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Aug 1, 2011 (Vol. 31, No. 14) , Jul 1, 2011 (Vol. 31, No. 13)

aCGH Opens Up Novel Avenues of Study

Technique that Augments Karotyping Now Being Used in Prenatal Testing, Cancer, and Autism

  • Not Only for Somatic Cells

    Click Image To Enlarge +
    Comparison of the detection of chromosomal aberrations on a human iPSC line using karyotype analysis and the Ambry StemArray: (A) Standard G-banding metaphase karyotype analysis only identified trisomy 20. (B) The StemArray detected three deletions and six amplifications including the trisomy 20 (C) detected by karyotype. (D) An example of copy-number changes identified by the StemArray on chromosome 8 include a 500 Kb deletion containing 25 genes (green arrow) and a multiple copy amplification of the MYC gene introduced during iPSC transformation (red arrow). [Ambry Genetics]

    Ambry Genetics has extensive experience with aCGH, other array types, and next-generation sequencing. The company has performed commercial aCGH for several years, mostly for detecting deletions and amplifications implicated in common genetic diseases. About two years ago Ambry began running research tests for academic labs and pharmaceutical companies, mostly on cancer tissue samples.

    Around this time the company realized that aCGH analysis of stem cell lines could provide insights into how a cell line behaved, particularly when used therapeutically. “No arrays existed at the time that targeted regions in the genome implicated in stem cell differentiation and proliferation,” said Aaron Elliot, Ph.D., senior scientist at Ambry.

    Working with Roche NimbleGen, Dr. Elliot designed an aCGH microarray that covered the genomic backbone but also targeted specific regions of interest for stem cells at a resolution of 15 kilobases. “We can detect the deletion or duplication of a single exon,” Dr. Elliot explained.

    This level of sensitivity is critical, for example, in assuring that implanted stem cells are not lacking an obvious tumor suppressor gene or overexpressing a tumor promoter. “You would never be able to find defects that small through karyotyping.” The lower detection limits of karyotyping, said Dr. Elliot, is about five megabases.

    Ambry recently reached a collaborative agreement with Cell Line Genetics (CLG) that combines Ambry's experience in microarrays with CLG's knowledge of preclinical cell-line characterization. The goal is the introduction of additional microarray-based products for stem cell analysis.

    When working with stem cell lines it is not unusual for an embryonic or induced pluripotent stem cell to begin with a normal karyotype, then develop abnormalities over time. “Cytogenetics can pick up emerging cell populations much earlier than array CGH, albeit at much lower resolution,” says Julie Johnson, director of laboratory operations.

    Johnson notes that some authors mistakenly claim that aCGH replaces karyotyping. “Actually, the techniques go hand-in-hand. Cytogenetics is better for detecting low-level, emerging cell populations and balance translocations, while array CGH offers higherresolution detection of chromosomal abnormalities and greater sensitivity.”

    Developing a specialized array is an iterative process that takes about six months. Companies like Ambry typically draw up a list of sequences they believe are relevant, and submit them to an array fabricator such as Roche NimbleGen, Agilent Technologies, or Oxford Gene Technology.

    The deeper the coverage of genes of interest, the higher the resolution. Probes may be deleted in subsequent versions of the array if testing shows they do not perform as expected.

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