Rob Taylor #GRD23 on multi-omic approaches to dissect mitochondrial pathology.

Clinical mitochondrial diseases collectively have a prevalence of ~1 in 4000 and have functional, molecular, clinical, and prognostic heterogeneity. Rob Taylor #GRD23: Some of this complexity comes from the fact that cells have many copies of the mitochondrial genome. Pathogenic variants can either be homoplasmic (in all copies) or heteroplasmic (in some copies).

Kristine Bilgrav Saether #GRD23: Transposable elements jump through the genome via RNA intermediates. They make up ~50% of the genome. Multiple versions, some of which are autonomous (LINE) and some are non-autonomous (SVA). Kristine Bilgrav Saether #GRD23: Can use methods like MELT (👍 @DrGeneUK), xTEA, etc for short reads. For long reads, look at split reads so they wrote a new one called TELLR.

Studying 1KG and SweGen samples.

Kaiyue Ma #GRD23: Mutations in alpha-dystroglycan can lead to dystroglycanopathies.

Developing SMuRF (saturation mutagenesis-reinforced functional assays) to test variants in alpha-DG glycosylation enzymes like FKRP. Kaiyue Ma #GRD23: SMuRF scores have the expected distributions for variant type (e.g. synonymous look neutral, nonsense functional). Missense mutations in the catalytic domain tend to be more disruptive (vs those in stem). Good correlation of score with ClinVar classifications.

Gosia Borowiak #GRD23: The field figured out how to make progenitor cells in culture, but trying to get homogenous populations of human beta cells was a challenge.

Time an endocrine progenitor is formed matters in likelihood of developing into a alpha vs beta cell. Gosia Borowiak #GRD23: Digging into the microenvironment that influence human endocrine development. Found that WNT5A is necessary and sufficient for beta cell in vitro induction.

nature.com/articles/s4146…

Danny Miller (@danrdanny) #GRD23: Starts with his take home points
- long-read sequencing will fundamentally change clinical genetic testing
- will reduce barriers to accessing comprehensive testing
- this will happen even if the cost of generating other types of data falls to $0 .@danrdanny #GRD23: Traditional genetic workup (mircoarray -> panel -> exome) is diagnostic in <50% of cases.

Pitches that we can use long-read sequencing as a single test that could then be analyzed in different ways (SV -> repeat expansion -> genome, etc).

Now on is David Liu (@davidrliu) walking through programmable nucleases. >200 patients have been treated with therapies enabled by CRISPR nucleases thus far #GRD23 .@davidrliu #GRD23: While nucleases are good for gene disruption, they aren't great for gene correction.

Developed base editing and prime editing to address this gap and have editors now that can address all single nucleotide base changes.

Hannah Verdin #GRD23: Over the last few years, just started carrier screening in Belgium via BeGECS (Belgian Genetic Expanded Carrier Screening). 400 couples have been studied to date.

Recruited pre-conception, but couples have to pay 1.5keuros. Hannah Verdin #GRD23: Couple report is generated to inform of an increased couple risk. Also generate individual reports to provide information about specific high impact variants.

Lidewij Henneman #GRD23: Aim of carrier screening is to find carrier couples of recessive disorders with the goal of increasing reproductive autonomy.

A big challenge of screening preconception is that it is difficult to identify and reach the target population. Lidewij Henneman #GRD23 also notes that screening is not the same as diagnostics. Frequently couples are low-risk, and this is for reassurance. Need to ensure equal access -- should be inexpensive, simple, and socially accepted.

Zeid Kuzbari #GRD23: Tumor-only sequencing remains the most frequent approach, but that means you need to distinguish between germline and somatic variants.

Working on recommendations of when to suggest germline follow-up after tumor-only. Zeid Kuzbari #GRD23: Starting with 49k tumors, but focused on 45k with certain features [that I missed]. Of the 58 cancer susceptibility genes, separated in different actionability classes.

Nathalie Charmi (@Nathalie_Chami) #GRD23: There are rare forms of obesity that are monogenic (typically early onset), which are to be distinguished from syndromic obesity.

Leptin-Melanocortin pathway regulates energy balance -> disruptions in this can lead to overeating .@Nathalie_Chami #GRD23: Using 500k exomes from UK Biobank and focused on 1.3k rare variants in 6 monogenic obesity genes. For each variant, calculated penetrance and the odds ratio.

At least for MC4R LoF, seems like there is a correlation between penetrance and OR

Jay Gopalakrishnan on brain organoids #GRD23: The human brain is one of the most complex tissue systems with many different cell types that have highly orchestrated interactions.

