FINALS LEC: DNA POLYMORPHISM & HUMAN IDENTIFICATION

Question 1

Variations of DNA sequences (ranging from a single base pair to thousands of base pairs) that are shared by 1%-2% or more of a given population

Answer 1

POLYMORPHISM

Question 2

Highly repeated sequences (6-8kbp in length), containing RNA polymerase promoters & open reading frames

Answer 2

Long interspersed nucleotide elements (LINES)

Question 3

Highly repeated sequences approximately 0.3 kbp in length, including Alu elements

Answer 3

Short interspersed nucleotide elements (SINES)

Question 4

Head-to-tail repeats of DNA sequences with <10-bp repeat units

Answer 4

Short tandem repeats (STRs)

Question 5

Head-to-tail repeats in DNA with 10-50-bp repeat units

Answer 5

Variable-number tandem repeats (VNTRs)

Question 6

A sequence variation that results in creating, destroying, or moving a restriction site

Answer 6

Restriction fragment length polymorphisms (RFLPs)

Question 7

are A.K.A. mobile elements/transposable elements/transposons

Answer 7

LINES & SINES

Question 8

is used to form patterns by breaking down DNA

Answer 8

RFLP

Question 9

Differences in sizes & number of fragments generated by restriction enzyme digestion of DNA

Answer 9

Restriction Fragment Length Polymorphisms (RFLPs)

Question 10

RFLP typing in humans required the use of ____

Answer 10

Southern blot technique

Question 11

Only the fragments with complementary sequences to a probe to the B region (top) can be visualized
>2,000 RFLP loci have been described in human DNA

Answer 11

Restriction Fragment Length Polymorphisms (RFLPs)

Question 12

The uniqueness of the collection of
polymorphisms in each individual is the basis for human ID at the DNA level. t or f?

Answer 12

true

Question 13

RFLP protocols for human ID:
▪ Sources of genomic DNA:

Answer 13

blood, saliva, or tissue

Question 14

RFLP protocols for human ID:

North American Labs:

Answer 14

HaeIII restriction enzyme

Question 15

RFLP protocols for human ID:

European labs:

Answer 15

HinfI restriction enzyme

Question 16

Regulation of results from independent labs:

Answer 16

Standard Reference Material (SRM) DNA Profiling Standard for RFLP analysis (1992)

Question 17

Polymorphisms can be used as landmarks/markers in the genome to determine the location of other genes

Answer 17

Genetic Mapping with RFLPs

Question 18

More frequently a particular polymorphism is present in
persons with a disease phenotype = more likely an affected gene is located close to the polymorphism

Answer 18

Genetic Mapping with RFLPs

Question 19

Inherited breast cancer:

Answer 19

RFLP location
BRCA1 gene

Question 20

RFLP location:

Answer 20

17q21

Question 21

BRCA1 gene:

Answer 21

mapped to this position

Question 22

Fragment sizes of an individual are a combination of those from each parent

Answer 22

RFLP & PARENTAGE TESTING

Question 23

alleles/fragment sizes of the child & the mother are analyzed

Answer 23

Paternity test

Question 24

provide the remaining alleles/fragments (inclusion)

Answer 24

Alleged fathers (AFs)

Question 25

1st genetic tool for human ID:

Answer 25

ABO blood group antigens

Question 26

1st human DNA profiling/fingerprinting system:

Answer 26

UK Forensic Science Service (1985) using Sir Alec Jeffrey’s Southern blot multiple-locus probe (MLP)RFLP system

Question 27

Single-locus probe (SLP) (1990) in Europe & N. America

Answer 27

HUMAN ID USING RFLPs

Question 28

Requires 0.7% gels

Answer 28

HUMAN ID USING RFLPs

Question 29

RFLP Southern blot technique:

Answer 29

100 ng to 1 ug of DNA (1-20 kbp)

Question 30

HUMAN ID USING RFLPs Results:

Answer 30

5-7 days

Question 31

Head-to-tail repeats of DNA sequences with <10-bp repeat units

Answer 31

Short Tandem Repeats (STRs)

