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Sept2016 sv bio_nano
The document discusses updates to genome mapping technology. It describes how high-throughput, high-resolution imaging can generate contiguous DNA molecules up to megabase lengths. Labeled DNA is imaged repeatedly to scan the entire genome. Genome maps can be used to discover structural variants by comparing patterns of labeled sequences. Genome maps can also be used as scaffolds to align sequencing contigs. The document provides examples of detecting insertions, deletions, and other structural variants between samples or to a reference genome. It also discusses using genome maps to validate structural variants found through other methods like PacBio sequencing.
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Sept2016 sv bio_nano
- 1. Genome in aBottle Update September 15th, 2016
- 2. 2 ©2015 BioNano Genomics AlgorithmsConvert Images into Molecules Assembly Algorithms Align Molecules de novo for Constructing Consensus Genome Maps Cross-Mapping Across Multiple Samples or to a Reference High Throughput, High Resolution Imaging Gives Contiguous Molecules up to Mb Length • Automated SV Detection • Gap Sizing • Genome Finishing Isolate High Molecular Weight DNA Label Specific Sequences Across the Entire Genome Transfer Labeled DNA into Cartridge for Scanning Insertion Irys® Workflow- Overview Load, Linearize & Image Labeled DNA in Repeated Cycling to Scan Whole Genome
- 3. 3 ©2015 BioNano Genomics Irys®Applications Structural Variation (SV) discovery Compare to a reference or gold standard, looking for changes in the patterns: • Shifts in barcode patterns reveal insertion (addition), deletion (subtraction), inversion (re-orientation), translocation of genome segments. Hybrid Scaffolding BioNano maps are used as a scaffold: • Sequencing contigs are converted in silico into molecular barcodes by highlighting the same sequence motifs • These sequencing based barcodes are then aligned to the BioNano maps Two Fundamental Applications
- 4. 4 ©2015 BioNano Genomics LabelSite Gain/ Loss Balanced SVs Tandem Array Deletion Insertion Cross-Map Analysis: Look for Similarities and Differences Between Maps Deletion Insertion 26.6kb 21.0kb IrysView® SV Detection BCR ABL1Chr 9 Chr 22 ~200kb ~70kb
- 5. 5 ©2015 BioNano Genomics SimulatedDiploid Genome – Sensitivity and PPV Estimate • BioNano SV calls in two homozygous hyditidaform mole cell lines were used as a gold standard • Variants that are the same in both lines are considered homozygous and variants found in only one line are considered heterozygous in the mixture • We do not have a measurement of FN rate related to missing coverage (e.g. at fragile sites) in this set up
- 6. 6 ©2015 BioNano Genomics BioNanosize PacBiosize (bp) Size Concordance for Insertions and Deletion Between PacBio and BioNano SVs BioNanosize PacBio size (bp) Pac Bio calls from: Chaisson et al., Resolving the complexity of the human genome using single-molecule sequencing Deletions Insertions Good size concordance between BioNano and PacBio SVs facilitates cross validation of findings.
- 7. 7 ©2015 BioNano Genomics NewSV Calls – Better Heterozygous SV Detection, Confidence Scores Sample Nickase Input data Diploid assembly size Genome map N50 Insertion Deletion Father Nt.BspQI 319 Gb 5.24 Gb 4.46 Mb 4436 1935 Mother Nt.BspQI 385 Gb 5.22 Gb 3.93 Mb 5047 2210 Son Nt.BspQI 508 Gb 5.52 Gb 2.55 Mb 3626 1775 Check son-specific SVs: i. low assembly, alignment (repetitive, ambiguous), variant scores ii. FP in child iii. FN in parents iv. putative de novo SVs Aggressive SV calling 2311 3229 1034 son-specific SVs 523 803 679 3089 Father Mother
- 8. 8 ©2015 BioNano Genomics FPvariant in the son – low local coverage 1.055 Mbp ins Heterozygous Insertion on chr18:31,368,891-31,419,488 size=159.8 kbp Note that the coverage at the variant region is abnormally low. Hence this is a false call, and is filtered by automated molecule alignment check Son map Son map chr18 Son molecule pileup
- 9. 9 ©2015 BioNano Genomics FNin a parent’s assembly (1) Son 302 kbp chr8 Mother Father A heterozygous deletion found only in the son by assembly comparison. chr8:5,594,272-5,609,910 size: 10.2 kbp On the mother’s assembly (blue arrow), there seem to be some kind of aberration, but it does not match the son’s deletion Del
- 10. 10 ©2015 BioNano Genomics FNin a parent’s assembly (2) Mother’s molecule aligned to the son’s genome map Son Mother molecules 302 kbp A heterozygous deletion found only in the son by assembly comparison. chr8:5,594,272-5,609,910 size: 10.2 kbp Note that the mother’s molecules actually align well to the son’s genome map
- 11. 11 ©2015 BioNano Genomics 23113229 3 son-specific SVs 523 803 679 3089 Father Mother SV shared among trio members i. 792 with low assembly, alignment (repetitive, ambiguous), variant scores ii. 20 FP in child iii. 219 FN in parents iv. 3 putative de novo SVs Sample Nickase Input data Diploid assembly size Genome map N50 Insertion Deletion Father Nt.BspQI 319 Gb 5.24 Gb 4.46 Mb 4436 1935 Mother Nt.BspQI 385 Gb 5.22 Gb 3.93 Mb 5047 2210 Son Nt.BspQI 508 Gb 5.52 Gb 2.55 Mb 3626 1775
- 12. 12 ©2015 BioNano Genomics Summary •Fullyde novo genome map assembly for genome structure •Validation of sequence assembly by orthogonal verification •Hybrid scaffolding of sequence assemblies •Structural variation detection •Structural variation validation by genome map and single molecule alignment
- 13. 13 ©2015 BioNano Genomics Acknowledgements •Genome in a bottle consortium • BioNano Genomics − Andy Pang − Joyce Lee − Ernest Lam − Tiff Liang − Thomas Anantharaman − Khoa Pham − Will Stedman − Han Cao • Mt. Sinai − Ali Bashir
Editor's Notes
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