CHAPTER 10 MB

Question 1

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.

Answer 1

POLYMORPHISMS

Question 2

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.

Answer 2

98%

Question 3

May occur in gene-coding regions or in intergenic sequences

Answer 3

SINGLE NUCLEOTIDE POLYMORPHISMS

Question 4

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.

Answer 4

human leukocyte antigen (HLA) ; peptides

Question 5

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

Answer 5

Long Interspersed Nucleotide Elements (LINEs)

Question 6

0.3 kbp in size, are present in over 1,000,000 copies per genome.

Answer 6

Short Interspersed Nucleotide Elements (SINEs)

Question 7

Short Interspersed Nucleotide Elements (SINEs) include __________ - named for harboring recognition sites for the Alu(I) restriction
enzyme.

Answer 7

Alu elements

Question 8

• There are well in excess of 1 million Alu elements, accounting for almost __________
• The majority of transcribed genes contain Alu elements in their _____

Answer 8

11% of the human genome ; introns

Question 9

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.

Answer 9

cryptic splice and polyadenylation sites

Question 10

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 _______

Answer 10

mobile elements ; transposable elements ; pseudogenes

Question 11

Shorter blocks of repeated sequences also undergo expansion or shrinkage through generations.

Answer 11

SHORT TANDEM REPEATS (STRs) and VARIABLE-NUMBER TANDEM REPEATS (VNTRs)

Question 12

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 _________

Answer 12

restriction fragment length polymorphisms (RFLPs).

Question 13

Analysis of restriction fragments by Southern blot

Answer 13

RESTRICTION FRAGMENT LENGTH POLYMORPHISMS (RFLPs)

Question 14

One or more nucleotide changes that affect the size of restriction enzyme products

Answer 14

RESTRICTION FRAGMENT LENGTH POLYMORPHISMS (RFLPs)

Question 15

STRUCTURE: One or more nucleotide changes that affect the size of restriction enzyme products

DETECTION METHOD: SOUTHERN BLOT

Answer 15

RFLP - RESTRICTION FRAGMENT LENGTH POLYMORPHISMS

Question 16

STRUCTURE: Repeats of 10–50 base sequences in tandem

DETECTION METHOD: SOUTHERN BLOT, PCR

Answer 16

VNTR - VARIABLE-NUMBER TANDEM REPEATS

Question 17

STRUCTURE: Repeats of 1–10 base sequences in tandem

DETECTION METHOD: PCR

Answer 17

STR - SHORT TANDEM REPEATS

Question 18

STRUCTURE: Alterations of a single nucleotide

DETECTION METHOD: SEQUENCING, OTHER

Answer 18

SNP - SINGLE NUCLEOTIDE POLYMORPHISMS

Question 19

In RFLP typing, Original DNA targets used for ________, ___________, and __________.

Answer 19

gene mapping ; human identification ; parentage testing

Question 20

Observed as differences in the sizes and number of fragments generated by restriction enzyme digestion of DNA

Answer 20

RFLP TYPING

Question 21

__________ may also destroy, change, or create restriction enzyme sites, altering the number of fragments

Answer 21

Nucleotide changes

Question 22

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

Answer 22

to construct a restriction enzyme map of the DNA region under investigation

Question 23

___________ are detected by observing fragment numbers and sizes different from those expected from the reference restriction map.

Answer 23

Polymorphisms

Question 24

RFLP typing in humans required the use of the
___________. DNA was cut with _______-, resolved by ________, and blotted to a _________.

Answer 24

Southern blot technique ; restriction enzymes ; gel electrophoresis ; membrane

Question 25

Human beings are diploid with two copies of every locus. In other words, each person has ____ alleles of each locus.

Answer 25

two

Question 26

If these alleles are the same, the locus is ________; if the two alleles are different, the locus is ___________.

Answer 26

homozygous ; heterozygous

Question 27

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.

Answer 27

HaeIII ; HinfI

Question 28

_________ are used to determine the probability that an unknown gene is located close to a known marker in the genome.

Answer 28

Formal statistical methods

Question 29

__________ used RFLP to map one of the genes mutated in inherited breast cancer.

Answer 29

Mary Claire King

Question 30

A parentage test requires analysis of at least _______. The more loci tested, the higher the probability of positive identification of the father.

Answer 30

eight loci

Question 31

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.

Answer 31

ABO blood group antigens

Question 32

The initial use of DNA as human identification tool relied on ______ detectable by Southern blot

Answer 32

RFLP

Question 33

DNA Fingerprinting With RFLP The first human DNA profiling system was introduced by the ____________ in 1985 using ______________ system

Answer 33

United Kingdom Forensic Science Service ; Sir Alec Jeffrey’s Southern blot multiple-locus probe (MLP) -RFLP

Question 34

___________ system could take 5 to 7 days to yield clear results

Answer 34

P-based probe

Question 35

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

Answer 35

continuous allele

Question 36

__________, 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

Answer 36

Professor Sir Alec John Jeffreys

Question 37

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

Answer 37

HLA DQ alpha system ; DQA1; 28

Question 38

with the addition of the __________, the analyst could type five additional genetic markers.

Answer 38

Polymarker (PM) system

Question 39

The ________ is a set of primers complementary to sequences flanking STRs, or microsatellites.

Answer 39

PM system

Question 40

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.

Answer 40

microvariants

Question 41

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

Answer 41

Silver-stained gels ; capillary electrophoresis with fluorescent dyes

Question 42

was developed for surname testing and forensic identification of male offenders or victims. This primer set only amplifies STR located on the Y chromosome

Answer 42

Y-STR

Question 43

sets of fragments representing all possible alleles of a repeat locus

Answer 43

allelic ladders

Question 44

_____ 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.

Answer 44

STR TH01 ; TPOX

Question 45

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).

Answer 45

DNA ; segment

Question 46

GENDER IDENTIFICATION _________ is a very useful marker often analyzed along with STR

Answer 46

amelogenin locus

Question 47

GENDER IDENTIFICATION The __________, which is not an STR, is located on the X and Y chromosomes.

Answer 47

amelogenin gene

Question 48

a term used to express the situation where all locus genotypes (alleles) from two sources are the same.

Answer 48

Genetic concordance

Question 49

________ 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

Answer 49

Technical artifacts

Question 50

_______ 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.

Answer 50

Stutter

Question 51

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.

Answer 51

bin

Question 52

Collection of all peaks or bands within a characteristic distribution of positions and areas is called _______.

Answer 52

binning

Question 53

The _________ is an approximation of the more conservative floating-bin approach. An alternative assessment of allele certainty is the use of _________

Answer 53

fixed-bin approach ; locus-specific brackets

Question 54

_____________, or the ___________. The population frequency of two alleles, p and q, can be expressed mathematically as p^2 + 2pq + q^2 = 1.0

Answer 54

Hardy–Weinberg equilibrium ; Hardy–Weinberg law

Question 55

_________ was the basis for the National DNA Database (NDNAD) launched in Britain in 1995

Answer 55

Sir Alec Jeffreys’ DNA profiling

Question 56

The ___________ is the federal level of the CODIS used in the United States. There are three levels of CODIS: the ____________, ____________, and ____.

Answer 56

National DNA Index System (NDIS) 1. Local DNA Index System (LDIS) 2. State DNA Index System (SDIS) 3. NDIS

Question 57

Peter Gill developed a forensic DNA identification method for minimal samples called ____________

Answer 57

low copy-number analysis

Question 58

Low-copy-number analysis is reportedly performed on less than _______ (about 16 diploid cells)

Answer 58

100 pg DNA

Question 59

_______ 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

Answer 59

Paternity index

Question 60

__________, which summarizes and evaluates the genotype information

Answer 60

Combined paternity index (CPI)

Question 61

Probability of paternity, a number calculated from the combined _________ (genetic evidence) and _______ (nongenetic evidence)

Answer 61

paternity index ; prior odds

Question 62

ratio generated by sibling test.

Answer 62

kinship index, sibling index, or combined sibling index

Question 63

A _________ is a determination of the likelihood that two people tested share a common mother and father.

Answer 63

full sibling test

Question 64

A ________ is a determination of the likelihood that two people tested share one common parent (mother or father).

