Table 1

Overview of cases followed up by optical genome mapping (OGM), including the respective findings and their final classification on OGM analysis.

Case No	Sample material	Finding by SOC testing and information on the locus	OGM result	Additional testing	Origin of SV	Classification after OGM	Phenotype
P1	Amniotic cells	CMA: arr[GRCh38] Xp22.31(7341220_7534466)x2, Xp21.2p21.1(30871431_31525874)x2	Complex rearrangement of a duplicated segment containing exons of STS and DMD without disrupting any known gene	Fetal PCR, maternal MLPA	Maternal	Likely benign	Sonographically inconspicuous
P1	Amniotic cells	Two hemizygous X-chromosomal duplications involving exons 56–79 of DMD and exon 11 of STS		Fetal PCR, maternal MLPA	Maternal	Likely benign	Sonographically inconspicuous
P2	Chorionic villi	Karyotyping: 46,XX,inv(7)(q?11.2q?22)	Inversion involving the region 7q11.23q22.1, breakpoints do not disrupt any known genes	Fetal FISH, parental karyotyping, maternal OGM and FISH	Maternal	Likely benign	Sonographically inconspicuous
P2	Chorionic villi	Exact breakpoints of inversion unknown; similar inversions are reported to cause haematological malignancies		Fetal FISH, parental karyotyping, maternal OGM and FISH	Maternal	Likely benign	Sonographically inconspicuous
P3	Chorionic villi	Familial WES: putative, unspecified genetic variant prohibiting sequencing of exon 13 of SCNN1B	Cryptic, homozygous inversion involving the region 16p13.12, proximal breakpoint maps to SCNN1B exon 13	Fetal FISH and PCR, parental OGM and PCR, maternal karyotyping and FISH	Biparental	Biallelic pathogenic	Sonographically inconspicuous
P4	Blood	Karyotyping: 46,XX,t(3;5)(q22.3;q22)	Breakpoint localised ca 300 kb upstream of FOXL2	Parental karyotyping	De novo	Likely benign	Blepharophimosis
P4	Blood	Potential disruption of gene FOXL2 (localised in band q22.3 of chromosome 3) suspected as causative for patient’s blepharophimosis	Breakpoint localised ca 300 kb upstream of FOXL2	Parental karyotyping	De novo	Likely benign	Blepharophimosis
P5	Amniotic cells	Karyotyping: 46,XX,?inv(15)(q26q26)	Inconspicuous in OGM	–	n/a	Likely artefact of karyotyping	Sonographically inconspicuous
P5	Amniotic cells	Possible inversion on chromosome 15	Inconspicuous in OGM	–	n/a	Likely artefact of karyotyping	Sonographically inconspicuous
P6	Amniotic cells	Karyotyping: 46,XX,?inv(12)(p11.2p13)	Inconspicuous in OGM	Parental karyotyping	n/a	Likely artefact of karyotyping	Sonographically inconspicuous
P6	Amniotic cells	Possible inversion on chromosome 12	Inconspicuous in OGM	Parental karyotyping	n/a	Likely artefact of karyotyping	Sonographically inconspicuous
P7	Amniotic cells	CMA: arr[GRCh38] 9q34.3(135848046_136246353)x3	Partial duplication of CAMSAP1, likely in tandem, not disrupting the gene	Parental MLPA	Maternal	Likely benign	Hygroma colli
P7	Amniotic cells	Duplication involving exons 1–7 of CAMSAP1		Parental MLPA	Maternal	Likely benign	Hygroma colli

P1–P3 are discussed in detail in this study.
CMA, chromosomal microarray; MLPA, multiplex ligation-dependent probe amplification; SOC, standard of care; SV, structural variant; WES, whole-exome sequencing.