January 16, 2014

Finally the sub-$1000 sequencing of a genome and chip sequencing and nanopore sequencing trying to get to sub$100 genome sequencing

The Illumina HiSeq X™ Ten is the world’s first system to deliver full coverage genomes for less than $1,000. Purpose-built for large-scale human whole genome sequencing, it enables population-scale sequencing of tens of thousands of samples per year with high-quality, high-coverage SBS data, delivering a comprehensive catalog of human variation within and outside coding regions.

The less than $1000 cost is about 3 to 4 times less than what Illumina customers were experiencing in 2013. Many companies were claiming far prices at or near $1000 but those might not have being reading as thoroughly.

Building on the proven performance of Illumina SBS technology, HiSeq X Ten utilizes a number of advanced design features to generate massive throughput. Patterned flow cells, which contain billions of nanowells at fixed locations, combined with a new clustering chemistry deliver a significant increase in data density (6 billion clusters per run). Using state-of-the art optics and faster chemistry, HiSeq X Ten can process sequencing flow cells more quickly than ever before – generating a 10x increase in daily throughput when compared to current HiSeq® 2500 performance.

The HiSeq X Ten is sold as a set of 10 or more ultra-high throughput sequencing systems, each generating up to 1.8 terabases (Tb) of sequencing data in less than three days or up to 600 gigabases (Gb) per day, per system, providing the throughput to sequence tens of thousands of high-quality, high-coverage genomes per year.

The HiSeq X™ Ten, composed of 10 HiSeq X Systems, is the first sequencing platform that breaks the $1000 barrier for a 30x human genome. The HiSeq X Ten System is ideal for population-scale projects focused on the discovery of genotypic variation to understand and improve human health. (Photo: Business Wire)

Illumina announced the immediate availability of a transformative addition to its industry-leading next-generation sequencing portfolio with the launch of the NextSeq 500 System. The new sequencer packs high-throughput performance into an affordable desktop form factor, enabling researchers to perform the most popular sequencing applications in less than a day. The NextSeq 500 System is priced at $250,000.

Cost per genome to sequence up to April 2013

Who are the main contenders in the race to less than $100 genome sequencing ?

Dozens of startups are trying to carve off their chunk of a genetic testing market that UnitedHealthcare estimates could reach $25 billion annually by 2021.

Innovations like "ion torrent" sequencing, created by a startup acquired in 2010 by Life Technologies, aim to slash costs. Sequencing has traditionally been done optically, by flooding DNA snippets with chemicals called reagents that contain one of DNA's four bases. Every base has only one match; when a base finds a match, a light flashes. The sequencer sees it and records the base.

With the Ion Proton System -- a $100,000 machine that can sit on top of a table -- it's not light that's being recorded, but changes in pH balance. The DNA snippets being sequenced are attached to tiny beads sitting in as many as a billion tiny wells on a custom-designed semiconductor chip. The chip is flooded with DNA nucleotides, and when a base snaps into place, a hydrogen ion is released and recorded.

Eric Topol, a professor of genomics and director of the Scripps Translational Science Institute in San Diego, says chip sequencing -- without expensive reagents -- has the potential to be "remarkably cheaper" than traditional optical sequencing.

Illumina's arrays are quickly becoming cheaper and denser. Other advances are also driving down prices.

Topol cites innovations like nanopore sequencing, which passes DNA through a protein nanopore: "That's a very efficient way of getting millions and millions of bases read." That approach still has "significant problems with accuracy," he noted.

Oxford Nanopore is a leader in nanopore sequencing.

Government grants focus on nanopore sequencing

The use of nanopore technology aimed at more accurate and efficient DNA sequencing is the main focus of grants awarded by the National Institutes of Health. The grants – nearly $17 million to eight research teams – are the latest awarded through the National Human Genome Research Institute (NHGRI)'s Advanced DNA Sequencing Technology program, which was launched in 2004. NHGRI is part of NIH.

"Nanopore technology shows great promise, but it is still a new area of science. We have much to learn about how nanopores can work effectively as a DNA sequencing technology, which is why five of the program's eight grants are exploring this approach," said Jeffery A. Schloss, Ph.D., program director for NHGRI's Advanced DNA Sequencing Technology program and director of the Division of Genome Sciences.

