Whole Genome and Transcriptome Sequencing
| WGTS Clinical and Research (RUO) | WGS Clinical and Research (RUO) | WTS Research Only (RUO) | pWGS Clinical and Research (RUO) | |
| Sample Requirements | DNA 230 ng (gDNA from buffy coat) 80 ng (gDNA from fresh frozen) 130 ng (gDNA from FFPE) RNA 80 ng (RNA from fresh frozen) 275 ng (RNA from FFPE) | 230 ng (gDNA from buffy coat) 80 ng (gDNA from fresh frozen) 130 ng (gDNA from FFPE) | 80 ng (RNA from fresh frozen) 275 ng (RNA from FFPE) | 10 ng (cfDNA from plasma) |
| Sequencing Depth and Coverage (NovaSeq X Plus) | 2×150 PE Clinical and RUO 80X Tumor | 30X Normal 40X Tumor | 30X Normal | 2×150 PE Clinical and RUO 80X Tumor | 30X Normal 40X Tumor | 30X Normal RUO 80X 40X 30X 0.2X (shallow WGS) | 2×100 or 2×150 PE RUO 100M Clusters (Paired ends) | 2×150 PE 30X |
| Turnaround time (clinical only) | 45 days | 45 days | N/A | 45 days |
| Deliverables | Clinical Clinical Report (see example here) RUO FASTQ or RUO Standard Analysis Pipeline | Clinical Clinical Report (see example here) RUO FASTQ or RUO Standard Analysis Pipeline | FASTQ or RUO Standard Analysis Pipeline | Clinical Clinical Report (see example here) RUO FASTQ or RUO Standard Analysis Pipeline |
Targeted Sequencing
| Targeted Sequencing Clinical and Research (RUO) | Whole Exome Sequencing Research Only (RUO) | |
| Sample Requirements | 20 ng (cfDNA from plasma) 40 ng (gDNA from buffy coat) 40 ng (gDNA from fresh frozen) 40 ng (gDNA from FFPE) | 230 ng (gDNA from buffy coat) 80 ng (gDNA from fresh frozen) 130 ng (gDNA from FFPE) |
| Sequencing Depth and Coverage | 2×150 PE (NextSeq 2000) Clinical and RUO 15 000X Tumor 5000X Normal | 2×150 PE (NovaSeq X Plus) 100X 200X |
| Turnaround time (clinical only) | 21 days | n/a |
| Deliverables | Clinical Clinical Report (see example here) RUO FASTQ or RUO Standard Analysis Pipeline | FASTQ |
Methylome Sequencing
| EM-Seq (NEBNext Enzymatic Methyl-Seq Kit) Research Only | Biomodal 6-letter (Biomodal Duet Multiomic solution) Research Only | |
| Sample Requirements | 10 ng (cfDNA from plasma) 50 ng (genomic DNA from fresh frozen) 100 ng (genomic DNA from FFPE) *Additional DNA needed for WGS or 5hmC | 10 ng (cfDNA from plasma) 50 ng (genomic DNA from fresh frozen) 100 ng (genomic DNA from FFPE) *One library for both WGS and Methylome |
| Library Preparation | Approximate 1.5 days of prep time and automation friendly. Separate prep for genome and methylome. | Approximate 2.5 days of prep time. Same prep for both genome and methylome. |
| Sequencing (Nova Seq X Plus) | -2×150 -30x genome /400M Clusters/ 800 Paired-end reads -Genome and Methylome can be sequenced at different depths | -2×150 -30x genome-methylome/ 1B Clusters/ 2B Paired-end reads -15X genome-methylome/ 0.5B Clusters/ 1B Paired-end reads -Same depth /coverage for both genome and methylome |
| Informatics and Analysis | -Relatively low duplication rate -Ultra deep genome sequencing possible (separate prep) -Insert size should be compatible for fragmentomics studies -May use same pipeline as bisulfite sequencing | -Tend to have higher duplication rate -Difficult to sequence at ultra-depth -Optimization may be needed for fragmentomics studies. -Require access to biomodal pipeline for “read-out” |
| Deliverables | FASTQ | FASTQ |
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