FINALS: DNA POLYMORPHISMS AND HUMAN ID

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

POLYMORPHISMS

Question 2

STRUCTURE:
Single-nucleotide differences (1-bp), may occur in gene-coding
regions or in intergenic sequences

DETECTION METHODS;
Sequencing, other

Answer 2

SINGLE NUCLEOTIDE POLYMORPHISMS (SNPs)

Question 3

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

DETECTION METHODS;
Sequencing

Answer 3

LONG INTERSPERSED NUCLEOTIDE ELEMENTS (LINES)

Question 4

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

DETECTION METHODS:
Sequencing

Answer 4

SHORT INTERSPERSED NUCLEOTIDE ELEMENTS (SINES)

Question 5

STRUCTURE:
Head-to-tail repeats of DNA sequences with
(LESS THAN) <10-bp repeat units

DETECTION METHODS;
PCR

Answer 5

SHORT TANDEM REPEATS (STRs)

Question 6

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

DETECTION METHODS;
Southern Blot, PCR

Answer 6

VARIABLE - NUMBER TANDEM REPEATS (VNTRs)

Question 7

STRUCTURE:
A sequence variation that results in CREATING, DESTROYING
, or MOVING a restriction site

DETECTION METHODS;
Southern Blot

Answer 7

RESTRICTION FRAGMENT LENGTH POLYMORPHISMS (RFLPs)

Question 8

RFLP IS USED TO FORM PATTERN BY?

Answer 8

BREAKING DOWN DNA

Question 9

• DIFFERENCES IN SIZE & NUMBER of FRAGMENTS generated by restriction enzyme digestion of DNA

 Nucleotide changes may also destroy, change, or create restriction enzymes sites, altering the number of fragments.

Answer 9

RESTRICTION FRAGMENT LENGTH
POLYMORPHISMS (RFLPs)

Question 10

RFLP typing in humans required the use
of

Answer 10

Southern blot technique

Question 11

The ________of the collection of polymorphisms in each individual is the BASIS FOR HUMAN ID AT THE DNA LEVEL.

Answer 11

uniqueness

Question 12

RFLP protocols for human ID:
North American labs use?

Answer 12

Haelll restriction enzyme
(Haemophilus aegyptius)

Question 13

RFLP protocols for human ID:
European labs use?

Answer 13

Hinfl restriction enzyme
(Haemophilus influenzae strain Rd.)

Question 14

A. GENETIC MAPPING WITH RFLPs
Polymorphisms can be used as __________ in the genome to determine the location of other genes

Answer 14

landmarks/markers

Question 15

A. GENETIC MAPPING WITH RFLPs

More frequently a particular polymorphism is present in persons with a disease phenotype =

Answer 15

MORE LIKELY THE AFFECTED GENE IS LOCATED CLOSE TO THE POLYMORPHISM

Question 16

❖ Inherited breast cancer:
RFLP location:

Answer 16

17q21

Question 17

❖ Inherited breast cancer:
_____: mapped to this position

Answer 17

BRCA1 gene

Question 18

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

Answer 18

RFLP & PARENTAGE TESTING

Question 19

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

Answer 19

Paternity test

Question 20

provide the remaining alleles/fragments (inclusion)

Answer 20

Alleged fathers (AFs)

Question 21

C. HUMAN ID USING RFLPS
- 1st genetic tool for human ID:

Answer 21

ABO blood group antigens

Question 22

C. HUMAN ID USING RFLPS
- 1st human DNA profiling/fingerprinting
system:

Answer 22

UK Forensic Science Service (1985) using Sir Alec Jeffrey’s Southern blot multiple-locus probe (MLP)-RFLP system
- Single-locus probe (SLP) (1990) in Europe & N. America

Question 23

RFLP Southern blot technique:
(how much/many?)

Answer 23

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

Question 24

• HEAD-TO-TAIL repeats of DNA sequences with <10-bp repeat units
• Detection method: PCR

Answer 24

SHORT TANDEM REPEATS (STRS)

Question 25

used to determine the no. of repeats in the locus by the SIZE OF THE AMPLICONS

Answer 25

Allelic ladders

Question 26

SHORT TANDEM REPEATS (STRS)
Specimen required:

Answer 26

10 ng (key factor for forensic analysis)

Question 27

SHORT TANDEM REPEATS (STRS)
Analysis:
Analysis time:

Answer 27

• Fluorescent detection
  systems (capillary electrophoresis)
• 24-48 hours

Question 28

STR NOMENCLATURE

Answer 28

International Society for Forensic
Genetics (1997)

Question 29

STR & SEX ID
Amelogenin gene:

Answer 29

located on the X & Y
chromosomes

Question 30

likelihood of paternity

Answer 30

Paternity index

Question 31

summarizes & evaluates the genotype information

Answer 31

Combined paternity index (CPI)

Question 32

likelihood that 2 people tested share a common mother & father

Answer 32

Full-sibling test:

Question 33

likelihood that 2 people tested share 1 common parent

Answer 33

Half-sibling test:

Question 34

likelihood ratio

Answer 34

Kinship index/sibling
index/combined sibling index:

Question 35

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

Answer 35

Avuncular testing:

Question 36

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

Answer 36

Probability of relatedness:

Question 37

• 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 37

Y-STR

Question 38

2 or more males have a common paternal
ancestors

Answer 38

Y-STR/paternal lineage test:

Question 39

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

Answer 39

SURNAME TEST

Question 40

• Single-nucleotide differences (1-bp)
• HGP: human nucleotide sequence
  differs every 1,000-1,500 bases from 1
  individual to another
• International SNP Map Working Group:
  2 haploid genomes differ at 1
  nucleotide per 1,331 bp
  o 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 40

SINGLE-NUCLEOTIDE
POLYMORPHISMS (SNPs)

Question 41

• COLLECTIONS of DNA sequence variants
  used as a reference for screening
  genomic sequencing data
• Detection of variant: sequencing, may
  already be described or associated with
  a disease phenotype as noted in the
  databases
• Include short deletions, insertions, &
  duplications involving more than 1
  nucleotides
• dbSNP, dbVar, ClinVar, & others

Answer 41

SNP DATABASES

Question 42

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

Answer 42

MITOCHONDRIAL DNA
POLYMORPHISMS

Question 43

OTHER ID METHODS
- Amino acid variations

Answer 43

PROTEIN BASED ID

Question 44

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

Answer 44

EPIGENETIC PROFILES