Cancer Genomics

The Cancer Genomics Shared Resource (CGSR) provides comprehensive genomic services and many state-of-the-art technologies via the MCC Cytogenomics Shared Service and the University of Minnesota Genomics Center (UMGC).

Investigators are encouraged to utilize one or both of the resources, depending on goals of the project, whether the need is for classic cytogenetics or the newest molecular genetic sequencing assay. Contact either facility for guidance on technology selection.

Services

High quality G-band karyotype analyses of human, mouse, rat and swine cell lines, embryonic stem (ES) cells, induced Pluripotent Stem (iPS) cells, blood, bone marrow or fresh tissue.

Fluorescence-in-situ-hybridization (FISH) studies performed on cell lines, fresh or paraffin-embedded tissue samples, including:

  • Generation of site-specific probes from genome resources BAC/PAC clones or investigator-provided DNA sequences
  • Use of commercially-available probes
  • Focused gene mapping of human or mouse genes using sequential G-banding and FISH and/or FISH and Spectral Karyotyping (SKY).
  • Metaphase and interphase FISH analyses to investigate the presence of, or monitor, a specific chromosomal or gene rearrangement, or XX/XY chimeras.

Spectral Karyotyping (SKY) multi-color FISH analyses for human, mouse and rat cell lines and tissues to identify structural chromosome abnormalities, and clarify tumor heterogeneity on a cell by cell basis

Genomic Microarrays for detection of Copy Number Variants and Copy Neutral changes.

This technology permits evaluation of tissues not amenable to conventional cytogenetics (solid tumors and mature nondividing tissues)

Human, mouse and rat arrays are available for detection of genome-wide copy number changes (e.g., gene duplication and deletions):

  • 4x180K, 2x400K and other array platforms
  • CUSTOM array platforms can be designed at no additional cost
  • Hybrid CGH+SNP and SNP microarrays

Mulitplex Ligation-Dependent Probe Assay (MLPA) analyses performed on DNA samples for detection of abnormal copy numbers and single gene aberrations. PCR primer probe sets for genetic syndromes, cancers and tumors are commercially available. MLPA can also be performed with Investigator designed primers or primers designed in collaboration with the Biomedical Genomics Center or MRC Holland.

Images

g banding followed by fish
G-banding followed by FISH identifies the integration site of a transposon plasmid probe to mouse chromosome band 6B3-6C2
human bone marrow karyotype
Human bone marrow karyotype (Fanconi anemia): G-band karyotyping reveals a chromosome fragment resembling a portion of chromosome 3
spectral karyotyping m fish
Spectral Karyotyping (SKY) or M-FISH (Multicolor FISH) confirms the G-band chromosomal fragment to be extra copy of a portion of chromosome 3
microarray comparative genomic hybridization
Microarray comparative genomic hybridization (aCGH) identifies multiple gains (green) and losses (red) within this human DNA sample