E-MTAB-1984 - DNA-seq conducted to generate targeted resequencing data covering a region associated with osteosarcoma in greyhounds

Status
Released on 16 November 2013, last updated on 2 May 2014
Organism
Canis familiaris
Samples (15)
Protocols (9)
Description
This experiment was conducted to generate targeted resequencing data covering a region associated with osteosarcoma in greyhounds. 8 greyhounds diagnosed with osteosarcoma and 7 greyhounds without tumors were sequenced. DNA from the 15 dogs was used to prepare libraries and hybrid capture performed to enrich the region of interest prior to paired-end sequencing using Illumina Genome Analyzer II. The reads were aligned to the dog-genome CanFam2.0 using bwa and pre-processed using Picard and GATK. Variant discovery was performed using GATK. The resulting list of variants were used in the study to finemap the associated region and look for causal variants. We submit the preprocessed BAM-files that still have all reads although some reads are flagged. We also submit the resulting vcf-file with called and filtered variants in all individuals.
Experiment types
DNA-seq, disease state design, genotype design, in vitro
Contact
Citation
Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B. Elinor K. Karlsson, Snaevar Sigurdsson, Emma Ivansson, Rachael Thomas, Ingegerd Elvers, Jason Wright, Cedric Howald, Noriko Tonomura, Michele Perloski, Ross Swofford, Tara Biagi, Sarah Fryc, Nathan Anderson, Celine Courtay-Cahen, Lisa Youell, Sally L. Ricketts, Sarah Mandlebaum, Patricio Rivera, Henrik von Euler, Bill Kisseberth, Eric S. Lander, Guillermo Couto, Kenine Comstock, Mike P. Starkey, Jaime Modiano, Matthew Breen, Kerstin Lindblad-Toh.
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-MTAB-1984.idf.txt
Sample and data relationshipE-MTAB-1984.sdrf.txt
Processed data (1)E-MTAB-1984.processed.1.zip
Links