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Open Access Highly Accessed Methodology article

Weighted pedigree-based statistics for testing the association of rare variants

Yin Yao Shugart1, Yun Zhu2, Wei Guo1 and Momiao Xiong23*

Author Affiliations

1 Unit of Statistical Genomics, Division of Intramural Division Program, National Institute of Mental Health, National Institute of Health, Bethesda, MD, USA

2 Division of Biostatistics, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA

3 Human Genetics Center, The University of Texas Health Science Center at Houston, P.O. Box 20186, Houston, TX 77225, USA

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BMC Genomics 2012, 13:667  doi:10.1186/1471-2164-13-667

Published: 24 November 2012

Additional files

Additional file 1: Figure S1A:

The power curves of the family-based corrected single marker χ2 test statistic as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming an additive model, 20% of the risk variants and a baseline penetrance of 0.01.

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Additional file 2: Figure S1B:

The power curves of the family-based collapsing test (variants with frequencies ≤0.005 were collapsed) statistic as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming an additive model, 20% of the risk variants and a baseline penetrance of 0.01.

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Additional file 3: Figure S1C:

The power curves of the family-based VT test statistic as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a dominant model, 20% of the risk variants and a baseline penetrance of 0.01.

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Additional file 4: Figure S1D:

The power curves of the family-based WSS test statistic as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming an additive model, 20% of the risk variants and a baseline penetrance of 0.01.

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Additional file 5: Figure S2A:

The power curves of the family-based corrected single marker χ2 test statistic as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a multiplicative model, 20% of the risk variants and a baseline penetrance of 0.01.

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Additional file 6: Figure S2B:

The power curves of the family-based collapsing test (variants with frequencies ≤0.005 were collapsed) statistic as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a multiplicative model, 20% of the risk variants and a baseline penetrance of 0.01.

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Open Data

Additional file 7: Figure S2C:

The power curves of the family-based VT test statistic as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a multiplicative model, 20% of the risk variants and a baseline penetrance of 0.01.

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Open Data

Additional file 8: Figure S2D:

The power curves of the family-based WSS test statistic as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a multiplicative model, 20% of the risk variants and a baseline penetrance of 0.01.

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Additional file 9: Figure S3A:

The power curves of the family-based corrected single marker χ2 test statistic as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a recessive model, 20% of the risk variants and a baseline penetrance of 0.01.

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Open Data

Additional file 10: Figure S3B:

The power curves of the family-based collapsing test (variants with frequencies ≤0.005 were collapsed) statistic as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a recessive model, 20% of the risk variants and a baseline penetrance of 0.01.

Format: PDF Size: 5KB Download file

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Open Data

Additional file 11: Figure S3C:

The power curves of the family-based VT test statistic as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a recessive model, 20% of the risk variants and a baseline penetrance of 0.01.

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Open Data

Additional file 12: Figure S3D:

The power curves of the family-based WSS test statistic as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a recessive model, 20% of the risk variants and a baseline penetrance of 0.01.

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Open Data

Additional file 13: Figure 4A:

The power curves of the family-based corrected single marker χ2 test statistic as a function of the proportion of risk variants at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming an additive model, a total of 1,800 sampled individuals and a baseline penetrance of 0.01.

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Open Data

Additional file 14: Figure 4B:

The power curves of the family-based collapsing test (variants with frequencies 0.005 were collapsed) statistic as a function of the proportion of risk variants at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming an additive model, a total of 1,800 sampled individuals and a baseline penetrance of 0.01.

Format: PDF Size: 11KB Download file

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Open Data

Additional file 15: Figure 4C:

The power curves of the family-based VT test statistic as a function of the proportion of risk variants at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming an additive model, a total of 1,800 sampled individuals and a baseline penetrance of 0.01.

Format: PDF Size: 11KB Download file

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Open Data

Additional file 16: Figure 4D:

The power curves of the family-based WSS test statistic as a function of the proportion of risk variants at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming an additive model, a total of 1,800 sampled individuals and a baseline penetrance of 0.01.

Format: PDF Size: 11KB Download file

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Open Data

Additional file 17: Figure S5A:

The power curves of the family-based corrected single marker χ2 test statistic as a function of the proportion of risk variants at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a multiplicative model, a total of 1,800 sampled individuals and a baseline penetrance of 0.01.

Format: PDF Size: 5KB Download file

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Open Data

Additional file 18: Figure S5B:

The power curves of the family-based collapsing test (variants with frequencies ≤0.005 were collapsed) statistic as a function of the proportion of risk variants at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a multiplicative model, a total of 1,800 sampled individuals and a baseline penetrance of 0.01.

