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Golden Triangle, NC, United States

Papenhausen P.,Laboratory Corporation of Cytogenetics | Schwartz S.,Laboratory Corporation of Cytogenetics | Risheg H.,Laboratory Corporation of America Cytogenetics | Keitges E.,Laboratory Corporation of America Cytogenetics | And 6 more authors.
American Journal of Medical Genetics, Part A | Year: 2011

Single nucleotide polymorphism (SNP) based chromosome microarrays provide both a high-density whole genome analysis of copy number and genotype. In the past 21 months we have analyzed over 13,000 samples primarily referred for developmental delay using the Affymetrix SNP/CN 6.0 version array platform. In addition to copy number, we have focused on the relative distribution of allele homozygosity (HZ) throughout the genome to confirm a strong association of uniparental disomy (UPD) with regions of isoallelism found in most confirmed cases of UPD. We sought to determine whether a long contiguous stretch of HZ (LCSH) greater than a threshold value found only in a single chromosome would correlate with UPD of that chromosome. Nine confirmed UPD cases were retrospectively analyzed with the array in the study, each showing the anticipated LCSH with the smallest 13.5Mb in length. This length is well above the average longest run of HZ in a set of control patients and was then set as the prospective threshold for reporting possible UPD correlation. Ninety-two cases qualified at that threshold, 46 of those had molecular UPD testing and 29 were positive. Including retrospective cases, 16 showed complete HZ across the chromosome, consistent with total isoUPD. The average size LCSH in the 19 cases that were not completely HZ was 46.3Mb with a range of 13.5-127.8Mb. Three patients showed only segmental UPD. Both the size and location of the LCSH are relevant to correlation with UPD. Further studies will continue to delineate an optimal threshold for LCSH/UPD correlation. © 2011 Wiley-Liss, Inc.

Choi S.M.,University of Pennsylvania | Choi S.M.,Childrens Hospital of Philadelphia | Papenhausen P.,Laboratory Corporation of Cytogenetics | Wertheim G.,University of Pennsylvania | And 3 more authors.
Journal of Hematopathology | Year: 2014

Molecular genetic analysis is indispensible in both classification and prognostication of hematopoietic malignancies. The evolution of genetic analysis from conventional cytogenetics to novel genomic technologies has increased our ability to detect subtle and nonconventional mutations in leukemia and lymphoma. Near haploidy, a subtype of hypodiploidy, is a rare entity that carries a particularly poor prognosis in B lymphoblastic leukemia (B-ALL). Near-haploid B-ALL usually quickly evolves by doubling of the chromosome number, creating confusion with the prognostically favorable hyperdiploid B-ALL subtype. Here, we describe a case of B-ALL in which single-nucleotide polymorphism (SNP) microarray analysis was used to identify a hyperdiploid clone that had evolved from a presumptive, near-haploid clone. By conventional methods, this clone may have been easily misinterpreted as a common hyperdiploid clone. Given the extreme prognostic differences of the two clones, this distinction is especially critical to accurately guide therapy. In this case report and brief review, we discuss the role of SNP microarray analysis in the diagnosis and proper subclassification of B-ALL as well as its potential in the identification of genetic therapeutic targets. © 2013 Springer-Verlag Berlin Heidelberg.

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