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Kaitlin Samocha Profile picture
@ksamocha
Apr 25 • 5 tweets • 2 min read Twitter logo Read on Twitter
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.
Zeid Kuzbari #GRD23: ~16% of the filtered variants (by MAF, consequence, etc) were from the germline. But this is highly variable. Example: BRCA1 has a much higher germline rate vs APC.
Zeid Kuzbari #GRD23: A sub-analysis of age shows that the fraction of germline variants looks different for some genes (RB1) when studying patients with onset < 5 vs all patients.
Zeid Kuzbari #GRD23: More details on the specific guidelines can be read here:
annalsofoncology.org/article/S0923-…

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More from @ksamocha

Kaitlin Samocha Profile picture
Apr 26
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.
Read 6 tweets
Kaitlin Samocha Profile picture
Apr 26
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.
Read 4 tweets
Kaitlin Samocha Profile picture
Apr 26
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.
Read 4 tweets
Kaitlin Samocha Profile picture
Apr 26
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…
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].
Read 4 tweets
Kaitlin Samocha Profile picture
Apr 26
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…
Read 8 tweets
Kaitlin Samocha Profile picture
Apr 25
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.
.@davidrliu #GRD23: Have been able to show both ex vivo and in vivo base editing. Example of in vivo base editing for progeria in mice:
nature.com/articles/s4158…

Untreated mice live ~7.5months, but the ABE-treated mice live much longer.
Read 6 tweets

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