the gel
(which, like gelatin desserts, is difficult to handle and
preserve intact) onto a sheet of a paper-like substance
(usually either made of nylon or nitrocellulose) called a
“filter" or "membrane."
The separated DNA fragments are then permanently
attached to the filter either by exposure to ultraviolet light
or cross-linking chemicals.
The RFLP method of creating DNA profiles-
Hybridization
A restriction enzyme that recognizes a four nucleotide
long restriction site (like HaeIII mentioned above)
should find such a site once every 256 base pairs on
average if each of the nucleotides are equally represented
in a random sequence.
For a 3.2 billion nucleotide sequence such as that of the
human genome, cutting with such an enzyme results in
literally millions of fragments of a very wide variety of
sizes.
As a result, the gel electrophoresis of a restriction
enzyme digested human genome is best described as a
smear of fragments that contains no distinct bands.
 The particular bands of interest to forensic scientists are recognized
through the use of "probes" that seek out and bond with a locus of
interest and no other.
 The tendency for A's and T's to interact and for G's and C's to interact
allows single stranded DNA molecules to be designed that stick more
stably to complementary sequences of nucleotides attached to the
membrane of the Southern blotting step described above.
 Such probes can either be made through the use of recombinant
technology, or chemically synthesized.
 These probes were originally tagged with radioactive markers that made
it possible to determine where they had attached to a membrane but
safer and more convenient fluorescent markers are also now available.
 Probes that do not find a complementary sequence to which they can
bind are simply washed away while those that do bind give rise to a bar
code type of pattern that is characteristic of the VNTR DNA typing
methodology.
First application of DNA profiling in
a criminal investigation.
SLP was used to analyze samples. A
= hair roots from the first victim. B
= mixture of semen and vaginal
fluid from first victim. C = blood
from second victim. D = vaginal
swab from second victim. E =
semen stain on clothing from
second victim. S = blood from
suspect. Alleles (arrows) are
matched with the profiles of the
two cases but not with the suspect
profile.
Classes of VNTRs
There are two principal families of VNTRs:
microsatellites and minisatellites.
The former are repeats of sequences less than about 5 base pairs in
length (an arbitrary cutoff ), while the latter involve longer blocks.
Confusing this distinction is the recent use of the terms Short
Tandem Repeat (STR) and Simple Sequence Repeat (SSR), which are
more descriptive, but whose definitions are similar to that of
microsatellites.
VNTRs with very short repeat blocks may be unstable - dinucleotide
repeats may vary from one tissue to another within an individual,
while trinucleotide repeats have been found to vary from one
generation to another.
The 13 assays used in the CODIS database are usually referred to as
STRs, and most analyze VNTRs that involve repeats of 4 base pairs.
Summary
VNTR alleles are hypervariable regions of human
DNA that differ from each other in:
A. location of internal sites recognized by restriction
enzymes.
B. variable number of point mutations.
C. number of copies of an internally repeated DNA
sequence.
D. variable location on different chromosomes.
E. ability to hybridize with a specific single locus probe.
 Introduction
STRs are currently the most commonly analysed genetic polymorphism in forensic
genetics. They were introduced into casework in the mid-1990s and are now the
main tool for just about every forensic laboratory in the world – the vast majority
of forensic genetic casework involves the analysis of STR polymorphisms.
A short tandem repeat (STR) in DNA occurs when a pattern of two or more
nucleotides are repeated and the repeated sequences are directly adjacent to each
other. The pattern can range in length from 2 to 10 base pairs (bp) (for example
(CATG)n in a genomic region) and is typically in the non-coding intron The
number of repetitions varies from one person to another and a particular number
of repetitions is known as an allele of the marker.
A short tandem repeat polymorphism (STRP) occurs when homologous STR
loci differ in the number of repeats between individuals. By identifying repeats of
a specific sequence at specific locations in the genome, it is possible to create a
genetic profile of an individual. There are currently over 10,000 published STR
sequences in the human genome. STR analysis has become the prevalent analysis
method for determining genetic profiles in forensic cases.
They are scattered through out the genome and occur on average every 10,000
nucleotides.
Analysis and types of STR
Determine the flanking regions surrounding the repeats.
Design PCR primers, amplify the repeat region.
New STR markers are identified in 2 ways-
Search DNA sequence data bases for regions with more
than 6 or so contiguous repeat units, or
Performing molecular biology isolation methods.
The STR repeat sequences are named by the length of the
repeat unit. They are-
dinucleotides, trinucleotides, tetranucleotides,
pentanucleotides and hexanucleotides.
Tetranucleotide repeats are the most popular STR
markers for human identification.
Statistical Analysis of DNA
Simple Repeats
Identical length and sequence
 agat agat agat agat agat
Compound Repeats
Two or more adjacent simple repeats
 agat agat agat ttaa ttaa ttaa
Complex Repeats
Variable unit length & possible intervening seq
 agat agat aggat agat agat ttaacggccat agat agat
STR LOCI ALLELES

