3 ms·

But it's a crucial subset. It's not that WGS is that expensive, but what can you do with it that cant be done with 23andme?

farresito 5y ago
Correct me if I'm wrong. The issue with SNPs is that they are common in the population, and hence they tend to have small effects, because if a variant is common and gives the carrier a big advantage, the variant will over time get absorbed by most of the population, and the same applies the opposite way. So the interesting variants are those that rare, because they are the ones that often cause genes to malfunction.
yread 5y ago
point mutations?
- cblconfederate 5y ago
  but are the ones that are not already in the covered snps interesting ?
  - yread 5y ago
    23andMe only has an overlap of ~30k with the ~500k (?) ClinVar variants. So less than 10% is covered.
- hwillis 5y ago
  That's what SNPs are. Specifically, point mutations that are associated with known outcomes (ie diseases) or with group differences. Point mutations occurring outside SNPs are almost by definition not yet useful. If we know what the gene does or is related to, it's an SNP.
  - otherme123 5y ago
    You second paragraph is wrong. SNPs are interesting because they exist in a significant part of the population. But a new mutation never reported before can as dangerous as you want. A case we found: a woman already developed an illness in her adult life, lets supose it was renal failure. We suspected a genetic root, so we sequenced her exome, founding a never reported mutation that frameshifted a gene previously associated with renal failures. We quickly panel-sequenced her parents and children to check if they had the mutation, which none of them had. So the woman had a de novo mutation in heterozygosis that their little kids were lucky enough to avoid. Imagine the relief. Not useful? I disagree.

3 ms·

But it's a crucial subset. It's not that WGS is that expensive, but what can you do with it that cant be done with 23andme?

by cblconfederate 5y ago

farresito 5y ago
Correct me if I'm wrong. The issue with SNPs is that they are common in the population, and hence they tend to have small effects, because if a variant is common and gives the carrier a big advantage, the variant will over time get absorbed by most of the population, and the same applies the opposite way. So the interesting variants are those that rare, because they are the ones that often cause genes to malfunction.
yread 5y ago
point mutations?
- cblconfederate 5y ago
  but are the ones that are not already in the covered snps interesting ?
  - yread 5y ago
    23andMe only has an overlap of ~30k with the ~500k (?) ClinVar variants. So less than 10% is covered.
- hwillis 5y ago
  That's what SNPs are. Specifically, point mutations that are associated with known outcomes (ie diseases) or with group differences. Point mutations occurring outside SNPs are almost by definition not yet useful. If we know what the gene does or is related to, it's an SNP.
  - otherme123 5y ago
    You second paragraph is wrong. SNPs are interesting because they exist in a significant part of the population. But a new mutation never reported before can as dangerous as you want. A case we found: a woman already developed an illness in her adult life, lets supose it was renal failure. We suspected a genetic root, so we sequenced her exome, founding a never reported mutation that frameshifted a gene previously associated with renal failures. We quickly panel-sequenced her parents and children to check if they had the mutation, which none of them had. So the woman had a de novo mutation in heterozygosis that their little kids were lucky enough to avoid. Imagine the relief. Not useful? I disagree.