CGI Celebrates Kidney Cancer Awareness Month with #KidneyLive Tweet Event

Published on: Thursday, June 26th, 2014 View all Articles

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In March, CGI marked Kidney Cancer Awareness Month with a live-tweet event #KidneyLive. We followed Lonnie around the lab as she performed a UroGenRA-Kidney test – CGI’s proprietary test that can diagnose and sub-type kidney tumors!

The sample we followed for #KidneyLive was “sample 921,” a kidney tumor sample sent to CGI for diagnosis and sub typing.

Kidney sample is placed in thermoblock

CGI’s kidney cancer test, which is called UroGenRA-Kidney, can determine whether a tumor is benign or malignant, and also what tumor subtype is. The sub-type of the tumor is helpful to doctors, as different subtypes may respond differently to treatments.

Approximately 65,000 new cases of kidney cancer are diagnosed in the US each year. Renal cell carcinoma (RCC) is the common and lethal form of kidney cancer, and there are three main subtypes of RCC: clear
cell (ccRCC), papillary (pRCC), and chromophobe (chrRCC). The next most frequent subtype is oncocytoma (OC), which is benign and can be followed by active surveillance. Choice of treatment depends upon the kidney cancer subtype as well as the patient’s age and health history.

The UroGenRA-Kidney test is a micro-array test. Here’s a diagram explaining how it works: Array CGH diagram

UroGenRA Kidney tumor samples can be acquired either through fine needle aspirate or surgically resected kidney specimen. While traditional methods of diagnosis rely on removing a section of the tumor in order to inspect it, because Cancer Genetics’ UroGenRA-Kidney test can be performed with the DNA from fine needle aspirate, some unnecessary surgeries may be avoided.

Sample 921, which we followed for the #KidneyLive event, came in paraffin. The paraffin must be removed by placing the sample in a thermoblock. This essentially melts the paraffin, allowing the tumor sample to be separated from the paraffin.

Here’s a picture of 921 going into the thermoblock:
sample is put into thermoblock
Next, Sample 921’s DNA must be extracted. The process used to extract the DNA is called tissue lysis, which breaks down the cell and allows for the genomic DNA to be purified.

Once the DNA has been extracted from the cells, the DNA must be cut into smaller pieces using enzymes. Some of the digested DNA is run in an electrophoresis gel to ensure that the process worked. Here, Lonnie is taking the gel to be photographed. The photo will tell her whether the enzymes did, in fact, cut the DNA.

gel is removed

The DNA in the gel is stained using ethydium bromide, a chemical that makes it visible under UV light. When Lonnie looks at the gel under UV, she’s able to see that it worked! Sample 921’s DNA was successfully digested by the enzymes, so now she can move on to labeling the DNA.

scientist checks gel electrophoresis

 

In the microarray, the sample DNA is labeled and compared to a labeled control. The DNA is labeled with a dye that will fluoresce and give it color. Sample 921 is labeled with blue dye. A control DNA is labeled with Pink dye.

DNA for microarray test are labeled with dye

(Fun Fact: In real life, the dyes are photosensitive – which means they would have been ruined by the flash! The dye used for the KidneyLive test of sample 921 are not the ones we photographed!)

After they’ve been dyed, the samples must be prepped for hybridization on the microarray. This requires mixing the labeled control DNA and the labeled sample 921 DNA together. Then the solution can be placed onto the microarray slide.

samples are placed in microarray slide

The microarray slide has thousands of tiny probes, and each probe has a specific DNA sequence to which complementary DNA will attach (hybridize). UroGenRA has 101 regions of the human genome represented!

After we’ve loaded the DNA, the microarrray slide is placed on top of the samples, and KidneyLive 921 is ready to hybridize to the microarray! The slide is placed into a rotating microarray hybridization machine, which works sort of like a rotisserie oven, rotating the slides and baking them for 24 hours.
microarray slide is prepared for hybridization

Getting ready for the microarray machine!

hybridization oven

The next day, after sample 921 had been rotating for 24 hours, it’s time to take the slide out.

Now that the samples have hybridized to the slide, the slides must be washed to remove excess DNA.

microarray slides are washed

Once washed, the microarray slide must be put into an Agilent scanner in order to be analyzed. Just like a photo scanner shows different colors in a picture, this scanner will detect color variations on the #KidneyLive microarray slide.

microarray slide is placed in Agilent scanner

Once the slide has been scanned, scientists look at the image and ensure that the hybridization was complete. Each dog shows a place where a sequence of DNA from our samples has hybridized to the slide.

microarray slide

We want to know how different sample 921 is from the control, which will tell us about genomic changes that have occurred in the DNA. The software used for the UroGenRA-Kidney test can determine the difference based on color differences. Based on these color differences, the software can determine how different the #KidneyLive sample is from the control.

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After our scientists review and analyze the results, they are reported to the doctor, who can then create a treatment plan with the patient.

In addition to determining whether a tumor sample is benign or malignant, UroGenRA-Kidney can subtype between the four main types of Kidney Cancer. Sample 925’s subtype is chrRCC, a type of Renal Cell Carcinoma.

If you’d like to learn more about Cancer Genetics Inc’s UroGenRA-Kidney test, you can visit our website at http://cancergenetics.com/products/urogenra/. You can see the original live tweet on our twitter feed: @Cancer_Genetics

A big shout out and thanks to Lonnie from our Research & Development team, who let us follow her around the Lab for #KidneyLive!

Lonnie Seo at the CGI lab