TPOX
THYROID PEROXIDASE
Chromosome 2
AATG repeat
6 to 13 repeats
TH01
TYROSINE HYDROXYLASE
Chromosome 11
TCTA repeat (Bottom strand)
4 to 11 repeats
Common microvariant 9.3
STR LOCI ALLELES
vWA
von Willebrand Factor
Chromosome 12
TCTA with TCTG repeat
10 to 22 repeats
D3S1358
Chromosome 3
AGAT with AGAC repeat
12 to 20 repeats
 13 CODIS Core STR Loci
with Chromosomal
Positions
TPOX

D3S1358

TH01
D8S1179
D5S818 VWA
FGA D7S820
CSF1PO

AMEL

D13S317
D16S539 D18S51 D21S11 AMEL
Forensic DNA Analysis

One Region of DNA

Sample 10 million copies
Buccal swab
Blood stain
Semen stain

PCR
Extraction

All DNA
Hundreds of
copies

PCR

16 Regions of DNA
10 million copies
This is what we want to
Run on Genetic Analyzer
do this week.
Short Tandem Repeats > Capillary Electrophoresis

12

If we race 2 alleles down the tube and measure

them.
DNA Detection > Fluorescent Label

DNA fragments are labeled with a fluorescent

dye.

Fluorescent Light

Laser

DNA
Short Tandem Repeats > Capillary Electrophoresis

12

We’ll add the dyes to our drawing.

Short Tandem Repeats > Capillary Electrophoresis
TPOX
Sample Size Allele
(base pairs)

194

206

We can determine the size of the fragments

(when compared to the size standard).
Short Tandem Repeats > Capillary Electrophoresis
TPOX TPOX
Size Allele Sample Size Allele
(base pairs) (base pairs)

186 7
190 8
194 9 194 9
198 10
202 11
206 12 206 12
210 13

The sizes are compared to the allelic ladder to

determine the alleles.
Short Tandem Repeats > Capillary Electrophoresis

From TPOX
9

12

From vWA
10

11

What if we wanted to look at 2 loci at the same

time?
Short Tandem Repeats > Capillary Electrophoresis

9 From TPOX

12

From vWA
10

11

What if we wanted to look at 2 loci at the same

time?
Short Tandem Repeats > Capillary Electrophoresis

Size Allele Sample Size Allele

186 7
190 8
194 9 194 ?
TPOX 198 10
TPOX
202 11
206 12 206 ?

210 13

Size Allele Sample Size Allele

186 7
190 8

vWA 194 9 vWA

198 10 198 ?

202 11 202 ?

206 12
210 13

Who knows what size goes with which loci?

Short Tandem Repeats > Capillary Electrophoresis

Size Allele Sample Size Allele

186 7
190 8
194 9 194 ?
TPOX 198 10 198 ?
TPOX
202 11
206 12
210 13

Size Allele Sample Size Allele

186 7
190 8

vWA 194 9 vWA

198 10
202 11 202 ?

206 12 206 ?

210 13

Who knows what size goes with which loci?

Short Tandem Repeats > Capillary Electrophoresis

From TPOX
9

12

From vWA
10

11

There are 2 ways to differentiate loci.

Short Tandem Repeats > Capillary Electrophoresis

From TPOX
9

12

From vWA
10

11

#1. Use a different fluorescent dye.

