2 ms·

Later: > Variants (SNP/ InDel) generated with this method were compared with a normal dataset using Archer’s analysis pipeline to distinguish noise from a true

Later: > Variants (SNP/ InDel) generated with this method were compared with a normal dataset using Archer’s analysis pipeline to distinguish noise from a true call. The normal dataset was created with sequencing data from seven young, healthy individuals.

gus_massa 4y ago
From the article: > in this astronaut cohort (median age 44 years, range 37–67), I'd like to see also a comparison with 7 normal persons with ~45 years old. How many mutations is the expected value for a ~45 years old person?
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hedora 4y ago
Archer's analysis pipeline isn't a well defined statistical test. It's a UI that browses results from the type of machine they used: https://www.enzymatics.com/news/archer-analysis-pipeline-update-version-3/ https://www.enzymatics.com/news/archer-analysis-pipeline-upd... They filtered the results with various p-values < 0.01. Their supplementary data: https://www.nature.com/articles/s42003-022-03777-z#Sec9 https://www.nature.com/articles/s42003-022-03777-z#Sec9 doesn't say how many samples the machine produced in the first place, but it does say the filter resulted in 35 hits. That tells us absolutely nothing about the rate of mutations in the astronauts vs the general population, or even if astronauts produce more novel mutations on average vs. the general population. On top of that, they seem to have the data to answer these questions, but don't report it anywhere: Do zero-mission astronauts also show a "true call" in Archer's analysis pipeline? They ran multiple samples from the same astronauts (before and after missions). On average, does the same astronaut have more/more-novel mutations after each mission? These would require additional experiments or data, but seem obvious to check: Do they have unusually high or low numbers of mutations vs. the general population at the same age? If so, grouping the general population sample, what other professions also show a "true call" according to the pipeline?

gus_massa 4y ago

From the article: > in this astronaut cohort (median age 44 years, range 37–67), I'd like to see also a comparison with 7 normal persons with ~45 years old. How many mutations is the expected value for a ~45 years old person?

deleted 4y ago
[deleted]

hedora 4y ago

Archer's analysis pipeline isn't a well defined statistical test. It's a UI that browses results from the type of machine they used: https://www.enzymatics.com/news/archer-analysis-pipeline-update-version-3/ https://www.enzymatics.com/news/archer-analysis-pipeline-upd... They filtered the results with various p-values < 0.01. Their supplementary data: https://www.nature.com/articles/s42003-022-03777-z#Sec9 https://www.nature.com/articles/s42003-022-03777-z#Sec9 doesn't say how many samples the machine produced in the first place, but it does say the filter resulted in 35 hits. That tells us absolutely nothing about the rate of mutations in the astronauts vs the general population, or even if astronauts produce more novel mutations on average vs. the general population. On top of that, they seem to have the data to answer these questions, but don't report it anywhere: Do zero-mission astronauts also show a "true call" in Archer's analysis pipeline? They ran multiple samples from the same astronauts (before and after missions). On average, does the same astronaut have more/more-novel mutations after each mission? These would require additional experiments or data, but seem obvious to check: Do they have unusually high or low numbers of mutations vs. the general population at the same age? If so, grouping the general population sample, what other professions also show a "true call" according to the pipeline?