Bionano Optical Genome Mapping (OGM)
What does the platform do?
Optical Genome Mapping is non-sequencing technology capable of analyzing large eukaryotic genomes and their structural features at a high resolution by evaluation of patterns generated by fluorophore tags labeled to specific sequence motifs within extremely long DNA molecules, of more than 300 kb (3, 4).
The use of long molecules allows repetitive regions and other regions that are complicated to map, to be spanned more easily than with short molecules, leading to the creation of maps that may cover the hole arm of a chromosome (3).
View the service pricing schedule for more information about Optical Genome Mapping pricing.
Background
Most large genomes contain thousands of large structural variants (SVs), repetitive regions composed of identical or similar stretches of sequences, mobile elements such as transposons, large insertions, deletions, translocations, and inversions up to millions of bases, with even partial or entire chromosomes altered. Some SVs, such as deletions and duplications, change the dosage of DNA and are considered copy number variations (CNVs). Others, such as inversions and balanced translocation, do not change the DNA dosage. The gain and losses of important genes and regulatory elements due to SVs will impact phenotype causing disease such as cancer and sex development disorders.
Structural Variants (SVs) caused by the reorganization of the DNA may connect two distal fragments together leading to gene fusions and chimeric proteins when two distant genes are joined into one. Gene fusions are often major cancer driving events, especially in pediatric cancers and liquid tumors.
An extremely complex form of SVs called chromothripsis, in which dozens to hundreds of breakpoints on one or more chromosomes are involved, was originally reported in different types of cancers as well as in germlines genomes causing developmental and neuronal disorders.
Optical Mapping
Bionano Optical Genome Mapping directly observes structural variations by linearizing and imaging DNA in its native state using massively parallel Nano-Channels.
This direct observation results in some of the longest read lengths in genomic research. As a result, Bionano mapping yields hundreds of times more contiguous assembly than sequencing technologies alone can provide with unparalleled sensitivity for large structural variations (SVs) from 500 bp to mega base pair lengths.
Bionano OGM Applications
- Detects all types of Structural Variants (SVs) down to 5% Variant Allele Fraction for mosaic samples or heterogeneous cancer samples.
- Detects repeats and complex rearrangements.
- Detects genome wide CNVs and fusions, including fusion partners.
- Identify genes of interest, their locations, and how SVs impact them for downstream Applications.
Bionano Optical Genome Mapping Technology
Megabase size molecules of genomic DNA are isolated and labelled at a specific 6 or 7 base pair sequence motifs. The motifs occur approximately 8–28 times per 100 kbp, depending on its frequency in a particular genome. The label patterns allow each long molecule to be uniquely identified and aligned.
Labelled DNA is loaded onto a Saphyr chip and placed into the Saphyr instrument where electrophoresis initiates to move mega base length molecules from bulk solution into the silicon chip micro-environment before unwinding and linearizing the DNA in the Nano-Channel arrays. Cycles of loading of the Nano Channels followed by imaging are performed until sufficient data is collected.
Bionano image detection software extracts molecules from raw image data. The backbone stain signal of the DNA molecules is used to identify molecules and to determine their position and size. The distance between the labels on each molecule is recorded to generate an extracted molecule file called a BNX file. The BNX file is the only input needed for the Bionano Results Analysis.
SV calls are made based on analyses of a multiple local alignment between consensus maps and the reference. The pipeline supports calling of major SV types: insertions, deletions, inversions, and translocation breakpoints.
Note: Optical Genome Mapping can detect variation throughout most of the genome however it does not include coverage of centromeres, short arms of acrocentric chromosomes and some exceptionally long paracentric low copy repeat regions.
Bionano Optical Genome Mapping Data Analysis
Bionano Access software enables users to perform a variety of bioinformatic analysis and visualize structural variations (SV) that have been detected through Optical Genome Mapping (OGM) including insertions, deletions, duplications, inversions, translocations, ring chromosomes, complex rearrangements, absence of heterozygosity (AOH) and triploidy.
