Legends to Supplementary Figures
Supplementary Fig 1 Phenotypic features of the index patient (III:2) and affected
relatives (II:2, II:4), and reverse FISH painting of genomic amplicons
(a, b) Clinical details of III:2 – large nose with high nasal bridge and bulbous tip and
lower limbs with asymmetry in size and fixed posture of left limb associated with
contractures of hip, knee and foot.
(c) Nose of subject II:4 showing typical aspect of TRPS I nose with large bridge and
base and bulbous depressed tip.
(d) Hand x-ray of subject II:2 showing the lack of cone-shaped epiphyses.
(e) Reverse FISH painting with genomic amplicons of flow sorted der chromosomes.
Genomic amplicon of der(8) chromosome is labelled in red whereas of der(13) in green.
Contamination of laser flow sorted der(8) chromosome amplicon with chromosome 6
specific material is observed.
Supplementary Fig 2 Overview of the evolutionary conservation according to the UCSC
Genome Browser of the pathogenic der(8) breakpoint
(a) Ideogram of the derivative chromosome 8.
(b) Evolutionary conservation of a 12.6 kb (chr8:116,755,723-116,768,309) fragment upstream
to the der(8) breakpoint. The solid lines without conservation adjacent to the breakpoint
correspond to the transposon type I L1PA3 element.
(c) Evolutionary conservation of a 15 kb fragment downstream to the der(8) breakpoint
corresponding to chr13:65,101,510-65,116,509 region. Adjacent to the breakpoint is the highly
conserved VISTA hs874 CNE.
Supplementary Fig 3 Comparative sequence electropherograms of the TRPS1 coding
strand demonstrating differential allelic expression
From each subject the sequence electropherogram of the same polymorphic region is
shown from genomic DNA (gDNA) and RNA. The primer pair for amplification of
gDNA is TRPS1-Ex2F / TRPS1-Ex2R whereas of RNA or cDNA is TRPS1-RT1 /
TRPS1-RT7 (sequencing primers are underlined). Allelic ratios were calculated by
dividing the peak height of the translocation associated alleles (in black) by that of the
1
wild-type (in gray). Translocation associated or wild-type alleles with more than 50%
increase in the peak heights are underlined.
(a) SNP rs2721939 (HGVS name NM_014112.2:c.-78G>A) from the index patient
(III:2).
(b-c) SNP rs35329862 (HGVS name NM_014112.2:c.-9_-8insT) from the patient’s
father (II:4) and aunt (II:2). The peak heights of an adjacent 29 nucleotide sequence
were analysed using the PeakPicker.
2