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Table 1 Characteristics of participants, complex structural variants, and individual rearrangement events

From: Complex structural variants in Mendelian disorders: identification and breakpoint resolution using short- and long-read genome sequencing

Details of participant Details of whole cxSV Details of individual rearrangement events
Participant Phenotype Sex cxSV type Nomenclature Inheritance Pathogenicity (implicated gene) GT Chr Start End SV Included segmentsb Size Confirmation method
P1 Coffin-Siris syndrome; Atrial septal defect; Cleft soft palate F dupINVinvDEL 46,XX,der(6)(q25.1,q28)dn seq[GRCh37/hg19]der(6)(6pter->6q25.2(+)(154768570):: q25.2(+)(154778901),q25.2(+)154778992:: q25.2(-)(154774047),q25.2 (-)(154768570):: q25.2(-)(154768570),q25.1(-)(~151443182-151443482))dn De novo Pathogenic (ARID1B) Het 6 151443332a 154768570 Dup B 3.3 Mb Microarray
151443332 154778901 Inv B-C-E 3.3 Mb Sanger
154774047 154778992 Inv D-E 4.9 kb Sanger
154778901 171115067 Del D-F 16.3 Mb Sanger and Microarray
P2 Tonic-clonic seizures; Intellectual disability; Learning difficulties M delINVdup 46,XX,der(1)(q44,q44). seq[GRCh37/hg19]der(1) (1pter->1q44(+)(244867200):: TCGCC{5}:: q44(-)(246816211),q44(-)(246064238}):: GGG...TAG{48}:: q44(+)(246569871)->1qter)dn De novo Pathogenic (HNRNPU) Het 1 244867200 246064238 Del B 1.2 Mb Sanger and Microarray
246064238 246816211 Inv C-D 505 kb Sanger
246569871 246816211 Dup D 246 kb Sanger and Microarray
P3 Cone-rod dystrophy; Sensorineural hearing loss M delINVdel 46,XX,der(9)(q21.2,q21.2) seq[GRCh37/hg19]der(9) (9pter->9q21.2(+)(80843698):: q21.2(-)(80849760}),q21.2(-)(80849462}):: q21.2(+)(80859678}->9qter) Not available Pathogenic (CEP78) Hom 9 80843698 80849462 Del B 5.7 kb Sanger and Microarray
80849462 80849760 Inv C 298 bp Sanger
80849760 80859678 Del D 9.9 kb Sanger and Microarray
P4 HIE Grade 2, birth asphyxia; Fetal distress; Intrauterine hypoxia F dupINVdup 46,XX,der(X)(p22.13,p22.13)dn seq[GRCh37/hg19]der(X) (Xpter->Xp22.13(+)(18074005):: GCA…CAC{100}:: p22.13(-)(18532312),p22.13(-)(17793009):: p22.13(+)(18248955)->Xqter)dn De novo VUS (CDKL5) Het X 17793009 18074005 Dup B 280 kb Sanger and Microarray
17793009 18532312 Inv B-C-D 458 kb Sanger and ONT
18248955 18532312 Dup D 283 kb Microarray
  1. cxSVs are described using Next-Gen Cytogenetic Nomenclature [49]. For details of all affected genes, see Additional file 2: Table S1
  2. cxSV complex structural variant, GT genotype, Chr chromosome, SV structural variant
  3. aNot confirmed by Sanger sequencing; coordinate obtained from direct observation of WGS data in IGV
  4. bRefers to genomic segments as shown in Fig. 1