Answer 64

half-sibling test

Question 65

_______, which measures the probabilities that two alleged relatives are related as either an aunt or an uncle of a niece or nephew.

Answer 65

avuncular testing

Question 66

The ________ can determine whether two or more males have a common paternal ancestor

Answer 66

Y-STR/paternal lineage test

Question 67

_________ is calculated from the frequency of occurrence of a given haplotype in a tested population.

Answer 67

Haplotype diversity (HD)

Question 68

________ is determined by the number of different haplotypes seen in the tested population and the total number of samples in the population

Answer 68

Discriminatory capacity (DC)

Question 69

The European Y chromosome typing community has established a set of Y-STR loci termed the ______

Answer 69

minimal haplotype

Question 70

An “___________” includes all of the loci from the minimal haplotype plus the highly polymorphic dinucleotide repeat YCAII

Answer 70

extended haplotype

Question 71

LINKAGE ANALYSIS Three basic approaches are used to map genes: _________. _______ and _______.

Answer 71

family histories, population studies, and sibling analyses

Question 72

___________ is to look for gene associations in large numbers of unrelated individuals in population studies.

Answer 72

linkage analysis

Question 73

__________ is a method used to treat malignant and nonmalignant blood disorders as well as some solid tumors.

Answer 73

Bone marrow transplantation

Question 74

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 (_________).

Answer 74

conditioning

Question 75

The allogeneic stem cells are then expected to reestablish a new bone marrow in the recipient (_______).

Answer 75

engraftment

Question 76

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.

Answer 76

donor matching

Question 77

After conditioning and infusion with the donor cells, the patient enters the __________.

Answer 77

engraftment phase

Question 78

The engraftment of donor cells in the recipient must be monitored (___ days). ______ has become the method of choice for engraftment monitoring.

Answer 78

90 ; DNA typing

Question 79

In the laboratory, there are two parts to engraftment/ chimerism DNA testing.

Answer 79

1. screening to find at lease one informative locus 2. engraftment analysis

Question 80

_________ are those in which the donor and the recipient have the same alleles.

Answer 80

Noninformative loci

Question 81

After the transplant, analysis of the gel band pattern from the blood or bone marrow of the recipient revealed one of three different states:

Answer 81

1. Full Chimerism 2. Mixed Chimerism 3. Graft Failure

Question 82

in which only the donor alleles were detected in the recipient

Answer 82

Full Chimerism

Question 83

in which a mixture of donor and recipient alleles was present

Answer 83

mixed chimerism

Question 84

in which only recipient alleles were detectable

Answer 84

graft failure

Question 85

qPCR of SNP advantage:

Answer 85

higher throughput and lower sample requirements.

Question 86

In PSTR Testing, Donor and recipient DNA for allele screening prior to transplant can be isolated from ___ or _____.

Answer 86

blood or buccal cells

Question 87

Multiple loci can be screened simultaneously using ________.

Answer 87

multiplex PCR

Question 88

isolated granulocytes may show full chimerism, whereas the T-cell fraction still shows mixed chimerism.

Answer 88

Split chimerisms

Question 89

- 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.

Answer 89

The Human Haplotype Mapping (HapMap) Project

Question 90

Mitochondrial genome has two noncoding regions that vary in DNA sequence, the ______ and the ________, or HV1 and HV2

Answer 90

hypervariable region 1 ; hypervariable region 2

Question 91

Mitochondrial nucleotide sequence data are divided into two components:

Answer 91

1. Forensic 2. Public

Question 92

- consists of anonymous population profiles - used to assess the extent of certainty of mtDNA identifications in forensic casework.

Answer 92

Forensic

Question 93

provide information on worldwide population groups not contained within the forensic data and can be used for investigative purposes.

Answer 93

Public

Question 94

OTHER IDENTIFICATION METHODS

Answer 94

1. Protein Based Identification 2. Epigenetic Profiles

Question 95

______________ produce single-amino-acid polymorphisms in proteins.

Answer 95

Nonsynonymous DNA polymorphisms

Question 96

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.

Answer 96

Epigenetic changes

Question 97

_________ change in the absence of cell division or DNA sequence alterations.

Answer 97

Epigenetic alterations