Aug2015 analysis team 04 10x genomics

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

6. GemCode Platform Workflow

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