Anchored Assembly is a structural variant caller built as a use case of the BioGraph Analysis Format.
One of the biggest challenges in large-scale sequencing is the ability to detect complex changes in the genome. These complex structural changes are important for understanding cancer, neurological disorders like autism, rare childhood disorders, investigating changes across individuals and understanding evolution. Often, considerable time is spent evaluating tools or sifting through results to find real variants.
Anchored Assembly is a bioinformatics method that can be used on regular, short read NGS data to detect longer indels (changes of 30-50bp) and structural variants (changes > 50bp). Using a combination of mapping and assembly of reads, we can accurately detect changes often not detected by other methods.
Specifically, it searches for reads that have not aligned to the reference and then follows the read overlap assembly in both directions until over 70% of the reads match the reference. This is reported as a variant. Utilizing the backbone of the BioGraph Analysis Format, this search for structural variants can be completed in approximately 12 hours.
NGS sequencing is moving toward comparing samples, whether a family trio or a large case-control study. Accuracy in calling breakpoints is important for comparing samples. Adam English, lead bioinformatics programmer at the Baylor College of Medicine, says that “Spiral Anchored Assembly breakpoints matched very closely if not exactly with PCR-validated breakpoints.”
Often, structural variant callers are good to detect only a particular type or size range of structural variant. The Baylor College of Medicine compared multiple structural variants callers. William Salerno, Bioinformatic Scientist at Baylor, says that “when looking at our high-confidence SV events with long-read PacBio support, we often found that Spiral AA was the only Illumina-based method contributing to that discovery. We even assemble long insertions with sufficient resolution to identify differences from parents.” See publications.
Low false discovery rate
Even if variant callers are able to detect variants, often there is a high rate of false discoveries. Anchored Assembly has a false discovery rate of around 4%, up to around 10 times less than current standard structural variant callers. See publications.
We have published one paper validating the method and have others in preparation. See publications.