Table 2 Association analysis for the ANGPTL4 gene and triglycerides.

From: Beyond Rare-Variant Association Testing: Pinpointing Rare Causal Variants in Case-Control Sequencing Study

Genomic position (bp)32

Variant name32

Pinpointed by the method (marked by ‘V’)

Non-synonymous(marked by ‘Y’)

No. of variant carriers in casesc

No. of variant carriers in controlsc

ADAa

BE-SKATb

BE-BURDENb

8335323

E40K

V

V

 

Y

1

8

8337000

  

V

V

 

2

0

8337027

   

V

 

1

0

8337155

E167K

   

Y

0

1

8337250

     

0

1

8340030

     

0

1

8340185

P210P

    

1

0

8340204

K217X

   

Y

0

1

8341802

   

V

 

1

0

8341945

G223R

   

Y

0

1

8342029

P251T

  

V

Y

1

0

8342288

P307P

    

1

0

8342289

V308M

  

V

Y

1

0

8342373

R336C

   

Y

1

3

8342438

  

V

V

 

2

0

8344630

G361S

   

Y

0

1

8344771

   

V

 

1

0

Total pinpointed causal variants

 

1

3

7

   
  1. aThe ADA method was implemented with 1,000 permutations.
  2. bThe BE procedure (for both SKAT and BURDEN) was implemented with 1,000 random subsamples.
  3. cVariant carriers were heterozygotes for all the 17 loci. We did not observe any subject with homozygous minor alleles at any locus.
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