FOR505 Exam 1 Study Guide - Forensic DNA Analysis

Comprehensive vocabulary flashcards generated from lecture notes on biological evidence collection, DNA extraction, qPCR quantitation, PCR amplification, and capillary electrophoresis.

Allele

A variant form of a gene, representing alternative possibilities for a genetic locus, with one inherited from the maternal line and one from the paternal line.

Locus

A specific physical location or position in the genome, such as on a chromosome, where a gene, marker, or sequence resides.

Marker

A DNA sequence with a known physical location on a chromosome used for specific types of testing, such as forensic DNA markers.

Touch DNA

DNA cells left behind on an object when an individual touches or comes into contact with it.

Transfer DNA

DNA that moves from one surface or object to another, either through direct contact (primary transfer) or indirectly via an intermediate object or person (secondary or tertiary transfer).

Locard's Exchange Principle

The principle stating that whenever contact occurs between two surfaces, there will be a mutual exchange of physical material.

Presumptive Tests

Non-confirmatory screening tests that are fast, cheap, safe, and non-destructive, used to indicate the presence or absence of a specific biological fluid.

Confirmatory Tests

Specific tests for a suspected biological fluid that conclusively identify the substance for inclusion or exclusion.

Kastle-Meyer Test

A presumptive blood test where phenolphthalin is oxidized to pink phenolphthalein by the peroxidase-like activity of hemoglobin's heme group in the presence of hydrogen peroxide.

Acid Phosphatase (AP) Test

A presumptive semen test detecting an enzyme secreted by the prostate gland, which turns purple when sodium alpha-naphthylphosphate and Fast Blue B are added.

Prostate Specific Antigen (PSA / p30) Test

A test detecting a glycoprotein produced by the prostate gland, useful for identifying seminal fluid from aspermic or vasectomized males.

Christmas Tree Staining

A confirmatory microscopic staining technique for sperm where nuclear fast red colors sperm heads red and picroindigocarmine colors mid-pieces blue and tails yellow/green.

Phadebas Test

A presumptive saliva test identifying $\alpha$-amylase using filter paper containing insoluble starch and a water-soluble blue dye that releases dye upon enzymatic reaction.

Restriction Fragment Length Polymorphisms (RFLP)

Variations in DNA sequences at restriction enzyme recognition sites, resulting in differing lengths of cleaved DNA fragments used as historical genetic markers.

Single Nucleotide Polymorphisms (SNPs)

Sequence polymorphisms consisting of single base pair changes at a specific locus in the genome.

Population Genetics

The branch of genetics describing the distribution of genetic variation and allele frequencies within and between populations.

Hardy-Weinberg Equilibrium

A model stating that allele and genotype frequencies in a population remain constant over generations under conditions of large population size, random mating, and no migration, mutation, or selection.

Linkage Equilibrium

The independent inheritance of alleles at different loci, allowing the product rule to be applied to estimate combined profile frequencies.

Organic Extraction

A solvent-based DNA extraction technique using phenol/chloroform to separate denatured proteins in an organic phase from DNA in an aqueous phase.

Chelex Extraction

A rapid single-tube DNA extraction method using a resin that chelates metal ions and polar molecules to prevent DNA degradation during boiling.

Silica-based Extraction

A DNA extraction technique where DNA reversibly binds to silica substrate in the presence of high concentrations of chaotropic salts.

Reagent Blank

A negative control containing all extraction reagents but no evidence sample, processed through the entire lab procedure to monitor for contamination.

Differential Extraction

A procedure used on mixed biological evidence to separate non-sperm DNA from sperm DNA by selectively lysing non-sperm cells before breaking sperm head disulfide bonds with DTT.

Quantitative PCR (qPCR)

A real-time PCR technique that measures DNA amplification after each cycle using fluorescence to determine the quantity of amplifiable human and male DNA.

Internal PCR Control (IPC)

A synthetic DNA target co-amplified in qPCR assays to verify proper reagent/instrument function and detect PCR inhibitors.

Degradation Index (DI)

A ratio of the small autosomal (SA) target to the large autosomal (LA) target in real-time PCR used to quantify DNA degradation.

Hot Start PCR

A PCR method utilizing a modified DNA polymerase activated by high heat to prevent non-specific target amplification during reaction set-up.

Multiplex PCR

A technique that simultaneously amplifies multiple target loci within a single reaction tube using distinct fluorescently-tagged primer sets.

Non-nucleotide Linkers

Flexible chemical structures incorporated into primers to alter molecular mobility and space out amplicons of different loci in a multiplex assay.

Preferential Amplification

An unequal amplification efficiency of specific alleles or loci during PCR, leading to peak-height ratio imbalance or allele drop-out.

Stutter

A minor PCR artifact generated by strand-slippage during polymerisation, producing a product typically one repeat unit (e.g., $\text{N}-4\,\text{bp}$) shorter than the true allele.

Direct Amplification

A rapid protocol for known reference standards where samples are lysed with specialized buffer (e.g., Prep-N-Go) and amplified without prior extraction or quantitation.

$-A$ Artifact

An artifact occurring when Taq polymerase fails to add a terminal non-templated adenine ($A$) to the $3'$ end of an amplicon, leaving an incomplete fragment.

Formamide

A strong chemical denaturant added to capillary electrophoresis samples to maintain DNA as single-stranded fragments.

Allelic Ladder

A standard reference mixture of common population alleles for specific STR loci used to assign precise genotype names to unknown DNA peaks.

Internal Lane Size Standard (ILS)

A set of synthetic, fluorescently labeled DNA fragments of known sizes run with each sample in capillary electrophoresis to establish a calibration curve for sizing.

Local Southern Method

An algorithm used in capillary electrophoresis to calculate unknown fragment sizes by averaging two sigmoidal curves generated from surrounding size standard peaks.