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Table 1 Descriptive statistics of different grouping or binning strategies based on annotations of sequence variants on chromosome 3

From: Evaluation of gene-based association tests for analyzing rare variants using Genetic Analysis Workshop 18 data

Strategies of grouping variants in a gene

Total # of variants

Restricting to variants with MAF ≤ 0.05

  

# of genes with ≥1 variant

# of genes with ≥2 variants

Average # of variants per gene with ≥1 variant

Average MAF

a. Coding variants

7435

900

690

4.34

0.012

b. Protein changing

4099

729

479

2.95

0.011

c. Protein damaging

1791

462

210

1.94

0.011

d. Protein changing or conservative T1

15,326 (4099 + 11227)

1034

841

8.17

0.011

e. Protein damaging or conservative T2

5987 (1791 + 4196)

735

438

4.31

0.012

  1. Descriptive statistics for rare variants with minor allele frequencies of 0.05 or less were constructed from the sample of 103 unrelated individuals. The number of genes and average number of variants per gene were slightly reduced when we analyzed the real data because the number of individuals was reduced to 96 after consideration of missing phenotype and covariates.