<p>Is anyone aware of a publication or pre-publication data set that includes the following for a single human tumor/normal sample pair:</p>

<ul>
	<li>Illumina whole genome sequence (WGS) to at least 30-50X depth for both tumor and normal (e.g. blood). Preferably this would be HiSeq paired end data generated with v3 chemistry</li>
	<li>Illumina exome sequence data for the same tumor/normal pair but to considerably higher depth (say at least 150-200X)</li>
	<li>Illumina RNA-seq data generated for the same tumor sample. Bonus points if there is also RNA-seq for a matched normal sample (same tissue as the tumor as opposed to blood DNA that would typically be used for a normal comparison at the DNA level).</li>
</ul>

<p>Since this data would primarily be used for methods development, the tumor/normal pair could be from a tumor cell line and matched lymphoblastoid &#39;normal&#39; cell line derived from the same individual. Some data along these lines is being made available here:</p>

<p><strong>TCGA Mutation/Variation Calling Benchmark 4 at CGHub</strong></p>

<p><a href="https://cghub.ucsc.edu/benchmark_download.html">https://cghub.ucsc.edu/benchmark_download.html</a></p>

<p>However, this is whole genome data only. No exome or RNA-seq data yet. Plenty of RNA-seq data can be found in GEO and elsewhere but I&#39;m not aware of any projects where there is corresponding WGS or Exome data. Plenty of exome data and WGS data are being generated for TCGA but again I&#39;m not aware of any publications describing combinations of all three types.</p>

<p>Large scale cancer sequencing projects that <em>might</em> have performed such a comparison:<br />
<a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a><br />
<a href="http://www.sanger.ac.uk/genetics/CGP/">Cancer Genome Project (CGP)</a><br />
<a href="http://icgc.org/">International Cancer Genome Consortium (ICGC)</a></p>

We eventually created such a data set ourselves and made it publicly available via FTP [here](https://github.com/genome/gms/wiki/HCC1395-WGS-Exome-RNA-Seq-Data)

The data are from a matched tumor/'normal' pair of cell lines: HCC1395 and HCC1395/BL whole genome (WGS), exome, and/or RNA-seq data. All data are 2x100 bp reads generated on an Illumina HiSeq 2000 instrument. The exome data was generated by use of a NimbleGen SeqCap EZ Human Exome Library v3.0 reagent.

If you find this data useful, please cite:

Griffith et al. <a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004274">Genome Modeling System: A Knowledge Management Platform for Genomics</a>. PLoS Comput Biol. 2015 Jul 9;11(7):e1004274. doi: 10.1371/journal.pcbi.1004274. eCollection 2015 Jul. PubMed PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/26158448">26158448</a>;

Since these data corresponds to cell line material we were able to make them available without using dbGaP.