Unlock Powerful Genomics Insights with Linked-Reads: Introducing the GemCode Platform

Michael Schnall-LevinVice 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

Cycle

Collect

DNABarcodedprimer 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 onLinked-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 Detected50 Kb Deletion in NA24385

Large-Scale Structural Variants Easily DetectedPhasing of 50 Kb Deletion in NA24385

Father

Child

Mother

Wide Classes of Structural Variants Now Accessible1 Kb Distal Insertion in NA24385

Wide Classes of Structural Variants Now AccessiblePhasing of 2 Kb Distal Insertion in NA24385

Wide Classes of Structural Variants Now AccessibleRetrotransposon in NA12878

Serafim Batzoglou: Critical-Content Rescue

Serafim BatzoglouAlex BisharraYuling Liu

Zero evidence for variants in short-readsAll found with Linked-Reads

All variants in this region would be missed by short-reads

Serafim Batzoglou: Critical-Content Rescue