LAMPLINK - detection of statistically significant epistatic interactions

The LAMPLINK can detect statistically significant epistatic interactions of two or more SNPs from GWAS data. This software can be used in the same way as the widely used GWAS analysis software PLINK, but LAMPLINK has the additional options for the detection of epistatic interactions with LAMP, which is a multiple testing procedure for combinatorial effects discovery. You can apply LAMPLINK to an analysis pipeline with PLINK simply by replacing plink with lamplink and adding the --lamp option.

Installation

Linux binary of LAMPLINK and its C++ source code are available.

The LAMPLINK binary should be placed in the current working directory or the directory in your command path. Then, typing lamplink or ./lamplink will run LAMPLINK.

Demonstration

We show an example of LAMPLINK using a sample GWAS dataset in example/ (example.zip).

  • lamplink_sample.map: Annotation file for each SNP locus
  • lamplink_sample.ped: Sample information file such as phenotype and genotype
  • phenotype_sample.txt: An example file for quantitative trait

The following command finds all of the significant combinations with Fisher’s exact test. The significance level was set as 0.05.

$ ./lamplink --file ./example/lamplink_sample --lamp --model-dom --sglev 0.05 --upper 0.5 --out example --fisher

When LAMPLINK completes successfully, the result is output in example.lamplink and example.lamp.

example.lamp:

COMBID     Raw_P           Adjusted_P   COMB
 COMB1     0.006993     0.034965     rs7817762,rs2631899,rs1841195

This file indicates that one combination of SNPs (rs7817762, rs2631899, and rs1841195) was significantly associated with the phenotype after the multiple testing correction. The raw and adjusted P-values are 0.006993 and 0.034965, respectively.

example.lamplink:

 CHR    SNP                 A1   A2    TEST            AFF          UNAFF    P                      OR       COMB1
 8        rs7817762    2      1       DOM            5/2            1/7      0.0405594     17.5    1 
 8        rs2631899    2      1       DOM            5/2            2/6      0.131935        7.5      1 
 8        rs1841195    2      1       DOM            5/2            1/7      0.0405594     17.5    1 
 8        rs1564125    2      1       DOM            2/5            4/4      0.608392        0.4      0

This file reports detailed information about each of the SNPs. Column P shows the P-value of the SNP. If the value in COMB1 is 1, the SNP is a member of COMB1 in example.lamp.

The output file formats are described in Output file format.

For the quantitive trait, Mann-Whitney U test can be used by the following command.

$ ./lamplink --file ./example/lamplink_sample --pheno ./example/phenotype_sample.txt --lamp --model-dom --sglev 0.05 --upper 0.5 --out example_utest --utest --alternative "greater"

Usage

LAMPLINK contains the following user-selectable functions.

  • Main function: Detect significant epistatic interactions (--lamp option)
  • Post-processing: Eliminate SNP combinations that show linkage disequilibrium (LD) (--lamp-ld-remove option)
  • All functions implemented in PLINK v1.07 (list of PLINK options).

Detect significant epistatic interactions

The following options are available in LAMPLINK to enumerate significant epistatic interactions.

Option Description
--lamp Find combinatorial elements using LAMP
--file (or --bfile) <filename> Input filename without the extension
--out <filename> Output filename (default “lamplink.***”)
--model-dom (or –model-rec) dom: minor allele is dominant, rec: minor allele is recessive
--fisher Use Fisher’s exact test as the statistical significance test (default is Chi-square test)
--utest Use Mann-Whitney U test as the statistical significance test (default is Chi-square test)
--alternative Select which alternative hypothesis is used from "greater", "less" or "two.sided" (default is two.sided)
--ci <value> Output confidence interval for CMH odds ratios
--sglev <value> Set statistical significance level used in LAMP (default is 0.05)
--upper <value> Set maximum MAF value (default is 0.1)
   

Input file format

Input files should be set with the --file or --bfile option. For inputs using --file filename, filename.ped and filename.map files should exist. For inputs using --bfile, filename.bed, filename.bim, and filename.fam files should exist.

