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
.@cgonzagaj#GRD23: REMEXER project to start a rare disease registry in Mexico. Can start to understand the number of patients, the challenges/needs, and the diagnoses.
144 patients registered in the first year.
.@cgonzagaj#GRD23: Only ~27% of patients have had genetic testing and many of these patients had to pay out of pocket for this, which can be costly.
Via ReMexER, starting to do genomic sequencing. Of the first patients, 36% have a diagnosis in a known gene, 36% novel candidate.
@cgonzagaj .@cgonzagaj#GRD23 walked through a few patient cases. Now mentioning an initiative for rare diseases in Latin American & the Caribbean (ERCAL) to bring together patients, researchers, clinicians, and regulators. Goals to promote/establish early diagnosis programs + registries.
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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).
Rob Taylor #GRD23: High throughput sequencing has helped identify pathogenic variants + new disease genes.
A few examples shown, including POLRMT, UQCRH, etc.
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.
Kristine Bilgrav Saether #GRD23: TELLR finds split reads and insertions, then uses DBSCAN to cluster, minmap2 --> TE calls.
Long reads also give methylation information, which is useful since TE activity is controlled via epigenetics.
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.
Kaiyue Ma #GRD23: SMuRF, EVE, and REVEL all do well in AUC analysis of computational predictors. REVEL is the best, but high correlation between SMuRF scores and REVEL. Improvements to SMuRF underway.
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.
Gosia Borowiak #GRD23: Re-emphasizes a point from yesterday: need to have a "factory" to be able to make large amounts of high quality cells if you want to do disease modelling / testing.
Figured out a way to allow serial expansion of these cells [MMP2, I believe].
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).
.@danrdanny#GRD23: Long-reads are 1kb+ in length. Read accuracy varies (90-99%) and the cost is $500-$3k.
Long-read sequencing finds 2x as many structural variants as short reads. See: cell.com/ajhg/pdfExtend…
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.