Question 32

Detection Method of Short Tandem Repeats (STRs)

Answer 32

PCR

Question 33

used to determine the no. of repeats in the locus by the size of the amplicons

Answer 33

Allelic ladders

Question 34

Specimen required for Short Tandem Repeats (STRs):

Answer 34

10 ng (key factor for forensic analysis

Question 35

Analysis of Short Tandem Repeats (STRs):

Answer 35

Fluorescent detection systems (capillary electrophoresis)

Question 36

Analysis time of Short Tandem Repeats (STRs):

Answer 36

24-48 hours

Question 37

(microsatellites or simple sequence repeats) are short tandemly repeated DNA sequences of 1-6 bp in a DNA sequence

Answer 37

Short tandem repeat

Question 38

is a sequence of two or more DNA bases that is repeated many times in a head-to-tail manner on a chromosome.

Answer 38

tandem repeat

Question 39

STR within genes:

Answer 39

according to gene name

Question 40

intron 1 of human tyrosine hydroxylase gene on chromosome 11

Answer 40

TH01

Question 41

lintron 10 of human thyroid peroxidase gene on chromosome 2

Answer 41

TPOX

Question 42

test subject is the father/not

Answer 42

Paternity test

Question 43

likelihood of paternity

Answer 43

Paternity index

Question 44

summarizes & evaluates the genotype information

Answer 44

Combined paternity index (CPI)

Question 45

CPI = 5.719 x 8.932 x 15.41 x 10.22 = 8,044.931

Answer 45

Indicate that the child is 8,045x more likely to have inherited the 4 observed alleles from the AF than from another man

Question 46

5 STR & Sibling Tests

Answer 46

Full-sibling test Half-sibling test Kinship index/sibling index/combined sibling index Avuncular testing Probability of relatedness

Question 47

likelihood that 2 people tested share a common mother & father

Answer 47

Full-sibling test

Question 48

likelihood that 2 people tested share 1 common parent

Answer 48

Half-sibling test

Question 49

likelihood ratio

Answer 49

Kinship index/sibling index/combined sibling index

Question 50

2 alleged relatives are related as either an aunt/uncle of a niece/nephew

Answer 50

Avuncular testing

Question 51

based on the no. of shared alleles between the tested individuals

Answer 51

Probability of relatedness

Question 52

▪ STR located on the Y chromosome, paternally related men share all Y loci ▪ Represented only once per genome & only in males ▪ Applications: forensic, lineage, population studies, kinship testing

Answer 52

Y-STR

Question 53

2 or more males have a common paternal ancestors

Answer 53

Y-STR/paternal lineage test

Question 54

group of males having the same surnames is expected to be related to a common male ancestor, sharing the same Y-chromosome alleles

Answer 54

Surname test

Question 55

Single-nucleotide differences (1-bp)

Answer 55

Single-Nucleotide Polymorphisms (SNPs)

Question 56

human nucleotide sequence differs every 1,000-1,500 bases from 1 individual to another

Answer 56

HGP

Question 57

2 haploid genomes differ at 1 nucleotide per 1,331 bp ❖ 11 million sites in genome of 3 billion bp that vary in at least 1% of the world’s population = 11 million SNPs in each individuals

Answer 57

International SNP Map Working Group

Question 58

▪ Genetic mapping, disease production, and human ID ▪ Detection: direct sequencing ▪ Approx. 10 millions SNPs have been identified (99% have no biological effects; over 60,000 within genes; some are associated with disease) ▪ Classification: according to location, relation to coding sequences, & whether they cause a conservative/nonconservative sequence alteration

Answer 58

SNPs

Question 59

Contribute to individual differences in function & susceptibility to various diseases such as Parkinson disease, Alzheimer disease, bipolar disorder, & cancer

Answer 59

MITOCHONDRIAL DNA POLYMORPHISMS

Question 60

Amino acid variations

Answer 60

PROTEIN BASED ID

Question 61

• Epigenetic alterations (DNA methylation) • Result of environmental events: Profile is unique = no 2 individuals will have the same environmental exposures

Answer 61

EPIGENETIC PROFILES