Format: PDF Size: 5KB Download file

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Open Data

Additional file 19: Figure S5C:

The power curves of the family-based VT test statistic as a function of the proportion of risk variants at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming the multiplicative model, a total of 1,800 sampled individuals and a baseline penetrance of 0.01.

Format: PDF Size: 5KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 20: Figure S5D:

The power curves of the family-based WSS test statistic as a function of the proportion of risk variants at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming the multiplicative model, a total of 1,800 sampled individuals and a baseline penetrance of 0.01.

Format: PDF Size: 5KB Download file

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Open Data

Additional file 21: Figure S6A:

The power curves of the family-based corrected single marker χ2 test statistic as a function of the proportion of risk variants at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a recessive model, a total of 1,800 sampled individuals and a baseline penetrance of 0.01.

Format: PDF Size: 5KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 22: Figure S6B:

The power curves of the family-based collapsing test (variants with frequencies ≤0.005 were collapsed) statistic as a function of the proportion of risk variants at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a recessive model, a total of 1,800 sampled individuals and a baseline penetrance of 0.01.

Format: FIG Size: 15KB Download file

Open Data

Additional file 23: Figure S6C:

The power curves of the family-based VT test statistic as a function of the proportion of risk variants at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming the recessive model, a total of 1,800 sampled individuals and a baseline penetrance of 0.01.

Format: PDF Size: 5KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 24: Figure S6D:

The power curves of the family-based WSS test statistic as a function of the proportion of risk variants at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming the recessive model, a total of 1,800 sampled individuals and a baseline penetrance of 0.01.

Format: PDF Size: 5KB Download file

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Open Data

Additional file 25: Figure S7A:

The power curves of the family-based corrected single marker χ2 statistic under opposite directions of association as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming an additive model, 20% of the risk variants and a baseline penetrance of 0.01.

Format: PDF Size: 11KB Download file

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Open Data

Additional file 26: Figure S7B:

The power curves of the family-based collapsing test (variants with frequencies ≤0.005 were collapsed) statistic under opposite directions of association as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming an additive model, 20% of the risk variants and a baseline penetrance of 0.01.

Format: PDF Size: 11KB Download file

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Open Data

Additional file 27: Figure S7C:

The power curves of the family-based VT statistic under opposite directions of association as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming an additive model, 20% of the risk variants and a baseline penetrance of 0.01.

Format: PDF Size: 11KB Download file

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Open Data

Additional file 28: Figure S7D:

The power curves of the family-based WSS test statistic under opposite directions of association as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming an additive model, 20% of the risk variants and a baseline penetrance of 0.01.

Format: PDF Size: 11KB Download file

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Open Data

Additional file 29: Figure S8A:

The power curves of the family-based corrected single marker χ2 statistic under opposite directions of association as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a multiplicative model, 20% of the risk variants and a baseline penetrance of 0.01.

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Open Data

Additional file 30: Figure S8B:

The power curves of the family-based collapsing test (variants with frequencies ≤0.005 were collapsed) statistic under opposite directions of association as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a multiplicative model, 20% of the risk variants and a baseline penetrance of 0.01.

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Open Data

Additional file 31: Figure S8C:

The power curves of the family-based VT statistic under opposite directions of association as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a multiplicative model, 20% of the risk variants and a baseline penetrance of 0.01.

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Open Data

Additional file 32: Figure S8D:

The power curves of the family-based WSS test statistic under opposite directions of association as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a multiplicative model, 20% of the risk variants and a baseline penetrance of 0.01. (PDF 4 kb) (PDF 4 kb)

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Additional file 33: Figure S9A:

The power curves of the family-based corrected single marker χ2 statistic under opposite directions of association as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a recessive model, 20% of the risk variants and a baseline penetrance of 0.01.

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Open Data

Additional file 34: Figure S9B:

The power curves of the family-based collapsing test (variants with frequencies ≤0.005 were collapsed) statistic under opposite directions of association as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a recessive model, 20% of the risk variants and a baseline penetrance of 0.01.

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Open Data

Additional file 35: Figure S9C:

The power curves of the family-based VT statistic under opposite directions of association as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a recessive model, 20% of the risk variants and a baseline penetrance of 0.01.

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Open Data

Additional file 36: Figure S9D:

The power curves of the family-based WSS test statistic under opposite directions of association as a function of the total number of individuals at the significance level α = 0.05 in the test under seven settings: unrelated individuals in cases-controls study, nuclear family groups 1 and 2, sib-pair groups 1 and 2 and three generation family groups 1 and 2, assuming a recessive model, 20% of the risk variants and a baseline penetrance of 0.01.

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Open Data