Short Tandem Repeats > Capillary Electrophoresis

9 From TPOX

12

From vWA
10

11

When TPOX fragments cross, the camera sees red

light.
Short Tandem Repeats > Capillary Electrophoresis

12

From vWA
10

11

When vWA fragments cross, the camera sees blue

light.
Short Tandem Repeats > Capillary Electrophoresis

Size Allele Sample Size Allele

186 7
190 8
194 9 194 9
TPOX 198 10
TPOX
202 11
206 12 206 12

210 13

Size Allele Sample Size Allele

186 7
190 8

vWA 194 9 vWA

198 10 198 10

202 11 202 11

206 12
210 13

Now the alleles can be determined.

Short Tandem Repeats > Capillary Electrophoresis

From TPOX
9

12

From vWA
10

11

#2. The location of primers can be moved so all

alleles for vWA come out after TPOX.
Short Tandem Repeats > Capillary Electrophoresis

From TPOX
9

12

From vWA
10

11

#2. The location of primers can be moved so all

alleles for vWA come out after TPOX.
Short Tandem Repeats > Capillary Electrophoresis

Size Allele Sample Size Allele

186 7
190 8
194 9 194 9
TPOX 198 10
TPOX
202 11
206 12 206 12

210 13

Sample Size Allele

vWA vWA
232 ?
236 ?

Moving primers changes the sizes of alleles on

the vWA allelic ladder.
Short Tandem Repeats > Capillary Electrophoresis

Size Allele Sample Size Allele

186 7
190 8
194 9 194 9
TPOX 198 10
TPOX
202 11
206 12 206 12

210 13

Size Allele Sample Size Allele

220 7
224 8

vWA 228 9 vWA

232 10 232 10

236 11 236 11

240 12
244 13

Moving primers changes the sizes of alleles on

the vWA allelic ladder.
Short Tandem Repeats > Capillary Electrophoresis

Size Allele Size Allele Size Allele

186 7 186 7 186 7

190 8 190 8 190 8

194 9 194 9 194 9

198 10 198 10 198 10

202 11 202 11 202 11

206 12 206 12 206 12

210 13 210 13 210 13

Size Allele Size Allele Size Allele

220 7 220 7 220 7

224 8 224 8 224 8

228 9 228 9 228 9

232 10 232 10 232 10

236 11 236 11 236 11

240 12 240 12 240 12

244 13 244 13 244 13

A multiplex reaction analyzes >1 loci at one time.

 Profiler Plus Allelic Ladders

D3S1358 VWA FGA

AMEL D8S1179 D21S11 D18S51

D5S818 D13S317
D7S820
ALLELIC LADDERS
 PCR Product Size (bp) Same DNA Sample Run with Each of
the ABI STR Kits
D3S1358 vWA FGA
Power of Discrimination
Blue 1:5000

TH01 TPOX CSF1PO

Amel 1:410
Green I

D3S1358 TH01 D13S317 CSF1PO 1:3.6 x 109

Amel D5S818 vWA TPOX FGA D7S820 Profiler
1:9.6 x 1010
Amel D8S1179 vWA D13S317
D7S820
D3S1358 D5S818 D21S11 FGA Profiler Plus
D18S51
1:8.4 x 105

D3S1358 TH01 D7S820

TPOX
Amel D16S539
CSF1PO COfiler
1:3.3 x 1012
D3S1358 vWA
Amel D8S1179 TH01
D21S11 D16S539 D18S51
D19S433 D2S1338 SGM Plus
FGA
 Why use STRs?
STRs satisfy all the requirements for a forensic marker:
they are robust, leading to successful analysis of a wide range
of biological material;
the results generated in different laboratories are easily
compared; they are highly discriminatory, especially when
analysing a large number of loci simultaneously
(multiplexing);
they are very sensitive, requiring only a few cells for a
successful analysis;
it is relatively cheap and easy to generate STR profiles; and
there is a large number of STRs throughout the genome that
do not appear to be under any selective pressure.
Single Nucleotide Polymorphisms(SNPs)
 Introduction
The simplest type of polymorphism is the SNP; single base
differences in the sequence of the DNA.
A single-nucleotide polymorphism (SNP, pronounced snip)
is a DNA sequence variation occurring when a single nucleotide
— A, T, C, or G — in the genome differs between members of a
species or paired chromosomes in an individual. For example,
two sequenced DNA fragments from different individuals,
AAGCCTA to AAGCTTA, contain a difference in a single
nucleotide. In this case we say that there are two alleles : C and T.
Almost all common SNPs have only two alleles.
SNPs are formed when errors (mutations) occur as the cell
undergoes DNA replication during meiosis. Some regions of the
genome are richer in SNPs than others, for example chromosome
1 contains a SNP on average every 1.45 kb compared with
chromosome 19, where SNPs occur on average every 2.18 kb.
 Single Nucleotide
Polymorphism
Single base-pair differences occurring in a
population with a frequency of >1%

