The New York Genome Center has begun to move into its new home in downtown Manhattan and plans to have its sequencing operations up and running next month, prior to a "ribbon-cutting ceremony" in mid-September.
The center is in the process of recruiting several principal investigators – both experimental researchers and bioinformaticians – who will set up their groups in the brand-new labs and office space.
Its staff has already grown to about 40, approximately 25 on the scientific side and 15 administrators, and it is currently hiring bioinformaticians and lab technicians to support its growth.
Click to EnlargeDuring a visit last week, parts of the new facilities, which occupy six floors of an office building at 101 Sixth Avenue, still looked like a construction site, with workers installing lab benches and many offices still unfurnished. Five Illumina HiSeq 2500 sequencers sat in crates in the empty sequencing laboratory, ready to be installed starting this week, while Bob Darnell, the center's president and scientific director, and his administrative team have already moved into fully-operational offices.
Click to EnlargeConstruction work to renovate the space and convert offices into labs began a year ago, when the center signed a 20-year lease with its landlord, Edward J. Minskoff Equities (IS 7/24/2013). According to Bill Fair, director of business development and institutional relations for the NYGC, construction costs will total more than $50 million, a large portion of the close to $140 million the center has raised in funding so far. "Putting in the heating and the cooling and the electrical systems and the data systems to support labs, that's a huge expense," he told In Sequence last week.
By the end of the month, the center plans to vacate its pilot sequencing laboratory at Rockefeller University and move its existing instrumentation – including six Illumina HiSeq 2500s and one MiSeq sequencer – into the new lab, where they will join the five new HiSeqs. Four Ion Torrent Protons that are currently housed at Memorial Sloan-Kettering Cancer Center will remain there for now, though the center might move one or more of them over in the future, said Kevin Shianna, NYGC's deputy scientific director of sequencing operations. "All the demand is Illumina right now," he said.
The center is also bringing in an Irys single-molecule DNA mapping instrument from BioNano Genomics – the first genome center to do so – which it purchased after testing the technology in a genome sequencing project in collaboration with research groups in New York. BioNano recently showed proof-of-concept for being able to analyze human-size genomes (IS 6/11/2013).
The sequencing center is scheduled to be up and running in early August. Sequencing operations will be spread across two separate laboratories, allowing for a "clean split" between projects for the center's institutional founding members and associate members and work for others, such as pharmaceutical companies. The plan is to ramp up the number of Illumina HiSeqs to 20 by the end of the year, and more if necessary. As sequencers are added, sample prep work will move into in its own dedicated room.
NYGC's Innovation Center will be housed in yet another laboratory so that companies' technologies tested under early access programs or methods under development at the center can be shielded from the prying eyes of visitors. According to Shianna, the center has already beta-tested several sample prep kits from Illumina, and it had access to Moleculo's technology before the company was acquired by Illumina earlier this year.
Click to EnlargeIn addition to its research sequencing space, the center has been setting up its CLIA laboratory, spread over three currently empty rooms marked for sample reception, pre-PCR, and post-PCR that can be expanded in size if needed. The CLIA lab will initially house one or two of the HiSeq instruments and is headed by Liying Zhang, director of the diagnostic molecular genetics laboratory at Memorial Sloan-Kettering Cancer Center, who serves as its interim director until the NYGC hires a permanent director.
The genome center has already submitted an application for certification of the lab to the New York State Department of Health and expects to be inspected by the department later this year. Zhang, who has a certificate of qualification from the State of New York in molecular oncology and in molecular genetics, will help the center with the certification process and the development of its first tests. In addition, the center has hired a senior clinical laboratory technician, Michelle Lamendola-Essel, who is also certified by the State of New York, to run the lab on a day-to-day basis.
Click to EnlargeOn the bioinformatics side, the center recently recruited Toby Bloom as deputy scientific director for informatics from the Broad Institute, where she was director of informatics for the past 10 years. Bloom will have "similar responsibilities" to Dirk Evers, who was hired as senior vice president of informatics last year and left the center unexpectedly this spring. Data analysis will be a key focus of the NYGC – the 6th floor, 30,000 square feet in total, is dedicated to bioinformatics, including a large open space currently equipped with a few scattered desks and bundles of data cables, a training room for classes and courses, and several conference rooms.
While its facilities are being completed, the center is "actively recruiting" scientists to conduct in-house research, with a goal of hiring approximately five to 10 principal investigators – some of whom might bring a dozen postdocs with them – and up to 10 junior principal investigators, according to Fair. "We're being opportunistic, because it's not as if we've got a plan to hire three people this week and five people next week," he said. And while most of the current funding is dedicated to building out the facility, equipment, and staff salaries, "we're willing to reallocate dollars to get really good people here and to fund really interesting projects." By the end of 2014, the NYGC hopes to have grown to about 250 people, he added.
In the meantime, the center's pilot lab has been conducting sequencing projects, many in collaboration with its 12 institutional founding members and its two – soon to be three – associate members, with a focus on rare diseases, cancer, and population studies. While most of these projects have been small, many have "the ability to evolve into a much bigger story," Fair said.
Among the completed projects is one where the center sequenced the genomes of a parent-child trio, where the child was afflicted with a rare genetic disease, and was able to identify the causative mutation within seven days.
Genome center staff are intimately involved in these projects, providing sequencing data as well as an extensive initial consultation and analysis of data quality. "We don't see ourselves as a service provider, more of a collaborator," Shianna explained. For example, "oftentimes people say they want an exome at 50x coverage. It's so much more complicated than saying '50x coverage.' We make sure that they understand what's different between 50x coverage and an even distribution of reads."
Meanwhile, Darnell and the center's scientific and clinical steering committee, which has at least one representative from each institutional founding member and one from each associate member and was established last year, have been identifying projects that the center and its collaborators plan to take on (IS 3/12/2013).
Many of these projects will require funding, and "we're constantly in the process of writing grants," Fair said. Researchers from different institutions with similar interests often find each other through the steering committee, he said, allowing them to partner on grant applications. "And that's one of the things that is really powerful about this, because with the effects of sequestration and decreases in other funding sources, the competition for grant dollars is going to increase tremendously, and in order to best position the genome center and its member institutions, we think these collaborative approaches to grant writing are absolutely essential," he said.
In the end, the large number of medical institutions in New York, as well as its large patient population, is what will set this genome center apart from others, Fair said, helping it to fulfill its mission of providing translational research.
Click to Enlarge"We get that question asked quite a bit: Why would you set up a genome center in New York City? It's not inexpensive to start here − everything from construction costs to hiring costs to facility operation costs − it's a really high-cost place to do business," he said. "But if you think about the concentration of academic medical centers that are here, the access to talent that is here, [and] you look at the ethnic diversity of the New York City population, the sheer number of inpatient visits and outpatient procedures that are done here, you really have a rich environment from which to gather clinical information."