Services and resources

Clinical Reporting Services

CAP, IQMH and ISO 15189-compliant, high-quality sequencing and analysis services available for clinical diagnostics. These services utilize our Requisition System and generate clinical reports, which are completed by certified geneticists. Prices per case are listed below and are valid as of March 2022.

Clinical Resources

• Clinical Project Initiation Form
• Requisition and Reporting System User Manual
  • Requisition System Access Request Form
• Sample Submission Instructions
• Terms and Conditions and Acknowledgement Policy.
• Whole Genome Library Preparation Protocol
• Whole Transcriptome Library Preparation Protocol

Sequencing Services

From tissue extraction to targeted, whole genome/exome/transcriptome, or customized sequencing, we can help at any stage of your genomics research, even if you are working with low input and/or low quality biospecimens. We utilize a fleet of Illumina instruments, including the MiSeq, NextSeq 550 and NovaSeq 6000, as well as the Oxford Nanopore MinION and PromethION. Prices per sample are listed below and are valid as of March 2022.

Sequencing Resources

• Project Initiation Form
• Sample Submission Instructions
  • Sample Submission Form
• Library Submission Form
• Terms and Conditions and Acknowledgement Policy.
• Whole Genome Library Preparation Protocol
• Whole Transcriptome Library Preparation Protocol

Bioinformatics Services

The Genome Sequence Informatics group develops and uses a variety of automated and semi-automated analysis workflows to fulfill every project’s unique needs. Our pipelines use industry-standard bioinformatics tools together with software developed in-house.

Bioinformatics services for sequencing are offered in three levels of data analysis and return, with increasing costs.

Types of analysis:

• Raw data (Fastq) : we return only the sequence data in Fastq format. Choose if you have a non-standard or non-human reference (e.g. T2T or mouse), or if you have your own bioinformatics team.
• Aligned sequence : we return sequence aligned to the human reference (hg38) in BAM or CRAM format. Choose if you have specific bioinformatics analysis you want to run that’s distinct from our full packages.
• Full package: we return all of our standard analysis types for your sequencing choice, which may include: fastqs, BAM/CRAM, somatic variant calls, copy number calls, etc. Note that some sequencing types have less in the full package than others, and you will be charged accordingly. Details for each sequencing type are below.

FULL PACKAGES

• Shallow whole genome: BAM files, ichorCNA results
• Whole Genome: Pre-processed call ready BAMs, Somatic variants, Structural variants, Copy number variants
• Exome: Pre-processed call ready BAMs, Somatic variants, Copy number variants
• Targeted sequencing/Panels: Aligned BAMs, UMI Deduplication, Somatic variants
• smMIPs: Fastq files
• cfMeDIP: Fastq files
• Nanopore epigenome: BAM files
• Transcriptome: STAR BAM files, RSEM expression, STAR-Fusion fusion calls
• Nanopore transcriptome: Aligned BAMs

We return data to you in different ways depending on the service requested. Clinical reports are always returned through the Genomics Requisition System. We can provide genomic data via SFTP or rsync download or upload. We also provide data deposition services to EGA or cBioPortal. 

Finally, we can accept data sequenced elsewhere for analysis through one of our packaged services, listed above. Please contact us for a quote.