...C C A T T G A C...
…G G T A A C T G...
...C C G T T G A C...
…G G C A A C T G...
Identification of SNPs has been one of the most significant
outcomes of the Human Genome Project.
They are found in the human genome about once in every
1000 bp. It has been estimated that > 1 million common
SNPs, each with a frequency of 10% - 50% account for the
bulk of human DNA sequence difference. This represents
about 85% of the human genetic variation.
They are an important part of the future of differentiating
between individuals. A no. of technologies are being
developed to miniaturize and automate the procedure for
SNA analysis.
Single nucleotide polymorphisms may fall within
Types of SNPs

1) coding sequences of genes,

2) non-coding regions of genes,
3) or in the intergenic regions between genes.
 SNPs within a coding sequence will not necessarily change
the amino acid sequence of the protein that is produced.
 STRs Vs. SNPs
Characteristics STRs SNPs
Occurrence in human ~1 in every 15 kb ~1 in every 1 kb
genome
General informativeness High Low: only 20-30% as
informative as STRs
Marker type Di-, tri-, tetranucleotide Bi-allelic markers
repeat markers
Number of alleles per Typically >5 Typically 2
marker
Detection methods Gel/capillary Sequence analysis
electrophoresis
Multiplex capability >10 markers with multiple Potential of 100s on
fluorescent dyes microchip
Forensic Relevance (PROS)
better potential to discriminate between mixtures and
single source samples.
Can be multiplexed to a higher level than STRs.
Sample processing and data analysis may be more fully
automated because a size based separation is not needed.
The PCR products from SNPs can be less than 100 bp in
size, so these markers will be able to withstand degraded
DNA samples better tan STRs that have amplicons as large
as 300-400bp.
SNPs can be population specific because of their low
mutation rate. Thus it may be possible to predict a
perpetrator’s ethnic origin with the analysis of a few
population specific SNP loci.
 CONS
Since each SNP locus possesses only two possible alleles,
more markers are needed to obtain a high discriminatory
power.
On an average approx. 25-45 SNP loci are needed to yield
equivalent random match probabilities as 13 core STR loci
 Utility in Forensics
With the exception of the analysis of mitochondrial DNA,
SNPs have not been used widely in forensic science to date,
and the dominance of tandem repeated DNA will continue
for the foreseeable future .
The major attraction of using SNPs with the current
technology is that SNP analysis can provide results from
highly degraded DNA when conventional STR profiling has
failed.
Autosomal SNPs that have different frequencies in different
major population groups can provide valuable information on
geographic ancestry. Many of the SNPs selected for this
purpose are associated with coding regions that have been
subjected to selection pressures. These include pigmentation
genes and genes involved with the metabolism of xenobiotics.
To summarise:
Several potential applications of SNPs exist for human
identity testing. These center around three areas:
estimating ethnic origin of a sample
SNPs have a much lower mutation rate than STRs and
therefore are more likely to become ‘fixed’ in a population.
SNPs change on the order of once every 108 generations
(Brookes 1999) while STR mutation rates are approximately
one in a thousand). Because of their low mutation rate,
SNPs are often found to be population-specific (Bamshad et
al. 2003). These loci could thus be useful in predicting a
perpetrator’s ethnic origin to aid criminal investigations. But
results from genetic tests attempting to predict ethnic origin
or ancestry should always be interpreted with caution and
only in the context of other reliable evidence.
predicting physical traits of a perpetrator, and
As more and more information becomes uncovered
about the nature and content of the human genome, we
will be able to identify the genetic variants that code for
phenotypic characteristics (e.g., red hair or blue eyes).
For example, the Forensic Science Service has developed
an SNP typing assay involving mutationsin the human
melanocortin 1 receptor gene that are associated with red
hair phenotype (Grimes et al. 2001). The company
DNAPrint is also developing a genetic test for inference
of eye color (Frudakis et al. 2003b).
recovering more information from a degraded DNA
sample.