Jonathan Sebat

Great turnout!

Decoding Genetics of Autism

Speakers:
Prof Jonathan Sebat - UCSD
Prof Lilia Lakoucheva - UCSD
Dr. Alan Ma - Children’s Hosp Westmead,
Prof. Katrina Williams - @MonashUni

Hosted by BMC/Child Neurodevelopment team @adamguastella.bsky.social

I doubt that there is a single family in America that hasn’t benefitted directly from the NIH.

True story, as an undergrad I did an experiment with green Anole lizards where I kept a constant number of flies in their cage by running a hose from my scuba tank through a jar of flies and into the tank. Lizards really are the mothers of invention

Leaf blowers on lizards is pretty innovative if you ask me

Not the most accurate analogy. In this example there is a real difference between the 4th percentile and the 15th percentile

YouTube video by The Late Show with Stephen Colbert A Scientific Brain Drain Has Followed Trump’s Gutting Of The NIH - Dr. Francis Collins

The former NIH director on the catastrophe unfolding for American research. youtu.be/lW9c6t4potU

I'm pretty sure that there would not be any context in my chatGPT conversations in which the chatbot would inclined to say "Hail Satan". I'm really missing out.

Agreed. Theres alot to learn from single cell LR-WGS of somatic tissues!

I’m not sure I understand.

TL;DR LRs boost detection of de novo and inherited coding SVs and longer TRs, which boosts detection of causal variants. But long reads are game changer WRT to resolving complex genetic variation and its functional consequences and regulatory effects.

Power is limited in N=243. But the signal is quantifiable. Rare SVs, TRs and rare SNVs combined explained 7.6% of the heritability. We will need larger samples to get precise estimates, but the combined common and rare is starting to reach a substantial fraction.

Gray zone carriers typically look like panel E. Only FMR1 methylation is skewed. X chromosome inactivation is not skewed. The one exception (panel D) was a girl that carried an X-linked dominant mutation in DDX3X a gene that escapes XCI and, for unknown reasons, is know to cause skewed XCI

Skewed methylation was a characteristic of all "gray zone" alleles of FMR1 (>35 repeats). But in all but one sample, the skewing was specific to FMR1. X chromosome inactivation was NOT skewed. 10/N

In the fragile X repeat FMR1, we went full long-read nerd with PHASED repeats AND methylation. Phased reads in one female (REACH365) shows random methylation (red) on the X. In another female (REACH561) with an expanded 49 repeat allele, methylation was totally skewed to expanded haplotype H2 9/N

Long-Read Genome Sequencing in Clinical Psychiatry: RFX3 Haploinsufficiency in a Hospitalized Adolescent With Autism, Intellectual Disability, and Behavioral Decompensation - PubMed Long-Read Genome Sequencing in Clinical Psychiatry: RFX3 Haploinsufficiency in a Hospitalized Adolescent With Autism, Intellectual Disability, and Behavioral Decompensation

We and @abesterman.bsky.social detected a TAN-DUP-DEL in a clinical case. Assembly of the complex SV was essential for determining the genetic diagnosis of RFX3 haploinsufficiency. It showed that the DEL occured within the FUNCTIONAL copy of the gene pubmed.ncbi.nlm.nih.gov/40200712/

Where long reads really shine is when you need to map out and assemble large complex SVs. In doing so, we found a class of duplication/deletion events (TAN-DUP-DEL and INV-DUP-DEL) events. They also produce distinct signatures in short read coverage data

Phase information of individual reads ends up being useful for a variety of purposes including assembling SVs, genotyping and detection of de novo and mosaic SVs and TRs (more to come on this) 6/N

De novo SVs have been bread-and-butter of ASD genetics, and LRs detect novel de novo and somatic MOSAIC coding SVs. In this example, a de novo in-frame duplication, was present on most (but not all) reads on the H2 haplotype in the offspring and coverage also showed copy number of 2.5 instead of 3.

Panel C (coding SVs in constrained genes) are a class variants with well-established associations with ASD. To maximize detection of these, one needs a combination of short reads and long reads. For large (>50 bp) tandem repeat variants, long reads alone do a good job 4/N.

a susbstantial fraction of SVs are only detetable with LRs. However, there is also a significant fraction of SVs that are detectable only with Illumina WGS, particularly large CNVs that are detectable based on coverage. (A) All SVs (B) coding SVs (C) coding SVs in constrained genes (pLI>0.9).

We WGS'd 267 subjects from 63 ASD families, 109 with ONT (GridION) and 158 with PacBio HiFi platform (Sequel IIe) and 109 with ONT(GridION). Standard structural variant (SV) and tandem repeat (TR) calling pipelines were applied to both platforms. 2/N

Structural variants are significant contributor to autism. But many SVs & TRs are hard to detect with short reads. Long read sequencing with @pacbio.bsky.social and @nanoporetech.com captures and maps out alot of what short reads miss. So what can LR-WGS tell us about autism? 🧵

That's a good way to cleanse the palette before starting #21

Is there a limit to how many times someone can listen to “war pigs“ in one day? Asking for a friend.

Four of the 18 loci are on Chr 16, see table S3

I totally agree! bsky.app/profile/seba...

If you didn't see the thread on the first paper, don't forget to check it out bsky.app/profile/did:...

While not attributable to the major loci, patterns are consistent within them. When you look closely at cell-type specific gene expression in DUP 16p11.2 or DEL 22q11.2, you begin to appreciate how the effects of a CNV can be mediated through distinct pathways across a variety of cell types

Factor F2 was driven by differential DUP effects in neuronal vs non-neuronal cell types in mood disorders. F3 by differential spatial patterns of DEL effects in MDD and ADHD. The 3 factors, factor loadings and factor scores remain concordant after we remove all 18 genome-wide significant loci

As a reminder, DEL effects are concentrated in visual, auditory, sensorimotor. DUP effects are more frontal. Dose dependent effects in SCZ appear to show differential patterns at multiple levels synaptic/regulatory, excitatory/inhibitory, sensory/association