DNA Sequence Analysis

Question 1

a letter prefix is used to indicate…

Answer 1

typw of reference sequence use
c = coding DNA
g = genomic DNA
m =mitochondrial DNA
p = protein
r = RNA

Question 2

”>”

Answer 2

substitution (DNA and RNA level)

Question 3

“del”

Answer 3

deletion

Question 4

“dup”

Answer 4

duplication

Question 5

“ins”

Answer 5

insertion
duplicating insertiosn described as DUPLICATIONS, not insertions

Question 6

“inv”

Answer 6

inversion

Question 7

“fs”

Answer 7

frame shift
more so for proteins, not so much for nucleotides

Question 8

“ext”

Answer 8

extension

Question 9

most common type of variant

Answer 9

substition

Question 10

“delins”

Answer 10

one or more letters in the DNa cose are missing and replaced by several new letters
deletion and insertion indicated by “delins”

Question 11

3’ rule

Answer 11

Always name the last T (most 3’) to be duplicated

Biologically we don’t know what is truly duplicated, but for CONSISTENCY = use 3’ rule = last nucleotide that is duplicated or deleted

Question 12

each allele should go in these

Answer 12

brackets
cis = indicates that all in one chromosome = [;]
trans = [];[]
(;) = means unknown

Question 13

types of variants detected by Sanger sequencing

Answer 13

SNVs = synonymous, missense, nonsense
insertions
duplications
deletions
in/dels

Question 14

5 categories that you can place a variant into:

Answer 14

1) pathogenic; class 5; >99% certainty
2) likely pathogenic; class 4; >90% certainty
3) variant of uncertain significance (VUS); class 3
4) likely benign; class 2; >90% certainty
5) benign; class 1; >99%