Open Access Research article

A comprehensive candidate gene approach identifies genetic variation associated with osteosarcoma

Lisa Mirabello1*, Kai Yu1, Sonja I Berndt1, Laurie Burdett2, Zhaoming Wang2, Salma Chowdhury2, Kedest Teshome2, Arinze Uzoka2, Amy Hutchinson2, Tom Grotmol3, Chester Douglass4, Richard B Hayes5, Robert N Hoover1, Sharon A Savage1 and the National Osteosarcoma Etiology Study Group

Author Affiliations

1 Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20852, USA

2 Core Genotyping Facility, National Cancer Institute, SAIC-Frederick, Inc., Gaithersburg, MD, USA

3 Cancer Registry of Norway, PO Box 5313 Majorstuen, NO-0304 Oslo, Norway

4 Harvard School of Dental Medicine, Boston, MA, USA

5 Division of Epidemiology, Department of Environmental Medicine, New York University, New York, NY, USA

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BMC Cancer 2011, 11:209  doi:10.1186/1471-2407-11-209

Published: 29 May 2011

Additional files

Additional file 1:

Table S1. SNPs from 255 candidate genes by functional pathway. This table shows the genes analyzed in each pathway, the number of SNPs in each gene, the P value for the most significant SNP in each gene, and the gene- and pathway-level P values.

Format: XLSX Size: 52KB Download file

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Additional file 2:

Table S2. Significant SNPs (P < 0.05) in each pathway associated with osteosarcoma before correction for multiple tests. This table lists the statistics (minor allele, MAF, OR, and P values) for each of the 241 SNPs significantly (P < 0.05) associated with osteosarcoma before correction for multiple tests by gene and pathway.

Format: XLSX Size: 53KB Download file

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Additional file 3:

Supplementary Figures S1 and S2. Figure S1. Linkage disequilibrium across FANCM using the HapMap Caucasian (CEU) population data (A), and our control data (B) determined using Haploview. This figure illustrates the linkage disequilibrium across FANCM and highlights the significant SNPs associated with osteosarcoma after correction for multiple tests. Figure S2. Linkage disequilibrium across GH1 using the HapMap Caucasian (CEU) population data (A), and our control data (B) determined using Haploview. This figure illustrates the linkage disequilibrium across GH1 and highlights the significant SNPs associated with osteosarcoma after correction for multiple tests

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