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A research project aimed at evaluating methods for predicting human disease mutations, specifically focusing on the cftr gene in nine species. The team, led by dr. Mark miller, aims to classify mutations as neutral or deleterious and potentially improve on existing prediction methods using the grantham difference (gd) and grantham variation (gv) approach. Data for replacement mutations causing and not causing cf, as well as definitions and criteria for determining mutation categories.
Typology: Study Guides, Projects, Research
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Advisor: Advisor:
Dr Mark Miller Dr Mark Miller
Team Members: Team Members:
Lakshmi Pillai Lakshmi Pillai
Anusha Davuluri Anusha Davuluri
Rajesh Kolla Rajesh Kolla
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60]
#human
ATGCAGAGGTCGCCTCTGGAAAAGGCCAGCGTTGTCTCCAAACTTTTTTTCAGCTGGACC
#olive_baboon
ATGCAGAGGTCGCCTCTGGAAAAGGCCAGCGTTGTCTCCAAACTTTTTTTCAGCTGGACC
#macaca_mulatta
ATGCAGAGGTCGCCTCTGGAAAAGGCCAGCGTTGTCTCCAAACTTTTTTTCAGCTGGACC
#cow
ATGCAGAGGTCGCCTCTGGAAAAGGCCAGCGTCGTCTCCAAAGTTTTTTTCAGCTGGACC
#sheep
ATGCAGAGGTCGCCTCTGGAAAAGGCCAGCGTCGTCTCCAAACTTTTTTTCAGCTGGACC
#new_rabbit
ATGCAGAAGTCGCCTCTGGAGAAGGCCGGCGTCCTCTCCAAACTTTTTTTCAGCTGGACT
#mouse
ATGCAGAAGTCGCCTTTGGAGAAAGCCAGCTTTATCTCCAAACTCTTCTTCAGCTGGACC
#killifish
ATGCAGAAGTCACCGGTGGAAGATGCGAACTTCCTCTCCAGATTTGTCTTTTGGTGGATT
#salmon
ATGCAGAAGTCACCCGTGGAAGATGCAAACTTCCTCTCCAAATATTTCTTCTGGTGGACA
1
A
G
2
T
A
3
G
T
3
G
A
14
C
T
28
A
C
AGC->CGC = Serine->Arginine (109.0)
Grantham Deviation= 109.
Multiple Sequence Alignment
Sample Disease Mutation Data
AGC -> Serine GGC-> Glycine AAC-> Asparagine Serine -> Glycine (56.0) Glycine -> Asparagine (94.0) Serine -> Asparagine (65.0) Grantham Variation= 94.
Definitions : Definitions :
GD : the Grantham difference between the GD : the Grantham difference between the
‘ ‘
wild wild
type type
’ ’
and mutated AA and mutated AA
GV : maximum Grantham score observed at that GV : maximum Grantham score observed at that
site in MSA site in MSA
If GD=0, then mutation is likely neutral If GD=0, then mutation is likely neutral
If (GV > 61.3) and (0<GD<=61.3), then the mutation is If (GV > 61.3) and (0<GD<=61.3), then the mutation is
likely neutral likely neutral
If (GV=0) and (GD>0) then the mutation is likely If (GV=0) and (GD>0) then the mutation is likely
deleterious deleterious
If (0<GV<=61.3) and (GD > 0) then the mutation is If (0<GV<=61.3) and (GD > 0) then the mutation is
likely deleterious likely deleterious
( Disease Mutations) ( Disease Mutations)
Category Category
Expected Expected
results results
Experimental Experimental
results results
Neutral Neutral
Deleterious Deleterious
Unclassified Unclassified
( Non ( Non
- -
Disease Mutations) Disease Mutations)
Category Category
Expected Expected
results results
Experimental Experimental
results results
Neutral Neutral
Deleterious Deleterious
Unclassified Unclassified
(1) Calculate GD, GV
values
(2) Classify mutations
based on criteria
Tasks to be done
√ √
July 18
Status
Date