Analysis Pipelines
- Rare Variant Analysis Pipeline detects SVs genome-wide without bias, including analysis of heterogeneous tumor/mosaic samples down to an average level of detection of 5% variant allele fraction
- De novo Assembly Pipeline calls heterozygous structural variants with unmatched sensitivity and precision
- Copy Number Variation Pipeline detects copy number changes from 500 kbp up to aneuploidies, down to 10% variant allele fraction with high sensitivity
- Variant Annotation Pipeline calculates all SV calls based on the frequency of variants in a built-in control database, and external databases. It annotates calls by providing overlapping gene information, and performs trio-analysis and tumor-normal comparison
Data Visualization: The Circos Plot provides a whole genome summary of variants detected.
Data Visualization: The Genome Browser displays alignment of all assembled maps on single Chromosomes.
Bionano Optical Genome Mapping Service Requirements
When preparing samples for analysis by Bionano Genome Mapping (OGM) Systems, maintaining the integrity of the samples is critical, as DNA molecules must be 150 kb or larger to be assessed.
Service Scheduling
The OGM Service is by appointment only. Please contact Marisela Mendoza mgmendoz@mdanderson.org to schedule the date and time of sample submission.
Sample Types
- Fresh Cell Cultures
- Cryopreserved Cells
Sample Requirements
Fresh Cell Cultures
- Dissociate and harvest cells according to the user’s established protocol.
- Transfer samples to the ATGC in wet ice.
- Required input is ≥1.5 million live mammalian cells from adherent or suspension cell cultures (preferred input of 5-7 million cells).
- Submit cells in 5 ml - 10 ml cell culture media of choice or in 5ml -10 ml cold PBS without Calcium or Magnesium.
- Cells viability ≥75%
- Submit cells as taken from -80◦C storage. Do not thaw or add cell culture media or buffer.
- Transfer samples to the ATGC in dry ice.
- Required input is ≥1.5 million live mammalian cells (preferred input of 5-7 million cells).
- Cells viability ≥75%
Note: Samples delivered to the OGM Service by 10 am on the scheduled service date will begin same day processing.
Samples received after 10 am will be prepared for freeze-storage by the OGM Service personnel and placed in queue for processing on the next available date.
Selecting Coverage
Please see the “Initial Structural Variant Analysis” information to select the Coverage and Analysis Pipeline according to the project requirements.
Initial Structural Variant Analysis Performed by the ATGC
| Application | Germline DNA Analysis |
Cancer Analysis |
| Data Collected |
400 Gbp |
1.5 Tbp |
| Coverage Setting |
100X |
400X |
| Effective Coverage |
80X | 300X |
| Variant Allele Frequency (VAF) |
50% | ≥5% |
| Analysis Pipeline |
DeNovo Assembly | Rare Variant Analysis |
Service Output
At project completion, investigators will be provided with access to raw molecules data, assemblies and SV calls as well as a username and password for the Access software to allow for additional analysis.
Note: The ATGC does not provide biostatistical analysis as a service.
Contact Information
Marisela Mendoza: mgmendoz@mdanderson.org
Erika Thompson: ejthomps@mdanderson.org
Viju Varghese: vivarghes@mdanderson.org
References
- Yang, L. A practical guide for structural variation detection in human genome. Curr Protoc Hum Genet. 2020; 107(1): e103.
- Visualizing Different Classes of Structural Variants in Bionano Access Software. Bionano Genomics, 2022; Doc 30548, Rev A.
- Dremsek, P, et al. Optical Genome Mapping in Routine Human Genetic Diagnostics – Its Advantages and Limitations. Genes, 2021; 12(1958): 1-15
- Yang, H, et al. High Resolution structural variant profiling of myelodysplastic syndromes by optical genome mapping uncovers cryptic aberrations of prognostic and therapeutic significance. Leukemia, 2022; 36: 2306-2316.