Corporate Banner
Satellite Banner
Scientific Community
Become a Member | Sign in
Home>News>This Article

Using Qlucore Omics Explorer for Interpreting Leukemia Proteomics Data

Published: Monday, November 18, 2013
Last Updated: Monday, November 18, 2013
Bookmark and Share
Qlucore software has speeded up the process and enabled discovery for leukemia researcher Steven Kornblau.

There are many things that can be limiting factors in the research process. In the case of medical professor Steven Kornblau, the time pressures of the biological infomaticians he works with have been significant limitations.

Kornblau, a Professor of Medicine in the Department of Leukemia & Department of Stem Cell Transplantation and Cellular Therapy at UT MD Anderson Cancer Center in Houston, Texas, US, uses proteomics - the large-scale study of proteins - in the fight against leukemia. The approach that he and his colleagues take is to look simultaneously at hundreds of proteins to define patterns of protein activation in acute myeloid leukemia (AML) and identify proteins whose function are key to the survival of leukemic cells.

His laboratory developed the techniques required to use a reverse phase protein array (RPPA), which measures the relative expression levels of a protein in many samples simultaneously, for the study of leukemia and he is recognized as the leader in this field. Another key feature of Kornblau's work is the vast repository of leukemia patient samples that he has collected and can use for studies.

Kornblau and his colleagues - which includes five people in the lab, two coordinators that collect samples from the patients, and a database manager - make DNA, RNA, protein, serum and cryopreserve viable cells. He explained that ‘these materials can be used for a huge list of experiments by the researchers that we send samples to.'

Gaining insight from these many experiments is a complex task. The repository includes samples from over 2000 AML patients and the RPPA that Kornblau's team has built uses samples from 511 AML cases. This approach enables many studies to go on simultaneously, speeding up research and enabling patterns to be uncovered. However, the volumes of data are huge, particularly considering that there are around 80 different fields of clinical information for each patient, which all need to be treated differently depending whether they are simple details like the patient's name or more complicated features such as the patient's response to a particular drug or combination chemotherapy regimen. These samples are then screened against hundreds of antibodies.

The volumes and complexities of the data prevent patterns being spotted without in-depth statistical analysis that is outside the normal range of expertise of biologists, even biologists like Kornblau who also has an economics degree.

As a result, data is taken to statistician colleagues for analysis, a process that can take time as these colleagues' expertise is very much in demand. ‘I was always having to rely on statisticians. They did a great job but it involved a lot of going back and forth,' explained Kornblau.

All this changed in June 2013 when Kornblau purchased Qlucore Omics Explorer. ‘Qlucore allows me to do analysis on my own,' he said. ‘I can now check things that I know are biologically relevant on the fly.' This, he said, has ‘speeded up the process and facilitated discovery. It has definitely been a big enabler.'

The software allows Kornblau to explore his data statistically and, for example, change outlier parameters. It also enables him to generate heat maps that quickly show relevant patterns. "We can look at proteins, see why some are particularly important compared with other functionally-related proteins and look for correlations between protein clusters from one functional group. We can see how proteins are interacting with antibodies and can classify them into groups. Formerly my statistician would do all this," he observed. "The more I use the software the more I keep discovering new things."

He said that the most common functions that he uses in Qlucore Omics Explorer are the heatmap generator and the ability to do principal component analysis (PCA). He also uses the 3D functions within the PCA.

The change has been dramatic. "I've been working with protein arrays for seven years and always had to get bioinfomaticians to do the analysis. They are very much in demand so they are a rate-limiting step." In fact, he said that it usually took a couple of months to get results. "Now it is pretty easy to put my data in and I can get results within an hour - and I play with my dataset more now that I can do it myself."

Kornblau is one of the first researcher to apply the Qlucore software to proteomics.. However, he believes that it is well suited to his area of research and to other areas too.

He has found the software quite straightforward to use, with advice from Qlucore. "Like all complicated software it has a learning curve. However, once I'd learnt how the program set up its dataset there was almost nothing that I needed to do. I just had to rearrange my dataset a bit, for example to ensure that my 230 antibodies are at the end. I don't think it's any more difficult to learn than something like Excel," he explained, although he added that it does help to have some statistical background in order to get the most out of it.

And when he has found things that could be improved he has fed these ideas back to Qlucore, which is working on improvements to the software based on user feedback.

When Kornblau purchased the Qlucore solution it was following a free trial period. "I played with it pretty heavily and it was clear to me that it would be worth the money," he recounted. What's more, he has recommended it to colleagues in the proteomics space and some of them have also now purchased the tool.

Further Information
Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 2,800+ scientific posters on ePosters
  • More than 4,000+ scientific videos on LabTube
  • 35 community eNewsletters

Sign In

Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Related Content

Researchers Develop Animal Free Methods for Testing Chemical Compounds for Allergens
EU-funded research project developing in vitro (‘out of body’) test strategies to reduce or replace animal testing use gene expression analysis software.
Monday, April 08, 2013
New Biomarkers Could Offer Vital Clues for Cancer Research
European funding for cancer research has led to some interesting results in recent years, says Carl-Johan Ivarsson, CEO at Qlucore.
Friday, May 04, 2012
Scientific News
New Class of RNA Tumor Suppressors Identified
Two short, “housekeeping” RNA molecules block cancer growth by binding to an important cancer-associated protein called KRAS. More than a quarter of all human cancers are missing these RNAs.
Mathematical Model Forecasts the Path of Breast Cancer
Chances of survival depend on which organs breast cancer tumors colonize first.
Exploring the Causes of Cancer
Queen's research to understand the regulation of a cell surface protein involved in cancer.
Nanocarriers May Carry New Hope for Brain Cancer Therapy
Berkeley lab researchers develop nanoparticles that can carry therapeutics across the brain blood barrier.
RNA-Based Drugs Give More Control Over Gene Editing
CRISPR/Cas9 gene editing technique can be transiently activated and inactivated using RNA-based drugs, giving researchers more precise control in correcting and inactivating genes.
University of Glasgow Researchers Make An Impact in 60 Seconds
Early-career researchers were invited to submit an engaging, dynamic and compelling 60 second video illuminating an aspect of their research.
Metabolic Profiles Distinguish Early Stage Ovarian Cancer with Unprecedented Accuracy
Studying blood serum compounds of different molecular weights has led scientists to a set of biomarkers that may enable development of a highly accurate screening test for early-stage ovarian cancer.
Dead Bacteria to Kill Colorectal Cancer
Scientists from Nanyang Technological University (NTU Singapore) have successfully used dead bacteria to kill colorectal cancer cells.
CRISPR-Cas9 Gene Editing: Check Three Times, Cut Once
Two new studies from UC Berkeley should give scientists who use CRISPR-Cas9 for genome engineering greater confidence that they won’t inadvertently edit the wrong DNA.
Genetically Engineering Algae to Kill Cancer Cells
New interdisciplinary research has revealed the frontline role tiny algae could play in the battle against cancer, through the innovative use of nanotechnology.

Skyscraper Banner
Go to LabTube
Go to eposters
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
2,800+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
4,000+ scientific videos