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Bionano
Data Services
The Gold Standard for Genome Wide Detection of Structural Variation
Submit your research samples to Bionano Data Services and receive an appropriately filtered set of structural variant (SV) calls. SV data is shared using the Bionano Access visualization software. SV calls can be exported as vcf-files and used with any software of your choice. The Bionano Support team will work with you on experiment design and analysis training.
Data Services
Germ Line DNA Analysis
Bionano Solve de novo assembly, SV calling and Variant Annotation Pipeline will be run, which yields SVs 500 bp and up for heterozygous and homozygous variants.
Cancer or Heterogeneous Samples
The Rare Variant Pipeline and Variant Annotation Pipeline will be run, which yields SVs 5 kbp and up for insertions and deletions and ~30kbp and up for balanced variants down to 5% VAF.
Tumor-normal Comparison, or Trio Analysis
Duo or trio variant annotation will be run to identify de novo or somatic variants. Variants will be called against GRCh37/hg19, or GRCh38/hg38. Based on the project description and goals, variants will be appropriately filtered against a control database or a gene-list of choice, but filtering options can be changed after data delivery. For projects needing duo or trio variant annotation, please indicate the relationship between samples in the sample intake spreadsheet.
Sample Types Accepted - Frozen, Mammalian Only
We do not accept isolated DNA. Samples must be intact as lysed cells will have degraded DNA. Blood samples collected with EDTA must be frozen within 4 days of draw. Samples collected in heparin tubes must be frozen immediately, and we recommend adding Bionano DNA stabilization buffer to those. Frozen samples should NOT be thawed before shipping. If a larger aliquot has already been frozen, do not thaw and re-freeze. Detailed sample collection and shipping instructions are available for the sample type of interest.
Bionano optical genome mapping enables efficient, economical and accurate genome assembly and SV-identification in the genomes of non-human model organisms. In particular, the platform now offers a comprehensive solution to study the mouse genome SV. Specifically, we provide a mouse C57BL/6J strain specific CNV profile, control database as well as gene annotation for deeper investigation of candidate structural variants. For other non-human model organisms, we are able to perform SV analysis with customer provided high-quality reference genome. The users can also perform the case-control or trio comparison with their own control samples.
| Accepted Sample Types and Minimum Quantities | ||
|---|---|---|
| Sample Types | Minimum Quantity Per Aliquot | |
| Blood | Frozen blood (EDTA) | 650 μL |
| Frozen blood (heparin) | 650 μL (with Bionano DNA stabilizer added) | |
| Cultured Cells | Frozen cell line (cryopreservation medium) | 1.5 million cells (in cryopreservation medium) |
| Frozen cell line (dry pellet) | 1.5 million cells (washed with Bionano DNA stabilizing buffer) | |
| Bone Marrow Aspirates | Frozen bone marrow aspirate (EDTA) | 1 mL |
| Frozen bone marrow aspirate (heparin) | 1 mL (with Bionano DNA stabilizer added) | |
| Tissue Biopsies | Human tissue | ≥ 10 mg |
| Human breast tissue or muscle | ≥ 60 mg | |
| Non-human mammalian tissue | ≥ 10 mg | |
Data Collection
- 400 Gbp (~120x) of raw data for diploid samples/genetic disease studies
- 1500 Gbp (~400x) for heterogeneous/cancer/
mosaic samples that pass QC - 5000 Gbp (~1600x) for 1% allele fraction for SVs (10% allele fraction for CNVs), available after consultation with data services technical team
Data Delivery
All data will be uploaded to Bionano’s web-based visualization software bionanoaccess.com for visualization, filtering, report generation and download. SV calls can be exported as .vcf files, for use in the software of your choice. The Bionano Support team will work with you on analysis training.
All data will be removed after 6 and before 12 months of storage unless otherwise requested.
Sample Failures
If samples fail at one of the quality control steps, and you have provided an extra aliquot, they will be re-prepped and run at no cost, one additional time. If the sample fails a second time, a $100 fee will apply instead of the full price.
How It Works
- 1
Contact your Bionano Regional Business Manager or click here to contact us if you are new to Bionano.
- 2
Fill out the Bionano Services Intake From.
- 3
Once the project has been approved and the quote and PO issued, samples can be sent in using specific sample submission guidelines.
- 4
Expect a turnaround time of 6-8 weeks. We will inform you when samples pass QC with an updated delivery estimate.
Pricing
- $950 per sample
for diploid/genetic disease cases collected
at 120x coverage - $1,150 per sample
for mosaic/cancer samples collected at 400x - Pricing available upon request
for mosaic/cancer samples collected at 1600x
Forms/Guides
- 30179 Blood Shipping Instructions
- 30180 Cell Line Shipping Instructions
- 30186 Tissue and Tumor Shipping Instructions
- 30187 Agarose Plug Shipping Instructions
- 30358 Bone Marrow Aspirate Shipping Instructions
- 30359 Bionano Services Sample Sheet and Shipping Form
- 30378 Bionano Data Services Intake Form
