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Roche NimbleGen, Neuromuscular Disorder Group to Merge CGH, Sequencing Data in Study

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Roche NimbleGen announced last month that the Neuromuscular Disorder-Chip Consortium, a European Union's Seventh Framework Programme for Research and Technical Development, will use its microarrays for genetic research on neuromuscular disorders.

Roche said that the NMD-Chip researchers will use custom-designed NimbleGen Human CGH 12x135K microarrays to look for NMD-related gene- and exon-level rearrangements, deletions, or insertions — particularly for NMDs such as Duchenne/Becker muscular dystrophies, limb girdle muscular dystrophies, congenital muscular dystrophies, hereditary motor-sensory neuropathies, and Charcot-Marie-Tooth neuropathies.

The consortium also plans to use customized NimbleGen Human Sequence Capture 385K arrays for capturing DNA fragments representing all known genes in groups of NMDs. These fragments can then be coupled with high-throughput sequencing to assess genetic variation in NMDs.

According to Roche, the NMD-Chip project is one of several projects underway that use the firm's CGH and sequence capture arrays together, though none of these projects have published on their findings or methodology to date. A company spokesperson described the sequence capture and CGH arrays as "complementary technologies," and noted that the two approaches in concert "allow you to analyze the full spectrum of variation – from single base-pair changes to larger structural variation."

Patrice Bourgeois, a professor at the Département de Génétique Médicale in the Hôpital d'Enfants la Timone of Marseille, France, who is involved in the NMD-Chip project, told BioArray News this week that NMD-Chip plans to run around 800 DNA samples on two sets of custom CGH arrays, one batch representing "published and identified genes involved in NMDs to date," the other batch including "candidate loci" thought to play a role in NMDs. Separately, NMD-Chip will use the sequence capture arrays to capture targets of interest that will then be screened using Roche 454 Life Sciences' sequencing platform for point mutations.

Bourgeois said that Roche NimbleGen's ability to offer both CGH and sequence capture at the time the project grant was being developed in 2007 convinced the NMD-Chip researchers to work with the Madison, Wis.-based Roche business. Specifically, Bourgeois said NimbleGen offered the "largest density of probes, as high as 2.1 million per array"; a "maximum flexibility of array design"; and a "more complete multiplexing" solution."

Roche 454's sequencing technology, meantime, offers the "longest pyrosequencing mean fragment length," on the market, he said.

Beyond the initial 800 samples, Bourgeois said the chips will be distributed to NMD researchers, so that it is "difficult to answer" how many samples will eventually be run on the arrays. "The tools developed within this project are planned to be commercialized among interested genetic testing laboratories," Bourgeois said. "It is difficult to evaluate the impact of that tech-transfer, compared to the old but currently used 'gene-by-gene approach'," he said. The availability of the new arrays could "concern potentially all the genetic tests in the neuromuscular disease field," he added.

NMD-Chip is a three-year, €2.91 million ($3.72 million) project funded through the European Union's Seventh Framework Programme for Research and Technical Development. It includes researchers from 13 European institutions in eight countries, including: the French National Institute for Health and Medical Research (INSERM); Association Institut de Myologie and Genethon in France; Julius-Maximilians University in Würzburg, Germany; University College London; the University of Newcastle upon Tyne in the UK; the University of Ferrara in Italy; Karolinska Institute in Sweden; Technical University of Dresden, Germany; Association Genethon in France; Leiden University Medical Center in the Netherlands; and the National Institute of Environmental Health in Hungary. Additionally, two private companies, France's Partnerchip and Belgium's Phenosystems, are taking part in NMD-Chip.

Ultimately, the consortium aims to use the technology to identify new genes or mutations involved in these inherited NMD, and increase the molecular diagnosis per patient ratio. The group eventually hopes to develop a "novel sensitive and reliable diagnostic tool, with time and cost effectiveness dedicated to neuromuscular disorders," according to NMD-Chip. Bourgeois said that the project is currently split into several groups with different specializations. One group has explicitly been charged with designing software to integrate the data generated by the array and sequencing platforms.

Roche's Role

According to Roche NimbleGen spokesperson Kary Staples, the company will not only provide products and support to NMD-Chip, but will be "working in collaboration with the researchers and the group in terms of design, bioinformatics, annotations, technical follow-up, and any early access to new products for the project."

Staples said that Roche NimbleGen already has a relationship established with NMD-Chip coordinator Nicolas Levy of the Université de la Méditerranée in Marseille, as well as NMD-Chip participant Jamel Chelly of INSERM. He noted that Chelly recently co-authored a paper that described work using Roche NimbleGen CGH arrays.

[Saillour Y, et al. Detection of exonic copy-number changes using a highly efficient oligonucleotide-based comparative genomic hybridization-array method. Human Mutation. 2008 Sep;29(9):1083-90

Staples said that the NMD-Chip project will be running samples within its own laboratories, rather than ordering the analyses via Roche NimbleGen's services lab in Iceland. He said the firm has seen an increase in customers who prefer to use its platform rather than outsource their work.

According to Staples, NimbleGen also plans to enter the instrument market this year. For customers who prefer to use its technology in house, NimbleGen this year debuted its MS 200 Microarray Scanner, which includes an autoloader, an integrated barcode reader, ozone control, and on-demand calibration combined with adjustable 2- or 5-micron pixel resolution. A higher resolution scanner is planned for launch later this year (see BAN 1/6/2009).

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