For detailed descriptions of the required formats, please refer to Basic usage / data formats (PLINK web page).

Output file format

Results are output in two files.

  • lamplink.lamp: result file of LAMP
  • lamplink.lamplink: integrated file of the results of LAMP and PLINK

The filename can be changed using the --out option.

lamplink.lamp

The lamplink.lamp file contains the following columns:

Column Description
COMBID Combination ID corresponding to COMBID in lamplink.lamplink
Raw_P P-value
Adjusted_P Adjusted P-value
COMB SNPs that are members of the combination
   

The lamplink.lamplink file contains the following columns independent of the statistical significance test:

Column Description
CHR Chromosome number
SNP SNP name
A1 Minor allele name (calculated from the input ped file)
A2 Major allele name
Test DOM: minor allele is dominant, REC: minor allele is recessive (This output depends on the input option)
AFF Frequency of this allele in cases
UNAFF Frequency of this allele in controls
P P-value for this SNP
OR Estimated odds ratio (for A1, i.e., A2 is the reference)
COMBx 1: This SNP is a member of COMBx, 0: This SNP is absent from COMBx, x: Combination ID that corresponds to COMID in lamplink.lamp
   

The lamplink.lamplink file contains the following additional columns when the Chi-square test is used:

Column Description
CHSQ Chi-square score
DF Degree of freedom
   

The lamplink.lamplink file contains the following additional columns when the --ci option is used:

Column Description
Lx Lower bound of x% confidence interval for odds ratio
Ux Upper bound of x% confidence interval for odds ratio
   

Post-processing

The following options can be used to eliminate redundant SNP combinations.

Option Description
--lamp-ld-remove Eliminate SNP combinations in LD
--file (or --bfile) <filename> Input filename without the extension
--comb <filename> Result filenames set with the --lamp option (“***.lamplink” and “***.lamp”) without the extension
--out <filename> Output filename (default is “lamplink.***”)
--lamp-r2 Set the threshold for the r-squared value (default is 0.8)
   

The commands used to detect significant combinations and to eliminate redundant SNP combinations are shown using the example files example/lamplink_sample.map and example/lamplink_sample.ped.

$ ./lamplink --file ./example/lamplink_sample --lamp --model-dom --sglev 0.3 --upper 0.5 --out example2 --fisher
$ ./lamplink --file ./example/lamplink_sample --comb example2 --lamp-ld-remove --out example2_elimld --lamp-r2 0.5

When the results in example2.lamp and example2_elimld.lamp were compared, COMB1 was eliminated from example2_elimld.lamp.

example2.lamp:

COMBID     Raw_P           Adjusted_P    COMB
 COMB1     0.006993     0.034965      rs7817762,rs2631899,rs1841195
 COMB2     0.040559     0.2028           rs7817762
 COMB3     0.040559     0.2028           rs1841195

example2_elimld.lamp:

COMBID     Raw_P           Adjusted_P    COMB
 COMB2     0.040559     0.2028           rs7817762 
 COMB3     0.040559     0.2028           rs1841195

FAQ

Q. LAMPLINK is still running after a few days.
A. Please test --model-rec and/or set --upper to smaller value.
Q. Can I run LAMPLINK on Mac or Windows?
A. We have a plan to distribute Mac and Windows binary. Wait a sec!

Compile

LAMPLINK source code is available from Github. LAMPLINK can be compiled using the following command on Linux. C++ and Boostlibrary should be installed in advance.

$ git clone https://github.com/a-terada/lamplink.git
$ cd lamplink
$ ./install.sh

License

LAMPLINK is distributed under the GNU General Public License, Version 2. Please see GNU General Public License, version 2 for more details.

Contributors

LAMPLINK was developed through discussions with Aika Terada, Jun Sese, and Koji Tsuda.

Contact

Please contact us at the address below if you find a bug or need further information.

  • lamp_staff(AT)googlegroups.com

Reference