Type of Model

Parameters | Genetics | Type of Model

Type of Model

Use this parameter to select the type of model to use for testing for rare variant association .

Available models are described in the following table:

Select:

When you want to:

Regression-based

Include the weighted sum method described by Madsen and Browning (2009) ¹ ; a variable -threshold approach (Price et al . 2010) ² with or without weights such as PolyPhen-2 scores; models taking the direction of the variant's effect into account, similar to Han and Pan's data-adaptive sum model (2010) ³ ; as well as combinations of these approaches that can be put into the framework described by Hoffmann, Marini, and Witte (2010) ⁴ .

KBAC

Perform the kernel-based adaptive cluster method described by Liu and Leal (2010) ⁵ .

CMAT

Perform the cumulative minor- allele test described by Zawistowki et al . (2010) ⁶ .

C-alpha

Perform the C - alpha test described by Neale et al . (2011) ⁷ when the trait is binary.

1

Madsen, B.E. and S.R. Browning. 2009. A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic. PLoS Genet. 5: e1000384.

2

Price A.L., G.V. Kryukov, P.I. de Bakker, S.M. Purcel, J. Staples, L.J. Wei, and S.R. Sunyaev. 2010. Pooled Association Tests for Rare Variants in Exon-Resequencing Studies. Am J Hum Genet. 86:832-838.

3

Han, F. and W. Pan. 2010. A Data-Adaptive Sum Test for Disease Association with Multiple Common or Rare Variants. Human Heredity 70:42-54.

4

Hoffmann, T.J., N.J. Marini, and J.S. Witte. 2010. Comprehensive approach to analyzing rare genetic variants. PLoS Genet. 5: e13584.

5

Liu, D.J. and S.M. Leal. 2010. A novel adaptive method for the analysis of next generation sequencing data to detect complex trait associations with rare variants due to gene main effects and interactions. PLoS Genet. 6: e1001156.

6

Zawistowski M, Gopalakrishnan S, Ding J, Li Y, Grimm S, Zöllner S. 2010. Extending rare-variant testing strategies: analysis of noncoding sequence and imputed genotypes. Am J Hum Genet. 87:604-17.

7

Neale B.M., M.A. Rivas, B.F. Voight, D. Altshuler, B. Devlin, et al. 2011. Testing for an Unusual Distribution of Rare Variants. PLoS Genet 7(3): e1001322.

To Specify the Type of Model:

Select the desired model by clicking within the appropriate radio button.

Select:	When you want to:
Regression-based	Include the weighted sum method described by Madsen and Browning (2009) ¹ ; a variable -threshold approach (Price et al . 2010) ² with or without weights such as PolyPhen-2 scores; models taking the direction of the variant's effect into account, similar to Han and Pan's data-adaptive sum model (2010) ³ ; as well as combinations of these approaches that can be put into the framework described by Hoffmann, Marini, and Witte (2010) ⁴ .
KBAC	Perform the kernel-based adaptive cluster method described by Liu and Leal (2010) ⁵ .
CMAT	Perform the cumulative minor- allele test described by Zawistowki et al . (2010) ⁶ .
C-alpha	Perform the C - alpha test described by Neale et al . (2011) ⁷ when the trait is binary.