Table 1.

Overview of investigated inversions

Case ID	Ascertainment	Karyotype	GRCh37	GRCh38	T2T	Chimpanzee	Bonobo	Sequencing data
RD_P525	Repeated IVF without pregnancy	46,XY,inv(5)(p13q23)	✓	✓	✓	✓	✓	lrGS
P4855_501	Neurodevelopmental disorder, hearing loss, visual impairment, anosmia, hypogonadism	46,XY,inv(6)(p12q16.3)	×	✓	✓	✓	✓	srGS^a, lirGS^a, lrGS
P5371_208	Recurrent miscarriages	46,XY,inv(9)(p13q22)	×	×	×	×	×	srGS^a, lirGS^a
BH16643-1	Hypotonia, global developmental delay	46,XX,inv(9)(q12q34.3)dn	×	×	✓	×	×	srGS, lrGS, OGM
P4855_106	Family investigation	46,XY,inv(10)(q11q23)pat	×	×	✓	×	×	srGS^a, lirGS^a
P4855_208	Neurodevelopmental disorder	46,XY,inv(11)(p11.1q12)mat	×	×	×	×	×	srGS^a, lirGS^a, lrGS
RD_P541	Recurrent miscarriages	46,XX,inv(12)(p11.23q13.3)	✓	✓	✓	✓	✓	lrGS, OGM
RD_P549	Family investigation	46,XY,inv(14)(q24q32)	✓	✓	✓	✓	✓	lrGS
P5370_201	Diabetes type II, Hodgkins lymphoma, hearing loss, hypogonadism, retinitis pigmentosa, acanthosis nigricans, beta thalassemia	46,XY,inv(18)(p11.3q11.2)	×	×	×	×	×	srGS^a, lirGS^a
RD_P526	Family investigation	46,XX,inv(18)(p11.23q21.1)	✓	✓	✓	✓	✓	lrGS
RD_P542	Repeated IVF without pregnancy	46,XX,inv(19)(p13.2q13.4)	✓	✓	✓	✓	✓	lrGS
RD_P546	Family investigation	46,XY,inv(19)(p13.2?q13.4)	✓	✓	✓	✓	✓	lrGS

The table displays the reference genome in which the inversion breakpoint junctions were mapped (✓) or absent (×), and the data available (short-read [sr], linked-read [lir], long-read [lr] genome sequencing [GS], and optical genome mapping [OGM]).
^aPreviously reported in Pettersson et al. (2020).

Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps