5 ms·

Anytime you perform a sequencing experiment you will get _some_ microbial/fungal contamination. Every time. You can even check this yourself today. Analyse any

by axg11 4y ago

Anytime you perform a sequencing experiment you will get _some_ microbial/fungal contamination. Every time. You can even check this yourself today. Analyse any publicly available (unprocessed) whole genome sequencing data. Usually the contamination is <1% but it’s there. This study hasn’t ruled out contamination as the cause for the results. Given that, it’s very likely to be BS.

greggsy 4y ago
> You can even check this yourself today. As much as I would love to be able to do this, I’m unsure where to start, and while I’m certain there would be a stackoverflow community for it, I wouldn’t even know what to ask. I know this sounds like a joke comment, but I feel like we live in a time where someone could post some Jupyter notebooks on the matter, and for someone to create a step by step video on YouTube to guide people through the process.
- yellsatclouds 4y ago
  we cerntainly have the technology... just not the social-political will to do it.
  - penumbragement 4y ago
    Not to be pedantic, but we do have the social-political will, just not enough of it. Yet.
- aaauaucuggaa 4y ago
  Start with downloading SRA toolkit: https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-To... Find some data of interest: https://www.ncbi.nlm.nih.gov/sra?term=(%22Homo%20sapiens%22[Organism]%20AND%20%22strategy%20wgs%22[Properties]%20AND%20%22platform%20illumina%22[Properties]%20AND%20%22filetype%20fastq%22[Properties])&cmd=DetailsSearch https://www.ncbi.nlm.nih.gov/sra?term=(%22Homo%20sapiens%22[... (This searches SRA for human genome sequences on illumina with fastq files available) Run fasterq-dump on the SRR (listed as "Runs" in the SRA page of your choice): fasterq-dump SRR21812682 Download a microbial genome of interest, here is the link for common yeast: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF_000146045.2_R64/GCF_000146045.2_R64_genomic.fna.gz https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF... Install an alignment tool like bwa: https://github.com/lh3/bwa https://github.com/lh3/bwa Unzip the the genome file and create a bwa index: gunzip GCF_000146045.2_R64_genomic.fna.gz && bwa index GCF_000146045.2_R64_genomic.fna Align: bwa GCF_000146045.2_R64_genomic.fna SRR21812682.fastq (or whatever the fastq files are named) If you get any alignment results, you've "found" fungal DNA in a human sample. This is a highly simplified workflow, but covers the basic ideas. One of the papers is free and the method sections covers their workflow (it is much more complicated): https://www.cell.com/cell/fulltext/S0092-8674(22)01127-8 https://www.cell.com/cell/fulltext/S0092-8674(22)01127-8 Useful resources: https://www.biostars.org/ https://www.biostars.org/ https://rosalind.info/problems/list-view/?location=bioinformatics-armory https://rosalind.info/problems/list-view/?location=bioinform... https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga https://www.cancer.gov/about-nci/organization/ccg/research/s... (source data for this paper, cancer specific sequencing data)
  - mbreese 4y ago
    If anyone is thinking of doing this, it is both this easy and way harder. Yes, this is an approximate workflow. It doesn’t take that much specialized knowledge to get it running. However step 2/3 (find/download a dataset of interest) is harder. Finding whole genome sequencing data for a cancer that you can download without being part of a research institution is difficult. There are a lot of controls over who can access raw DNA sequences from patients. RNA data are much more readily available as they are less identifiable. Specifically, here is the type of access you need: https://gdc.cancer.gov/access-data/obtaining-access-controlled-data https://gdc.cancer.gov/access-data/obtaining-access-controll... The reasons for this are good and I’m not trying to say otherwise. Just that from a practical perspective, being able to technically perform the analysis is doable for many non-biomedical people here. However, accessing the raw data is much more difficult.
  - lifeisstillgood 4y ago
    I am reaching for something - that software is now enabling a minimal access level to amazing corners of science and technology - we can luck satellite photos from the ether, have whole dna sequences on our desktop. I feel there is a "basic bootcamp for the 21C" that I missed
- biophysboy 4y ago
  If you just wanted to see if a particular sequence was fungi, you could just use BLAST. If you had thousands of sequence reads from multiple unknown organisms, then you’d have to implement a meta genomics pipeline. All the software for this is already made. You take your sequence reads, trim them a bit, assemble them into “contigs”, and then map those contigs to known genomes in the magical tree of life.
vavooom 4y ago
Assuming this was true and well documented, this sounds like an interesting classification problem to identify and quickly flag such instances in genome sequencing. As always - this requires good clean data!
jcampbell1 4y ago
This is newsworthy because the Swedish healthcare system recently discovered that prostate cancer patients who took oral Terbinafine to treat toenail fungus had much better cancer outcomes. The same holds for Terbinafine and colon cancer. We are currently in the WTF is going on here phase. $5 of anti-fungal medication cuts some cancer death rates in half? Is a tiny amount of fungus in cancer tissue driving growth and metastasis? Does Terbinafine have some other anti-cancer mechanism?
- smt88 4y ago
  > $5 of anti-fungal medication cuts some cancer death rates in half? I read an interesting hypothesis that many cancers can be treated by changing (perhaps unpredictable) variables in the patient's body. We already know cancers thrive in nutrient-rich environments and that many tumors have a narrower set of survival conditions than the normal tissue around them. That's why chemo works: you start to kill the whole person and the tumor (hopefully) dies first. So what if you just randomly messed around with the conditions of the body? Give someone a diabetes drug, change their diet, add an antifungal... we've seen random successes like this, and the unifying theory might be that the cancer was thriving because it had exactly the right conditions, and now we can change them to cause the cancer to stop thriving.
- dev_throw 4y ago
  Thanks for giving me my reading material this week, as someone with stage 4 colon cancer :) I also read about promising outcomes with fenbendazole (dog deworming medicine) and colon/lung cancer, hope these finally unlock the fix for metastasis.
  - yunobcool 4y ago
    Sorry to hear about the stage 4 prognosis. I know its insanely unlikely, but here's hoping for a quick game changing recovery that will flip the table on your cancer.
tjpnz 4y ago
>Anytime you perform a sequencing experiment you will get _some_ microbial/fungal contamination. Can you provide a source for this? There are a lot of cranks right now claiming that there's no such thing as a virus because we've never been able to get a non-contaminated sequence (something I've assumed was due to culturing). If this is true of everything there's no limit to what can and cannot exist per their insane arguments.
- saurik 4y ago
  Did you even try to look before throwing FUD? Into is really sketchy to me when people call for citations without noting at least in passing that they either found the opposite or tried something reasonable and failed to find something. In this case, I don't really know much about this either way, but 30 seconds of effort by just copy/pasting the exact sentence you quoted into Google found me something that seems to fit the bill, showing that contaminants in sequencing is "pervasive" and must be accounted for--such as by filtering things that look out of scope--to get reasonable results. https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-020-0748-z https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-02... > Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability > We found that contamination is pervasive and can introduce large biases in variant analysis. We showed that these biases can result in hundreds of false positive and negative SNPs, even for samples with slight contamination. Studies investigating complex biological traits from sequencing data can be completely biased if contamination is neglected during the bioinformatic analysis, and we demonstrate that removing contaminant reads with a taxonomic classifier permits more accurate variant calling.
  - tokai 4y ago
    You are using the term FUD incorrectly.
    - deleted 4y ago
      [deleted]
  - throwaway290 4y ago
deleted 4y ago
[deleted]

