Table 2.

Genetic Disease and Complex Variants.^*

Disease	Variant or Variants and Location	Gene or Genes	Locus Structure Represented in Human Reference Genome†	Variant Detectable by Whole-Exome Sequencing	Variant Detectable by Whole-Genome Sequencing‡	Method of Discovery
X-linked dystonia-parkinsonism	SVA insertion, noncoding region21§	TAF1	Yes	No	No	Long-read transcript sequencing
Bipolar disorder and schizophrenia	VNTR composition, noncoding region20	CANA1C	No	No	No	Long-read sequencing
Schizophrenia	Complex structural variant of C4 genes, coding and noncoding regions48	C4A, C4B	Yes/No	No	Yes/No	Digital droplet PCR
Benign adult familial myoclonic epilepsy	TTTTA expansion, noncoding region22	SAMD12	No	No	No	Long-read sequencing
Baratela-Scott syndrome	CCG expansion, noncoding region49	XYLT1	No	No	Yes	Southern blot and lllumina sequencing
Fascioscapulohumeral muscular dystrophy	Macrosatellite D4Z4 contraction and permissive SNVs, coding and noncoding regions26	FSHD1	Yes/No	No	Yes/No	Southern blot
Amyotrophic lateral sclerosis-frontal temporal dementia	GGGCC repeat expansion, noncoding region50,51	C90RF72	No	No	Yes/No	Southern blot, FISH, and repeat-primed PCR

^*FISH denotes fluorescence in situ hybridization, PCR polymerase chain reaction, SNV single-nucleotide variant, and VNTR variable-number tandem repeat.

^†“Yes/No” indicates that the locus structure was incompletely represented in the human reference genome.

^‡“Yes/No” indicates that the variant could be partially detected (depending on the size of the allele — i.e., sequences of the larger alleles are not completely resolved).

^§SVA (SINE-VNTR-Alu) is a class of retrotransposon found in humans and great apes.