Figure 5. Long-read data provides insights into the biological relevance of structural variation and human evolution and diversity.

a) The NOTCH2NLA, B, and C genes are located within chromosome 1q21.1, a segmental duplication-rich region of the genome partially assembled by PacBio CLR sequencing of BAC clones¹¹⁶. The region was originally incorrectly assembled in the human reference genome¹¹⁶. Deletions and duplications mediated by the segmental duplication-rich region can cause thrombocytopenia-absent radius (TAR) syndrome¹⁶⁵ as well as distal 1q21.1 deletion/duplication syndrome^119,166. High-quality sequencing of the region allowed the breakpoints of these disease-causing rearrangements to be better defined and improved the annotation of human-specific NOTCH2NL duplicate genes¹¹⁶. Subsequent sequencing of patients affected with neuronal intranuclear inclusion disease (NIID) and leukoencephalopathy using long-read PacBio CLR and ONT sequencing recently identified a GGC repeat expansion in Exon 1 of NOTCH2NLC in affected patients⁶⁶ (exons are in red; untranslated regions (UTRs) are in gray). Expansion of the repeat is associated with the production of anti-sense transcripts whose role is uncertain but may interfere with the expression and regulation of the gene family. Figure adapted from Ref. 66. SDs, segmental duplications; SVs, structural variants. b) Heatmap of differentially expressed genes located near structural variants in chimpanzee and human. Differences in macaque, chimpanzee, and human brain expression are shown for genes where a human-specific structural variant maps within 50 kbp of a transcription start and end. Structural changes, such as a deletion of an enhancer region as shown here, can cause changes in gene expression fundamental to brain development³⁰.