by axg11 4y ago

greggsy 4y ago

> You can even check this yourself today. As much as I would love to be able to do this, I’m unsure where to start, and while I’m certain there would be a stackoverflow community for it, I wouldn’t even know what to ask. I know this sounds like a joke comment, but I feel like we live in a time where someone could post some Jupyter notebooks on the matter, and for someone to create a step by step video on YouTube to guide people through the process.

yellsatclouds 4y ago
we cerntainly have the technology... just not the social-political will to do it.
- penumbragement 4y ago
  Not to be pedantic, but we do have the social-political will, just not enough of it. Yet.
aaauaucuggaa 4y ago
Start with downloading SRA toolkit: https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-To... Find some data of interest: https://www.ncbi.nlm.nih.gov/sra?term=(%22Homo%20sapiens%22[Organism]%20AND%20%22strategy%20wgs%22[Properties]%20AND%20%22platform%20illumina%22[Properties]%20AND%20%22filetype%20fastq%22[Properties])&cmd=DetailsSearch https://www.ncbi.nlm.nih.gov/sra?term=(%22Homo%20sapiens%22[... (This searches SRA for human genome sequences on illumina with fastq files available) Run fasterq-dump on the SRR (listed as "Runs" in the SRA page of your choice): fasterq-dump SRR21812682 Download a microbial genome of interest, here is the link for common yeast: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF_000146045.2_R64/GCF_000146045.2_R64_genomic.fna.gz https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF... Install an alignment tool like bwa: https://github.com/lh3/bwa https://github.com/lh3/bwa Unzip the the genome file and create a bwa index: gunzip GCF_000146045.2_R64_genomic.fna.gz && bwa index GCF_000146045.2_R64_genomic.fna Align: bwa GCF_000146045.2_R64_genomic.fna SRR21812682.fastq (or whatever the fastq files are named) If you get any alignment results, you've "found" fungal DNA in a human sample. This is a highly simplified workflow, but covers the basic ideas. One of the papers is free and the method sections covers their workflow (it is much more complicated): https://www.cell.com/cell/fulltext/S0092-8674(22)01127-8 https://www.cell.com/cell/fulltext/S0092-8674(22)01127-8 Useful resources: https://www.biostars.org/ https://www.biostars.org/ https://rosalind.info/problems/list-view/?location=bioinformatics-armory https://rosalind.info/problems/list-view/?location=bioinform... https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga https://www.cancer.gov/about-nci/organization/ccg/research/s... (source data for this paper, cancer specific sequencing data)
- mbreese 4y ago
  If anyone is thinking of doing this, it is both this easy and way harder. Yes, this is an approximate workflow. It doesn’t take that much specialized knowledge to get it running. However step 2/3 (find/download a dataset of interest) is harder. Finding whole genome sequencing data for a cancer that you can download without being part of a research institution is difficult. There are a lot of controls over who can access raw DNA sequences from patients. RNA data are much more readily available as they are less identifiable. Specifically, here is the type of access you need: https://gdc.cancer.gov/access-data/obtaining-access-controlled-data https://gdc.cancer.gov/access-data/obtaining-access-controll... The reasons for this are good and I’m not trying to say otherwise. Just that from a practical perspective, being able to technically perform the analysis is doable for many non-biomedical people here. However, accessing the raw data is much more difficult.
- lifeisstillgood 4y ago
  I am reaching for something - that software is now enabling a minimal access level to amazing corners of science and technology - we can luck satellite photos from the ether, have whole dna sequences on our desktop. I feel there is a "basic bootcamp for the 21C" that I missed
biophysboy 4y ago
If you just wanted to see if a particular sequence was fungi, you could just use BLAST. If you had thousands of sequence reads from multiple unknown organisms, then you’d have to implement a meta genomics pipeline. All the software for this is already made. You take your sequence reads, trim them a bit, assemble them into “contigs”, and then map those contigs to known genomes in the magical tree of life.

