• Summary
• Structural and copy number variant inputs
  • Private SV / CNV inputs
    • PG-pop
    • Pop-Manta
  • Public SV / CNV inputs
    • PopIns Icelandic insertions
    • Parliament insertions
• References

Input for variants characterized on Polaris cohorts can be derived from any number of public or private datasets.

In the case of public datasets, Polaris provides additional validation to increase confidence in calls that are either common or found in a characterized pedigree. For private datasets, Polaris additionally provides a means of sharing variants and supporting alignments that might have been difficult or impossible to share otherwise. Additionally, candidates may be provided as input without any prior evidence from an SV dataset, based on, for instance population genetic signals or other, novel means, of variant detection.

A set deletion and compound deletion / insertion calls that were initially identified as pedigree-consistent in the Platinum Genomes from a variety of SV callers. Reads from these regions were then extracted in a larger population and reassembled using SPAdes¹. Any SVs that produced a single unique breakpoint contig within the cohort were taken as input candidates.

Population calls identified by Manta² that were re-identified in a Polaris cohort.

Insertions described in Kehr, et al ⁵ identified in a population of Icelandic individuals using PopIns⁴. Candidates were limited to those that could be converted to a graph input and contained flanking sequence matching the reference.

Insertions described in English, et al³ identified using Parliament and incorporating data types and SV calling methods to call SVs in a single subject.

1. Bankevich, et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 19(5):455-77. doi:10.1089/cmb.2012.0021
2. Chen, et al (2016) Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics 32(8):1220-1222. doi:10.1093/bioinformatics/btv710
3. English, et al (2015) Assessing structural variation in a personal genome-towards a human reference diploid genome. BMC Genomics. 16:286 doi:10.1186/s12864-015-1479-3
4. Kehr, et al (2016) PopIns: population-scale detection of novel sequence insertions. Bioinformatics. 32(7):961-7. doi: 10.1093/bioinformatics/btv273
5. Kehr, et al (2017) Diversity in non-repetitive human sequences not found in the reference genome. Nat Genet. 49(4):588-593. doi: 10.1038/ng.3801