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.