Identification of structural variants leading to non-reference gene structure


Grace Koo

Document Type


Publication Date

Summer 2023



JAX Location

In: Student Reports, Summer 2023, The Jackson Laboratory


The GRCh38 reference genome and its annotation have been gradually improved for two decades. However, it has limitations in measuring gene expressions mainly due to a lack of diversity derived from structural variants (SVs). Here, we aim to identify SVs that cause non- reference gene structure using high-quality haplotype-resolved genomes and corresponding RNA-seq data from a diverse sample group to address the limitation. This analysis allowed us to identify 202 SVs that potentially change the gene structure of the reference genome in protein- coding exons. Our findings exemplify that SVs indeed contribute to a more diverse gene structure, suggesting that diversity is needed in the annotation as well as in the genome to better represent the landscape of gene expression across human populations.

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