The center for Pediatric Genomic Medicine (CPGM) at Children's Mercy was the first genome center in the world to focus exclusively on pediatric sequencing. While most genome centers focus on research, the CPGM develops new clinical tests as a starting point for next-generation medical treatments to improve patient outcomes at Children's Mercy and around the world, as well as works to enable genome driven applications at every phase of pediatric medical care.
The three most common assays in are center are:
The data warehouse does not contain only data from affected pediatric samples. Often as part of the Stat-Seq analysis the available parents and siblings (affected or unaffected) may also be sequenced. As part of several on going Exome collaborations data from exome analysis represent a wide variety of ages and ethnicities. TAGSCAN samples are primarily pediatric samples but contain several adult samples as well.
Whole Genome data was generated using PCR free sequencing kits. Exome sequencing data has been generated using a variety of exome kits including but not limited to. Sequencing for both Whole Genome and Exome sequencing occurred on a variety of instruments including but not limited to HiSeq 2000, HiSeq 2500, and HiSeq x4000. TAGSCAN data was generated using, and sequencing occurring on Miseq, HiSeq 2000, and HiSeq 2500.
Alignment of raw sequencing data occurred using a variety of different algorithm and algorithm combinations. Aligners include Gsanp, BWA, ISAAC, and Dragen. Variant callers include Alpheus, GATK 1.3 - 3.4, and Illumina Starling. Many combinations of aligners and variant callers were used: Gsnap-alpheus was used for many of the very earl analysis done, with GSnap-GATK and BWA-GATK occurring roughly equally. ISAAC-Starling analysis occurring as part of our STAT Seq rapid analysis pipeline. A few DRAGEN analysis exist on our system currently with the hopes of replacing ISAAC=Starling with DRAGEN in the near future.
Current warehouse version: 2017-07-01.4