High resolution genomic analysis of 18q- using oligo-microarray comparative genomic hybridization (aCGH)

Patricia L. Heard, Erika M. Carter, Analisa C. Crandall, Courtney Sebold, Daniel E. Hale, Jannine D. Cody

Research output: Contribution to journalArticle

39 Scopus citations

Abstract

The advent of oligonucleotide array comparative genomic hybridization (aCGH) has revolutionized diagnosis of chromosome abnormalities in the genetics clinic. This new technology also has valuable potential as a research tool to investigate larger genomic rearrangements that are typically diagnosed via routine karyotype. aCGH was used as a tool for the high-resolution analysis of chromosome content in individuals with known deletions of chromosome 18. The aim of this study was to clarify the precise location of the breakpoints as well as to determine the presence of occult translocations creating additional deletions and duplications. One hundred eighty-nine DNA samples from individuals with 18q deletions were analyzed. No breakpoint clusters were identified, as no more than two individuals had breakpoints within 2 kb of each other. Only two regions of 18q were never found to be haploid, suggesting the existence of haplolethal genes in those regions. Of the individuals with only a chromosome 18 abnormality, 17% (n = 29) had interstitial deletions. Six percent (n = 11) had a region of duplication immediately proximal to the deletion. Eight percent (n = 15) had more complex rearrangements with captured (non-18q) telomeres thus creating a trisomic region. The 15 captured telomeres originated from a limited number of other telomeres (4q, 10q, 17p, 18p, 20q, and Xq). These data were converted into a format for ease of viewing and analysis by creating customtracks for the UCSC Genome Browser. Taken together, these findings confirm a higher level of variability and genomic complexity surrounding deletions of 18q than has previously been appreciated.

Original languageEnglish (US)
Pages (from-to)1431-1437
Number of pages7
JournalAmerican Journal of Medical Genetics, Part A
Volume149
Issue number7
DOIs
StatePublished - Jul 2009

Keywords

  • 18q-
  • Chromosome 18
  • Chromosome abnormality
  • Chromosome deletion
  • aCGH

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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