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GIANT consortium data files – Giant Consortium

http://portals.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files

Dataset of 100 freely available STAD T/N pairs

http://www.nature.com/ng/journal/v46/n6/full/ng.2983.html#affil-auth

Kai Wang,
Siu Tsan Yuen,
Jiangchun Xu,
Siu Po Lee,
Helen H N Yan,
Stephanie T Shi,
Hoi Cheong Siu,
Shibing Deng,
Kent Man Chu,
Simon Law,
Kok Hoe Chan,
Annie S Y Chan,
Wai Yin Tsui,
Siu Lun Ho,
Anthony K W Chan,
Jonathan L K Man,
Valentina Foglizzo,
Man Kin Ng,
April S Chan,
Yick Pang Ching,
Grace H W Cheng,
Tao Xie,
Julio Fernandez,
Vivian S W Li,
Hans Clevers,
Paul A Rejto,
Mao Mao
& Suet Yi Leung

Nature Genetics 46, 573–582 (2014) doi:10.1038/ng.2983Received 01 August 2013 Accepted 18 April 2014 Published online 11 May 2014

Looks like 88 freely available liver cancer genome datasets
http://gigadb.org/dataset/100034

http://genome.cshlp.org/content/early/2013/01/02/gr.144600.112.abstract

QT:{{”
To demonstrate the promise of personalized genome analysis, the genome of HuRef was sequenced using the Life SOLiD™ platform. Nimbus Informatics performed the analytical work for this project and has made the resulting data available here, running entirely on the Amazon Cloud.
“}}
http://huref.nimbusinformatics.com

http://www.nature.com/nature/journal/v488/n7409/full/nature11284.html
Appears there’s germline variant calls (from JK) for potentially ~125 matched pairs