Bulk Tissue and Cell-Free Sequencing
Whole Exome Sequencing & MSK-NeoQual:
| Description: | A capture-based assay to assess the entire exome. |
|---|---|
| Starting Material: | DNA or DMP Library |
| Library Chemistry: | KAPA EvoPrep |
| Capture Chemistry: | xGen v2.0 from IDT (human); SinglePlex Mouse Exome from Twist (mouse) |
| Sequencing Read Length: | PE100 |
| Sequencing Coverage: | 30-250X+ |
| Deliverable: | FASTQ; NeoQual pipeline analysis (human); Pipeline analysis options available from CMO or BIC with additional charges |
Targeted Sequencing:
| Description: | Capture-based assays to assess specific genes within the exome. |
|---|---|
| Starting Material: | DNA or DMP Library |
| Library Chemistry: | KAPA EvoPrep |
| Capture Chemistry: | Custom probes |
| Sequencing Read Length: | PE100 |
| Sequencing Coverage: | 500X T/250X N (IMPACT); 60M reads (ACCESS); 30M reads (CMO-CH) |
| Deliverable: | FASTQ (IMPACT; pipeline analysis options available from BIC with additional charges), pipeline analysis (ACCESS); in development (CMO-CH) |
Transcriptome Sequencing:
| Description: | Techniques to enrich RNA and assess expressed transcripts |
|---|---|
| Starting Material: | RNA or cells (SMARTer only) |
| Library Chemistry: | Watchmaker mRNA (polyA), Watchmaker w/ Polaris Depletion (Ribodepletion), SMART-Seq v4 + KAPA EvoPrep (SMARTer) |
| Sequencing Read Length: | PE100 |
| Sequencing Coverage: | 10-100M+ |
| Deliverable: | FASTQ + BAM; analysis options from BIC at an additional cost |
Whole Genome Sequencing:
| Description: | Assess the entire genome using PCR-free methods, minimal PCR cycles, or a shallow sequencing for CNV. |
|---|---|
| Starting Material: | DNA |
| Library Chemistry: | KAPA EvoPrep |
| Sequencing Read Length: | PE150 (deep WGS); PE100 (shallow/bacterial WGS) |
| Sequencing Coverage: | 1-120X+ |
| Deliverable: | FASTQ |
Epigenome Sequencing:
| Description: | Various methods to assess the epigenetic structure of the genome |
|---|---|
| Starting Material: | Cells - no more than 24 samples/batch (ATAC), Transposed DNA (ChIP), gDNA (Methyl) |
| Library Chemistry: | Nextera XT (ATAC), KAPA EvoPrep (ChIP), NEBNext + Twist probes (Methyl) |
| Sequencing Read Length: | PE100 |
| Sequencing Coverage: | 40-50M (ATAC), 10M (ChIP; more reads can be requested), 30-40X (Methyl) |
| Deliverable: | FASTQ + methylation report (Methyl) |
TCR Sequencing:
| Description: | Methods to enrich T-cell receptor sequences |
|---|---|
| Starting Material: | Cells (10X Genomics), RNA - IGO-TCR |
| Deliverable: | FASTQ + Pipeline output |
Other Bulk Sequencing:
| Description | Sequencing Read Length | Sequencing Coverage | Deliverable |
|---|---|---|---|
Amplicon Sequencing | varies | varies | FASTQ |
| CRISPR Cut Site Sequencing | PE150 | 75K reads | FASTQ + CRISPRESSO analysis |
Single Cell Sequencing
10x Genomics Single Cell:
| Description: | Single-cell platforms to interrogate gene expression, immune repertoire, and/or protein expression. |
|---|---|
| Starting Material: | Single cell or nuclei suspension |
| Library Chemistry: | Chromium Single Cell |
| Sequencing Read Length: | PE28/88 |
| Sequencing Coverage: | 20K reads/cell (GEX), 5K reads/cell (V(D)J & cell hashing) |
| Deliverable: | FASTQ, Cell Ranger output |
10x Genomics Multiome:
| Description: | Single-cell ATAC-Seq + RNA-Seq from the same nucleus. |
|---|---|
| Starting Material: | Single nuclei suspension |
