Welcome, Guest

Joshua Schiffman, MD

Joshua Schiffman, MD

The University of Utah's Joshua Schiffman, MD, discusses the use of molecular inversion probe (MIP) technology for studying copy number alterations in pediatric cancers

Scientists at the University of Utah, led by Dr. Joshua Schiffman, are using MIP technology to identify unique genetic aberrations that can distinguish between different types of pediatric cancers. Their work has uncovered patterns of copy number aberrations and regions of allelic imbalance that could be used to guide risk stratification and future treatment.

Some of our experiments have samples that are up to 15 years old, and we're still able to get very clean copy number data from very little DNA, as little as 75 ng.

In 2009, Dr. Schiffman collaborated with Affymetrix using a 24K MIP panel and GeneChip® 30K Universal Tag Arrays to analyze 45 pediatric leukemia samples in order to detect unique copy number aberrations. Their study identified 69 regions of copy number changes, including unique patterns of copy number loss in samples with a deletion of the CDKN2A gene. These patterns differentiated between two similar subtypes of acute lymphoblastic leukemia (ALL), precursor B-cell ALL and precursor T-cell ALL. Recently, Schiffman and colleagues used Affymetrix MIP Copy Number Services to perform a genome-wide analysisof copy number alterations in different malignancy grades of pediatric astrocytomas. The study identified several genomic amplifications that characterized the different tumor grades. Specifically, the study revealed distinct BRAF gene rearrangements that occurred in grade 1 versus grade 2 to 4 tumors and indicated BRAF mutation as a frequent mutation target in pediatric astrocytomas. They also found that BRAF mutations were significantly associated with homozygous CDKN2A deletions, suggesting the possibility of a new subset of pediatric astrocytomas.

"With the MIP assay, we can easily correlate patient outcome with higher copy numbers," said Schiffman. "Once we collect enough samples and enough outcome data, we"ll better understand the relationship between high copy number value and clinical outcome in many different types of cancer." Schiffman recently spoke with Jessica Parra, Associate Marketing Manager at Affymetrix, about his use of the MIP copy number platform to study different forms of pediatric cancers. The two discussed:

  • The advantages of being able to analyze formalin-fixed, paraffin-embedded (FFPE) samples
  • The MIP copy number platform design and the linear dynamic range of the assay
  • The clinical importance of being able to identify copy number changes that can characterize different forms of pediatric cancers
Read the full article. Download the pdf version to enjoy the article in it's entirety and also keep it for future reference. Avaliable in PDF (2.8 MB)

More Scientist Spotlights

  • Mady Hornig, MD Mady Hornig, MA, MD, Director of Translational Medicine at Columbia University, discusses the use multiplexed immunoassays for studying chronic fatigue syndrome, known as myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS).
  • Jizeng Jia, PhD Jizeng Jia, PhD, from the Institute of Crop Sciences, Chinese Academy of Agriculture Science, Beijing, discusses the limitations of current technologies and how they were overcome to develop the highest density wheat array commercially available.
  • Gordon Mills, MD Gordon Mills, MD, PhD, of the University of Texas MD Anderson Cancer Center and "Dream Team" co-leader in Stand Up To Cancer®, discusses the importance of genomic profiling in the discovery of novel predictive markers to improve the effectiveness of cancer treatment.
  • Mark I. McCarthy, MD Professor Mark McCarthy, from the University of Oxford, UK, outlines how the intersection of biobank capabilities, new study designs, and technological advances will improve our understanding of complex trait genetics.
  • Bruno Stuhlmüller, PhD Bruno Stuhlmüller, PhD, head of the scientific laboratory and team leader at the Institute of the Rheumatology and Clinical Immunology department at the Charité Free University and Humboldt University, Berlin, discusses working with whole blood samples to identify mRNA and miRNA biomarkers for predictive rheumatoid arthritis treatments.
  • Peter Ambros, PhD Peter Ambros, PhD, Associate Professor at the Children's Cancer Research Institute (CCRI) in Vienna, Austria discusses the way in which arrays are helping to unravel the complexities of the cancer genome and guiding patient-tailored treatment strategies.
  • Austin Tanney, PhD Austin Tanney, PhD, Scientific Liaison Manager for Almac Diagnostics, UK, discusses the opportunities and challenges of working with FFPE tissue, and his visions for technologies driving towards personalized medicine.
  • Jay Tiesman, PhD Procter & Gamble Company's Jay Tiesman, PhD, discusses the role of genomics in the cosmetics industry.
  • Joshua Schiffman, MD The University of Utah's Joshua Schiffman, MD, discusses the use of molecular inversion probe (MIP) technology for studying copy number alterations in pediatric cancers.
  • Lisa Baumbach, MD The University of Miami's Lisa Baumbach and Maastricht University's Torik Ayoubi discuss how ethnicity-specific genetic changes govern aggressive breast cancer risks.
  • Chris Smith, PhD Chris Smith of Cambridge University, Tyson Clark of Affymetrix and Melissa Cline of UCSC discuss EURASNET's approach for comparing commercial microarrays.
  • Robert Norgren, PhD Rob Norgren of The University of Nebraska Medical Center and Katja Nowick of Lawrence Livermore National Laboratory discuss the development of the Rhesus Macaque Genome Array.
  • Yong-Jie Lu, PhD Yong-Jie Lu of Queen Mary, University of London and Colleen Elso of the Walter and Eliza Hall Institute discuss a method for rapidly identifying chromosome rearrangements.

Scientist Spotlights

Publications

Archived Webinars

Warning! The earliest signals for cancer – miRNA regulation

Joshua Schiffman, MD | Researchers | Community