Studied by 64 peopleSTR genotype
the alleles at a particular locus
STR profile
the combination of all of the locus genotypes for a sample
STR genotyping
the process of analyzing the raw data from an electrophoretic run and determining a samples genotype at all tested loci
matrix, ILS, allelic ladder
factors affecting genotyping
analytical threshold
dependent on instrument sensitivity-- Usually around 50 RFUs. Peaks below this are unreliable, whereas peaks above this get called.
dropout threshold
dependent on biological sensitivity-- Usually around 150-200 RFUs. Important in mixture interpretation.
interpretation threshold
if a peak is higher than this threshold, it can be used for inclusions. If it is between the analytical threshold and this threshold, it can only be used for exclusions.
analytical threshold
the lowest RFU value at which a peak can be distinguished from noise
greater than
the interpretation threshold is ________ the analytical threshold
local southern method
using two calibration points on either side of the unknown fragment of DNA to estimate its size
global southern method
using all peaks to create a calibration curve
internal size standard
the alleles in the allelic ladder are sized using the ________
allelic ladder
genotyping is performed by comparing the sample results to the _______
0.5
There is a +/- bin of ____ around each allele
extra peaks
stutter, incomplete adenylation, tri-allele patterns, bleed through, dye blobs, and mixed samples may lead to...
stutter
a minor product of one repeat unit shorter than the main allele peak, caused by slippage of taq polymerase
less
stutter is _____ pronounced with larger repeat unit sizes
stutter cutoff value
a threshold set by the lab-- peaks above this threshold are called, whereas peaks below this threshold are considered stutter.
stutter percentage
peak height of suspected stutter/peak height of main peak x 100
non-template addition
refers to the addition of an extra nucleotide to the end of a PCR product by taq polymerase. Can be enhanced with an extension soak at the end of the PCR cycle
incomplete adenylation
excess template DNA can result in...
three peak patterns
caused by an extra chromosomal fragment present in a sample, shown as an extra peak at a single locus
pull-up
the inability to properly resolve dye colors due to a matrix failure
bleedthrough
pull-up is also referred to as...
dilution of PCR product
pull-up may be resolved by...
spikes
caused by air bubbles, urea crystals, or voltage spikes. appears in all colors at the same location.
microvariant off ladder alleles
alleles that are not exact multiples of the basic repeat motif
STRbase
the summary of alleles that have been submitted and sequenced
null allele
when an allele is present in a DNA sample but fails to be amplified due to a nucleotide change in the primer binding site
allelic dropout
can be caused by degradation or inhibition
population database
the goal of a ______ is to identify common alleles and sample them multiple times to estimate their fequency in the population
degraded DNA
a sign of ______ is a loss of signal at larger size loci
mixtures
a sign of ________ is more than two alleles visible at multiple loci
partial profile
the failure to obtain a complete set of results for the DNA loci examined
mini-STR
a kit run where the primers are as close as possible to the repeat region, increasing the chances to get results off of degraded DNA
mixtures
arise when more than one individuals contribute to the sample being tested
heterozygote percent
measures the height ratio between two peaks-- If less than 70%, the peaks must have been contributed by different individuals
15%
the stutter region is below _____
low copy number DNA
analysis of a small quantity of DNA, often performed by increasing PCR cycles. Increases risk of contamination and stochastic effects.
database
a collection of computer files containing entries of DNA profiles that can be searched to look for potential matches
databank
a collection of samples
population database
used to estimate allele frequency and random match probability
local, state, and national
the three tiers of CODIS
combined dna index system
CODIS stands for...
criminal justice information services wide area network
CJIS-WAN stands for
CJIS-WAN
network that connects labs and allows for exchange of information
database hit
a confirmed match between two or more DNA profiles discovered by the database search
forensic hit
when one or more samples are linked (case to case)
offender hit
when one or more forensic samples are linked to a convicted offender sample (case to offender)
investigations aided
the number of criminal investigations where CODIS has added value to the investigation process
high stringency
when all alleles must match
moderate stringency
when all available alleles match but may have a different number of alleles
low stringency
when only one or more alleles match
5
and allele should be observed at least ____ times in order to ensure a reliable estimate of frequency
population database evaluation
when population geneticists evaluate allele frequencies and population data with statistical tests to ensure linkage equilibrium and independence
random match probability
the chance of a specific profile occurring in a specific population based on observed allele frequencies for that population
nonrandom mating
population substructure is caused by _______
theta
an empirically determined measure of population subdivison
100-500
generally _______ samples are needed to obtain reliable allele frequency estimates
likelihood ratio
ratio of two probabilities of the same event under different hypothesis
prosecutor's fallacy
switching the meaning and the language of a random match probability; ex.) the chance that someone is guilty, or the chance that the DNA is from somebody else
source attribution
a statement reflecting that to a high degree of confidence, a tested individual is the source of an evidentiary DNA sample
Note
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