Sequencing

11th Annual Sequencing, Finishing, and Analysis in the Future Meeting
DIRECT DETERMINATION OF GENOME SEQUENCES
Thursday, 2nd June 15:50 La Fonda Ballroom Tech Talk (TT‐2.01)
David Jaffe, Neil Weisenfeld, Vijay Kumar, Kamila Belhocine, Rajiv Bharadwaj,
Deanna Church, Paul Hardenbol, Jill Herschleb, Chris Hindson, Yuan Li, Patrick Marks,
Pranav Patel, Andrew Price, Michael Schnall Levin, Alex Wong, Indira Wu
10x Genomics, Inc
We introduce a new method for determining the genome sequence of an organism. Our method has
the following key advantages:
1. Our starting material consists of 1 ng of high molecular weight DNA, as compared to typical requirements
of 1,000‐10,000 ng or more.
2. We create a single library, as compared to typical methods which require creation of multiple
libraries and often multiple data types. This makes our process fundamentally more robust than
typical methods.
3. Our costs are about ten times lower.
4.The entire process, including assembly, is not organism‐specific. For example, there are no
parameters to specify to the algorithm.
5. We produce a genome sequence that mirrors the actual chromosomes in the sample, as contrasted
with prior methods for which a contig is a mélange of homologous sequences.
To accomplish this, we create a single 10X Genomics Linked‐Read (Chromium Genome) library and
sequence it on the HiSeq X instrument. The data type consists of barcoded pools of reads, each
originating from several very long molecules, with each molecule represented by many reads, and
shallowly covered. Our new turn‐key software, the Supernova Assembler, exploits these pools, first to
create local assemblies, that can capture difficult regions, and then to phase homologous chromosomes.
Using human genomes, we obtain contigs of size 100 kb, in scaffolds of size larger than 10 Mb, and
composed of phase blocks of size 3‐4 Mb. Notably, these phase block lengths greatly exceed those
obtained from any other method, in spite of being constructed from dramatically less expensive data.
We rigorously assess the accuracy of our assemblies, including by means of a HGP sample for which
340 Mb of finished sequence is available. We further demonstrate our method on a wide range of
organisms (both animal and plant), obtained from diverse starting materials. For many purposes, our
method supplants all prior methods for obtaining genome sequences by providing a direct and
inexpensive path to the true sequence of the sample.
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