Brain organoids are self-assembling 3D structures that could be used to model neurological disorders Jay Gopalakrishnan #GRD23: Brain organoids have some of the layers seen in the brain. Have been able to make organoids with two eye-like structures (are light sensitive).

Have worked out a way to make ~1000 nearly homogeneous brain organoids per batch. "Hi-Q" brain organoids.

Gabrielle Lemire up next on how genome sequecing can be more than just a fancy exome. #GRD23

Genomes are more expensive than exomes and have a higher analytical burden, but could offer additional benefit. Want to evaluate that benefit here. Gabrielle Lemire #GRD23: 744 families with short read genome sequencing, some also have RNAseq.

Need genomes for deep intronic variants, tandem repeats, small/intronic CNVs, or coding variants in regions that weren't well covered in exome sequencing.

Dana Marafi (@Danamarafi) #GRD23: Founder effect is a loss of genetic variation due to a population being established by a small group of individuals (due to a bottleneck or geographical/cultural isolation).

See allele frequency differences to originating population. .@Danamarafi #GRD23: These leads to founder mutations, some of which can contribute to disease. Can identify these founder mutations via haplotype analysis, genealogical investigation, or minor allele frequency in a matched genetic ancestry group.

Claudia Gonzaga-Jauregui (@cgonzagaj) starts off this morning describing rare disordes in Latin America. Variable definitions between countries. #GRD23 @cgonzagaj .@cgonzagaj #GRD23: Barriers for implementation of molecular diagnostics in Latin America:
- limited testing coverage by healthcare/insurance
- high cost/low availability
- lack of awareness from PCPs
- low testing demands
- few trained professionals
-> etc

Alexandre Reymond #GRD23: Found out a few years ago that CNV carriers in the general population tend to be at the mild end of the phenotypic spectrum, see:
jamanetwork.com/journals/jama/…

With larger database/biobanks, can do a CNV-GWAS to find CNVs as phenotypic modifiers. Alexandre Reymond #GRD23: In a CNV-GWAS, found 131 signals across 47 phenotypes in:
pubmed.ncbi.nlm.nih.gov/35240056/

Found a few new associations, including a novel gene association for MARF1 in female reproduction time.

Nechama Wieder (@NechamaWieder) #GRD23 starts by reminding us of how critical 5'UTRs are.

Start codons within the 5'UTRs (uAUGs) can decrease translation of the downstream coding sequence.

Start-stop: "minimum ORF" impedes ribosome scanning without peptide production of uORFs. .@NechamaWieder #GRD23: Start-stop contribute to ribosome pausing and decreasing downstream translation.

~5% of all MANE Select transcripts have these start-stops and most of them only have one.

Peter Robinson #GRD23 on splicing-impacting variants.

Diagnostic rates have improved over time, but still are low. Where are the other diagnoses?

Notes that bioinformatics can help increase efficiency by improving variant prioritization and interpretation. Peter Robinson #GRD23: Field is slowly moving to focus on prioritizing noncoding variants (vs missense).

For splice sites, know about the importance of the canonical sites (e.g., donor +1/+2), but variants that fall outside of those regions are harder to interpret.

Morton #LupskiLecture #GRD23: Walking through a specific case with a balanced rearrangement (an inversion) that disrupted HMGA2.

Described more here:
sciencedirect.com/science/articl… Morton #LupskiLecture #GRD23: Reminds the room that 97% of the genome does not code for proteins and highlights that there are >15k lncRNAs in the human genome. See more lncRNAs in mice, meaning that we may be missing some in humans.

Maureen Pittman #ASHG22: Oligogenic inheritance describes situations were there are some loci (more than one, less than thousands) that contribute to a disease.

Congenital heart disease (CHD) is potentially one of these situations. Maureen Pittman #ASHG22: Example of a family where GATA6 was passed on from an unaffected parent to a child with CHD. Common variants don't seem to contribute much -- could it be due to other rare variants?

Graham Erwin (@grahamserwin) #ASHG22: Half of the human genome is repetitive, most are transposons but about 3% is made up of tandem repeats. Tandem repeats cause >40 human diseases. Graham Erwin (@grahamserwin) #ASHG22: Friedreich's ataxia is caused by a triplet expansion in the first intron of FXN gene. Patients have 70++ repeats, which leads to lower expression/protein levels.

Scott Younger #ASHG22: Genomic Answers for Kids (GA4K). Currently have >10k subjects enrolled and have returned ~1k diagnoses.

Focus here is large scale assays, specifically establishing a protocol to do patient-derived iPSC reprogramming at scale. Have generated 250 iPSC lines Scott Younger #ASHG22: Using antisense oligonucleotides (ASOs) to modulate gene expression. Proof of their use in TNNT2 gene.