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UPD detection using homozygosity profiling with a SNP genotyping microarray.
MedLine Citation:
PMID:  21594998     Owner:  NLM     Status:  In-Data-Review    
Abstract/OtherAbstract:
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 13.5 Mb 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 46.3 Mb with a range of 13.5-127.8 Mb. 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.
Authors:
Peter Papenhausen; Stuart Schwartz; Hiba Risheg; Elisabeth Keitges; Inder Gadi; Rachel D Burnside; Vikram Jaswaney; John Pappas; Romela Pasion; Kenneth Friedman; James Tepperberg
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Publication Detail:
Type:  Journal Article     Date:  2011-03-15
Journal Detail:
Title:  American journal of medical genetics. Part A     Volume:  155     ISSN:  1552-4833     ISO Abbreviation:  Am. J. Med. Genet. A     Publication Date:  2011 Apr 
Date Detail:
Created Date:  2011-05-19     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101235741     Medline TA:  Am J Med Genet A     Country:  United States    
Other Details:
Languages:  eng     Pagination:  757-68     Citation Subset:  IM    
Copyright Information:
Copyright © 2011 Wiley-Liss, Inc.
Affiliation:
Laboratory Corporation of Cytogenetics Triangle Park, North Carolina. papenhp@labcorp.com.
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