Thread by @thatdnaguy

#ASHG20 VAY
The added value of RNA sequencing over WES for variant interpretation and diagnosis of patients with rare genetic disorders.
Vicente A. Yepez.

#ASHG20 VAY 50-75% of rare genetic disease patients don't get a diagnosis after whole exome. Either not found reasonable variants, or variants are of uncertain significance.

#ASHG20 VAY Example of mitochondrial disease. Prevalence ~1/5000. Disruptions in energy metabolism.

#ASHG20 VAY 105 fibroblasts from patients with mitochondrial disorders unsolved by whole exome. Aberrant expression and splicing diagnosed about 10% of them.

#ASHG20 VAY Used OUTRIDER to remove technical effects and find true expression outliers. Associated with rare vars in the patients. Under expression outliers are enriched in rare, LoF variants.

#ASHG20 VAY Used FRASER to look at splicing events in these patients (loss, gain, alterations in splicing). Use percent splicing and splicing efficiency measures.

#ASHG20 VAY Splicing outliers are enriched in rare splice, *INTRONIC*, and *CODING* rare variants.

#ASHG20 VAY Look at mono-allelic expression of rare allele per allele per patient. Rare vars are less frequent mono-allele expressed (ref alleles more likely mono-expressed).

#ASHG20 VAY Each strategy contributed to different cases. Called variants from the RNA-Seq also to bolster things missed in the WES.

#ASHG20 VAY Example - homozygous synonymous variant in WTNK. Leads to a *splicing* defect. Another - intronic variant in NDUFAF5 intronic variant makes a cryptic intron (splice to intronic variant, would be missed in whole exome).

#ASHG20 VAY Negative case - homozygous splice acceptor rare variant in BUB1 doesn't cause a splicing defect at the RNA level.

#ASHG20 VAY integrated methods in DROP pipeline.
bit.ly/34Ia09I