Human Exome Sequencing

Standard Exome Sequencing

The Standard Exome includes sample plating, library preparation, hybrid capture, sequencing (76bp paired reads), sample identification QC check, and data storage. This product utilizes the Agilent Sure-Select Human All Exon v2.0, 44Mb baited target with the Broad in-solution hybrid selection process. With >5Gb PF of data, our hybrid selection libraries meet or exceed 80% of targets at 20x and a mean target coverage >80x.

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 rates are high with 50ng (1ng/uL minimum concentration) or greater.
  • Tumor/Normal or Case/Control pairs must be received together if indel co-cleaning is required.

 

Exome Express

The Exome Express pipeline is a uniquely designed workflow optimized for speed and utilizes the Agilent Sure-Select Human All Exon v2.0, 44Mb baited target with the Broad in-solution hybrid selection process. Our Exome Express hybrid selection libraries meet or exceed 80% of targets at 20x (+/- 5%) The Exome Express product includes sample plating, library preparation, hybrid capture, sequencing (76bp paired reads), sample identification QC check, and data storage. Turnaround time from verified* sample receipt to aggregated BAM file generation is 21 calendar days or less.

Deliverable
Data delivery will include a de-multiplexed, aggregated BAM file which will be accessed via the BASS file server system or FTP for non-Broad users. Turnaround time from verified* sample receipt to aggregated BAM file generation is 21 calendar days or less. Samples that fail to meet this deliverable will be charged at the Standard Exome rate.

*Verified sample receipt includes a validation of funding and compliance agreements

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, Gender.
  • Genomic DNA, fresh frozen or FFPE tissue, blood, stool, saliva, slides, cell pellets, or buffy coats that preferably yield >500ng of DNA (note extra cost will be applied for extractions). Samples below 250ng (2ng/uL minimum concentration) and non-standard input materials e.g. FFPE, WGA, CTC samples will be considered 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.
  • All samples >0ng will proceed through the process once ordered.

 

Exome Plus

Exome Plus includes sample plating, library preparation, hybrid capture, sequencing (76bp paired reads), sample identification QC check, and data storage. The Exome Plus utilizes the Broad-designed expanded human content, manufactured by Agilent, with ~160Mb baited target and the Broad in-solution hybrid selection process. Exome Plus includes the standard exome targets with the following additions: intronic and promoter sequences for known cancer genes and significant targets identified in Cancer GWAS studies, The Cancer Genome Atlas (TCGA), and the Cancer Cell Line Encyclopedia (CCLE). Also included are novel exons identified in the 29 mammals comparative study, regulatory motifs from ENSEMBL as well as lincRNA sequence and additional sequence in known areas of copy number alterations. With 1 HiSeq lane, which typically yields 25Gb PF or more of delivered data, our hybrid selection libraries typically meet or exceed 80% of targets at 20x.

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 50ng (1ng/uL minimum concentration) or greater.
  • Tumor/Normal or Case/Control pairs must be received together if indel co-cleaning is required.