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Forensic Biology > Exam 3 > Flashcards

Exam 3 Flashcards

master (54 cards)

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1
Q

Fluorescent Dye functions

A

Fluorescent dye is attached to the TaqMan probe in quantitation step.
For amplification, dyes are attached to the primers
They can be used in multiplex PCR reactions

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2
Q

Singleplex PCR reaction

A

a single primer set used to amplify a single region (amplicon)

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3
Q

Multiplex PCR reaction

A

amplify over 20 loci at the same time
saves a large amount of time
can differentiate between individuals

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4
Q

How does having multiple dyes allow for multiplexing of PCR

A

It enables a clear differentiation of multiple targets, even when similar in size, by assigning fluorescence signals to each target, allowing for both simultaneous detection and better resolution in the analysis

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5
Q

How PCR products are labeled with fluorescent dyes for STR analysis

A

fluorescently labeled primers enable the differentiation of loci based on both size and dye color

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6
Q

How PCR products are labeled with a fluorescent dyes for mtDNA sequencing

A

fluorescently labeled ddNTPs allow for a sequential, base-by-base redout of the DNA sequence

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7
Q

How restriction endonucleases can be used to determine a person’s STR prodtfile

A

Restriction enzymes can be used to generate unique DNA fragment patterns based on STR length, but they lack specificity, sensitivity, and efficiency needed for reliable forensic STR profiling.

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8
Q

Basic function of restriction endonucleases

A

molecular “scissors” that enable precise cutting of DNA at specific sequences, playing a crucial role in genetic analysis, engineering, and forensic science

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9
Q

Structure of Variable Number Tandem Repeats (VNTRs)

A

consist of a sequence of DNA bases repeated back-to-back at a specific locus in the genome. Number of repeats can vary(genetic diversity)

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10
Q

Structure of Short Tandem Repeats (STRs)

A

subset of VNTRs where the repeating units are shorter, usually between 2-6 base pairs. vary in number of repeats, creating differences in length across individuals

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11
Q

Advantages of using PCR based assays in forensic investigation

A

high sensitivity
analysis of degraded samples
rapid and efficient process
ability to target specific regions
high throughput and multiplexing capability
compatibility with mixed and contaminated samples
standardization and databases
automation and portability

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12
Q

How PCR and capillary electrophoresis can be used to determine the number of repeats within an STR

A

by combining PCR to amplify STR regions and CE to separate and detect the amplified fragments, you can determine the number of repeats at each STR locus.

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13
Q

Advantages of using microsatellites over minisatellites

A

high sensitivity
efficiency
compatibility with degraded or small DNA samples
short length
ability to generate unique profiles
standardization in databases give an advantage

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14
Q

Basic information and characteristics for an STR to be usable

A

High variability
Stability and inheritance
Small size
low mutation rate
unique chromosomal locations
compatibility with PCR

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15
Q

STR types based on the number of base pairs in the repeat unit

A

Dinucleotide Repeats
Trinucleotide Repeats
Tetranucleotide Repeats
Pentanucleotide Repeats
Hexanucleotide Repeats

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16
Q

STR types based on Repeat pattern or sequence arrangment

A

Simple STR
Compound STR
Complex STR

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17
Q

STR based on Chromosomal Location

A

Autosomal STR
Y-STR
X-STR

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18
Q

Core loci

A

specific STR locations on the human genome that are routinely analyzed in forensic DNA testing.

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19
Q

why was core loci set expanded in 2017

A

Increased discrimination power
higher success rates with degraded samples
enhanced compatibility with international databases
improved kinship analysis

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20
Q

How can an internal lane standard be used to size the DNA fragments within an electropherogram peak

A

Calibration reference
Correction for variability
Fragment sizing

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21
Q

Allelic ladders and how they are used to “call” alleles for peaks

A

set of DNA fragments at a particular STR locus.
software visually compares the migration patterns of the sample peaks to the allelic ladder’s peaks

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22
Q

Steps in order to determine alleles, genotypes, and a profile

Study These Flashcards
A

understanding the electropherogram
identify the loci
compare peaks to the allelic ladder
determine the alleles
determine the genotype
construct the DNA profile

23
Q

Interpret results for autosomal STR data

Study These Flashcards
A

Inclusion (match): sample could come from the individual in question
Exclusion (non-match): excludes the individual as the source
Inconclusive: if sample is degraded or has low quality

24
Q

Interpret results for mtDNA data

Study These Flashcards
A

Inclusion (match): cannot uniquely identify an individual
Exclusion (non-match): individual is excluded
Inconclusive
cannot exclude

