Genome-wide association study of full body nevus count in the Brisbane Twin Nevus Study (BTNS)

The project uses the Brisbane Twin Nevus Study (BTNS) (N=3863)) to compare nevus counts on different anatomical sites to assess which anatomical site serves as best proxy for counting nevi on the whole body.In the project, a GWAS of nevus count on the whole body and GWAS of nevus count on the outer arm are performed.Here is the GWAS of total nevus count. Sample: GWAS analysis only includes samples of European ancestry. total nevus count were counted by trained research nurse. Genotype: All genotypes were imputed to a human haplotype map (HapMap) reference panel. Genome-wide association analyses were performed using Genome-wide Efficient Mixed model Association (GEMMA), which can account for genetically related individuals such as twins and siblings. Sex, age, age2, sex*age, sex*age2, sunburn, BSA, sun exposed hours weighted by UV index and 5 PCs, additionally two batch effect variables; were included as covariates. SNP imputation quality filter retained SNP with an INFO > 0.3. minor allele frequency frequency filter was applied to retain SNP MAF > 0.1 Columns include: CHR: Chromosome BP: Base pair SNP: rsID A1: Effect allele A2: Non-effect allele A1FQ: Effect allele frequency HWE: Hardy-Weinberg Equilibrium BETA: Effect estimate (of effect allele_ SEB: Standard error of beta PRB: P value N: Per SNP sample size本研究依托布里斯班双胎痣研究（Brisbane Twin Nevus Study, BTNS，样本量N=3863），通过对比不同解剖部位的痣计数情况，以明确哪一解剖部位可作为全身痣计数的最佳替代指标。 本项目开展了两项全基因组关联分析（Genome-wide Association Study, GWAS）：分别针对全身痣计数与手臂外侧痣计数，以下为全身总痣计数的GWAS分析结果。 【样本说明】本次GWAS分析仅纳入欧洲血统的受试者样本。全身总痣计数由经过专业培训的研究护士完成统计。 【基因型处理】所有基因型均被填充至人类单倍型图谱（Human Haplotype Map, HapMap）参考面板中。 【分析工具】全基因组关联分析采用基因组高效混合模型关联分析工具（Genome-wide Efficient Mixed model Association, GEMMA）开展，该工具可对存在遗传亲缘关系的个体（如双生子及兄弟姐妹）进行校正，以控制亲缘混杂偏倚。 【协变量设置】本次分析纳入的协变量包括：性别、年龄、年龄平方、性别×年龄交互项、性别×年龄平方交互项、晒伤史、体表面积（Body Surface Area, BSA）、按紫外线指数加权的日晒时长、5个主成分（Principal Components, PCs），此外还纳入了2个批次效应变量。 【SNP过滤标准】首先进行基因型填充质量过滤，保留INFO值大于0.3的SNP位点；随后通过次要等位基因频率（minor allele frequency, MAF）过滤，保留MAF大于0.1的SNP位点。 【结果字段说明】分析结果包含以下字段： CHR：染色体编号； BP：碱基对位置； SNP：rsID编号； A1：效应等位基因； A2：非效应等位基因； A1FQ：效应等位基因频率； HWE：哈迪-温伯格平衡检验结果； BETA：效应等位基因的效应估计值； SEB：β值标准误（Standard Error of Beta, SEB）； PRB：P值； N：每个SNP对应的样本量