Figure S1.
The process begins with a patient
presenting with a complex case and no family history. The first step
involves Trio Whole Exome Sequencing, which identifies MN1
haploinsufficiency but does not align with all symptoms. The next step is
Trio Transcriptional Analysis using RNA sequencing and exon-specific
quantitative PCR. This analysis reveals a loss of expression of SAMHD1
distal exons in the proband and partial loss in parents, with no exonic
variant detected, suggesting an intronic variant. Following this, Trio
Short-Read Whole Genome Sequencing is performed, which identifies a
potential translocation within SAMHD1 intron 4, though the identification of
the translocation partner region is hampered by mapping to a decay sequence,
indicating a poorly mapped region in the reference sequence. The process
then moves to Long-Read Whole Genome Sequencing, where the distal end of
SAMHD1 is still poorly mapped to GRCh38/hg38. The data is then aligned to
T2T-CHM13v2.0, which identifies a homozygous balanced translocation
t(17;20)(p11.2;q11.23). The final steps involve G-banded karyotyping to
confirm the translocation and immunoblotting to confirm SAMHD1
deficiency.
Flow chart showing iterative genetic testing of the proband. Iterative clinical and laboratory-based genetic testing was used to identify an uncommon homozygous balanced translocation in the proband from this study. An iterative approach such as that applied here can assist with identifying rare and unexpected variants from patients with inborn errors of immunity; however, this exact regimen is provided only as an example. The specific genetic tests and clinical decisions required should be assessed on a case-by-case basis in consultation with a multidisciplinary care team.