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Dec 1, 2010 (Vol. 30, No. 21)

Analyzing the Genome One Cell at a Time

Gene Expression and DNA Sequence Analysis at the Single-Cell Level Reveal Heterogeneity

  • Single-Cell Sequencing

    John Langmore, Ph.D., vp of commercial development at Rubicon Genomics, focused his presentation on methods designed to streamline the preparation of DNA derived from single cells for NGS for copy-number variation, mutation, and DNA-methylation analysis.

    The analytical robustness, reproducibility, and accuracy of current genomic analysis techniques including qPCR, microarrays, and NGS are sufficient for many cancer-research applications and could serve as the basis for diagnostic and prognostic tests performed at the single-cell level, according to Dr. Langmore.

    Rubicon introduced its single-cell PicoPlex™ whole-genome amplification kits for genetic analysis using PCR and microarrays in June 2009. In November of this year, Rubicon initiated beta testing of its new PicoPlex-NGS WGA kit optimized for next-generation sequencing, and in January the company plans to release PicoPlex-NGS whole methylome amplification (WMA) kits for methylation analysis using NGS.

    Earlier this year, the European Society for Human Reproduction and Embryology presented the results of a clinical study showing that a method utilizing Rubicon’s PicoPlex WGA kits and BlueGnome’s 24sure™ microarrays for diagnosing genetic abnormalities in human eggs in advance of IVF, called preimplantation genetic screening (PGS), could detect chromosomal abnormalities accurately 89% of the time.

    WGA was used to amplify the DNA present in polar bodies, which are small particles formed as a by-product of egg development. Analysis of the amplified DNA is used to infer whether the DNA remaining in the egg is euploid or aneuploid (having normal or abnormal chromosome number and structure, respectively).

    Rubicon designed its WGA kits to meet the needs of multiple markets, including determining which embryo(s) to implant during IVF using PGS to identify chromosomal abnormalities and preimplantation genetic diagnostics (PGD) to determine the presence/absence of a hereditary abnormality known to be carried by one or both parents, as well as the cancer and stem cell research markets. 

    The PGS and PGD fields stand to benefit from a large-scale prospective clinical trial planned in Europe that is designed to determine whether the application of a method for selecting healthy embryos before implantation will result in an increased number of live births. These findings could have economic implications as well, with the potential for implanting fewer embryos and reducing the rate of multiple births. At present, according to Dr. Langmore, only about 2% of the 1 million or so cases of IVF performed worldwide each year undergo PGS and PGD.

    In the prenatal testing arena, robust single-cell analytical techniques could lead to diagnostic applications using fetal cells isolated from the maternal bloodstream or short free fetal DNA fragments present in the maternal circulation or urine.

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