Expanding our understanding of the genetic contributions and etiologies of birth defects and childhood cancer will have a significant and direct impact on those affected by those conditions and also contributes significantly to related research in adult conditions. This application will create the HudsonAlpha-St Jude Genome Sequencing Center (HASJ-GSC) to provide an efficient and experienced genomics resource for the generation and analysis of high quality sequence and variant data from the largest number of pediatric cancer and birth defect cohorts as possible with available funds over a three year period. We present here the innovation, capabilities, and experience of the HASJ-GSC to produce data for the Gabriella Miller Kids First Research Program that will be accessible and available to the research community and leveraged to its maximal impact for years to come. We also present a cost reduction plan so the number of cases that can be sequenced and analyzed per dollar spent increases each year. The HASJ-GSC will generate exceptional quality whole- genome sequence and variant data for all samples and for the pediatric cancer samples, RNASeq and whole- exome data. The combine genome, exome and RNASeq will provide as much resolution as possible to understanding the genetic and functional genomic changes observed in pediatric cancer. The HASJ-GSC will provide sequence data, phased variant data, and phased structural variant data from cohorts of structural birth defect samples and childhood cancer samples that the Gabriella Kids First Program will provide. The HASJ- GSC will also provide a reliable and efficient data storage and data access capability that provides fast, reliable and efficient data access, sharing and reporting for the project/sample Program Directors/Principal Investigators (PDs/PIs) (X01 PDs/PIs). Finally, the HASJ-GSC will support efficient submission of sequence and variant data to the controlled public database of Genotypes and Phenotypes (dbGaP), and other databases that may be designated by the Gabriella Miller Kids First Program and coordinate with X01PDs/PIs who will submit the phenotypic data of the sequenced samples to the same databases.
PROJECT STATEMENT Understanding the fundamental genetic changes associated with structural birth defects and childhood cancers is an important step in developing tools to allow more advanced prediction, treatment and prevention of these devastating conditions. We propose to combine the resources of two world-class centers to support researchers in their investigations of the genetics of birth defects and childhood cancers. This centralized resource will provide researchers with the tools and support necessary to advance our understanding and drive us closer to curing or preventing these diseases.
