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

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

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

Tumor-normal Comparison, or Trio Analysis

Structural variants called against GRCh37/hg19 or GRCh38/hg38 will be appropriately filtered against a control database or a gene list of choice based on the project description and goals. Filtering options can be changed after data delivery. Where applicable, duo or trio variant annotation will be run to identify de novo or somatic variants. For projects needing duo or trio variant annotation, please indicate the relationship between samples in the sample intake form.

Sample Types Accepted

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 5 days of draw if stored at 4°C before freezing, or within 2.5 days if stored at room temperature. Fresh EDTA blood samples are accepted for domestic shipping only and must arrive at a Bionano laboratory within the time frames described above. Samples collected in heparin tubes must be frozen after adding Bionano DNA stabilizer, within 1 day of aspiration. 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 genomes. 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
BloodFrozen human blood (EDTA tube) preferred 650 μL
Fresh Human Blood (EDTA tube) 650 μL
Frozen human blood (Heparin tube + DNA stabilizer) 650 μL
(with Bionano DNA stabilizer added)
Fresh human blood (Heparin tube + DNA stabilizer) 650 μL
(with Bionano DNA stabilizer added)
Cultured CellsCryopreserved Amniocytes/ CVS cultures ≥ 1 million live cells
Frozen Amniocytes/ CVS culture dry pellets ≥ 1.5 million cells
Cryopreserved lymphoblastoid cell lines ≥ 1.5 million cells
Frozen lymphoblastoid cell line dry pellets ≥ 1.5 million cells
Other cryopreserved/frozen established human cell lines (known polyploidy, characteristics, culture media, storage media/conditions) ≥ 1.5 million cells
Bone Marrow AspiratesFrozen human bone marrow aspirate (EDTA tube) 1 mL
Frozen human bone marrow aspirate (Heparin + DNA Stabilizer) 1 mL
(with Bionano DNA stabilizer added)
Tissue BiopsiesHuman tumor tissue (breast, liver, lung, colon*, kidney*, bladder*, brain*, ovary*, prostate*, thyroid*) Minimum ≥ 10 mg
30 mg preferred

*Sample type has been tested but not validated.

Data Collection

  • 120x of raw data for diploid samples/genetic disease studies
  • 400x for heterogeneous/cancer/
    mosaic samples that pass QC
  • 1600x for 1% allele fraction for SVs (10% allele fraction for CNVs), available after consultation with data services technical team. Note: 1% allele fraction SV detection may not be possible for all sample types and may require 10+ weeks turnaround time. Accepted samples include cryopreserved LCL cultures, frozen blood, frozen bone marrow, and others upon consultation.

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 Data 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

Pricing is available upon request

  • Diploid/Genetic disease samples collected at 120X 
  • Mosaic/Cancer samples collected at 400X 
  • Mosaic/Cancer to Low frequency variant samples collected up to 1600X 

Please contact Bionano to request a detailed quote. 

Contact your Bionano Regional Business Manager to get started.

New to Bionano? Complete the form below and we will contact you about your project.
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