vavooom 4y ago

Assuming this was true and well documented, this sounds like an interesting classification problem to identify and quickly flag such instances in genome sequencing. As always - this requires good clean data!

jcampbell1 4y ago

This is newsworthy because the Swedish healthcare system recently discovered that prostate cancer patients who took oral Terbinafine to treat toenail fungus had much better cancer outcomes. The same holds for Terbinafine and colon cancer. We are currently in the WTF is going on here phase. $5 of anti-fungal medication cuts some cancer death rates in half? Is a tiny amount of fungus in cancer tissue driving growth and metastasis? Does Terbinafine have some other anti-cancer mechanism?

smt88 4y ago
> $5 of anti-fungal medication cuts some cancer death rates in half? I read an interesting hypothesis that many cancers can be treated by changing (perhaps unpredictable) variables in the patient's body. We already know cancers thrive in nutrient-rich environments and that many tumors have a narrower set of survival conditions than the normal tissue around them. That's why chemo works: you start to kill the whole person and the tumor (hopefully) dies first. So what if you just randomly messed around with the conditions of the body? Give someone a diabetes drug, change their diet, add an antifungal... we've seen random successes like this, and the unifying theory might be that the cancer was thriving because it had exactly the right conditions, and now we can change them to cause the cancer to stop thriving.
dev_throw 4y ago
Thanks for giving me my reading material this week, as someone with stage 4 colon cancer :) I also read about promising outcomes with fenbendazole (dog deworming medicine) and colon/lung cancer, hope these finally unlock the fix for metastasis.
- yunobcool 4y ago
  Sorry to hear about the stage 4 prognosis. I know its insanely unlikely, but here's hoping for a quick game changing recovery that will flip the table on your cancer.

tjpnz 4y ago

>Anytime you perform a sequencing experiment you will get _some_ microbial/fungal contamination. Can you provide a source for this? There are a lot of cranks right now claiming that there's no such thing as a virus because we've never been able to get a non-contaminated sequence (something I've assumed was due to culturing). If this is true of everything there's no limit to what can and cannot exist per their insane arguments.

saurik 4y ago
Did you even try to look before throwing FUD? Into is really sketchy to me when people call for citations without noting at least in passing that they either found the opposite or tried something reasonable and failed to find something. In this case, I don't really know much about this either way, but 30 seconds of effort by just copy/pasting the exact sentence you quoted into Google found me something that seems to fit the bill, showing that contaminants in sequencing is "pervasive" and must be accounted for--such as by filtering things that look out of scope--to get reasonable results. https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-020-0748-z https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-02... > Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability > We found that contamination is pervasive and can introduce large biases in variant analysis. We showed that these biases can result in hundreds of false positive and negative SNPs, even for samples with slight contamination. Studies investigating complex biological traits from sequencing data can be completely biased if contamination is neglected during the bioinformatic analysis, and we demonstrate that removing contaminant reads with a taxonomic classifier permits more accurate variant calling.
- tokai 4y ago
  You are using the term FUD incorrectly.
  - deleted 4y ago
    [deleted]
- throwaway290 4y ago

deleted 4y ago

[deleted]