Dinh 2011/NOTES/2011-9-29

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Penn African mQTL[edit]

./mQTL_2MB_plink.pl ../PennAfrican_Batch1_genotypes ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt > results.txt &
*Remember that tfam file must have extra "phenotype" column of values "-9" ('missing') for plink to work!

Divided high variance methylation matrix (77563 CpGs) to 8 groups:

2176  head -30000 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -10000 > no_20001_30000/UPenn46_hg19_methylMatrix_filtered_20001-30000.txt
2179  head -40000 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -10000 > no_30001_40000/UPenn46_hg19_methylMatrix_filtered_30001-40000.txt
2180  head -50000 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -10000 > no_40001_50000/UPenn46_hg19_methylMatrix_filtered_40001-50000.txt
2181  head -60000 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -10000 > no_50001_60000/UPenn46_hg19_methylMatrix_filtered_50001-60000.txt
2182  head -70000 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -10000 > no_60001_70000/UPenn46_hg19_methylMatrix_filtered_60001-70000.txt
2183  tail -7573 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt > no_70001_77573/UPenn46_hg19_methylMatrix_filtered_70001-77573.txt

I found out that the PennAfrican_Batch1_genotypes file has SNP positions in build 36.3 and not in build 37.1 Wrote script to lift over snp's RS values to hg19 positions

File:LiftOverRSvalues.txt

After using liftover, I found that there were multiple occurrences of the same SNPs in snp132.txt file.

wc -l 
PennAfrican_Batch1_genotypes_hg19.tped = 1109770 SNPs
PennAfrican_Batch1_genotypes.tped = 1083730 SNPs

Example of duplicated RS numbers in snp132.txt :

1266	chr2	89309681	89309682	rs3210114	0	-	C	C	A/G	cDNA	single	by-cluster	0	0	unknown	exact	3	  MultipleAlignments3ILLUMINA,KRIBB_YJKIM,LEE,	0				
1266	chr2	89345689	89345690	rs3210114	0	-	C	C	A/G	cDNA	single	by-cluster	0	0	unknown	exact	3	MultipleAlignments3ILLUMINA,KRIBB_YJKIM,LEE,	0				
1267	chr2	89513110	89513111	rs3210114	0	-	C	C	A/G	cDNA	single	by-cluster	0	0	unknown	exact	3	MultipleAlignments3ILLUMINA,KRIBB_YJKIM,LEE,	0				
1268	chr2	89619585	89619586	rs3210114	0	-	T	T	A/G	cDNA	single	by-cluster	0	0	unknown	exact	3	MultipleAlignments3ILLUMINA,KRIBB_YJKIM,LEE,	0				
1270	chr2	89901585	89901586	rs3210114	0	+	A	A	A/G	cDNA	single	by-cluster	0	0	unknown	exact	3	MultipleAlignments3ILLUMINA,KRIBB_YJKIM,LEE,	0				
1271	chr2	90007949	90007950	rs3210114	0	+	G	G	A/G	cDNA	single	by-cluster	0	0	unknown	exact	3	MultipleAlignments3ILLUMINA,KRIBB_YJKIM,LEE,	0				
1273	chr2	90193220	90193221	rs3210114	0	+	G	G	A/G	cDNA	single	by-cluster	0	0	unknown	exact	3	MultipleAlignments3ILLUMINA,KRIBB_YJKIM,LEE,	0	
  • Some rs were also mapped to gapped regions in hg19 and to the multiple haplotypes of chr6.
  • Rewrote mQTL_2MB_plink.txt to build the tped files for each CpG

Divided high variance methylation matrix (77563 CpGs) to 16 groups:

2472  head -5001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt > no_1_5000/methylMat.txt
2473  head -10001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_5001_10000/methylMat.txt
2474  head -15001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_10001_15000/methylMat.txt
2475  head -20001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_15001_20000/methylMat.txt
2476  head -25001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_20001_25000/methylMat.txt
2477  head -30001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_25001_30000/methylMat.txt
2478  head -35001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_30001_35000/methylMat.txt
2479  head -40001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_35001_40000/methylMat.txt
2480  head -45001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_40001_45000/methylMat.txt
2481  head -50001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_45001_50000/methylMat.txt
2482  head -55001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_50001_55000/methylMat.txt
2483  head -60001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_55001_60000/methylMat.txt
2484  head -65001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_60001_65000/methylMat.txt
2485  head -70001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_65001_70000/methylMat.txt
2486  head -75001 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt | tail -5000 > no_70001_75000/methylMat.txt
2487  tail -2575 ../UPenn46_hg19_Data/UPenn46_hg19_methylMatrix_filtered.txt > no_75001_77573/methylMat.txt

