Exam 2 Start: Lecture 6

Question 1

What would you expect to see for the following size standard and amplicons for a tetranucleotide STR locus?
- Allelic ladder (actual alleles 8-12 commonly observed in the pop)
- An individual who is heterozygous 9,11
- an individual who is homozygous 10

Answer 1

GEL:
- five bands evenly spaced for the ladder (8 at the bottom, 12 at the top)
- a band on 9 and on 11
- a thicker band at 10

CAP:
- ladder with 5 peaks, the leftmost is 8, rightmost is 12
- make sure to make samples and ladder diff colors
- t, or fragment length on x axis, relative fluorescence (RFU) on y axis
- two peaks on 9,11 and one bigger peak on 10

Question 2

WHAT DOES RFU STAND FOR?

Answer 2

Relative Fluorescence Unit

Question 3

What does RMP stand for and what does it mean?

Answer 3

Random match probability

probability that if you have a genotype, the probability of another person having that same genotype.

Question 4

What is a relatively inexpensive visualization system that can be used when only one locus is being analyzed?

Answer 4

Silver stain + white lilght

Question 5

What is amelogenin locus used for? Where does it come from? What does one band or two bands mean?

Answer 5

Sex determination; comes from a protein that functions in the deposition of tooth enamel (noncoding region)
- one band for female and two for male

Question 6

What allows for the conversion of electrophoresis time to base pair length?

Answer 6

The internal size standard

Question 7

What is a multiplex rxn

Answer 7

• more than one primer pair in reaction
• a lot of work, need to avoid preferential amplification of certain loci/ alleles

Question 8

What does HUMTH01 or TH01 stand for?

Answer 8

Human tyrosine hydroxylase gene

Question 9

If you use different primer sets from diff kits, what can be different in your results

Answer 9

The length of the fragments is different (bc where forward or rev binds)