CHAPTER 10 MB Flashcards
Are variations of DNA sequences that are shared by a certain percentage of a population. These sequences range from a single base pair to thousands of base pairs.
POLYMORPHISMS
The probability of polymorphic DNA in humans is great due to the relatively large size of
the human genome, ___ of which does not code for genes.
98%
May occur in gene-coding regions or in intergenic sequences
SINGLE NUCLEOTIDE POLYMORPHISMS
Polymorphisms are more frequent in some areas of the genome than in others. The _________ locus is a familiar example of a highly polymorphic regions of human DNA
- The variable nucleotide sequences in this locus code for _____ that establish self-identity of the immune system.
human leukocyte antigen (HLA) ; peptides
Are highly repeated sequences, 6 to 8 kbp in length, that contain RNA polymerase promoters and open reading frames related to the reverse transcriptase of retroviruses
Long Interspersed Nucleotide Elements (LINEs)
0.3 kbp in size, are present in over 1,000,000 copies per genome.
Short Interspersed Nucleotide Elements (SINEs)
Short Interspersed Nucleotide Elements (SINEs) include __________ - named for harboring recognition sites for the Alu(I) restriction
enzyme.
Alu elements
- There are well in excess of 1 million Alu elements, accounting for almost __________
- The majority of transcribed genes contain Alu elements in their _____
11% of the human genome ; introns
Alu elements have _______ and ________, which can become activated through the accumulation of mutations and lead to alternative splicing of RNAs or premature termination of translation.
cryptic splice and polyadenylation sites
LINEs and SINEs are also known as ______ or _________. They are copied and spread by recombination and reverse transcription and may be responsible for the formation of _______
mobile elements ; transposable elements ; pseudogenes
Shorter blocks of repeated sequences also undergo expansion or shrinkage through generations.
SHORT TANDEM REPEATS (STRs) and VARIABLE-NUMBER TANDEM REPEATS (VNTRs)
SNPs, larger sequence variants, and tandem repeats can be detected by observing changes in the restriction map of a DNA region. Analysis of restriction fragments by Southern blot reveals _________
restriction fragment length polymorphisms (RFLPs).
Analysis of restriction fragments by Southern blot
RESTRICTION FRAGMENT LENGTH POLYMORPHISMS (RFLPs)
One or more nucleotide changes that affect the size of restriction enzyme products
RESTRICTION FRAGMENT LENGTH POLYMORPHISMS (RFLPs)
STRUCTURE: One or more nucleotide changes that affect the size of restriction enzyme products
DETECTION METHOD: SOUTHERN BLOT
RFLP - RESTRICTION FRAGMENT LENGTH POLYMORPHISMS
STRUCTURE: Repeats of 10–50 base sequences in tandem
DETECTION METHOD: SOUTHERN BLOT, PCR
VNTR - VARIABLE-NUMBER TANDEM REPEATS
STRUCTURE: Repeats of 1–10 base sequences in tandem
DETECTION METHOD: PCR
STR - SHORT TANDEM REPEATS
STRUCTURE: Alterations of a single nucleotide
DETECTION METHOD: SEQUENCING, OTHER
SNP - SINGLE NUCLEOTIDE POLYMORPHISMS
In RFLP typing, Original DNA targets used for ________, ___________, and __________.
gene mapping ; human identification ; parentage testing
Observed as differences in the sizes and number of fragments generated by restriction enzyme digestion of DNA
RFLP TYPING
__________ may also destroy, change, or create restriction enzyme sites, altering the number of fragments
Nucleotide changes
The first step in using RFLPs is ________________________________. Once the restriction map is known, the number and sizes of the restriction fragments of a test DNA region cut with restriction enzymes are compared with the number and sizes of fragments expected based on the restriction map
to construct a restriction enzyme map of the DNA region under investigation
___________ are detected by observing fragment numbers and sizes different from those expected from the reference restriction map.
Polymorphisms
RFLP typing in humans required the use of the
___________. DNA was cut with _______-, resolved by ________, and blotted to a _________.
Southern blot technique ; restriction enzymes ; gel electrophoresis ; membrane
Human beings are diploid with two copies of
every locus. In other words, each person has ____ alleles of each locus.
two
If these alleles are the same, the locus is ________; if the two alleles are different, the locus is ___________.
homozygous ; heterozygous
RFLP protocols for human identification in most North American laboratories used the restriction enzyme ____ for fragmentation of genomic DNA, Many European laboratories used the ______ enzyme.
