A Bayesian Gene-Based Genome-Wide Association Study Analysis of Osteosarcoma Trio Data Using a Hierarchically Structured Prior

Cancer Informatics
Yi YangLin Zhang

Abstract

Osteosarcoma is considered to be the most common primary malignant bone cancer among children and young adults. Previous studies suggest growth spurts and height to be risk factors for osteosarcoma. However, studies on the genetic cause are still limited given the rare occurrence of the disease. In this study, we investigated in a family trio data set that is composed of 209 patients and their unaffected parents and conducted a genome-wide association study (GWAS) to identify genetic risk factors for osteosarcoma. We performed a Bayesian gene-based GWAS based on the single-nucleotide polymorphism (SNP)-level summary statistics obtained from a likelihood ratio test of the trio data, which uses a hierarchically structured prior that incorporates the SNP-gene hierarchical structure. The Bayesian approach has higher power than SNP-level GWAS analysis due to the reduced number of tests and is robust by accounting for the correlations between SNPs so that it borrows information across SNPs within a gene. We identified 217 genes that achieved genome-wide significance. Ingenuity pathway analysis of the gene set indicated that osteosarcoma is potentially related to TP53, estrogen receptor signaling, xenobiotic metabolism signaling, and ...Continue Reading

References

Apr 16, 1998·American Journal of Human Genetics·R S Spielman, W J Ewens
Dec 5, 1998·American Journal of Human Genetics·S Horvath, N M Laird
Mar 26, 1999·American Journal of Human Genetics·C R Weinberg
Jan 5, 2002·Genetic Epidemiology·Terri H BeatyI McIntosh
Jun 26, 2002·Neoplasia : an International Journal for Oncology Research·Jennifer L GoochDouglas Yee
Jan 31, 2004·Pediatric Blood & Cancer·Simon J CotterillUNKNOWN UKCCSG/MRC Bone Tumour Working Group
Jan 4, 2005·Biochemical Pharmacology·Mikael AhlströmChristel Lamberg-Allardt
Nov 16, 2006·British Journal of Cancer·R TroisiR N Hoover
Oct 30, 2007·American Journal of Human Genetics·Kai WangMaja Bucan
Dec 20, 2007·Journal of Pediatric Hematology/oncology·Nadezhda V KoshkinaErich M Sturgis
Feb 26, 2008·Biochemical and Biophysical Research Communications·Ben Hui LiWen Jie Zhang
Feb 26, 2009·Nuclear Receptor Signaling·Changcheng ZhouBruce Blumberg
Mar 10, 2010·Cancer Treatment and Research·Giulia Ottaviani, Norman Jaffe
Jun 10, 2010·Carcinogenesis·Lisa MirabelloUNKNOWN National Osteosarcoma Etiology Study Group
Apr 6, 2011·Cancer Causes & Control : CCC·Lisa MirabelloSharon A Savage
Jan 25, 2013·Veterinary Medicine International·John DaviesOssama Tawfik
Jun 4, 2013·Nature Genetics·Sharon A SavageStephen J Chanock
Jul 20, 2013·Current Molecular Medicine·C BergerX Chen
Sep 28, 2013·Tumour Biology : the Journal of the International Society for Oncodevelopmental Biology and Medicine·Maolin HeYang Wu
Feb 24, 2015·Journal of the Royal Statistical Society. Series C, Applied Statistics·Lin ZhangKim-Anh Do
Oct 13, 2017·Biometrics·Yang NiYuan Ji

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Citations

May 28, 2019·Veterinary Sciences·Kelly M MakielskiJaime F Modiano
Jul 30, 2020·BMC Genomics·Anna A IgolkinaMaria G Samsonova
Jul 8, 2020·International Journal of Molecular Sciences·Claudia Maria HattingerMassimo Serra
Jun 3, 2020·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Philip J Lupo, Logan G Spector

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Software Mentioned

GIANT
R package “ trio
Ensembl

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