25
Interpret results for Y-STR data interpretation
Inclusion (match): includes the individual Exclusion (non-match): excluded as a source Inconclusive Cannot exclude
26
Identify all different factors impacting STR genotyping
Sample quality, PCR conditions, Allelic variation, technical limitations, human error, and genetic factors
27
How Tri-allelic patterns form
biological mechanisms, genetic abnormalities, or technical issues
28
How point mutations in the STR flanking region can impact primer binding
Failure to bind; STR locus will appear as a null allele Reduced Binding Affinity; weaker PCR products Mispriming; lead to false peaks or primer-dimer artifacts
29
How point mutations in the STR flanking region can impact Amplification
Incomplete Amplification; partial STR profile will be generated Allelic Dropout; genotyping errors
30
How point mutations in the STR flanking region can impact STR profiling
Loss of information; difficult to distinguish between two individuals False Genotyping; lead to wrong conclusions
31
How strutter products are formed
byproducts of DNA polymerase slippage during PCR amplification of STR regions. shorter, smaller peaks, complicate interpretations of STR profiles
32
Basis of non-template adenylation
phenomenon where a polymerase (Taq polymerase) adds extra adenine residues to the 3' ends of PCR products.
33
Non-template adenylation and its impact on samples
Size shifts, false alleles, artifact peaks, or allelic misinterpretations
34
Cause of Pull up peaks in electropherograms
signal from a fluorescent dye is used for one STR locus "pulls up" into the detection range of another adjacent peak from a different fluorescent dye or locus spills or bleeds into adjacent channel
35
Cause of Spikes in Electropherograms
can arise from small technical issues with the capillary electrophoresis system contaminants like dust, bubbles electrical noise in the detection system
36
Identify a degraded DNA profile/ understand why it looks like that
characterized by shorter, fragmented STR products, missing alleles, and fainter peaks in the electropherogram can be caused due to environmental factors, time, microbial activity, handling conditions, or mechanical damage
37
Complications associated with low copy number DNA testing and increasing cycle numbers
increased stochastic effects, PCR artifacts, non-specific amplification, and a greater risk of contamination
38
Characteristics and identifying mixture profile
multiple alleles at one locus, imbalanced peak intensities, allelic drop-out, missing or additional peaks, and complex patterns careful interpretation is required when involved a low-quanitiy or degraded samples case
39
determine possible genotypes in a mixture sample
evaluate the number of peaks at each locus, their relative intensities, and their possible allele pairings
40
Characteristics of mtDNA
Inheritance circular structure size coding and non-coding regions high copy number small number of genes no recombination mutability absence of histones
41
General structure of the mtDNA genome
The two strands -heavy and light strand Control region -Non-coding region and D-loop Origin of Replication -Origin of Heavy strand replication -Origin of Light strand replication Gene Organization -Protein-coding genes -tRNA genes -rRNA genes Hypervariable Regions
42
Length Polymorphisms
refer to variations in the length of a DNA sequence between individuals STRs and VNTRs
43
Sequence Polymorphisms
refers to variations in the nucleotide sequence of a given region of DNA SNPs and Indels
44
What information can be gained from mtDNA
maternal ancestry degraded samples family lineage mothers side tracing
45
what information can be gained from Y-STR
Y chromosome paternal lineage tracing male family lines paternal relatives ancient male migration patterns
46
How the addition of ddNTPs is used to sequence regions of DNA
terminated DNA chain elongation at specific points=set of fragmented DNA sequences
47
Why sequence PCR reactions only include 1 primer instead of 2
because the sequencing reaction is designed to extend one strand of DNA in the 5' to 3' direction. starting point for DNA polymerase
48
Sequence Polymorphisms for mtDNA
Align the sequenced DNA to a reference Identify differences such as SNPs, insertions, or deletions report polymorphisms by position and type (transition, transversion, insertion, deletion) put the findings in the context of population databases or haplogroups to provide insight into ancestry, lineage, or forensic identification
49
Heteroplasmy
Refers to the presence of more than one type of mitochondrial DNA (mtDNA) in a single cell or organism
50
How to report sequence heteroplasmy
Identify document base change quantify the proportion of each variant contextualize the heteroplasmy
51
Y-STRs are all inherited together
they are located in close proximity on the Y chromosome and do not undergo recombination during meiosis
52
Exception to there only being one peak per locus and what causes it
homologous recombination or mutations that cause multiple alleles exception occurs when there is a duplicated locus or mutations causing more than one peak at a given Y-STR marker
53
Rapidly mutating Y-STRs
class of Y-chromosome Short Tandem Repeats that exhibit a higher mutation rate compared to typical Y-STR markers
54
Rapidly mutating Y-STRs potential advantages
Increased resolution for kinship testing forensic applications Genealogical and Ancestry research Personal Identification

Forensic Biology (3 decks)

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