The Chromium™ System

One System, One Workflow, Powerful New Sequencing Applications

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The Chromium™ System

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•Chromium™ Genome – The most comprehensive genome

–Long range genomes at population scale

–Call the full spectrum of variants and unlock previously inaccessible regions from a single library at equivalent coverage

•Chromium™ Exome – Reach beyond the exome

–Enable phasing of thousands of genes and detection of structural and copy number variation

–Optimized SureSelect baits to improve gene phasing by closing gaps, and recovering hard-to-map loci in the genome

•Chromium™ Single Cell 3’ – Cell-by-cell gene expression

–High-throughput single cell RNA sequencing

–Scalable transcriptional profiling of 1,000s to 10,000s of individual cells

Powerful new sequencing applications

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Complete solution from sample to answer with Chromium Exome and SureSelect baits

Sample input Target Enrichment Sequencers Analysis

Sample types• Cell lines• Demonstrated on

Whole blood and tissue

Sample prep methods• Qiagen MagAttract

HMW DNA kit

• Agilent All Exon V6 baits (available today)

• Agilent Optimized SureSelectBaits (2016H2)

• NextSeq• HiSeq 2000/2500• HiSeq 3000/4000

10x Software• Loupe 2.0• Long Ranger 2.0

Standard Outputs:• BAM• Fastq• VCF

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Partition Molecules and uniquely tag each short read to create Linked-Reads

Linked-Reads

• Input: Long DNA

• Output: Linked-Read data type enabling single molecule resolution

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GemCode™ Technology with millions of uniquely addressable partitions enables single molecule resolution and single cell sequencing

Conventional sequencing

100kb

Haplotype 1

Haplotype 2

Pos1 Pos2 Pos3

10x sequencing

Single Molecule ResolutionAverage of two molecules

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Mapping difficult in repetitive regions of genomes

Close Paralogs

Short Reads

Short Read Aligners Cannot Place Reads Correctly

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Long Range information Rescues Critical Content

1. Confident mapping provides anchors

2. Barcodes recruit short reads into paralogousregion

Close Paralogs

LariatTM Aligner Correctly Places Short Reads Even in Paralogous Loci

Linked-Reads

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Intelligent bait positioning improves phasing and mapping in difficult loci

Exome

Linked-Reads fromChromium Genome

Standard Exome Baits

Linked-Reads fromStandard Exome Baits

SureSelect OptimizedExome Baits

Linked-Reads fromOptimized Baits

Coming Q4 2016

Available Now

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10x Collaboration with Agilent Delivers High-Quality Constitutional Content

•Backbone: Agilent SureSelect Human All Exon V6

•Maximize ability to phase and call SV in all clinically relevant genes

•Optimize baits to improve mapping in clinically important genes –OPN1LW, OPN1MW, OPN1MW2

–SMN1, SMN2

–SRGAP2[ABCD]

Total design footprint: ~70 Mb

ClearSeq Inherited Disease2,874

TruSightOne4,811

MHC 26

ACMG56

257 10

2,194

Overlap of clinically relevant genes from various panels

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Similar coverage uniformity for 10x libraries vs standard libraries

• Chromium Exome (Agilent V6) library: 1.5 ng input DNA, 9 Gbsequencing

• Agilent SureSelect V6 library: 200 ng input DNA, 6 Gb sequencing

NA12878 Chromium Exome (9Gb)

vs. SureSelect (6Gb)

NIST Confident Regions

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Similar variant calling for 10x libraries vs standard libraries

• Chromium Exome (Agilent V6) library: 1.5 ng input DNA, 9 Gbsequencing

• Agilent SureSelect V6 library: 200 ng input DNA, 6 Gb sequencing

NA12878 Chromium Exome

(9Gb) vs. SureSelect (6Gb)

NIST Confident Regions

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• NA12878• RPS17: a ribosomal subunit gene in which mutations cause Diamond-Blackfan Anemia 4

Lariat Aligner: high quality mapping in the “dark”

BWA Aligner

Lariat Aligner

New TP variants

Same Data. Two Aligners. One Winner.

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Phasing of Compound Het in Titin with Chromium Exome

Confidential — Do not distribute

TTNCompound Het

189 kb (trans)

Work by: Daniel MacArthur

Mass General Hospital

“Seriously impressed with phased exome data from @10xgenomics -easily phases two causal TTN variants, 190 kb apart”

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• Autosomal recessive lysosomal storage disorder due to variants in CTNS

• Compound heterozygote is haplotype resolved for a 57kb deletion (exons 1-10 in CTNS) and a SNP

Compound Heterozygous Variant Resolution

chr17:3,563,221 (Gly308Arg)

CTNSSHPKTRPV1

57 kb deletion

G>A

Haplotype 1 Reads

Haplotype 2 Reads

Haplotype 1

Haplotype 2

NA17885 Chromium Exome

(SS v6) 9Gb

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•H2228: Non-small cell lung cancer

Identify Complex Structural Variants

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• VCaP: prostate cancer

Phasing Enables Detection of Single Exon Copy Number Changes

Copy Number Algorithms under active development

18• NA12214: Duplication of the PMP22 gene is associated with Charcot-Marie Tooth neuropathy type 1.

Larger CNVs are detected by read counts and classified/localized by Linked-Reads

CGH Confirmation using a 4x180k Agilent CGH array

CNV read count analysis of 10x libraries and SureSelect Exome plus phasing TE

The duplication is a tandem event, includes location and breakpoints

chr17:14,092,796

chr17:15,478,685

Copy 1 Copy 2

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Reaching Beyond Your Everyday Exome

Access genomic information from the Exome

Phase thousands of genes and assign cis or trans to heterozygous variants

Detect large SV and enable CNV detection

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10x Genomics products described are for Research Use Only. Not for use in diagnostic procedures.

Agilent products described are for Research Use Only. Not for use in diagnostic procedures.