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Hitachi High Technologies America, Inc. (HTA), in collaboration with Hitachi Ltd (Hitachi), jointly announced that HTA will showcase a wide range of genomic initiatives at the 2017 Annual Meeting of The American Society of Human Genetics (ASHG), in Orlando, Florida, to be held from October 17 through October 21, 2017. These initiatives include bioinformatics, nanopore sequencing, and droplet digital PCR.
Bioinformatics
Human Chromosome Explorer
Although there are numerous techniques used to identify Structural Variation (SV), none of them is feasible in practical applied use. This means the picture of human genomic variation is far from complete as significant sequenced regions containing SVs remain unread. HTA is developing the Human Chromosome Explorer(SM) (HCE), a cloud- and web-based analytical and visualization system used to discover SVs throughout the human genome from genome mapping technologies. At ASHG 2017, HTA will discuss how, as part of this development, HTA engaged in a prospective analysis of NA12878, and In Silico-derived samples, containing randomly assigned heterozygous SVs ranging from 1 kb to 1 Gb. This also will include a discussion about how the haplotype aware assembler and SV analysis pipeline exploit distributed computing across multiple compute nodes bringing the processing time down to one day. The ability to dynamically control compute nodes also controls cost and demonstrates HCE's feasibility as an emerging pipeline for rapid, cost-effective calling of SV in the human genome.
Since more data is always better, you can join the project! During this development period, and for a limited time, HTA offers to run and provide human genome maps without charge to qualified research organizations interested in sharing data to help HTA unlock the questions of Structural Variation.
Project {candi}
Candi is a research project whose name is derived from ©ondensed (An)alysis by (D)ata (I)ndexing. This API generates a dictionary of next-generation sequencing (NGS) short-read sequences that may enable high-sensitivity, high-accuracy, and high-throughput NGS data analysis. The dictionary is comprised of indexes on each of the reads which preserves all the reads from the sequence as opposed to a heuristic approach. This means that candi has the potential for high specificity and sensitivity for low allele frequency mutations in heterogeneous samples. It also has the potential to identify breakpoints with single base-pair resolution that may be indicative of SVs. The indexed dictionary provides fast querying capability and, because it is shared by all samples, may lend itself to lossless data compression.
Nanopore Sequencing
Also, at ASHG 2017, Hitachi will discuss the solid-state Nanopore DNA Sequencer, developed by Hitachi, which allows for single-nucleotide discrimination and bidirectional DNA translocation. The fabricated solid-state nanopore array has an ultrathin membrane with 1-3 nm diameter at 8-inch wafer scale. A piezo actuator with nanometer accuracy enables direct control of DNA motion at a single nucleotide scale. This bidirectional (pull-down and pull-up) translocation of DNA enables repetitive reads at target locations of the DNA sequence. For example, Hitachi recently demonstrated detection of a single cytosine in adenine 5-mer homopolymers, along with demonstrating the detection of these homopolymers, and short tandem repeats (STRs).
ddPCR
HTA also has developed a droplet digital polymerase chain reaction (ddPCR) system specifically with an eye toward liquid biopsy for cancer diagnostic research and the necessity for high sensitivity for the detection of circulating tumor DNAs (ctDNAs). At ASHG 2017, HTA will review how this system combines asymmetric PCR and melting curve analysis to overcome what are normally large fluctuations in the fluorescence intensity of the droplets, which may erode accuracy. Specifically, HTA will discuss how the melting temperatures of the dsDNAs in 2D-arrayed droplets could be evaluated in parallel. The double-stranded DNAs (dsDNAs) with different length could be distinguished in terms of melting temperature ™, suggesting that Tm can be used to detect targeted DNA in the droplet.
Please visit HTA and Hitachi at ASHG 2017 Booth #549 to learn more about these initiatives, including how your organization can get involved.
About Hitachi High Technologies America, Inc. (HTA)
Hitachi High Technologies America, Inc. (hitachi-hightech.com) is a privately-owned global affiliate company that operates within the Hitachi Group Companies. HTA sells and services semiconductor manufacturing equipment, analytical instrumentation, scientific instruments, and bio-related products as well as industrial equipment, electronic devices, and electronic and industrial materials.
About Hitachi Ltd
Hitachi Ltd (hitachi.com), headquartered in Tokyo, Japan, delivers innovations that answer society's challenges. The company's consolidated revenues for fiscal 2016 (ended March 31, 2017) totaled 9,162.2 billion yen ($81.8 billion). The Hitachi Group is a global leader in the Social Innovation Business, and it has approximately 304,000 employees worldwide. Through collaborative creation, Hitachi is providing solutions to customers in a broad range of sectors, including Power/Energy, Industry/Distribution/Water, Urban Development, and Finance/Government & Public/Healthcare.
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