Nanopore-based DNA sequencing involves threading single DNA strands through tiny pores. Individual base pairs – the chemical letters of DNA – are then read one at a time as they pass through the nanopore. The bases are identified by measuring the difference in their effect on current flowing through the pore. For perspective, a human hair is 100,000 nanometers in diameter; a strand of DNA is only 2 nanometers in diameter. Nanopores used in DNA sequencing are 1 to 2 nanometers in diameter.

This technology offers many potential advantages over current DNA sequencing methods, said Dr. Schloss. Such advantages include real-time sequencing of single DNA molecules at low cost and the ability for the same molecule to be reassessed over and over again. Current systems involve isolating DNA and chemically labeling and copying it. DNA has to be broken up, and small segments are sequenced many times. Only the first step of isolating the DNA would be necessary with nanopore technology.

Innovation is crucial in these as well as the other (non-nanopore) studies being funded. For example, one research team eventually hopes to use light to sequence DNA on a cell phone camera chip for under $100.

The new grants are awarded to:

* University of Illinois, Urbana-Champaign, $2.47 million over four years (pending available funds)
Principal Investigator: Oleksii Aksimentiev, Ph.D.

Dr. Aksimentiev and his colleagues plan to use nanopores as sensors. The researchers are studying the effects of combining synthetic nanopores with a light-based technique to control the flow of DNA molecules through the pores. They will use a type of spectroscopy to read the chemical sequence of the DNA.

* University of New Mexico Health Sciences Center, Albuquerque, $1.35 million over three years (pending available funds)
Principal Investigator: Jeremy Edwards, Ph.D.

Dr. Edwards and his colleagues plan to develop innovative molecular biology tools to improve whole-genome sequencing, which entails reading a person's entire genetic blueprint. The researchers hope that better methods of preparing the DNA molecules for sequencing will help scientists identify and link genetic variants to disease and, ultimately, lead to new treatments.

* University of Washington, Seattle, $3.83 million over four years (pending available funds)
Principal Investigator: Jens Gundlach, Ph.D.

The researchers plan to continue developing the use of nanopore DNA sequencing technology involving a type of protein nanopore called MspA. Part of their research will focus on improving the control of movement of DNA through the nanopore and on developing algorithms to identify DNA bases.

* Columbia University, New York City, $5.25 million over three years (pending available funds)
Principal Investigators: Jingyue Ju, Ph.D., George M. Church, Ph.D., (Harvard Medical School, Boston) and James John Russo, Ph.D. (Columbia University, New York City)

Dr. Ju and his colleagues plan to develop a miniaturized electronic system using nanopores to analyze single molecules of DNA in real time. They will construct large arrays of nanopores to create DNA sequencing chips, enabling them to determine DNA bases during a specific biochemical reaction. They hope this technique will enable them to read large sections of DNA more accurately and rapidly than is now possible.

* Eve Biomedical, Inc., Mountain View, Calif., $493,000 over two years (pending available funds)
Principal Investigator: Theofilos Kotseroglou, Ph.D.

Dr. Kotseroglou's research team intends to develop a DNA sequencing system that can sequence an entire human genome for under $100. The overall system will be based on using light to sequence DNA on a cell phone camera chip. For now, his group plans to continue studying ways to accurately read long sections of DNA and develop software tools and bioinformatics.

* University of Massachusetts, Amherst, $1.07 million over four years (pending available funds)
Principal Investigator: Murugappan Muthukumar, Ph.D.

Dr. Muthukumar's research group plans a theoretical approach to study several major challenges underlying nanopore-based DNA sequencing, including slowing down the rate at which DNA molecules flow through the pores, the effects of specific ions, changes in the shape of the DNA molecule and other aspects of the environment.

* University of North Carolina at Chapel Hill, $2.05 million over four years (pending available funds)
Principal Investigator: John Michael Ramsey, Ph.D.

Dr. Ramsey and his co-workers plan to develop a low-cost method for rapidly mapping individual genomes. Such maps will help determine how large mutations in DNA structure contribute to human disease and improve diagnostic testing using genomics.

* Electronic Biosciences, Inc., San Diego, $239,000
Principal Investigator: Anna Schibel, Ph.D.

Dr. Schibel and her co-workers will develop chemical methods to slow the rate by which single-stranded DNA molecules pass through protein nanopores. Such approaches may enable the development of faster, lower-cost DNA sequencing techniques.

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