title: Comparison of Multiple Methods for Determination ofFCGR3A/BGenomic Copy Numbers in HapMap Asian Populations with Two Public Databases.
abstract: LowFCGR3copy numbers (CNs) has been associated with susceptibility to several systemic autoimmune diseases. However, inconsistent associations were reported and errors caused by shaky methods were suggested to be the major causes. In large scale case control association studies, robust copy number determination method is thus warranted, which was the main focus of the current study. In the present study,FCGR3CNs of 90 HapMap Asians were firstly checked using four assays including paralog ratio test combined with restriction enzyme digest variant ratio (PRT-REDVR), real-time quantitative (qPCR) using TaqMan assay, real-time qPCR using SYBR Green dye and short tenden repeat (STR). To improve the comparison precision reproductively, the results were compared with those from recently released sequencing data from 1000 genomes project as well as whole-genome tiling BAC array data. The tendencies of inconsistent samples by these methods were also characterized. Refined in-home TaqMan qPCR assay showed the highest correlation with array-CGH results (r= 0.726,p< 0.001) and the highest concordant rate with 1000 genome sequencing data (FCGR3A91.76%,FCGR3B85.88%, andFCGR381.18%). For samples with copy number variations, comprehensive analysis of multiple methods was required in order to improve detection accuracy. All these method were prone to detect copy number to be higher than that from direct sequencing. All the four PCR based CN determination methods (qPCR using TaqMan probes or SYBR Green, PRT, STR) were prone to higher estimation errors and thus may lead to artificial associations in large-scale case-control association studies. But different to previous reports, we observed that properly refined TaqMan qPCR assay was not inferior to or even more accurate than PRT when using sequencing data as the reference.
authors.affiliation: Renal Division, Peking University First HospitalBeijing, China; Peking University Institute of NephrologyBeijing, China; Key Laboratory of Renal Disease, Ministry of Health of ChinaBeijing, China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of EducationBeijing, China.
authors.forename: Yuan-Yuan
authors.initials: YY
authors.lastname: Qi
authors.affiliation: Renal Division, Peking University First HospitalBeijing, China; Peking University Institute of NephrologyBeijing, China; Key Laboratory of Renal Disease, Ministry of Health of ChinaBeijing, China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of EducationBeijing, China.
authors.forename: Xu-Jie
authors.initials: XJ
authors.lastname: Zhou
authors.affiliation: Research Central Institute, Peking University First Hospital Beijing, China.
authors.forename: Ding-Fang
authors.initials: DF
authors.lastname: Bu
authors.affiliation: Renal Division, Peking University First HospitalBeijing, China; Peking University Institute of NephrologyBeijing, China; Key Laboratory of Renal Disease, Ministry of Health of ChinaBeijing, China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of EducationBeijing, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Hou
authors.affiliation: Renal Division, Peking University First HospitalBeijing, China; Peking University Institute of NephrologyBeijing, China; Key Laboratory of Renal Disease, Ministry of Health of ChinaBeijing, China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of EducationBeijing, China.
authors.forename: Ji-Cheng
authors.initials: JC
authors.lastname: Lv
authors.affiliation: Renal Division, Peking University First HospitalBeijing, China; Peking University Institute of NephrologyBeijing, China; Key Laboratory of Renal Disease, Ministry of Health of ChinaBeijing, China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of EducationBeijing, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Zhang
keywords: FCGR3; HapMap CHB; PRT; TaqMan qPCR assay; copy number