| Library Chemistry: | Chromium Single Cell |
| Sequencing Read Length: | PE 28/88 (GEX), PE50 (ATAC) |
| Sequencing Coverage: | 20K reads/cell (GEX), 25K reads/cell (ATAC) |
| Deliverable: | FASTQ, Cell Ranger output |
10x Genomics Visium:
| Description: | Transcriptome sequencing of 1-10 cells along with spatial information. |
|---|---|
| Starting Material: | Fresh Frozen, Fixed Frozen or FFPE tissue |
| Library Chemistry: | Visium Spatial Gene Expression v1 (frozen only) or CytAssis |
| Sequencing Read Length: | PE28/88 |
| Sequencing Coverage: | 25-50K reads/1-10 cells |
| Deliverable: | FASTQ, Space Ranger output |
10x Genomics Visium HD:
| Description: | Single cell resolution on the Visium platform |
|---|---|
| Starting Material: | FFPE, Fresh Frozen, or Fixed Frozen tissue |
| Library Chemistry: | Visium probe set v2 |
| Sequencing Read Length: | custom |
| Sequencing Coverage: | >50% sequencing saturation |
| Deliverable: | FASTQ, Space Ranger output |
10x Genomics Xenium:
| Description: | A single molecule imaging program for targeted single-cell spatial transcriptomics |
|---|---|
| Starting Material: | FFPE or Fresh Frozen |
| Sequencing Coverage: | N/A |
| Deliverable: | Analysis with Xenium Ranger |
Bruker CosMx:
Description: | A single molecule imaging program for targeted single-cell spatial transcriptomics |
|---|---|
Starting Material: | FFPE or Fresh Frozen |
Sequencing Coverage: | N/A |
Deliverable: | Analysis in the AtoMx |
SmartSeq:
| Description: | A single- or low-cell Smart-seq v3 method to accommodate projects without enough cells for 10X Genomics, or users interested in capturing the entire body of the gene. |
|---|---|
| Starting Material: | Sorted cells |
| Library Chemistry: | SMART-Seq + Nextera XT |
| Sequencing Read Length: | PE100 |
| Sequencing Coverage: | ~20K reads/cell |
| Deliverable: | FASTQ |
DLP:
| Description: | A method to detect CNV in single cells. |
|---|---|
| Starting Material: | Single cell suspension |
| Library Chemistry: | Custom protocol |
| Sequencing Read Length: | PE150 |
| Sequencing Coverage: | 2M reads/cell |
| Deliverable: | FASTQ |
Other Platforms
Digital PCR:
| Description: | PCR-based services for mutation detection, fusion detection, viral detection, or CNV. Hundreds of assays have been validated commercially or in house, but if your gene of interest is not on the list, IGO offers design & optimization services. |
|---|---|
| Starting Material: | DNA, RNA, Library |
| Deliverable: | Report |
Optical Genome Mapping:
| Description: | Structural variant detection on the Bionano platform |
|---|---|
| Starting Material: | Tissue or Cells |
| Sequencing Coverage: | Report in collaboration with MCCF |
| Deliverable: |
Tissue and Bulk Extraction:
| Description: | Manual and automated methods for purifying RNA, DNA, or both from a variety of starting materials and sample types. |
|---|---|
| Starting Material: | Plasma; Frozen tissue/cells (OCT, RLT, TRIzol, pellet); Viably frozen cells; Blood; FFPE; Fingernails Other? Contact us. |
| Deliverable: | Nucleic acid + QC report |
QC & Pathology:
| Description: | Other services offered by IGO. |
|---|---|
| QC Services: | BioAnalyzer or TapeStation QC; Quant-it; %Human for PDX |
| Pathology Services: | Sectioning (curls); Sectioning (slides); H&E Staining; Slide scraping; Macrodissection |
Please email [email protected] if your sequencing needs do not fit in one of these categories.