Missing the action at AGBT 2013 and want to know what is Illumina sequencing technology up to? Illumina has created special website for AGBT and shared a lot of interesting information.
The Illumina website titled “Seek The Truth” has lot of information on Illumina technology and its usage. As a rebuttal to a recent report suggesting that MiSeq is still lagging behind IonTorrent in terms of sales, Illumina is claiming that “85% of desktop data submitted to NCBI is done on MiSeq”. Using the data submitted to NCBI’s SRA, Illumina claims that among the 3243 studies that submitted data to NCBI, 2788 studies used MiSeq (85%) and 565 used other desktop sequencers (without naming IonTorrent).
Illumina Time Lapsed Video: Growth of BaseSpace Runs Across the World
Illumina also released a time-lapsed video showing Illumina BaseSpace data submission on a world map. The YouTube video shows that in a span of six months June 2012 to Dec 2012, Illumina BaseSpace MiSeq runs increased from about 11000 to 21000. And Illumina HiSeq BasSpace runs went from 2 to 287.
Illumina also has shared a few posters that it will presenting at AGBT this year. Interesting ones are obviously posters describing Moleculo technology and Illumina’s hint on future technology developments. Here are the abstracts and the link to the posters from Illumina at AGBT.
Accurate genome haplotyping using existing high-throughput sequencers, by Cuiping Pan,Dan Xie, Dmitry Pushkarev,Tim Blauwkamp,Volodymyr Kuleshov,Michael Snyder and Michael Kertesz.
Phasing information is of critical importance to personalized genomics and medicine. Many applications are expected to benefit from the deterministic assignment of variants to haplotypes. Those include diagnostics of compound heterozygous linked diseases, pharmacogenomics (genetically determined drug response) and noninvasive prenatal genome sequencing.
High throughput DNA sequencing allows whole human genomes to be resequenced rapidly and inexpensively, thus producing a
comprehensive list of variants relative to the reference genome. However, short read technologies do not allow the establishment of phasing information (i.e. assignment of variants to maternal and paternal chromosomes) and thereby produce non-phased heterozygous calls representing the average of variants located on maternal and paternal chromosomes.
We demonstrate a novel haplotyping method using Moleculo’s Clinical Sequencing method. Genomic DNA is modified by adding
custom DNA tags and converted into standard short read shotgun sequencing library. After sequencing, a proprietary algorithm based on a Hidden Markov Model establishes local genome phasing, which spans most of the heterozygous blocks. These blocks, averaging 100kb in length, are then phased relatively to each other using a large panel of previously sequenced genomes. Furthermore, the use of probabilistic graphical models provides accurate phasing confidence scores that can be used by downstream analysis pipelines.
De-novo haplotype resolved whole genome sequencing and assembly using Moleculo Long Read sequencing kit. by
Dmitry Pushkarev, Dmitri Petrov, Tim Blauwkamp, Michael Kertesz
Recent advances in sequencing technologies have led to orders of magnitude increase in the throughput of next generation short read sequencers. In spite of these achievements, read length and accuracy remain relatively flat at around 100-300 bases and Q15-Q30 depending on the platform. Moleculo has developed a new sequencing technology, which
extends the capabilities of existing short read sequencers to achieve continuous DNA read lengths of up to 10kb at over Q50 accuracy across the entire read length. One immediate application of such long and accurate DNA reads is de-novo genome assembly. Large genomes are plagued with thousands of repeats; using short reads to assemble them results in highly fragmented assemblies that are limited to the unique parts of the genome. Highly heterozygous genomes also pose significant problems for the assembly, as choosing the identity thresholds required to merge two haplotypes into consensus assembly inevitably leads to collapsing of nearly identical repeats. Long and accurate Moleculo reads address both of these problems by spanning across most of the repeats, while the high accuracy allows haplotype separation where necessary.
We describe the use of a single Moleculo run to generate over 5X coverage of the Drosophila Melanogaster (Fruit Fly) genome in long reads and the de-novo assembly of the genome using those long and accurate reads. We demonstrate that reference-quality genome assemblies can now be inexpensively generated by individual labs using Moleculo’s long read technology.