HaeIII ; HinfI
_________ are used to determine the probability that an unknown gene is located close to a known marker in the genome.
Formal statistical methods
__________ used RFLP to map one of the genes mutated in inherited breast cancer.
Mary Claire King
A parentage test requires analysis of at least _______. The more loci tested, the higher the probability of positive identification of the father.
eight loci
The initial use of DNA as an identification tool relied on RFLP detectable by Southern blot. The first genetic tool used for human identification was the ____________. Although this type of analysis could be performed in a few minutes, the discrimination power was low.
ABO blood group antigens
The initial use of DNA as human identification tool relied on ______ detectable by Southern blot
RFLP
DNA Fingerprinting With RFLP
The first human DNA profiling system was introduced by the ____________ in 1985 using ______________ system
United Kingdom Forensic Science Service ; Sir Alec Jeffrey’s Southern blot multiple-locus probe (MLP) -RFLP
___________ system could take 5 to 7 days to yield clear results
P-based probe
RFLP is an example of a ____________ system in which the sizes of the fragments define alleles. Therefore, precise band sizing was critical to the accuracy of the results
continuous allele
__________, a British geneticist, first developed techniques for genetic profiling, or DNA fingerprinting, using RFLP to identify humans. The technique has been used in forensics and law enforcement to resolve paternity and immigration disputes. The method can also be applied to nonhuman species, for example, in wildlife population genetic
Professor Sir Alec John Jeffreys
The first commercial and validated typing test based on polymerase chain reaction (PCR) specifically for forensic use was the _________, now called ______, developed in 1986. This system could distinguish ___ DQA1 types
HLA DQ alpha system ; DQA1; 28
with the addition of the __________, the analyst could type five additional genetic markers.
Polymarker (PM) system
The ________ is a set of primers complementary to sequences flanking STRs, or microsatellites.
PM system
STRs contain repeat units with altered sequences, or ________, repeat units missing one or more bases of the repeat. These differences have arisen through mutation or recombination events.
microvariants
The sizes of the PCR products are influenced by the number of embedded repeats. If one of each primer pair is labeled with a fluorescent marker, the PCR product can be analyzed in fluorescent detection systems. _______ may also be used; however, ___________ is the preferable method, especially for high-throughput requirements
Silver-stained gels ; capillary electrophoresis with fluorescent dyes
was developed for surname testing and forensic identification of male offenders or victims. This primer set only amplifies STR located on the Y chromosome
Y-STR
sets of fragments representing all possible alleles of a repeat locus
allelic ladders
_____ is located in intron 1 of the human tyrosine hydroxylase gene on chromosome 11, and ____ is located in intron 10 of the human thyroid peroxidase gene on chromosome 2.
STR TH01 ; TPOX
Non-gene-associated STRs are designated by the D#S# system.
- In this system, the “D” stands for ____; the following number designates the chromosome where the STR is located (1-22, X or Y).
- “S” refers to a unique _____, followed by a number registered in the International Genome Database (GDB).
DNA ; segment
GENDER IDENTIFICATION
_________ is a very useful marker often analyzed along with STR
amelogenin locus
GENDER IDENTIFICATION
The __________, which is not an STR, is located on the X and Y chromosomes.
amelogenin gene
a term used to express the situation where all locus genotypes (alleles) from two sources are the same.
Genetic concordance
________ such as air bubbles, crystals, and dye blobs, as well as sample contaminants, temperature variations, and voltage spikes, can interfere with consistent band migration during electrophoresis
Technical artifacts
_______ is another anomaly of PCR amplification, in which the polymerase may miss a repeat during the replication process, resulting in two or more different species in the amplified product.
Stutter
An acceptable range of sizes in this distribution is a ____. A ____ can be thought of as an uncertainty window surrounding the mean position (size) of multiple runs of each peak or band.
bin
Collection of all peaks or bands within a characteristic distribution of positions and areas is called _______.
binning
The _________ is an approximation of the more conservative floating-bin approach. An alternative assessment of allele certainty is the use of _________
fixed-bin approach ; locus-specific brackets
_____________, or the ___________. The population frequency of two alleles, p and q, can be expressed mathematically as p^2 + 2pq + q^2 = 1.0
Hardy–Weinberg equilibrium ; Hardy–Weinberg law
_________ was the basis for the National DNA Database (NDNAD) launched in Britain in 1995
Sir Alec Jeffreys’ DNA profiling
The ___________ is the federal level of the CODIS used in the United States. There are three levels of CODIS: the ____________, ____________, and ____.
