Fathers but not mothers preferentially transmit deletions of proximal cis-regulatory elements of genes, such as promoters, UTRs, and transcription start sites. This finding was the first report of inherited Autism risk coming from fathers. The prevailing wisdom was that mothers are the sole reservoirs of inherited Autism risk due the the female protective effect (women require more genetic load to be affected, therefore a male shouldn't transmit a risk mutation since he would be affected).

The results suggest that the genetics of Autism is more complex than previously thought and epigenetics, genetic modifiers, and selfish genes might play a role. This work was published in Science

Detecting structural variation in Illumina short paired-end genomes is extremely error prone with a false discovery rate of 40%. Likewise for sensitive SV detection, many calling tools need to be used, which complicates downstream analysis. To overcome these hurdles, I developed a machine learning model, SV² that genotypes structural variation with a False Discovery Rate between 1-4%.

SV² was trained on high quality genomes and SV genotypes from the phase 3 release of the 1000 Genome Project. Detailed performance results are summarized in our publication in Bioinformatics