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Bionano’s genome mapping technology makes it easy for researchers to identify the thousands of large structural variants that can be present in a single genome. But assessing the biological and clinical significance of these variants is a bit more challenging. Bionano’s Variant Annotation Pipeline (VAP) saves researchers valuable time (and frustration) by annotating structural variations observed by Bionano’s genome mapping platforms with information that can help determine the biological and functional significance of the call.

Bionano’s VAP is available as part of Bionano Access, free software available for download elsewhere on our website.


Variant Annotation for Disease Studies

The Bionano VAP automatically analyzes insertions, deletions, inversion breakpoints and translocations detected by Bionano genome mapping platforms. First, the tool collects all relevant data including size, zygosity, and confidence score for each variant call. Next, the calls are compared to Bionano’s database of structural variants of more than 160 phenotypically normal humans to identify the frequency of each variant in a control population.

Once we know how common all of the variants are in the control population, they are directly compared with other samples from the study. For example, a proband could be compared with one or both parents for duo or trio analysis, a tumor could be compared with a healthy sample from the same patient, or an engineered cell line could be compared with its parental line. This analysis includes comparisons of structural variation calls, assemblies and molecule alignments.

The power of Bionano’s extremely long molecules is demonstrated by this molecule alignment. Our SV calls have extremely low false positive and negative rates, but when filtering thousands of SVs down to a handful, you can not afford any false calls. By going back to the raw molecules and realigning the proband’s molecules to its assembly, the VAP ensures the de novo assembled genome maps are not chimeric (made of parts from different sources), that incorrect calls are removed, and that variant allele size is correct. Additionally, by comparing the proband with its parents, the VAP can identify true de novo events in the proband, and determine whether the proband’s structural variations are present in a low allelic fraction in the comparison sample, for instance when there is mosaicism in one of the parents.

Once all comparisons have been made, the VAP lists genes affected by the variant, or the closest gene and its distance to the variant. The output of these analyses is a data file that allows for simple filtering. Researchers can filter for only de novo calls, rare variants, or those likely to affect certain candidate genes or known oncogenic genes, if desired. The final result: from a long list of thousands of hard to interpret variants, the VAP delivers a handful of candidate genes for researchers to focus on.


“Variant curation can take up a significant amount of time, but with the introduction of Bionano’s VAP we were able to filter SVs based on frequency in databases such as the Database of Genomic Variants and Bionano’s Control Set consisting of 144 healthy individuals. With this information, we filtered out likely benign polymorphic variants. In addition, using VAP we can identify both inherited and de novo variants, genes overlapping, and in the vicinity of, structural variations and use a keyword-generated gene list to filter structural variations. These functions are essential for timely data analysis and identification of pathogenic variants.”

Dr. Hayk Barseghyan (not shown above), describing work he performed at UCLA on patients with undiagnosed genetic disease.  A recording of Dr. Barseghyan’s ASHG presentation covering his use of Bionano’s VAP can be seen here.


Identifying Rare, Potentially De Novo Variants in Families

Bionano’s VAP was recently used to help identify rare and potentially inherited de novo variants in a quartet family with two children with a neurological disorder. Using a family-based study design, we looked for rare or de novo structural variations in the two children. Using Bionano’s Saphyr optical genome mapping platform, 2,500 structural variations were detected in each sample.

The automated VAP determined the heredity of the calls, and selected 40–50 rare candidate variants, including a 174 kbp heterozygous deletion shared by the two affected children and the carrier father. This deletion overlaps ABCD3, a member of the ATP-binding cassette gene family. In addition, in one affected sample, researchers detected a rare 364 kbp heterozygous inversion, which was also inherited from the father.

In addition, we have also used this candidate-finding tool to help identify known rearrangements in leukemia. We were able to identify large translocations that could be verified by fluorescence in-situ hybridization. In addition, we detected many novel mutations whose size ranges from a few kilobases and up.

Read more about both studies here: Use of Bionano Optical Mapping to Identify Medically-Relevant Genomic Variation


Get Bionano Access

The Bionano VAP is part of the free Bionano Access software suite, which is available to download on our Software Downloads page. For a more technical description of the VAP’s functions, have a look at the VAP Theory of Operation.

For more information on the Bionano VAP or any of Bionano’s software and solutions, email us at info@bionanogenomics.com.



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