Answers.Body: <p>Please take a look at </p>
  
  <p><a href="https://www.nature.com/articles/sdata201610" rel="nofollow noreferrer">An open access pilot freely sharing cancer genomic data from participants in Texas</a></p>
  
  <p>Although I have not worked on this paper but author claimed that both tumor and normal data is publicly available. In case if you still need something more, than you can work on virtual normal data. And there are several papers which provide machnine learning techniques to overcome the deficiency of normal data (not much efficient but still they give considerable results). Hope this information will help you. Thanks</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-04-25T13:43:19.440Z
Answers.Text: Argh, this looks perfect, but the site seems to be down! I have emailed the author of the paper to see if it's just a temporary glitch. Thanks!
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-04-26T23:35:34.307Z
Answers.Text: [The site](http://txcrb.org/) is no longer maintained, but I contacted the authors and they very helpfully put it back up for me!
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-04-30T06:22:19.250Z
Answers.Text: @terdon: Then you should look for virtual normal database than or, if interested, machine learning techniques.
Answers.UserDisplayName: Lot_to_learn
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-04-25T10:07:55.363Z
Answers.LastActivityDate: 2018-04-25T10:07:55.363Z
Answers.UserDisplayName: Lot_to_learn
Body: <p>I am looking for a publicly available matched tumor-normal sample. I need Illumina fastq reads (or an aligned bam file, since I could extract the reads from it) from a tumor and a matching, non-tumor control set from the same patient. Ideally, I would also have a truth set of known variants in the sample, but I can live without that. </p>
  
  <p>I checked the <a href="http://gdc.cancer.gov" rel="nofollow noreferrer">Next Generation Cancer Knowledge Network</a> but although they do seem to have appropriate bam files, which I could convert to fastq, all of the ones I found were "controlled access" and getting access seems very complicated. </p>
  
  <p>Is there something like the public NA12878 sample for tumor-normal analyses? </p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-20T15:11:49.050Z
Comments.Text: The TCGA does provide the raw fastq too, and for some patients one has sample from the tumor and from a healthy region. But I am not sure it is public as without registration
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-20T15:37:49.803Z
Comments.Text: @Llopis as far as I can tell, the registration process is incredibly [convoluted](https://gdc.cancer.gov/access-data/obtaining-access-controlled-data) and involves getting the "Signing officer" of the organization (PI, CEO, whatever) to register the organization with two separate governmental bodies (eRA and then dbGAP) and then ask for access. It might be possible for me to ask my boss to do this, but I would much prefer to find more easily accessible data.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-20T15:49:05.917Z
Comments.Text: Most patient data is stored in dbGAP because of privacy issues, so you'll struggle to find anything that's unrestricted.
Comments.UserDisplayName: heathobrien
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-20T15:54:53.850Z
Comments.Text: @heathobrien yeah, which is why I've been struggling :) I was hoping there was a Henrietta Lacks analogue for the modern day or that NIST had released a tumor-normal pair or something.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-20T16:03:34.350Z
Comments.Text: I thought the HeLa genome got pulled down for exactly that reason. Is it available again?
Comments.UserDisplayName: heathobrien
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-20T16:08:41.440Z
Comments.Text: Not that I know of, no. Sorry, I was thinking of her cells and how they've been used for so many years, not about her genome. I come from the era before NGS.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-24T16:47:21.357Z
Comments.Text: If you work at a university, getting access to dbGap protected data is no where near as difficult as it seems. Getting registered on the system originally took about an hour of my time and about half a week of waiting. When I apply for a new dataset it takes me about half an hour per project.
Comments.UserDisplayName: Ian Sudbery
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-24T16:58:17.317Z
Comments.Text: @IanSudbery unfortunately, I am no longer in academia, so I would need to ask the CEO of the small startup I work at to do this, and he barely has enough time to breathe as it is.
Comments.UserDisplayName: terdon
Tags: <ngs><cancer><public-dataset>
Title: Is there a publicly available tumor-normal sample?
ThreadText: # Is there a publicly available tumor-normal sample?
  
  (Asked by: username_0 on 2018-04-20)
  
  I am looking for a publicly available matched tumor-normal sample. I need Illumina fastq reads (or an aligned bam file, since I could extract the reads from it) from a tumor and a matching, non-tumor control set from the same patient. Ideally, I would also have a truth set of known variants in the sample, but I can live without that.
  
  I checked the [Next Generation Cancer Knowledge Network](http://gdc.cancer.gov) but although they do seem to have appropriate bam files, which I could convert to fastq, all of the ones I found were "controlled access" and getting access seems very complicated.
  
  Is there something like the public NA12878 sample for tumor-normal analyses?
  
  **Tags:** ngs, cancer, public-dataset
  
  > **Comments:**
  > **username_1**: The TCGA does provide the raw fastq too, and for some patients one has sample from the tumor and from a healthy region. But I am not sure it is public as without registration  
  > **username_0**: @Llopis as far as I can tell, the registration process is incredibly [convoluted](https://gdc.cancer.gov/access-data/obtaining-access-controlled-data) and involves getting the "Signing officer" of the organization (PI, CEO, whatever) to register the organization with two separate governmental bodies (eRA and then dbGAP) and then ask for access. It might be possible for me to ask my boss to do this, but I would much prefer to find more easily accessible data.  
  > **username_2**: Most patient data is stored in dbGAP because of privacy issues, so you'll struggle to find anything that's unrestricted.  
  > **username_0**: @username_2 yeah, which is why I've been struggling :) I was hoping there was a Henrietta Lacks analogue for the modern day or that NIST had released a tumor-normal pair or something.  
  > **username_2**: I thought the HeLa genome got pulled down for exactly that reason. Is it available again?  
  > **username_0**: Not that I know of, no. Sorry, I was thinking of her cells and how they've been used for so many years, not about her genome. I come from the era before NGS.  
  > **username_3**: If you work at a university, getting access to dbGap protected data is no where near as difficult as it seems. Getting registered on the system originally took about an hour of my time and about half a week of waiting. When I apply for a new dataset it takes me about half an hour per project.  
  > **username_0**: @username_3 unfortunately, I am no longer in academia, so I would need to ask the CEO of the small startup I work at to do this, and he barely has enough time to breathe as it is.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_4 on 2018-04-25. Score: 3 | Accepted answer
  
  Please take a look at
  
  [An open access pilot freely sharing cancer genomic data from participants in Texas](https://www.nature.com/articles/sdata201610)
  
  Although I have not worked on this paper but author claimed that both tumor and normal data is publicly available. In case if you still need something more, than you can work on virtual normal data. And there are several papers which provide machnine learning techniques to overcome the deficiency of normal data (not much efficient but still they give considerable results). Hope this information will help you. Thanks
  
  > **Comments:**
  > **username_0**: Argh, this looks perfect, but the site seems to be down! I have emailed the author of the paper to see if it's just a temporary glitch. Thanks!  
  > **username_0**: [The site](http://txcrb.org/) is no longer maintained, but I contacted the authors and they very helpfully put it back up for me!  
  > **username_4**: @username_0: Then you should look for virtual normal database than or, if interested, machine learning techniques.  
  
  ---
  
  