Use MR Base to find the SNPs linked to lactate
- rs762523 on ch22
- rs1260326 on ch02
Move the files to a folder in my home directory using WinSCP and use gunzip to unzip ch22 and ch02
Pathway to folder: /panfs/panasas01/sscm/ca16591/ProtecT_genetic_Vanessa
Write a bash script to call Plink
I called the script lactate_snp_extract.sh
#!/bin/bash
#PBS -l walltime=00:05:00,nodes=1:ppn=1
#PBS -o snps.txt
#PBS -j oe
# Set the name of the job
#PBS -N lactate_snp22_extract
echo Running on host `hostname`
echo Time is `date`
echo Directory is `pwd`
echo PBS job ID is $PBS_JOBID
echo This jobs runs on the following machines:
echo `cat $PBS_NODEFILE | uniq`
# First change the MaCH files into Plink format with gcta. First get all in the zip format to use the --dosage-mach-gz option
# gcta64 --dosage-mach-gz data_chr22.step2.mldose.gz data_chr22.step2.mlinfo.gz --make-bed --out test
module add apps/plink-1.90
plink --bfile /panfs/panasas01/sscm/ca16591/ProtecT_genetic_Vanessa/test --snp rs762523 --recode A --out /panfs/panasas01/sscm/ca16591/ProtecT_genetic_Vanessa/Protect_lactate_22snps
Import the results for ch22 to R and select rs762523_A
Merge the genetic data for rs762523_A with the ProtecT metabolite data
Recode the rs762523_A such that the G is the risk allele
Tabulation of cases and controls by rs762523_A
| Case |
132 |
406 |
348 |
| Control |
77 |
283 |
263 |
Run a simple linear regression of genotype (rs762523) on log-transformed lactate
Results for rs762523
|
|
|
Lac
|
|
|
|
B
|
CI
|
std. Error
|
p
|
|
(Intercept)
|
|
0.55
|
0.50 – 0.60
|
0.02
|
<.001
|
|
rs762523_A
|
|
1
|
|
0.04
|
-0.02 – 0.09
|
0.03
|
.170
|
|
2
|
|
0.02
|
-0.03 – 0.08
|
0.03
|
.414
|
|
Observations
|
|
1509
|
|
R2 / adj. R2
|
|
.001 / .000
|
Write a bash script to call Plink
Could add a line to the script above for extracting the SNP on ch22, but I created a separate bash script called lactate_02.sh and ran plink --bfile /panfs/panasas01/sscm/ca16591/ProtecT_genetic_Vanessa/test02 --snp rs1260326 --recode A --out /panfs/panasas01/sscm/ca16591/ProtecT_genetic_Vanessa/Protect_lactate_02snps
Read in rs1260326_T data and merge on subjectid
Recode the rs1260326_T such that the C is the risk allele
Tabulation of cases and controls by rs1260326_T
| Case |
122 |
423 |
341 |
| Control |
115 |
291 |
217 |
Run a simple linear regression of genotype (rs1260326) on log-transformed lactate
Results for rs1260326
|
|
|
Lac
|
|
|
|
B
|
CI
|
std. Error
|
p
|
|
(Intercept)
|
|
0.56
|
0.52 – 0.61
|
0.02
|
<.001
|
|
rs1260326_T
|
|
1
|
|
0.03
|
-0.02 – 0.08
|
0.03
|
.286
|
|
2
|
|
-0.00
|
-0.06 – 0.05
|
0.03
|
.915
|
|
Observations
|
|
1509
|
|
R2 / adj. R2
|
|
.002 / .001
|
Sensitivity analysis (adding age as a covariate)
|
|
|
Lac
|
|
|
|
B
|
CI
|
std. Error
|
p
|
|
(Intercept)
|
|
0.59
|
0.38 – 0.81
|
0.11
|
<.001
|
|
rs762523_A
|
|
1
|
|
0.04
|
-0.02 – 0.09
|
0.03
|
.173
|
|
2
|
|
0.02
|
-0.03 – 0.08
|
0.03
|
.417
|
|
age
|
|
-0.00
|
-0.00 – 0.00
|
0.00
|
.681
|
|
Observations
|
|
1509
|
|
R2 / adj. R2
|
|
.001 / -.001
|
|
|
|
Lac
|
|
|
|
B
|
CI
|
std. Error
|
p
|
|
(Intercept)
|
|
0.61
|
0.39 – 0.82
|
0.11
|
<.001
|
|
rs1260326_T
|
|
1
|
|
0.03
|
-0.02 – 0.08
|
0.03
|
.287
|
|
2
|
|
-0.00
|
-0.06 – 0.05
|
0.03
|
.919
|
|
age
|
|
-0.00
|
-0.00 – 0.00
|
0.00
|
.685
|
|
Observations
|
|
1509
|
|
R2 / adj. R2
|
|
.002 / -.000
|