National DNA Index System (NDIS)
- Local DNA Index System (LDIS)
- State DNA Index System (SDIS)
- NDIS
Peter Gill developed a forensic DNA identification method for minimal samples called ____________
low copy-number analysis
Low-copy-number analysis is reportedly performed on less than _______ (about 16 diploid cells)
100 pg DNA
_______ is an expression of how many times more likely the child ’ s allele is inherited from the alleged father than by another man in the general population
Paternity index
__________, which summarizes and evaluates the genotype information
Combined paternity index (CPI)
Probability of paternity, a number calculated from the combined _________ (genetic evidence) and _______ (nongenetic evidence)
paternity index ; prior odds
ratio generated by sibling test.
kinship index, sibling index, or combined sibling index
A _________ is a determination of the likelihood that two people tested share a common mother and father.
full sibling test
A ________ is a determination of the likelihood that two people tested share one common parent (mother or father).
half-sibling test
_______, which measures the probabilities that two alleged relatives are related as either an aunt or an uncle of a niece or nephew.
avuncular testing
The ________ can determine whether two or more males have a common paternal ancestor
Y-STR/paternal lineage test
_________ is calculated from the frequency of occurrence of a given haplotype in a tested population.
Haplotype diversity (HD)
________ is determined by the number of different haplotypes seen in the tested population and the total number of samples in the population
Discriminatory capacity (DC)
The European Y chromosome typing community has established a set of Y-STR loci termed the ______
minimal haplotype
An “___________” includes all of the loci from the minimal haplotype plus the highly polymorphic dinucleotide repeat YCAII
extended haplotype
LINKAGE ANALYSIS
Three basic approaches are used to map genes: _________. _______ and _______.
family histories, population studies, and sibling analyses
___________ is to look for gene associations in large numbers of unrelated individuals in population studies.
linkage analysis
__________ is a method used to treat malignant and nonmalignant blood disorders as well as some solid tumors.
Bone marrow transplantation
In allogeneic transplant strategies, high doses of therapy completely remove the recipient bone marrow, particularly the stem cells that give rise to all the other cells in the marrow (_________).
conditioning
The allogeneic stem cells are then expected to reestablish a new bone marrow in the recipient (_______).
engraftment
The first phase of allogeneic transplantation is ______, in which potential donors are tested for immunological compatibility. This is performed by examining the HLA locus to determine which donor would be most tolerated by the recipient immune system.
donor matching
After conditioning and infusion with the donor cells, the patient enters the __________.
engraftment phase
The engraftment of donor cells in the recipient must be monitored (___ days). ______ has become the method of choice for engraftment monitoring.
90 ; DNA typing
In the laboratory, there are two parts to engraftment/ chimerism DNA testing.
- screening to find at lease one informative locus
- engraftment analysis
_________ are those in which the donor and the recipient have the same alleles.
Noninformative loci
After the transplant, analysis of the gel band pattern from the blood or bone marrow of the recipient revealed one of three different states:
- Full Chimerism
- Mixed Chimerism
- Graft Failure
in which only the donor alleles were detected
in the recipient
Full Chimerism
in which a mixture of donor and recipient alleles was present
mixed chimerism
in which only recipient alleles were detectable
graft failure
qPCR of SNP advantage:
higher throughput and lower sample requirements.
In PSTR Testing, Donor and recipient DNA for allele screening prior to transplant can be isolated from ___ or _____.
blood or buccal cells
Multiple loci can be screened simultaneously using ________.
multiplex PCR
isolated granulocytes may show full chimerism, whereas the T-cell fraction still shows mixed chimerism.
Split chimerisms
- Its goal was to develop a haplotype map of the human genome.
- It is used to identify common disease associations and patterns of human DNA sequence variation.
The Human Haplotype Mapping (HapMap) Project
Mitochondrial genome has two noncoding regions that vary in DNA sequence, the ______ and the ________, or HV1 and HV2
hypervariable region 1 ; hypervariable region 2
Mitochondrial nucleotide sequence data are divided into two components:
- Forensic
- Public
- consists of anonymous population profiles
- used to assess the extent of certainty of mtDNA identifications in forensic casework.
Forensic
provide information on worldwide population groups not contained within the forensic data and can be used for investigative purposes.
Public
OTHER IDENTIFICATION METHODS
- Protein Based Identification
- Epigenetic Profiles
______________ produce single-amino-acid polymorphisms in proteins.
Nonsynonymous DNA polymorphisms
occur as a result of environmental events, such that a putative epigenetic profile is unique to each individual because no two individuals will have the same environmental exposures.
Epigenetic changes
_________ change in the absence of cell division or DNA sequence alterations.
Epigenetic alterations
