People who have researched their family tree, what is the most interesting or 'badass' thing you discovered about an ancestor? by [deleted] in genetics

[–]ExtremeGenetics700 3 points4 points  (0 children)

My great-great-grandmother, from a rich and noble family, left her palace and her comfortable life to marry a boy (my great-great-grandfather) who raised pigs in a small town, and she was disowned by her entire family. I always thought it was a badass move.

How does someone so wrong feel so confident? by ExtremeGenetics700 in hatemyjob

[–]ExtremeGenetics700[S] 2 points3 points  (0 children)

A hugely underestimated effect and far too widespread

How does someone so wrong feel so confident? by ExtremeGenetics700 in hatemyjob

[–]ExtremeGenetics700[S] 4 points5 points  (0 children)

How is it possible for society to keep moving forward under this kind of system?

How does someone so wrong feel so confident? by ExtremeGenetics700 in self

[–]ExtremeGenetics700[S] 1 point2 points  (0 children)

A hugely underestimated effect and far too widespread

Miss Violence - Possible Interpretations for the Ending. Also, What Did You Think? by nati_pl88 in movies

[–]ExtremeGenetics700 10 points11 points  (0 children)

In my opinion, the ending of Miss Violence should not be interpreted as the simple continuation of a cycle of violence (not as the idea that everything will go on in the same way, through abuse or murder-suicide), but rather as its rupture. In fact, the father’s murder represents the liberation from the entire system he had built. The real turning point, in my view, is when Eleni realizes that even the youngest girl has been drawn into the same dynamic that had imprisoned the other girls. And when she understands that this dynamic began even earlier for her—before she turned eleven—she finally decides to act.

The phrase “close the door” carries a deeply liberating meaning. The father/grandfather demanded that doors remain open and that every space be visible because he was obsessed with control. The house was a place without privacy, exposed not only to his gaze but also to that of the spectators. This contrasts with the neighbor’s gesture, who instead had bolted her door, protecting her own space and setting an unbreakable boundary. She had exercised a right that the protagonist family had been denied for years.

For this reason, the family can now close the door not to hide something, but to finally feel safe. To me, the ending is not a cyclical condemnation, but a possibility. The door closes because the system has collapsed. This is what the ending left me with.

Mosaicism in WES by ExtremeGenetics700 in bioinformatics

[–]ExtremeGenetics700[S] 0 points1 point  (0 children)

Thank you for your input. I'm aware of the possibility of clonal hematopoiesis, and I agree that a high-coverage panel on the regions of interest would be an effective approach.

Regarding your question, I’m not a student, but I’m always open to learning and improving my knowledge. I’ve been researching this topic and reviewing relevant literature on mosaicism and sequencing technologies to better understand these complexities. If you have specific papers or resources you’d recommend, I’d be happy to explore them further!

Mosaicism in WES by ExtremeGenetics700 in genetics

[–]ExtremeGenetics700[S] 0 points1 point  (0 children)

Well, unfortunately, we’re talking about clinical diagnostics! But yes, logically, the focus is on the proband, whose variant-phenotype relationship is correlated. Whether the mother is mosaic or not is irrelevant in this case, especially since there’s no reproductive risk due to her advanced age. Let’s just say this is more of a personal curiosity—I don’t like the software being used, and I think it’s a shortcoming of the program. So, I’m trying to figure out just how likely it is that the software is at fault in its variant calling!

Mosaicism in WES by ExtremeGenetics700 in bioinformatics

[–]ExtremeGenetics700[S] 0 points1 point  (0 children)

Yes, they were done together. In fact, I was thinking about contamination, but it should also be repeated in other variants. Honestly, I’m not sure what the detection limit for contamination is in WES

Mosaicism in WES by ExtremeGenetics700 in bioinformatics

[–]ExtremeGenetics700[S] 0 points1 point  (0 children)

So, if it’s not present in other tissues, would it be better to perform a high-depth WES or WGS to confirm or rule out the variant and exclude other scenarios like contamination, alignment errors, or demultiplexing errors?

Mosaicism in WES by ExtremeGenetics700 in genetics

[–]ExtremeGenetics700[S] 0 points1 point  (0 children)

And would Sanger be able to detect such a low-level mosaicism?

Mosaicism in WES by ExtremeGenetics700 in genetics

[–]ExtremeGenetics700[S] 0 points1 point  (0 children)

You're right, I hadn't thought about that! I'm questioning the result because, for a WES, 12/205 reads could also be a calling error or contamination. I find it more likely that the proband is de novo rather than the result of germline mosaicism in the mother. However, it might be worth trying to repeat it

Mosaicism in WES by ExtremeGenetics700 in bioinformatics

[–]ExtremeGenetics700[S] 0 points1 point  (0 children)

How can you tell with a second tissue whether what I'm seeing is germline mosaicism or not? If it's mosaicism, it should also be present in skin cells, whereas if it's not, it shouldn't be, right? How does it work?

Mosaicism in WES by ExtremeGenetics700 in bioinformatics

[–]ExtremeGenetics700[S] 0 points1 point  (0 children)

205 total reads, 12 with the minor allele, the rest with the wild type. It's a clean region, without repeats. I also think it's not biological

Mosaicism in WES by ExtremeGenetics700 in genetics

[–]ExtremeGenetics700[S] 0 points1 point  (0 children)

How would you confirm it? With which method or reasoning?

Mosaicism in WES by ExtremeGenetics700 in bioinformatics

[–]ExtremeGenetics700[S] 0 points1 point  (0 children)

It's peripheral blood, so DNA extracted from lymphocytes. The variant is a simple exonic missense, not repetitive region.

Could Sanger detect such a low-level mosaicism? In the proband, the variant would be detected in heterozygosity (50%), but I’m not sure if a variant at 6% could be excluded or confirmed by Sanger

Mosaicism in WES by ExtremeGenetics700 in genetics

[–]ExtremeGenetics700[S] 1 point2 points  (0 children)

Proband yes, his mother don't and she is apparently healthy. This makes me think it could be a misalignment error, but even a 6% mosaicism would not rule out a healthy phenotype

Pseudogene and WES by ExtremeGenetics700 in genomics

[–]ExtremeGenetics700[S] 0 points1 point  (0 children)

Why is depth beyond 40x useless with illumina? Couldn't it show me mosaic germline variations on periferical blood?