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We have developed a new protocol for using molecular inversion probes to accurately and specifically measure allele copy number. The new protocol provides for significant improvements, including the reduction of input DNA (from 2 mug) by more than 25-fold (to 75 ng total genomic DNA), higher overall precision resulting in one order of magnitude lower false(More)
  • J Boger, R L Hahn, J K Rowley, A L Carter, B Hollebone, D Kessler +195 others
  • 2000
The Sudbury Neutrino Observatory is a second-generation water Cherenkov detector designed to determine whether the currently observed solar neutrino de"cit is a result of neutrino oscillations. The detector is unique in its use of D O as a detection medium, permitting it to make a solar model-independent test of the neutrino oscillation hypothesis by(More)
BACKGROUND A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE(More)
Detection of genomic copy number changes has been an important research area, especially in cancer. Several high-throughput technologies have been developed to detect these changes. Features that are important for the utility of technologies assessing copy number changes include the ability to interrogate regions of interest at the desired density as well(More)
High-throughput genotyping technologies that enable large association studies are already available. Tools for genotype determination starting from raw signal intensities need to be automated, robust, and flexible to provide optimal genotype determination given the specific requirements of a study. The key metrics describing the performance of a custom(More)
BACKGROUND Methylation of CpG islands within the DNA promoter regions is one mechanism that leads to aberrant gene expression in cancer. In particular, the abnormal methylation of CpG islands may silence associated genes. Therefore, using high-throughput microarrays to measure CpG island methylation will lead to better understanding of tumor pathobiology(More)
Quantification of minimal residual disease (MRD) following allogeneic hematopoietic cell transplantation (allo-HCT) predicts post-transplant relapse in patients with chronic lymphocytic leukemia (CLL). We utilized an MRD-quantification method that amplifies immunoglobulin heavy chain (IGH) loci using consensus V and J segment primers followed by(More)
In this study, we combined a novel sequencing method, which can identify individual clonotypes based on their unique T cell receptor (TCR) rearrangement, with existing immune assays to characterize antigen-specific T cell responses. We validated this approach using three types of assays routinely used to measure antigen-specific responses: pentamers which(More)
  • J Boger, R L Hahn, J K Rowley, A L Carter, B Hollebone, D Kessler +190 others
  • 1999
The Sudbury Neutrino Observatory is a second generation water Cerenkov detector designed to determine whether the currently observed solar neutrino deecit is a result of neutrino oscillations. The detector is unique in its use of D 2 O as a detection medium, permitting it to make a solar modellindependent test of the neutrino oscillation hypothesis by(More)
  • T C Andersen, R A Black, I Blevis, J Boger, E Bonvin, M Chen +37 others
  • 2002
As photodisintegration of deuterons mimics the disintegration of deuterons by neutrinos, the accurate measurement of the radioactivity from thorium and uranium decay chains in the heavy water in the Sudbury Neutrino Observatory (SNO) is essential for the determination of the total solar neutrino flux. A radium assay technique of the required sensitivity is(More)