Lecture 12/3 - Start Final

Question 1

What method is usually used to analyze mtDNA

Answer 1

Cycle sequencing

Question 2

what are the usual samples

Answer 2

hair, teeth, bones

Question 3

Is nDNA and mtDNA usually processed in the same facilities?

Answer 3

No, separate bc mtDNA is rlly sensitive to contamination

Question 4

AFDIL and AFMES (AFDIL came first)

Answer 4

Armed Forces DNA Identification Labratory ->
Armed Forces Medical Examiner System

Question 5

What did they do (AFDIL/AFMES)

Answer 5

develop pcr and cs protocols and primers etc. for human mtDNA

Question 6

what is used to grind up hair

Answer 6

tissue homogenizer

Question 7

How many base pairs is in D-Loop

Answer 7

1000 bp

Question 8

How many base pairs in mtDNA

Answer 8

16,569

Question 9

PS, MPS

Answer 9

Primer set, Mini primer set

Question 10

What are the 3 issues that cause trouble when working with mtDNA

Answer 10

1. Interpretation of a perfect match (maternally inherited)
2. Heteroplasmy
3. Contamination

Question 11

Why is interpretation of a perfect match an issue when analyzing mtDNA

Answer 11

not unique TO PERSONS, maternally inherited,
power rule does not apply bc haploid locus
Unique haplotypes are common

Question 12

SWGDAM guidelines

Answer 12

Exclusion (2+ nt differences)
inconclusive (1 nt difference)
cannot exclude (identical sequence/ no diff)

Question 13

SWG DAM

Answer 13

Scientific working group DNA analysis Methods

Question 14

What is a hot spot

Answer 14

A location that is too variable, can cause “failure to exclude” shouldn’t be useddddddddddd

Question 15

Proportion 95% confidence interval (of database for N)

Answer 15

p(hat?) +/- 1.96 (SQRT p(1-p)/N)

Question 16

What is heteroplasmy? Sequence and length?

Answer 16

The detection of >1 haplotype in a single organism

Sample has two different haplotypes within it, so one point mutation (SEQUENCE) or indel (LENGTH, one more base)

Question 17

What does the number after F or R tell you?

Answer 17

The base position at the 5’ end

Question 18

What are you looking for to exclude from your sequence after sequencing the forward primer amplicons

Answer 18

The reverse compliment of the reverse primer (6-7 b)

Question 19

remember homometric stretch of C’s

Answer 19

associated w length heteroplasmy

Question 20

What is the threshold of contamination

Answer 20

contamination < 1/10 of the sample DNA aka doesn’t affect the haplotype

Question 21

DGGE

Answer 21

Denaturing gradient gel electrophoresis