Molecular Biology - Lecture - 13 - Applications of Molecular Techniques in Genetic Testing and Forensics - Forensics - Part 3 - Complete

99.9%

Human genome is approximately the same between individuals by (%):

0.1%

It is the % of human genome that forensic scientists investigate or use to identify stains, recovered remains from accidents and mass disasters, and biological relatives

DNA

Useful as an identity marker because it is present throughout all cells of the body, except in mature red blood cells

Haploid sex gametes

DNA is the same in all cells of the body, except in:

Haploid sex gametes

These have half of the DNA material as compared to the other cells in the body

F

T/F

DNA changes throughout life from the time of conception

Progenitor stem cell transplantation

This procedure can result in the presence of the donor's DNA rather than the recipient's inherited DNA

Identical twins

DNA is also different in all individuals except in these specific people who have the same DNA.

Alternate light sources, Presumptive chemical tests

These can be used to visualize biological fluids and stains

Clean sterile swab

When a biological fluid has been deposited on a surface or an item that cannot be collected, the fluid should be sampled using a:

Clean sterile swab moistened with sterile distilled water

When a biological fluid is dry it should be sampled using a:

Air dry

After collection using a Clean sterile swab moistened with sterile distilled water, it should be allowed to ____ prior to packaging

Double swab technique

Technique for collecting swabs from bite marks on bodies and dried biological material

Double swab technique

This technique involves rubbing the evidentiary area with a wet swab followed by a dry swab.

T

T/F

Specimens should be collected one at a time, packaged separately, clearly labeled, and itemized.

EDTA, Citrate phosphate dextrose

Anticoagulants often used and requested for DNA testing

T

T/F

Any tissue may be used for DNA typing purposes.

Blood

For post-mortem samples, sources of DNA other than ___ are preferred if there is significant decomposition.

Liver tissue

DNA recovered from this soft tissue degrades quickly due to the presence of autolytic enzymes

Brain tissue

Soft tissue that is a relatively good source in the intermediate post-mortem period

Bone, Teeth, Nails

Stable sources of post-mortem tissue DNA

T

T/F

Informative DNA is routinely obtained from skeletal remains that are decades old

Incisional biopsy technique

Non-exposed tissue should be collected by this technique

T

T/F

Results from testing evidence are often used in legal proceedings. Thus, all aspects of the specimen collection procedure should be well-documented since they may be subjected to legal challenges. It is important to ensure clear documentation of the identification of the tested individuals, the collection of the evidence, and the labeling of the sample.

Extraction or purification of the DNA

After collecting the samples, the first and most critical step for DNA testing of evidence is:

F

T/F

DNA from a blood stain, a vaginal swab, or other source don't need to be isolated from other cell components and environmental contaminants

Solid phase column extraction methods, Magnetic resin particles

Most often used for DNA extraction since these methods are highly amenable to automated techniques.

Vaginal swabs

Specimen that require special conditions for extraction using a differential lysis procedure because of the need to separate the male DNA in sperm from the female DNA in epithelial cells.

Standard extraction procedures

The female fraction of vaginal swabs made up of the vaginal epithelial cells is separated by:

Vaginal epithelial cells

Female fraction of vaginal swabs

Spermatozoa

Male fraction of vaginal swabs

Centrifugation, Dithiothreitol

The male fraction of vaginal swabs is then extracted by ___ and breaking the disulfide bridges of the protective capsule of spermatozoa with ___ or other reducing agent solution.

DNA quantification

Once the samples are extracted, ____ is performed.

T

T/F

Knowing the amount of total DNA together with qualitative assessment is extremely useful in determining which assays to perform in the downstream analysis

Stop at quant procedure

DNA quantification procedure adopted by many laboratories

T

T/F

Samples are often times stopped at quantification if insufficient DNA is present

T

T/F

In forensics, multiple genetic marker systems are used.

T

T/F

Ideally, the system should have multiple alleles distributed in the population so that there is a high power of exclusion, and the least common phenotype has a frequency that can be determined reliably

Codominant

All markers in the genetic marker systems should be expressed as ___, with few to no null alleles

Known

Genetic marker systems

Mutation rates should be known or unknown?

T

Genetic marker systems

T/F

Phenotype should be unstable under usual storage conditions

T

Genetic marker systems

T/F

Methods for detecting the markers should be reliable, reproducible, and feasible for a large number of laboratories

Mendelian Laws

The genetics of the system must be known and follow established inheritance patterns, which is the ___, and the system should be independent of other markers routinely tested.

If the system is intended for calculating estimates of paternity or identity, the gene frequencies in various populations must also be established.

