Accepted samples are sequenced at the Broad’s Genomics Platform. After sequencing and processing completes, our project management team will send a notification and reminder to enter in phenotype information. This will be a required step before data can be loaded onto our seqr platform. Once data is available on seqr, our analyst team will send you a notification.
Libraries from DNA samples are created with an Illumina exome capture (37 Mb target) and sequenced (150 bp paired reads) to cover >85% of targets at 20x, comparable to ~55x mean coverage. Sample identity quality assurance checks are performed on each sample. The exome sequencing data is de-multiplexed and each sample's sequence data is aggregated into a single Picard CRAM file.
The transcriptome product combines poly(A)-selection of mRNA transcripts with a strand-specific cDNA library preparation, with a mean insert size of 550bp. Libraries are sequenced on the HiSeq 2500 platform to a minimum depth of 50 million STAR-aligned reads. ERCC RNA controls are included for all samples, allowing additional control of variability between samples. The RNA sequencing data is de-multiplexed and each sample's sequence data is aggregated into a single Picard BAM file.
Whole Genome Sequencing
Our PCR-free whole genome sequencing protocol process includes sample identification QC, sample preparation utilizing custom Broad indices (IDT) and Kapa Biosciences HyperPrep library construction kit, sequencing on an Illumina sequencer (2x150bp reads) with a mean target coverage of 30x. The genome sequencing data is de-multiplexed and each sample's sequence data is aggregated into a single Picard CRAM file.