molecular biology exam 4

STR 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 percent

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...

tri allele peaks

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