Array Riddles
Starts with "O" and is great at analyzing FFPE samples.
Who is OncoScan
A genetic abberation where one or more normal copies of a gene are irreversibly lost. Estimated to occur in at least 20% of cancer cells.
What is Loss of Heterozygosity
This technology uses an instrument the size of a sub-zero refrigerator. Requires between 50ng-500ng of DNA depending on read depth. Famous for producing a record output of data per flow cell in a minimum amount of time. Name technology & instrument.
My samples are precious. I am worried that your technology will not work on my FFPE cancer samples.
Has the customer heard about: OncoScan and MIP probes?
My volume has picked up and I would like to bring my CMA in house and buy an instrument.
Can I suggest: Datasheet: COL27965 0823, Brochure COL121348 0823
I consist of 216,000 SNP probes across the genome.
Who is OncoScan
A catastrophic chromosomal
rearrangement event that arises from breakage of
chromosomes at multiple sites and subsequent random
rejoining and repair. Associated with hihgly aggressive cancer.
What is Chromothripsis
This array which targets over 935,000 CPG sites. Requires 250ng of DNA per array. Can run FFPE tissue and uses iSCAN and the NextSeq500. One of its many use cases is in Brain Cancer.
What is Epic 850K Methyl Array
I am interested in SNPs and CNVs on FF and blood samples. Array data is just too limited vs. NGS.
Has the customer heard about CytoScan and Whole Genome Coverage?
I am really interested in the OncoScan CNV assay. I hear that the array has MIP probes. Is there a whitepaper that describes this?
Can I suggest: OncoScan CNV and CNV Plus White Paper.COL33128 0619. See Page 3.
With roughly 743,000 SNP probes across the genome I can analyze LOH and AOH with great finesse.
Who is CytoScan
Abberation where a chromosome copy (or part of a chromosome) is inherited from a single parent. No copies are received from the second parent.
What is Uniparental disomy (UPD)
This array is composed of 60mer oligos printed on a glass slide and requires 500ng of DNA. Contains 170,334 being biological features. 355 cancer genes covered with 1 probe and 280 cancer genes covered with 3 or more probes.
What is the SurePrint G3 Human 4x180K (Agilent)
The variant types are too limited on arrays. I would rather use NGS. I really need coverage near breakpoints.
Has the customer heard about Probe spacing for CytoScan and OncoScan - better resolution than most clinical pass NGS runs?
I am interested in CytoScan HD Accel.
Can I suggest: The HD accell Hip Hip Array Coverage Flyer: EXT5447 0823. See Page 3.
Unlike FISH, I cannot detect balanced rearrangements. However, I can detect cnLOH and call many thousands of SNP variants.
Who is CytoScan
This abberation is a chromosome segment that has broken off and reattached itself to the same chromosome, but in reverse orientation.
Inversion
This inexpensive array has targeted coverage of 4,800 genes in the genome, requires 200ng of DNA. Measures CNVs, LOH & Chromosomal abnormalities.
GDA Cyto Array (Illumina)
I am studying hemtological cancers, I am running an NGS targeted panel. I don't want to run an array as well.
Has the customer heard that CytoScan can complement that targeted panel with whole genome characterization of CNVs, LOH, cnLOH. In fact, arrays are on NCCN guidelines.
I heard that there was a webinar describing OncoScan and HRD. Do you know how to find it?
Can I suggest: The LabRoots webinar on HRD recorded in Oct 2023. It is on the LabRoots Web Page.
I am not a coin, but I can be a circle. My structure includes two universal primers, a DNA cleavage site, a unique DNA tag sequence, and a region that shares similarity with your genomic target sequence.
Who are MIP Probes in Oncoscan
A frequent cytogenetic alternation in brain tumors. Abberation is a chromosome fragments that lack centromeres and is circular. These fragment have combined via non-homologous end joining and microhomology - mediated break repair.
Double Minute Chromosomes (dMins)
This array family contains 60mer probes printed on glass slides. It combines long oligo probes along side SNP probes. The cancer designs are consortium designs(eg CMCC, Wellcome Trust). Wellcome Trust used it's design to study haploinisufficiency in human disease.
What are the CytoSure arrays from OGT.
I am using Oncomine HRR panel to study HRD.
Are you sure you are capturing all the cytogenetic information you need? OncoScan as the gold standard for capturing genomewide LOH?
MYSTERY
Can you suggest your favorite piece of collateral? If so You get double points!