forensic molecular biology ch 10, 11, 12, 14

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STR genotype

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STR genotype

the alleles at a particular locus

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STR profile

the combination of all of the locus genotypes for a sample

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STR genotyping

the process of analyzing the raw data from an electrophoretic run and determining a samples genotype at all tested loci

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matrix, ILS, allelic ladder

factors affecting genotyping

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analytical threshold

dependent on instrument sensitivity-- Usually around 50 RFUs. Peaks below this are unreliable, whereas peaks above this get called.

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dropout threshold

dependent on biological sensitivity-- Usually around 150-200 RFUs. Important in mixture interpretation.

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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.

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analytical threshold

the lowest RFU value at which a peak can be distinguished from noise

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greater than

the interpretation threshold is ________ the analytical threshold

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local southern method

using two calibration points on either side of the unknown fragment of DNA to estimate its size

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global southern method

using all peaks to create a calibration curve

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internal size standard

the alleles in the allelic ladder are sized using the ________

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allelic ladder

genotyping is performed by comparing the sample results to the _______

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0.5

There is a +/- bin of ____ around each allele

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extra peaks

stutter, incomplete adenylation, tri-allele patterns, bleed through, dye blobs, and mixed samples may lead to...

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stutter

a minor product of one repeat unit shorter than the main allele peak, caused by slippage of taq polymerase

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less

stutter is _____ pronounced with larger repeat unit sizes

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stutter cutoff value

a threshold set by the lab-- peaks above this threshold are called, whereas peaks below this threshold are considered stutter.

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stutter percentage

peak height of suspected stutter/peak height of main peak x 100

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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

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incomplete adenylation

excess template DNA can result in...

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three peak patterns

caused by an extra chromosomal fragment present in a sample, shown as an extra peak at a single locus

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pull-up

the inability to properly resolve dye colors due to a matrix failure

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bleedthrough

pull-up is also referred to as...

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dilution of PCR product

pull-up may be resolved by...

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spikes

caused by air bubbles, urea crystals, or voltage spikes. appears in all colors at the same location.

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microvariant off ladder alleles

alleles that are not exact multiples of the basic repeat motif

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STRbase

the summary of alleles that have been submitted and sequenced

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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

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allelic dropout

can be caused by degradation or inhibition

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population database

the goal of a ______ is to identify common alleles and sample them multiple times to estimate their fequency in the population

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degraded DNA

a sign of ______ is a loss of signal at larger size loci

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mixtures

a sign of ________ is more than two alleles visible at multiple loci

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partial profile

the failure to obtain a complete set of results for the DNA loci examined

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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

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mixtures

arise when more than one individuals contribute to the sample being tested

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heterozygote percent

measures the height ratio between two peaks-- If less than 70%, the peaks must have been contributed by different individuals

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15%

the stutter region is below _____

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low copy number DNA

analysis of a small quantity of DNA, often performed by increasing PCR cycles. Increases risk of contamination and stochastic effects.

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database

a collection of computer files containing entries of DNA profiles that can be searched to look for potential matches

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databank

a collection of samples

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population database

used to estimate allele frequency and random match probability

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local, state, and national

the three tiers of CODIS

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combined dna index system

CODIS stands for...

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criminal justice information services wide area network

CJIS-WAN stands for

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CJIS-WAN

network that connects labs and allows for exchange of information

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database hit

a confirmed match between two or more DNA profiles discovered by the database search

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forensic hit

when one or more samples are linked (case to case)

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offender hit

when one or more forensic samples are linked to a convicted offender sample (case to offender)

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investigations aided

the number of criminal investigations where CODIS has added value to the investigation process

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high stringency

when all alleles must match

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moderate stringency

when all available alleles match but may have a different number of alleles

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low stringency

when only one or more alleles match

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5

and allele should be observed at least ____ times in order to ensure a reliable estimate of frequency

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population database evaluation

when population geneticists evaluate allele frequencies and population data with statistical tests to ensure linkage equilibrium and independence

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random match probability

the chance of a specific profile occurring in a specific population based on observed allele frequencies for that population

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nonrandom mating

population substructure is caused by _______

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theta

an empirically determined measure of population subdivison

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100-500

generally _______ samples are needed to obtain reliable allele frequency estimates

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likelihood ratio

ratio of two probabilities of the same event under different hypothesis

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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

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source attribution

a statement reflecting that to a high degree of confidence, a tested individual is the source of an evidentiary DNA sample

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