Supplementary Note

There are 29 genes, three of which code for uncharacterized proteins, in the ~593 kb segment flanked by the segmental duplications on 16p11.2 (Supplementary Table 1). As both deletion and duplication of this region are sometimes associated with an abnormal phenotype, some of these genes are likely dosage-sensitive. Candidate genes in this segment and their expression patterns have been described elsewhere1-5. A majority of these genes has brain expression, some of which have been shown to alter synaptic function, behavior, and memory when knocked out in animals (MAP3K, DOC2A, SEZ6L2)1,4. Another gene of interest, especially when considering the three cases here with aortic and/or aortic valve abnormalities and the twins previously reported with bicuspid aortic valves, is HIRIP3, which encodes a protein that interacts with HIRA and acts as a chromatin/histone modifier2. HIRA is deleted in the 22q11.2 deletion syndrome, and it is a candidate for some of the features of that syndrome6. Another parallel to the 22q11.2 deletion syndrome comes from the MAP kinase pathway. Mouse models have suggested that there may be altered ERK1/2 (MAPK3/MAPK1) signaling in this deletion syndrome7. Additionally, hemizygous deletions of MAPK1 in humans have resulted in a phenotype similar to the 22q11.2 deletion syndrome8. Patients with the 16p11.2 microdeletion lack one copy of MAPK3. While mouse studies have shown that MAPK1 is necessary for survival, and MAPK3 is not9, this haploinsufficiency could be part of an additive affect impacting pathways that are also partially disrupted in 22q11.2 deletion syndrome. Two other genes within this 16p11.2 interval have been shown to be involved in another MAP kinase pathway, the JNK1/2/3 pathway. Mouse experiments have shown that JNK1/2/3 are involved in neuronal cell death and likely normal brain development9. Both PPP4C and TAOK2, within 16p11.2, are involved in JNK signaling10,11. Considering that the 16p11.2 microdeletion and microduplication could be impacting multiple pathways that are important in brain development, a possible explanation for the neurodevelopmental phenotype seen in these patients could be a cumulative effect of abnormal dosage of several genes in the region.

References

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