Hiseq 2000 or 2500 systems

Total RNA was isolated from tissue samples using the TriPure Isolation
Reagent (Roche Applied Science, Indianapolis, IN, USA). The RNeasy Mini Kit
(Qiagen, Valencia, CA, USA) was used for clean-up according to the
manufacturer's instructions. RNA-Seq from 74 canine HSA tissues is
published (17 (link),21 (link),32 (link),33 (link)) and an additional data set was
generated from two canine HSA tissues and from 10 non-malignant splenic hematoma
tissues. Total RNA was also extracted from 13 human AS tissues and from six
normal tissues. Two μg of total RNA from each sample were quantified and
assessed for quality; RNA-Seq libraries were generated as described (21 (link)) using the TruSeq RNA sample preparation
kit (Illumina Inc., San Diego, CA). Sequencing was performed using HiSeq 2000 or
2500 systems (Illumina Inc.). Each sample was sequenced to a targeted depth of
20 – 80 million paired-end reads with mate-pair distance of 50 bp.
Primary analysis and demultiplexing were performed using CASAVA software version
1.8.2 (Illumina Inc.) to verify the quality of the sequence data. The end result
of the CASAVA workflow was demultiplexed into FASTQ files for analysis.
Bioanalyzer quality control and RNA-Seq were performed at the University of
Minnesota Genomics Center (UMGC) or at the Broad Institute.

Whole-genome sequencing (WGS) was performed in the BRIDGES cohort using the Illumina HiSeq 2500 system. Library preparation was performed using Nimblegen SeqCap EZ Exome (RareBLISS and KPNC) or Agilent SureSelect Human All Exon v2 kit (Sweden), and whole-exome sequencing (WES) was performed using Illumina HiSeq 2000 or 2500 systems in RareBLISS, Sweden, and KPNC. Paired sequence reads were aligned to the human reference build hg19 using BWA ³⁹ . Variant calling was performed using the GotCloud sequence analysis pipeline ^{40 (link)} for WGS data in BRIDGES, and joint variant calling was performed using the Genome Analysis ToolKit (GATK) ^{41 (link)} for WES data within each of RareBLISS, Sweden, and KPNC. Genotypes with low sequence coverage or poor call quality were removed. Samples that were identified as population outliers, duplicates or relatives, or that failed study-specific sequencing metrics were removed. Variants with high missingness across samples, poor average genotyping quality, or found to significantly deviate from Hardy-Weinberg equilibrium were removed. A full description of sequencing and data quality control is provided in supplemental materials.