forensic biochem 2 exam 3

degraded DNA, PCR inhibition, low template DNA, DNA mixtures, population subdivision, CODIS, databases

heat, light, humidity, and time since deposit all affect the ___ of a DNA sample

quality

environmental exposure degrades DNA molecules via _______

hydrolysis

water is bad for a DNA sample as it contributes to ________ of the sample

hydrolysis

________ and _______ are bad for DNA bc they use it as food and “chew it up”

microorganisms, nucleases

______ is an old technique that can be used to evaluate the quality of the sample, or how degraded the sample is

agarose gel

high molecular weight DNA is ~_______ and of good quality for DNA analysis

20,000

the gel on the LEFT is of __________ DNA

good quality

the gel on the RIGHT is of ________ DNA

degraded

earlier DNA typing techniques used large allele sizes, which made analysis of degraded DNA _______

not possible

TRUE OR FALSE

with modern DNA analysis using STRs, obtaining a profile from a degraded sample is more likely than with earlier DNA typing techniques

true

for PCR amplification to occur with a degraded sample, ___________ must be intact

primer sequence and the sequence inbetween

the more degraded a sample is, the ______ PCR products are

shorter

there is an _______ relationship between the size of the locus and successful PCR amplification from degraded samples

inverse

the ski slope effect refers to how ________ using degraded DNA

signal strength is gradually lost with larger PCR products

this graph exhibits an example of

ski slope effect

created to generate a profile from degraded DNA

miniSTRs

miniSTRs have primers that ____, thus having a greater chance of obtaining a useful profile

anneal closer to the repeat region

outdoor crime scene PCR inhibitors

soil, sand, wood, leaves

interior crime scene PCR inhibitors

textile dyes, leather, wood

major PCR inhibitor found within blood

heme

PCR inhibitors can:

interfere with cell lysis, cause DNA degradation, inhibit pol activity

PCR inhibitor within tissue and hair

melanin

PCR inhibitor found within feces

bile salts

PCR inhibitor found within soil

humic compounds

PCR inhibitor found within urine

urea

PCR inhibitor found within blue jeans

textile dyes

amplification of a sample containing inhibitors can cause:

loss of alleles within larger loci, no profile, look like a degraded sample

solutions for trying to amplify a sample with inhibitors present:

dilution, add more pol, use alternative pol, use anti-inhibitor additives, purify sample

the most logical solution for dealing with a DNA sample with inhibitors is ____

purification prior to PCR

many casework samples do not contain the ________ ng amount of DNA required for amplification

0.5-1

category of samples where “specialized” techniques are needed for analysis

low template DNA

when a limited humber of target molecules exist within a sample (like within low template DNA), PCR primers ______ resulting in lower peak height or potential drop-out

may not always find all DNA molecules in the sample

strategies for improving sensitivity with low template DNA

increased cycle number, increased CE injection, post PCR purification, reduced volume PCR, nested PCR, mtDNA testing

DNA amplification technique that uses two successive PCR reactions and two sets of primers ("outer" then "inner") to amplify a specific target sequence

nested PCR

low template DNA has ______ stutter

increased

occurs when one allele is preferentially amplified in early rounds of PCR

heterozygous peak imbalance

when dealing with low template DNA, a peak height imbalance of greater than ___% can occur

60

2 “schools of thought” for dealing with random effects from testing low template DNA

stop testing/interpreting data from low template DNA, try and limit random variation by testing and research for implementation

approaches to improving reliability of results

improving DNA recovery at collection and extraction stages, improving profiling of samples, accounting for allele drop-out and other stochastic efforts during statistical interpretation

refers to a sample is amplified and profiled more than once to obtain a consensus for varied alleles

replicate analysis

arise when 2 or more individuals contribute to the sample

mixture

clues that help to determine if a mixture is present

loci have more than 2 alleles, really high stutter, severe peak imbalance

all possible genotypes for 4 peaks (A, B, C, D)

A, B + C, D

A, C + B, D

A, D + B, C

all possible genotypes for 3 peaks (A, B, C)

A, A + B, C

B, B + A, C

C, C + A, B

A, B + A, C

B, C + A, C

A, B + B, C

all possible genotypes for 2 peaks (A, B)

A, A + A, B

A, B + A, B

A, A + B, B

A, B + B, B

population subdivision entails a ________-like effect

inbreeding

population subdivision _______ the proportion of heterozygous genotypes

decreases

refers to when there is a perceived deficiency of heterozygotes in the population due to treating 2 different populations as one

Wahlund effect

H_I

heterozygosity of an individual in a population

H_S

expected heterozygosity of an individual in an equivalent random mating subpopulation

H_T

expected heterozygosity of an individual in an equivalent random mating total population

H_S is always equal to

2p_iq_i

p_i represents

allele frequency

H_T is always equal to

2p₀q₀

F_IS measures

reduction in heterozygosity of an individual due to nonrandom mating within a subpopulation

F_IS is equal to

(H_S-H_I)/H_S

the fixation index or F_ST refers to

reduction in heterozygosity of a subpopulation due to random genetic drift

F_ST is equal to

(H_T-H_S)/H_T

F_IT measures

reduction in heterozygosity of an individual relative to the total population

F_IT is equal to

(H_T-H_I)/ H_T

______ is the most inclusive measure of inbreeding, as it takes into account the effects of nonrandom mating within subpopulations and the effects of population subdivision

F_IT

mathematical relationship between F_IS, F_ST, and F_IT

(1-F_IS)(1-F_ST)=(1-F_IT)

in natural populations, F_IS is typically close to ___

0

when F_IS=0, then F_ST=___

F_IT

in some contexts, F_ST is referred to as ______ or ______

G_ST, theta

F_ST is used as a measure of

genetic differences among populations

F_ST is influenced by

random genetic drft, migration, natural selection, and mutation

F_ST= 0 - 0.05 can be interpreted as

little genetic differentiation “by no means negligible”

F_ST= 0.05-0.15 can be interpreted as

moderate genetic difference

F_ST= 0.15-0.25 can be interpreted as

great genetic differentiation

F_ST= greater than 0.25 can be interpreted as

very great genetic differentiation

of the total genetic variation between African, European, and Asain population groups, ~ __ % can be attributed to genetic differences between the population groups

7

~____% of the total genetic variation is found in individuals within the groups (African, European, Asain)

93

F_ST can be interpreted in terms of identity by descent → F_ST refers to the probability that

2 alleles chosen from the same subpopulation are ibd

as random drift occurs from generation to generation, the value of F will _____

increase

3 key components must be in-place before a DNA database can be established and actually be effective:

commitment for state and local governments to provide DNA samples, common set of DNA markers, quality standards

3 steps for entering DNA sample into database

collect specimen, analyze sample and enter into database, compare known samples to questioned sample

FBI launched the national DNA database, _______, in 1988

National DNA Index System

softwarre program used to access the national DNA database

Combined DNA Index System

Congress enacted the DNA Identification Act in _____

1994

Expressly authorized the NDIS and established the FBI’s authority to maintain it for law enforcement purposes

DNA Identification Act

SDIS stands for

State DNA Index System

LDIS stands for

Local DNA Index System

2 main categories for entry into NIBIN (excluding missing persons)

offender profiles, forensic profiles

DNA from known individuals are stored in the _______ section

offender

DNA from an unknown source, typically from evidence, is stored in the _______ category

forensic

before a DNA profile can be entered into the Forensic Index of CODIS, labs must promide assurance that _______

evidence is connected to a criminal offense

labs are able to prove that the evidence meets CODIS elements of offense typically by __________

witness statement