Animal Genome Research
Advancing animal genome research is crucial for feeding the world and maintaining healthy ecosystems. Most animal genomes are highly repetitive with large structural variations that sequencing-based tools alone cannot resolve. Bionano Saphyr™ offers hybrid scaffolding and structural variation discovery capabilities that are essential to overcoming these hurdles.
Generating high-quality finished animal genomes remains challenging. Assembly contiguity and accuracy is vital to driving discovery. Unlike next-generation sequencing (NGS), which is based on inferring genome structure information from fragmented DNA data, Bionano optical genome mapping directly observes long DNA molecules by linearizing and imaging DNA in its native state using massively parallel NanoChannels.
De novo Saphyr genome maps can be integrated with sequence assemblies to order and orient sequence fragments, identify and correct potential chimeric joins in the sequence assemblies, and estimate the gap size between adjacent sequences.
Bionano hybrid scaffolding considerably reduces the number of contigs found in initial NGS assemblies and improves contiguity up to 1000 times over NGS-based approaches alone.
The combination of Bionano maps with sequencing data improves assembly accuracy and quality while reducing the need for deep sequencing coverage. This improved contiguity significantly lowers costs associated with assembling reference genomes.
Saphyr also offers unparalleled sensitivity for large structural variations from 500 bp to megabase pair lengths.
- 99% sensitivity for homozygous insertions/deletions larger than 500 base pairs
- 95% sensitivity for heterozygous insertions/deletions larger than 500 base pairs
- 95% sensitivity for balanced and unbalanced translocations larger than 50,000 base pairs
- 99% sensitivity for inversions larger than 30,000 base pairs
- 97% sensitivity for duplications larger than 30,000 base pairs
For mosaic samples or heterogeneous cancer samples, Saphyr detects all types of structural variants down to 5% Variant Allele Fraction. Saphyr provides this performance typically with a false positive rate of less than 2%. Saphyr also detects repeats, copy number variants, and complex rearrangements.
See below for publications, white papers and other resources regarding Bionano genome mapping in animal genome research.
- Selective breeding – identify areas of biological interest for achieving desirable traits in livestock
- Evolutionary biology – see the complete picture of how genomes have evolved and been reorganized
- Disease discovery – call structural variations to identify variants of interest and their effect on genes and disease
- Reference genome assembly – perform de novo assembly and scaffold assemblies generated by sequencing-based systems
- A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals structural genome variation in rainbow troutbioRxiv 2020
- Molecular Ecology Resources 2020
- Gigascience 2020
- Isolating High-Quality Ultra-High Molecular Weight (UHMW) Genomic DNA (gDNA) from 5-10 mg of Fresh Frozen Animal and Human TissuesJanuary, 2020
- January, 2020
- January, 2020