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Circulating Cancer Cell Analysis for Personalizing Therapy
Blood samples can now analyzed for circulating tumor cells (CTCs) by nucleic acid
methods to isolate tumor-associated or tumor-specifi c mRNA. Detection of
extremely low concentrations of rare CTCs in the blood is still a challenge. IsoFlux
System (Fluxion Biosciences) utilizes a unique microfl uidic design to provide auto-
mated cell introduction, trapping, sealing, whole-cell formation and recording pro-
tocols. IsoFlux System is being used to isolate, recover, and analyze rare CTCs to
provide a real-time “liquid biopsy” of samples for molecular analysis. The focus is
on breast and lung cancers with the goal of subtyping different forms of the disease
and developing treatments personalized to each individual patient.
Detection of Loss of Heterozygosity
Many cancers are characterized by chromosomal aberrations that may be predictive of
disease outcome. Human neuroblastomas are characterized by loss of heterozygosity
(LOH), the deletion of one copy of a pair of genes at multiple chromosomal loci.
When the gene involved is a tumor suppressor gene, LOH removes a brake on uncon-
trolled cell growth, the growth that is the hallmark of cancer. A customized gene chip
has been developed to assess region-specifi c LOH by genotyping multiple SNPs
simultaneously in DNA from tumor tissues (Maris et al. 2005 ). Unlike gene expres-
sion microarrays, which detect varying levels of RNA to measure the activity levels of
different genes as DNA transfers information to RNA, the current microarray directly
identifi es changes in DNA. Rather than covering the entire genome, the microarray
focuses on suspect regions of chromosomes for signs of deleted genetic material
known to play a role in the cancer. Detection of LOH in this assay may not require
comparison to matched normal DNAs because of the redundancy of informative SNPs
in each region. This customized tag-array system for LOH detection is rapid, results
in parallel assessment of multiple genomic alterations, and may speed identifi cation of
and/or assaying prognostically relevant DNA copy number alterations in many human
cancers. Identifying the correct risk level allows doctors to treat aggressive cancers
appropriately, while not subjecting children with low-risk cancer to overtreatment.
BEAMing Technology for Analysis of Circulating Tumor DNA
Inostics’ BEAMing (Beads, Emulsions, Amplifi cation, and Magnetics) – a digital
technology that combines emulsion based digital PCR with magnetic beads and
fl ow cytometry – enables quantifi cation of mutant DNA. It is a non-invasive, highly-
sensitive, real-time “liquid biopsy” for screening, prognosis, prediction, and moni-
toring of cancer. Key features are:
- Starting material: plasma, serum, or tissue (FFPE/frozen)
- Starting DNA amount: ≥1 genome equivalent (6.6 pg human genomic DNA)