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Identification and clinical evaluation of segments of homozygosity, uniparental disomy and complex chromosomal abnormalities revealed by copy-number SNP arrays

  • Jia-Chi Wang1,
  • Leslie Ross1,
  • Loretta W Mahon1,
  • Renius Owen1,
  • Morteza Hemmat1,
  • Boris T Wang1,
  • Mohammed El Naggar1,
  • Kimberly A Kopita1,
  • Mary Haddadin1,
  • Fatih Z Boyar1,
  • Arturo Anguiano1,
  • Charles M Strom1 and
  • Trilochan Sahoo1Email author
Molecular Cytogenetics20147(Suppl 1):O4

Published: 21 January 2014


Chromosomal AbnormalityChromosomal SegmentImportant ClueTotal CoverageAutosomal Recessive Disorder


Presence of such segments of homozygosity (SOH) may be due to parental relatedness, chromosomal recombination or rearrangements and provides important clues regarding ancestral homozygosity, parental consanguinity or uniparental disomy. We have determined the frequency and nature of copy neutral segments with allelic homozygosity identified in cases interrogated by oligonucleotide-SNP microarrays.

Materials and methods

We collected cases from consecutive specimens sent to our clinical laboratory over the past two years. The cases were reported based on the presence of a contiguous SOH >10 Mb in a single region or >5 Mb in at least two regions. The percentage of the genome encompassed by SOH regions was calculated based on the total coverage of about 2,700 Mb.


Of 14,574 cases analyzed by SNP arrays, 872 (6%) cases harbored SOH, with 659 (76%) cases harboring multiple SOH and interpreted as arising due to identity by descent (IBD), 213 (24%) cases with SOH involving a single chromosomal segment and suspected or confirmed as resulting from UPD. For the cases with IBD, the coefficient of inbreeding was calculated: 5% cases due to first degree or closer parental relatedness, 9% second, 19% third, 16% fourth, and 51% fifth. Cases with UPD cases involved every single chromosome. In eight cases, identification of SOH was crucial to diagnosing autosomal recessive disorders.


This study demonstrates that the identification of SOH, in addition to CNVs, is much more frequent than previously recognized, reflecting close parental relatedness, and often ascertains autosomal recessive diseases or unravels UPD in many cases.

Authors’ Affiliations

Cytogenetics Laboratory, Quest Diagnostics Nichols Institute, San Juan Capistrano, USA


© Wang et al; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.