Coding vs Noncoding variation

Question 1

What are the 2 types of functional variants?

Answer 1

1. Coding variant
   - amino acid variation
   - splice/reading frame variation
2. Noncoding variant
   - transcriptional
   - post-transcriptional
   - non-coding RNA
   - epigenetic

Question 2

Most functional variation is?

Answer 2

Non-coding and regulatory

Question 3

What does DHS stand for?

Answer 3

DNASE I hypersensitive sites

Question 4

What is the workflow for variant functional identification?

Answer 4

• fine mapping
• in silico annotation
• SNP function
• target gene(s) identification
• target gene(s) function

Question 5

What are the approaches to functional ID?

Answer 5

• genetic linkage isn’t able to determine which SNPs are functionally important
• genetic association better BUT LD limits functional ID
• BIOINFORMATIC approaches good for coding SNPs

Question 6

What are the types of coding region variants?

Answer 6

• frame-shift (indels)
• base-substitutions:
  
  • synonymous: no AA change
  • non-synonymous: AA change
    
    • conservative = similar
    • semi conservation = +ve to -ve AA
    • radical - AA with different properties

Question 7

What are the bioinformatic approaches to predicting coding variant function?

Answer 7

• Genomic evolutionary rate profiling (GERP)

- Polymorphism Phenotyping

Question 8

What is GERP?

Answer 8

Where orthologous nucleotide sequences are compared to determine evolutionary constraints to change in sequence. Identifies constrained elements by quantifying substitution deficits.

R = sum (expected - observed) where higher score = more significant

Question 9

What does deficits represent in GERP?

Answer 9

Deficits represent substitutions that would have occurred if the element was neutral DNA, but didn’t occur due to selective pressure

Question 10

What is PolyPhen?

Answer 10

Predicts impact of AA substitution on stability and function of a protein, using physical and comparative evolutionary comparisons. Estimates probability of variant being damaging to protein function.

Question 11

What are the prediction outcomes of PolyPhen?

Answer 11

• Probably damaging, possibly damaging, benign or no prediction

Question 12

What is RegulomeDB?

Answer 12

Database which integrates functional data within ENCODE with genetic variation databases. Predicts whether variants are functional

Question 13

What are the prioritisation scores of RegulomeDB?

Answer 13

Category 1 = likely to affect binding and linked to expression of gene target

Category 2 = likely to affect binding

Category 3 = less likely to affect binding

Category 4 = minimal binding evidence