DNA in Forensics (#11)

Question 1

Human identity testing types

Answer 1

1. Forensic cases - matching suspect and victim with evidence
2. Parentage testing - identifying paternity and maternity
3. Mass disasters - putting pieces back together
4. Missing persons investigations
5. Military DNA - “dog tag”

Question 2

DNA use in forensic cases

Answer 2

Most are sexual assault cases (>2/3), homicides. etc..
Looking for an evidence match between suspect and/or victim
Must compare other individuals
Challenges:
1. Mixtures must be resolved
2. DNA is often degraded
3. Inhibitors to PCR are often present

Question 3

Basis of DNA profiling

Answer 3

The genome of each individual is unique (except identical siblings) and is inherited from parents (1/2 from each)
Probe subsets of genetic variation in order to differentiate between individuals (i.e. polymorphic) and then statistical probabilities of a random match are calculated
DNA typing must be performed efficiently and reproducible (hold up in court).
Current standard DNA tests DO NOT look at sensitive genetic information - little/no info on race, disease, or phenotypical info (eye color, height, hair color) is obtained

Question 4

Human genome

Answer 4

23 Pairs of chromosomes (3.2 billion bp):
1. 22 pairs of Autosomes
2. 1 pair of sex chromosomes
mtDNA - located in mitochondria (16,569 bp) 100s of copies per cell

Question 5

Short tandem repeats (STRs)

Answer 5

The repeat region is variable between samples while the flanking regions where PCR primers bind are constant.
Can be homozygote or heterozygote.
Types:
1. Dinucleotide
2. Trinucleotide
3. Tetranucleotide
4. Pentanucleotide
6. etc...

Question 6

How many STRs are in the human genome?

Answer 6

The efforts of the Human Genome Project have increased knowledge regarding the human genome, and hence there are many more STR loci available now than there were 13 years ago.
More than 20,000 tetranucleotide STR loci have been characterized in the human genome.
There may be more than a million STR loci present depending on how they are counted
STR sequences account for approximately 3% of the total human genome

Question 7

Advantages of using STR markers

Answer 7

1. Small product sizes are generally compatible with degraded DNA and PCR enables recovery of info from small amounts of material
2. Multiplex amplification with fluorescence detection enables high power of discrimination in a single test
3. Commercially available in an easy to use kit format
4. Uniform set of core STR loci provide capability for sharing of criminal DNA profiles through computer databases

Question 8

National DNA Index System (NDIS) and CODIS

Answer 8

Combined DNA Index System (CODIS)
Launched in October 1998 and now links all 50 states.
Used for linking serial crimes and unsolved cases with repeat offenders.
Convicted offender and forensic case samples along with a missing persons index
Requires 13 core STR markers
Contains more than 2.8 million DNA profiles

Question 9

Calculation of the quantity of DNA in a human cell

Answer 9

Slide 15

Question 10

Multiplex PCR

Answer 10

Up to 16 markers can be copied at once
Sensitive to less than 1 ng of DNA
Ability to handle mixtures and degraded samples
Different fluorescent dyes used to distinguish STR alleles with overlapping size ranges

Question 11

Challenges and Advantages of multiplex PCR

Answer 11

Challenges:
1. primer design to find compatible primers (no program exists)
2. reaction optimization is highly empirical often taking months
Advantages:
1. Increases the info obtained per unit times (increases power of discrimination)
2. Reduces labor to obtain results
3. Reduces template required (smaller sample consumed)

Question 12

Sources of biological evidence

Answer 12

Blood
Semen
Saliva
Hair roots
Teeth
Bone 
Tissue

Question 13

Uses of DNA as a lineage marker

Answer 13

Autosomal (passed on in part from ALL ancestors)
Y-Chromosome (passed complete, but only by sons
Mitochondrial (passed on complete, but only by daughters)

Question 14

Y-STRs and DNA compared to autosomal STRs

Answer 14

1. Autosomal STRs provide the highest power of discrimination and are the preferred method of Forensic DNA profiling whenever possible
2. Due to capabilities for male-specific amplification, Y-chromosome STRs can be useful in extreme female-male mixtures (e.g., when differential extraction is not possible such as fingernail scrapings)
3. Due to high copy number, mitochondrial DNA may be the only source of surviving DNA in highly degraded specimens or low quantity samples such as hair shafts

Question 15

DNA profile frequency with all 13 CODIS STR loci

Answer 15

Hardy-Weinberg equilibrium: p^2 + 2pq + q^2 = 1

The Random Match Probability for the given profile in U.S. Caucasion population is 1 in 837 trillion (Slides 38 and 39)