Whole Genome Sequencing

Standard Light Coverage Whole Genome Sequencing (6x)

Standard Light Coverage Whole Genome Sequencing (6x) includes plating, library preparation, size selection, sequencing (101bp paired reads), sample identification QC check, and data storage. The product provides one size-selected library (typical insert size of library is 385bp +/- 20%) and sequence coverage to 20Gb total aligned. This product is appropriate for the generation of low coverage human and mammalian genomes.

Deliverable
Data delivery will include a de-multiplexed, aggregated and aligned Picard BAM file, which will be accessed via the BASS file server system or FTP for non-Broad users.

Input Requirements

  • Funding and compliance requirements must be in place. This includes a valid IRB or letter of non-engagement where needed.
  • Minimum Sample data including Collaborator Participant ID, Collaborator Sample ID, and Gender.
  • Genomic DNA, fresh frozen or FFPE tissue, blood, stool, saliva, slides, cell pellets, or buffy coats that preferably yield >250ng of DNA (note extra cost will be applied for extractions). Samples below 250ng (2ng/uL minimum concentration) and FFPE samples will be accepted at risk, but success is expected with 50ng (1ng/uL minimum concentration) or greater.
  • Tumor/Normal or Case/Control pairs must be received together if indel co-cleaning is required.

 

Standard High Coverage Whole Genome Sequencing (30x)

Standard High Coverage Whole Genome Sequencing (30x) includes plating, library preparation, size selection, sequencing (101bp paired reads), sample identification QC check, and data storage. The product provides two size-selected libraries (typical insert sizes of libraries are 325bp and 355bp, +/- 20%) and sequence coverage to 95Gb total aligned. This product is appropriate for the generation of high coverage human and mammalian genomes.

Deliverable
Data delivery will include a de-multiplexed, aggregated and aligned Picard BAM file, which will be accessed via the BASS file server system or FTP for non-Broad users.

Input Requirements

  • Funding and compliance requirements must be in place. This includes a valid IRB or letter of non-engagement where needed.
  • Minimum Sample data including Collaborator Participant ID, Collaborator Sample ID, and Gender.
  • Genomic DNA, fresh frozen or FFPE tissue, blood, stool, saliva, slides, cell pellets, or buffy coats that preferably yield >250ng of DNA (note extra cost will be applied for extractions). Samples below 250ng (2ng/uL minimum concentration) and FFPE samples will be accepted at risk, but success is expected with 75ng (1ng/uL minimum concentration) or greater.
  • Tumor/Normal or Case/Control pairs must be received together if indel co-cleaning is required.

 

Standard Deep Coverage Whole Genome Sequencing (60x)

Standard Deep Coverage Whole Genome Sequencing (60x) includes plating, library preparation, size selection, sequencing (101bp paired reads), sample identification QC check, and data storage. The product provides two size-selected libraries (insert sizes of libraries are 325bp and 355bp, +/- 20%) and sequence coverage to 190Gb total aligned. This product is appropriate for the generation of deep coverage human and mammalian genomes.

Deliverable
Data delivery will include a de-multiplexed, aggregated Picard BAM file, which will be accessed via the BASS file server system or FTP for non-Broad users.

Input Requirements

  • Funding and compliance requirements must be in place. This includes a valid IRB or letter of non-engagement where needed.
  • Minimum Sample data including Collaborator Participant ID, Collaborator Sample ID, and Gender.
  • Genomic DNA, fresh frozen or FFPE tissue, blood, stool, saliva, slides, cell pellets, or buffy coats that preferably yield >250ng of DNA (note extra cost will be applied for extractions). Samples below 250ng (2ng/uL minimum concentration) and FFPE samples will be accepted at risk, but success is expected with 75ng (1ng/uL minimum concentration) or greater.
  • Tumor/Normal or Case/Control pairs must be received together if indel co-cleaning is required.

 

Non-Human Whole Genome Sequencing

Non-Human Whole Genome Sequencing includes plating, library preparation, sequencing (101bp paired reads), sample identification QC check, and data storage. The product provides a non-size selected library and sequencing coverage up to 300Mb (4Mb genome at ~30x coverage). This is appropriate for microbial and other small genome non-assembly needs such as SNP calling.

Deliverable
Data delivery will include a de-multiplexed, aggregated, and aligned (where ref seq is provided) Picard BAM file, which will be accessed via the BASS file server system or FTP for non-Broad users.

Input Requirements

  • Funding and compliance requirements must be in place. This includes a valid IRB or letter of non-engagement where needed (if sample is human derived).
  • Minimum Sample data including Genus, Species, Collaborator Participant ID, and Collaborator Sample ID.
  • 250ng or more of genomic DNA (2ng/uL minimum concentration). Samples below 250ng will be accepted at risk, but success is expected with 50ng (1ng/uL minimum concentration) or greater.