FINALS: DNA POLYMORPHISMS AND HUMAN ID Flashcards
- 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
POLYMORPHISMS
STRUCTURE:
Single-nucleotide differences (1-bp), may occur in gene-coding
regions or in intergenic sequences
DETECTION METHODS;
Sequencing, other
SINGLE NUCLEOTIDE POLYMORPHISMS (SNPs)
STRUCTURE:
Highly repeated sequences (6-8kbp in length), containing RNA
polymerase promoters & open reading frames
DETECTION METHODS;
Sequencing
LONG INTERSPERSED NUCLEOTIDE ELEMENTS (LINES)
STRUCTURE:
Highly repeated sequences approximately 0.3
kbp in length, including Alu elements
DETECTION METHODS:
Sequencing
SHORT INTERSPERSED NUCLEOTIDE ELEMENTS (SINES)
STRUCTURE:
Head-to-tail repeats of DNA sequences with
(LESS THAN) <10-bp repeat units
DETECTION METHODS;
PCR
SHORT TANDEM REPEATS (STRs)
STRUCTURE:
Head-to-tail repeats in DNA with 10-50-bp repeat units
DETECTION METHODS;
Southern Blot, PCR
VARIABLE - NUMBER TANDEM REPEATS (VNTRs)
STRUCTURE:
A sequence variation that results in CREATING, DESTROYING
, or MOVING a restriction site
DETECTION METHODS;
Southern Blot
RESTRICTION FRAGMENT LENGTH POLYMORPHISMS (RFLPs)
RFLP IS USED TO FORM PATTERN BY?
BREAKING DOWN DNA
- 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.
RESTRICTION FRAGMENT LENGTH
POLYMORPHISMS (RFLPs)
RFLP typing in humans required the use
of
Southern blot technique
The ________of the collection of polymorphisms in each individual is the BASIS FOR HUMAN ID AT THE DNA LEVEL.
uniqueness
RFLP protocols for human ID:
North American labs use?
Haelll restriction enzyme
(Haemophilus aegyptius)
RFLP protocols for human ID:
European labs use?
Hinfl restriction enzyme
(Haemophilus influenzae strain Rd.)
A. GENETIC MAPPING WITH RFLPs
Polymorphisms can be used as __________ in the genome to determine the location of other genes
landmarks/markers
A. GENETIC MAPPING WITH RFLPs
More frequently a particular polymorphism is present in persons with a disease phenotype =
MORE LIKELY THE AFFECTED GENE IS LOCATED CLOSE TO THE POLYMORPHISM
❖ Inherited breast cancer:
RFLP location:
17q21
❖ Inherited breast cancer:
_____: mapped to this position
BRCA1 gene
- Fragment sizes of an individual are a combination of those from each parent
RFLP & PARENTAGE TESTING
alleles/fragment sizes of
the child & the mother are analyzed
Paternity test
provide the remaining alleles/fragments (inclusion)
Alleged fathers (AFs)
C. HUMAN ID USING RFLPS
- 1st genetic tool for human ID:
ABO blood group antigens
C. HUMAN ID USING RFLPS
- 1st human DNA profiling/fingerprinting
system:
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
RFLP Southern blot technique:
(how much/many?)
100 ng to 1 ug of DNA (1-20 kbp)
- HEAD-TO-TAIL repeats of DNA sequences with <10-bp repeat units
- Detection method: PCR
SHORT TANDEM REPEATS (STRS)
used to determine the no. of repeats in the locus by the SIZE OF THE AMPLICONS
Allelic ladders
SHORT TANDEM REPEATS (STRS)
Specimen required:
10 ng (key factor for forensic analysis)
SHORT TANDEM REPEATS (STRS)
Analysis:
Analysis time:
- Fluorescent detection
systems (capillary electrophoresis) - 24-48 hours
STR NOMENCLATURE
International Society for Forensic
Genetics (1997)
STR & SEX ID
Amelogenin gene:
located on the X & Y
chromosomes
likelihood of paternity
Paternity index
summarizes & evaluates the genotype information
Combined paternity index (CPI)
likelihood that 2 people tested share a common mother & father
Full-sibling test:
likelihood that 2 people tested share 1 common parent
Half-sibling test:
likelihood ratio
Kinship index/sibling
index/combined sibling index:
2 alleged relatives are related as either an aunt/uncle of a niece/nephew
Avuncular testing:
based on the no. of shared alleles between the tested individuals
Probability of relatedness:
- 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
Y-STR
2 or more males have a common paternal
ancestors
Y-STR/paternal lineage test:
group of males having
the same surnames is expected to be
related to a common male ancestor,
sharing the same Y-chromosome
alleles
SURNAME TEST
- 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
SINGLE-NUCLEOTIDE
POLYMORPHISMS (SNPs)
- 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
SNP DATABASES
OTHER ID METHODS
- Contribute to individual differences in
function & susceptibility to various
diseases such as Parkinson disease,
Alzheimer disease, bipolar disorder, &
cancer
MITOCHONDRIAL DNA
POLYMORPHISMS
OTHER ID METHODS
- Amino acid variations
PROTEIN BASED ID
OTHER ID METHODS
- Epigenetic alterations (DNA methylation)
- Result of environmental events: Profile is unique = no 2 individuals will have the same environmental exposures
EPIGENETIC PROFILES