3-7, Short tandem repeats

Loci typically used in commercial assays consist of repeat units of how many nucleotides? These are called ___ that occur throughout the genome.

20 Core STR loci for CODIS

Most commonly used markers in forensic and parentage laboratories in the United States. These have been standardized for use in obtaining genetic profiles of individuals who have been convicted of various criminal offenses.

STR marker systems

Marker systems that have discrete alleles

3 or 4

STR locus may have ___ common alleles and several rare alleles. Alleles at these STR loci are defined by the number of repeat units in the PCR amplified product

Combined paternity index

CPI meaning

Cumulative probability of exclusion

CPE meaning

6>

It is usually necessary to test at least (how many) STR loci to obtain a high cumulative probability of exclusion or CPE and combined paternity index or CPI.

Amelogenin locus

Sex determination is commonly performed using this locus.

It differs from other routine identity markers in that it provides specific phenotypic information about the source individual, that is if the source is male or female.

It may be also important in the investigation of potential suspects as well as in the categorization of specimens as originating from a victim or a suspect.

Polymorphic Y chromosome markers

Markers not used for sex determination, but they are extremely useful in the typing of casework when there is a mixture of a male and a female, and a mixture of males

Polymorphic Y chromosome markers

Markers used to characterize the paternal lineage in human remain identification.

Y-STRs

These are excellent in obtaining a profile of the male subject with no interference from the female subject since its results are only obtained from males

Mitochondrial DNA

Composed of a circular piece of DNA that is 16,569 base pairs in length

16,569 base pairs

Mitochondrial DNA length

Non-coding displacement loop

Region of the mtDNA that is analyzed for human identification

D-loop

Non-coding displacement loop other name

Control region

Non-coding displacement loop other name

Mother

Mitochondria are inherited from the mother or father?

No

Does the father have any contribution to mitochondrial DNA?

Homoplasmic

This means that only a single mtDNA sequence is present in the cell and consequently no genetic recombination occurs. This means that mtDNA within a cell, tissue or individual are genetically identical.

Limited discriminatory power, Expensive, Time-consuming

Disadvantage of mtDNA sequencing

Single nucleotide polymorphisms

Methods used to detect these are used to determine a single base change in a sequence at a specific location.

70

Single nucleotide polymorphisms

Because of the limited variability at these loci, as many as ___ SNPs need to be tested to obtain the same level of information about relatedness, power of discrimination and mixture resolution as provided by a multiplex of several STR loci

T

T/F

Single nucleotide polymorphisms are also very powerful for identity testing.

Single nucleotide polymorphisms

Some of its advantages are that they provide information when traditional ones may not because they can be designed to amplify smaller amplicons.

Specific Single nucleotide polymorphisms

In addition, ___ may be used to provide information regarding the physical traits of an individual and it can be designed to predict the ethnic origin.

Next-generation sequencing

Method that simultaneously analyzes multiple markers.

Massively parallel pyrosequencing method

Next-generation sequencing other name

STRs, SNPs, mtDNA

Markers that are simultaneously analyzed by Next-generation sequencing

Next-generation sequencing

This method enables improved identification, ancestry estimation and phenotypic profiling from minimal evidence.

Next-generation sequencing

This method provides deeper, faster analysis of complex DNA samples compared to traditional methods.

Genotyping software

Parentage and forensic laboratories use ___ to size the alleles and make allele calls, and computer programs to perform kinship statistical analysis

Probabilistic genotyping software

Software system that calculates the probability of potential genotype combinations for a genotype result.

Probabilistic genotyping software

Software system that combines biologic modeling with mathematical processes to interpret complex DNA profiles.

Mixture deconvolution software tools

Software system used by some forensic laboratories to assist the forensic analyst in the review of mixed data as is often observed with sexual assault evidence.

So these tools separate complex DNA mixtures derived from two or more individuals into individual profiles.

To link a suspect to a crime, To exculpate falsely accused suspects, To recognize serial crimes, To distinguish copycat crimes, Aid in accident reconstruction

In the criminalistics context, DNA can be used for the following:

T

T/F, is this an application of DNA analysis in forensics?

For example, there is a car crash where the driver's identity is uncertain. Biological evidence such as blood stains on the driver's side of the windshield can be analyzed. The DNA profile obtained from these stains can help identify the individual who is most likely the driver.

In addition to the use of DNA for associative evidence at crime scenes, DNA is also used in the identification of human remains.

Inconclusive

DNA tests are reported as (conclusive/inconclusive) due to no or partial DNA results being obtained, profiles showing high levels of degradation or inhibition, and complex interpretation issues.