Added headers:

2491  cat header.txt no_1_5000/methylMat.txt > tmp
2492  mv tmp no_1_5000/methylMat.txt 
2494  cat header.txt no_5001_10000/methylMat.txt > tmp
2495  mv tmp no_5001_10000/methylMat.txt 
2497  cat header.txt no_10001_20000/methylMat.txt > tmp
2498  mv tmp no_10001_15000/methylMat.txt 
2500  cat header.txt no_15001_20000/methylMat.txt > tmp
2501  mv tmp no_15001_20000/methylMat.txt 
2502  cat header.txt no_20001_25000/methylMat.txt > tmp
2503  mv tmp no_20001_25000/methylMat.txt 
2504  cat header.txt no_25001_30000/methylMat.txt > tmp
2505  mv tmp no_25001_30000/methylMat.txt 
2506  cat header.txt no_30001_35000/methylMat.txt > tmp
2507  mv tmp no_30001_35000/methylMat.txt 
2508  cat header.txt no_35001_40000/methylMat.txt > tmp
2509  mv tmp no_35001_40000/methylMat.txt 
2510  cat header.txt no_40001_45000/methylMat.txt > tmp
2511  mv tmp no_40001_45000/methylMat.txt 
2512  cat header.txt no_45001_50000/methylMat.txt > tmp
2513  mv tmp no_45001_50000/methylMat.txt 
2514  cat header.txt no_50001_55000/methylMat.txt > tmp
2515  mv tmp no_50001_55000/methylMat.txt 
2516  cat header.txt no_55001_60000/methylMat.txt > tmp
2517  mv tmp no_55001_60000/methylMat.txt 
2518  cat header.txt no_60001_65000/methylMat.txt > tmp
2519  mv tmp no_60001_65000/methylMat.txt 
2520  cat header.txt no_65001_70000/methylMat.txt > tmp
2521  mv tmp no_65001_70000/methylMat.txt 
2522  cat header.txt no_70001_75000/methylMat.txt > tmp
2523  mv tmp no_70001_75000/methylMat.txt 
2524  cat header.txt no_75001_77573/methylMat.txt > tmp
2525  mv tmp no_75001_77573/methylMat.txt
In each folder:
../mQTL_2MB_plink.pl ../PennAfrican_Batch1_genotypes_hg19 methylMat.txt > results.txt &
File:MQTL 2MB plink.txt
Script to create WIG and BED files for CpG-SNP interactions
File:CreateBEDandWIGtracks.txt
File of all CpG-SNP (Benjamini p-val < 0.05)
File:Combined CpG-SNP results.txt

Files for chromosome 21 generated:
File:Chr21.dist.WIG.txt
File:Chr21.legend.BED.txt
File:Chr21.numCpGs.BED.txt
File:Chr21.p val.BED.txt

Plots of SNPs and their correlated CpGs, distances are in Mbp[edit]

  • Plot of CpG-SNPs on chromosome 21
File:African-mQTL-chr21.png
  • Plot of intergenic CpG-SNPs on chromosome 21
File:African-mQTL-chr21-snp-intergenic.png
  • Plot of intragenic CpG-SNPs on chromosome 21
File:African-mQTL-chr21-snp-intragenic.png
  • Plot of intragenic CpG-SNPs on chromosome 21 with high number of correlated CpGs
File:African-mQTL-chr21-snp-intragenic-highCG.png

Future direction[edit]

  • Double check Benjamini corrected P-values
  • Show the CpG site in the genome browser shots
  • Remove CpGs that lie on top of the SNPs
  • Separate out the CpGs based on distance from SNPs
  • Perform PCA - get SNPs that contributes the most to diversity - find out the CpGs which interacts with these SNPs.