Table 2. Comparison of advantages and limitations of genomic studies in ASD research.

Approach	Advantages	Disadvantages
GWAS	1) Relatively easy to perform technically 2) Meta-analysis can be used to increase the statistical power 3) Common variant in common disease model is often adopted	1) Sample size limitation is common in association studies 2) Population stratification or selection criteria for cases and controls are confounders in GWAS or meta-analysis 3) Replication of risk loci in different populations or labs is rarely seen 4) Biological relevance of risk loci is often very difficult to validate, especially for those SNPs located in the intergenic region 5) Rare pathogenic allele is often missing
WES	1) Sample collection is easy to obtain in a single center 2) Trio-WES is often adopted to analyze allele transmission and de novo variants 3) Candidate genes are easily selected from pathogenic or likely pathogenic variants 4) Rare variants are often focused 5) Cost-effective in identifying coding variants or de novo variants	1) Variants are limited to the exonic regions or exon/intron boundaries 2) VUSs are difficult to interpretate without functional assays 3) Multicenter validation is often limited
WGS	1) Sample collection is easy 2) SNV, CNV, SV can be simultaneously analyzed at the genomic level 3) De novo variants can be found in Trio-WGS 4) Variants from both coding and non-coding regions are covered	1) Relatively expensive for one sample 2) Length and depth of sequencing reads are important for the quality in expense of the costs 3) Variants in non-coding regions are difficult to replicate in animal models 4) Accuracy of prediction models for SVs needs to be improved