DNA Polymorphisms and ID: Exam 3

Polymorphism

presence of two or more inherited variant forms of a specific DNA sequence (genetic mutations in a population)

- can occur among different individuals or populations

- variations occurring in > 1% of population can be considered useful polymorphisms

Types of Polymorphisms

SNPS, polymorphic repetitive elements, microsatellites, small INDELS, and RFLPS

SNPs

single nucleotide polymorphisms 

- most common type; each individual has 11 million 

- 99% have no biological effect

- each SNP represents difference in single nucleotide in DNA sequence 

Polymorphic Repetitive Elements 

large or short blocks of repeated sequences 

- may be inverted, deleted, duplicated from one individual to another 

- LINEs or SINEs

- LINEs: long elements 6-8kbp

- SINEs: short elements 0.3kbps

Microsatellites

VNTRS or STRS

- variable number tandem repeats (VNTRs): 10-50bp

- short tandem repeats (STRs): 1-10bp

Small INDELs

insertion or deletion variations among individuals

- cause of similar levels of variations as SNPS

RFLPs

restriction fragment length polymorphisms

- one or more nucleotide change that affects the size of restriction enzyme products

RFLP Typing

differences in the sizes and number of fragments generated by RE digestion of DNA

- change in nucleotide sequence alters restriction site

RFLP Typing Steps

create a restriction map and compare the number and sizes of fragments

- detects polymorphisms by observing the number and size of fragments 

RFLP Inheritance

offspring inherit a combination of parental polymorphisms 

- single locus will have several alleles/versions 

- band patterns represent combination of RFLPs inherited from each parent 

- can test for paternity; 8 loci needed 

STR (short tandem repeat) Typing by PCR

uses a polymarker system to amplify loci; set of primers complementary to sequences

- used in forensics 

- number of repeats within an STR is referred to as an allele 

Y-STR Identification 

AMEL locus (amelogenin) is used to identify male individuals 

- amplification and electrophoresis reveals two bands for males and one band for females

Genotyping

peak or band patterns must be converted to genotype for allele identification 

- represents homologous chromosomes when repeated on both chromosomes

- if one has a repeat in one chromosome and a different one in another then it would be heterologous 

Partial Repeat Units

microvariant alleles indicated by the number of complete repeat units followed by a decimal point indicating the number of incomplete units

- 9.3 locus; full 9 TCAT and one 3bp repeat

Genetic Concordance

all alleles from two sources are the same

- indicates inclusion of a single individual as the donor of both genotypes

Genotyping Considerations

stutter: error due to pol missing a repeat during amplification

intragel precision: comparing bands in same gel

intergel precision: comparing bands between separate gels

Match Probability

the more loci tested, the higher the probability that the locus genotype positively identifies an individual 

Product Rule 

the frequency of a set of alleles or genotype in a population 

OF = F1 x F2 x F3 X…

- OF is overall frequency 

ex. calculate OF for penta D (1 in 10) and D7S829 (1 in 50) = 1/500

National DNA Index System (NDIS)

important to consider whether database is representative of a population or subpopulation 

- 13 million offender profiles

Allelic Frequencies in Paternity Testing 

H0 and H1

- an individual will share one allele of every locus with the paternal parent 

- H0: not the father

- H1: is the father 

Paternity Index (PI)

likelihood of paternity calculated for each locus which both the father and child share an allele

Combined Paternity Index (CPI)

product of all PI of each loci tested

Probability of Paternity

combines CPI and prior odds of someone being the father 

Linkage Analysis

used to map genes associated with disease

- if an allele of a particular locus is always present: disease

- linkage equilibrium: 2 or more alleles occur randomly

- linkage disequilibrium: whe they do not occur randomly

Marker for Disease (STR)

occurs if linkage is close to the gene