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GenomeInABottle
GenomeInABottle

Aug2015 analysis team 04 10x genomics

Health & Medicine
1 of 17
Unlock Powerful Genomics Insights with Linked-Reads: Introducing the GemCode Platform Michael Schnall-Levin Vice President, Computational Biology and Applications
750,000 Discrete Reagents in One Tube • 14bp barcode • Defined sequence • Highly uniform size and representation • Built-in sequencing adapter and primer content Gel bead scaffold Functional oligo with barcode High-diversity library 54 um P5 Barcode R1 N-mer
>100,000 Reactions Assembled in < 5 min Enzyme Cycl e Collect DNABarcoded primer library Oil GEMs Pool Solid phase reagent delivery Fluid partitioning Liquid phase biochemistry
1 ng gDNA ~ 100 kb Average Length > 100,000 Barcoded Partitions < 5 fg per Partition ~ 0.1% of Genome per GEM ~ 90% Gel Bead Fill Rate Haplotype Limiting Dilution
Linked-Reads – Whole Genome and Exome Whole Genome Exome GemCode Workflow Capture is Final Step on Linked-Read Library
GemCode Platform Workflow
Long Ranger Pipeline Details 7 Align w/ BWA, Mark PCR Duplicates, Barcoding Link Short Reads to Long Molecules Call SNPs and Indels Call SVs Phase SNPs, Indels, and SVs Visit http://software.10xgenomics.com to explore in detail
NIST Genome in a Bottle Data Release
Consistent Multi-Mb Phase Blocks Across Samples Mean Coverage 33.9X 25.4X 21.5X 23.8X PCR Duplication Rate 1.5% 1.1% 0.8% 1.2% Mapping Rate 96.7% 94.5% 94.5% 93.6% N50 Linked-Reads per Molecule (LPM) 104 145 71 183 Mean Molecule Length 130 Kb 165 Kb 109 Kb 146 Kb N50 Phase Block Length 16.7 Mb 20.5 Mb 12.5 Mb 21.6 Mb Longest Phase Block 40 Mb 40 Mb 40 Mb 40 Mb % SNPs Phased 96.2% 98.8% 98.6% 98.7% NA12878Metric NA24385 NA24149 NA24143
Phasing Scales to Entire Chromosome Arms Entire p arm of Chr10 in a single phase block (39.1 Mb) Subset of phase block (3.1 Mb) Subset of phase block (123 kb) showing linked-read coverage across ARHGAP12 gene
Large-Scale Structural Variants Easily Detected 50 Kb Deletion in NA24385
Large-Scale Structural Variants Easily Detected Phasing of 50 Kb Deletion in NA24385 Father Child Mother
Wide Classes of Structural Variants Now Accessible 1 Kb Distal Insertion in NA24385
Wide Classes of Structural Variants Now Accessible Phasing of 2 Kb Distal Insertion in NA24385
Wide Classes of Structural Variants Now Accessible Retrotransposon in NA12878
Serafim Batzoglou: Critical-Content Rescue Serafim Batzoglou Alex Bisharra Yuling Liu
Zero evidence for variants in short-reads All found with Linked-Reads All variants in this region would be missed by short-reads Serafim Batzoglou: Critical-Content Rescue

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Unlock Genomics Insights with Linked-Reads GemCode Platform

  • 1. Unlock Powerful Genomics Insights with Linked-Reads: Introducing the GemCode Platform Michael Schnall-Levin Vice President, Computational Biology and Applications
  • 2. 750,000 Discrete Reagents in One Tube • 14bp barcode • Defined sequence • Highly uniform size and representation • Built-in sequencing adapter and primer content Gel bead scaffold Functional oligo with barcode High-diversity library 54 um P5 Barcode R1 N-mer
  • 3. >100,000 Reactions Assembled in < 5 min Enzyme Cycl e Collect DNABarcoded primer library Oil GEMs Pool Solid phase reagent delivery Fluid partitioning Liquid phase biochemistry
  • 4. 1 ng gDNA ~ 100 kb Average Length > 100,000 Barcoded Partitions < 5 fg per Partition ~ 0.1% of Genome per GEM ~ 90% Gel Bead Fill Rate Haplotype Limiting Dilution
  • 5. Linked-Reads – Whole Genome and Exome Whole Genome Exome GemCode Workflow Capture is Final Step on Linked-Read Library
  • 7. Long Ranger Pipeline Details 7 Align w/ BWA, Mark PCR Duplicates, Barcoding Link Short Reads to Long Molecules Call SNPs and Indels Call SVs Phase SNPs, Indels, and SVs Visit http://software.10xgenomics.com to explore in detail
  • 8. NIST Genome in a Bottle Data Release
  • 9. Consistent Multi-Mb Phase Blocks Across Samples Mean Coverage 33.9X 25.4X 21.5X 23.8X PCR Duplication Rate 1.5% 1.1% 0.8% 1.2% Mapping Rate 96.7% 94.5% 94.5% 93.6% N50 Linked-Reads per Molecule (LPM) 104 145 71 183 Mean Molecule Length 130 Kb 165 Kb 109 Kb 146 Kb N50 Phase Block Length 16.7 Mb 20.5 Mb 12.5 Mb 21.6 Mb Longest Phase Block 40 Mb 40 Mb 40 Mb 40 Mb % SNPs Phased 96.2% 98.8% 98.6% 98.7% NA12878Metric NA24385 NA24149 NA24143
  • 10. Phasing Scales to Entire Chromosome Arms Entire p arm of Chr10 in a single phase block (39.1 Mb) Subset of phase block (3.1 Mb) Subset of phase block (123 kb) showing linked-read coverage across ARHGAP12 gene
  • 11. Large-Scale Structural Variants Easily Detected 50 Kb Deletion in NA24385
  • 12. Large-Scale Structural Variants Easily Detected Phasing of 50 Kb Deletion in NA24385 Father Child Mother
  • 13. Wide Classes of Structural Variants Now Accessible 1 Kb Distal Insertion in NA24385
  • 14. Wide Classes of Structural Variants Now Accessible Phasing of 2 Kb Distal Insertion in NA24385
  • 15. Wide Classes of Structural Variants Now Accessible Retrotransposon in NA12878
  • 16. Serafim Batzoglou: Critical-Content Rescue Serafim Batzoglou Alex Bisharra Yuling Liu
  • 17. Zero evidence for variants in short-reads All found with Linked-Reads All variants in this region would be missed by short-reads Serafim Batzoglou: Critical-Content Rescue

Editor's Notes

  1. May want to do second definition of GEM next time reference that
  2. Mention can tell which transcript variant was retrtransposed