Next-Generation Sequencing (NGS) has revolutionized our approach to understanding the genetic basis of human phenotypes. While SNP genotyping laid the groundwork, advancements in NGS, coupled with the ability to achieve a more detailed picture of genetic variations, have opened new opportunities for exploring complex traits. Our research emphasizes the transition from SNP genotyping to short-read and long-read sequencing technologies for identifying rare genetic variants and copy number variants (CNVs) that influence human traits. Additionally, we highlight the significant leap forward provided by the telomere-to-telomere complete human reference genome (T2T-CHM13), which offers an unprecedented level of genomic completeness. These advancements are enabling a more comprehensive characterization of disease-associated rare mutations and CNVs, as well as the discovery of pathogenic mutations, thus enhancing our understanding of the genetic architecture of human traits and diseases.