GENE gene marker blood typing , abo blood typing vntr

1. Importance of Genetic
Markers in Forensic
Analysis

2. What are Genetic
Markers?
• A gene or DNA seq. with aknown location on the
chromosome
• Single base pair changes such as SNPs and minisatellites
act as
common genetic markers
• These can be of two types:
a)biochemical markers which detect variation at the
translational level e.g. amino acid and protein changes
b)molecular markers which detect variation at the DNA
level such as nucleotide changes: duplication, inversion,
INDELs etc.
Uses of Genetic Markers
• Used for individual or species identification purposes

3. Types of Genetic
Markers
• RFLP (or Restriction fragment length
polymorphism) with PCR
• SSLP (or Simple sequence length
polymorphism) with PCR
• RAPD (or Random amplification of
polymorphic DNA)
• VNTR (or Variable number tandem repeat)
– SSR Microsatellite polymorphism, (or Simple
sequence repeat)
– SNP (or Single nucleotide polymorphism)
– STR (or Short tandem repeat)
• AFLP (or Amplified fragment length
polymorphism) with PCR

4. Basic Principle
• 40% of human genome is repetitive DNA
• These were first identified in Satellite DNA
• When a genome is digested with REs (e.g.
EcoRI) – it is seen that there are repeats
throughout the genome
• Some such repeats are actually
clustered at specific locations --
tandem repeats
(more common) and inverted repeats
• VNTRs are one of the class of clustered
tandem repeats that exhibit allelic
variation in their lengths.

5. Restriction Fragment Length
Polymorphism (RFLP)
• Difference in
homologous DNA
sequences that can be
detected by the
presence of fragments
of different lengths
after digestion of the
DNA samples in q
• Co-dominant (both
alleles in
heterozygous sample
will be detected) and
highly locus-specific
with specific restriction
endonucleases.

6. Simple Sequence Length
Polymorphisms (SSLPs)
• SSLPs are repeated sequences over varying base
lengths in intergenic regions of deoxyribonucleic
acid (DNA)
• Can be used to compare individual differences
Membership probability
of assigning genotypes
of the entire population
to
(a) two, (b) three, (c) four,
(d) five subgroups.
The height of each
bar represents
(b) the probability of
varieties belonging
to different
subgroups.
The varieties

7. Random Amplification of
Polymorphic DNA
(RAPD)
• Add primers (8-12) nt long
to the DNA sample and
PCR amplify it
• Resolve the resulting
pattern
• Primers would bind to
unknown sequences at
unknown sites thus there is
no need to have an existing
comparative database
• Degraded DNA samples are
not used
• Used to trace phylogenies
• There are problems in
reproducibility of results,
many scientific journals do
not accept experiments
merely based on RAPDs
A silver-stained polyacrylamide gel
showing three distinct RAPD profiles
generated by primer OPE15 for
Haemophilus ducreyi isolates from
Tanzania, Senegal, Thailand, Europe, and
North America
Different species produce different
bands
Nearly all RAPD markers are
dominant

8. Variable number tandem
repeat (VNTR)
• The tandem repeats in
various genes can be used
for personal and parental
identification
• The key is: repeats are
inherited and people differ
in terms of repeats –
children and parents match
in terms of
inheritance of repeating
pattern (which is unique
for each individual)
• The superset of parents’
VNTR contains children’s
pattern as a subset and the
grandparents’ pattern would
be related to grandchildren
in the same sense
Variations of VNTR (D1S80)
allele lengths in 6 individuals

9. • There are two types of VNTRs:
• 1.) Microsatellites: Near about 5 bps
– 2 nt differences among tissues in an individual
– 3 nt differences – across generations
– CODIS uses 13 assay STR with 4 nt
differences for forensic purpose
• 2.) Minisatellites: > 5 bps
– Short Tandem Repeat (STR) are sort of
minisatellites used in Forensic Analysis by
Forensic Geneticists
– Simple Sequence Repeat (SSR) are basically
the same but the term is more prevalent
among Plant Geneticists – these give
more crucial information

10. Amplified fragment length
polymorphism (AFLP)
• Although AFLP is commonly
referred to as "Amplified
fragment length
polymorphism", the resulting
data are not scored as length
polymorphisms, but instead
as presence-absence
polymorphisms.
• Used in criminal and paternity
tests
• To determine slight
differences within population
• Linkage studies to generate
maps for quantitative trait
locus (QTL) analysis
• Highest reproducibility,
sensitivity and resolution at
the whole genome level out

11. Forensic Analysis
• The first use of DNA fingerprinting was seen in 1986’s Dawn
Ashworth case in the UK
• Most human forensic casework is performed with
standardized commercial “multiplexes” that assay STRs at
multiple genetic loci simultaneously
• In the United States, the DNA Identification Act of 1994 authorized
the FBI to create a national DNA database: the Combined DNA
Index System (CODIS) -- contains profiles of DNA samples taken
from convicted offenders
• Criminal investigators can query CODIS with STR profiles taken
from biological samples found at a crime scene -- consists of 13
STR loci plus the amelogenin gene
• Laws regarding whose DNA goes into the database varies from
country to
country
• In some countries, investigators now search DNA databases not
only for full matches but also for partial matches to STR profiles
STR profile

12. • Researchers are now establishing useful
markers on the Y chromosome – to
screen out victim of sexual assault versus
the convict
• Other specialized markers such as
miniSTRs for which SNP profiles were
developed to identify the victims of
September 11, NYC terrorist attack
• The main disadvantage of SNP: not
many varieties as compared to STRs
• Almost 50 SNPs are required as compared
to 13 STRs
• mtDNA is useful in tracing the maternal lines
and thus determining the origin (the famous
Romanov family case) – historical analysis of

13. Complimentary Methods
• DNA profiling says nothing
about the tissue type which
can be determined by RNA
profiling
• Messenger RNA markers have
also been identified for saliva,
semen, and vaginal secretions
– this sort of Biological fluid
analysis screens out the
victim’s DNA
• Recent work in human genetic
variation suggests that
researchers may be able to
extract information about a
person's ancestry from certain
key genetic markers
• A major challenge in this area is
finding markers that can deal
with heavily admixed
populations, or those in which
people of very different
ancestries have blended
Consensus neighbour-joining
tree of the 249 non-admixed
human populations and six
chimpanzee populations

14. Conclusion
• Genetic markers such as VNTRs can be
used for identification purposes
• These marker techniques combined with PCR
can be used to study minute amount of DNA
samples present at crime site
• STR analysis of 13 sites and 1 gene forms a
DNA fingerprint which can be compared against
CODIS or similar databases
• In case of highly damaged DNA we miniSTR
and SNP analysis provides a useful basis of
identification (at ethnic level in un-admixed
populations)
• Y chromosome, mtDNA, RNA profile all add on
to the information one can obtain from a given
forensic sample