Characterization of Copy Number Variation in Genomic Regions Containing STR Loci Using Array Comparative Genomic Hybridization

• NCJ Number: 246417
• Journal: Forensic Science International: Genetics Volume: 7 Issue: 5 Dated: September 2013 Pages: 475-481
• Author(s): Elena A. Repnikova; Jill A. Rosenfeld; Andrea Bailes; Cecilia Weber; Linda Erdman; Aimee McKinney; Sarah Ramsey; Sayaka Hashimoto; Devon L. Thrush; Caroline Astbury; Shalini C. Reshmi; Lisa G. Shaffer; Julie M. Gastier-Foster; Robert E. Pyatt
• Date Published: September 2013
• Length: 7 pages
• Publication Format: Article
• Language: English
• Country: United States of America

Annotation

In this study, the researchers analyzed results from 32,850 samples sent for clinical array comparative genomic hybridization CGH analysis for the presence of CNV at regions containing the 13 CODIS Combined DNA Index System STR, and the Amelogenin X AMELX and Amelogenin Y AMELY loci.

Abstract

Short tandem repeat STR loci are commonly used in forensic casework, familial analysis for human identification, and for monitoring hematopoietic cell engraftment after bone marrow transplant. Unexpected genetic variation leading to sequence and length differences in STR loci can complicate STR typing, and presents challenges in casework interpretation. Copy number variation CNV is a relatively recently identified form of genetic variation consisting of genomic regions present at variable copy numbers within an individual compared to a reference genome. Large scale population studies have demonstrated that likely all individuals carry multiple regions with CNV of 1 kb in size or greater in their genome. To date, no study correlating genomic regions containing STR loci with CNV has been conducted. In this study, the researchers analyzed results from 32,850 samples sent for clinical array comparative genomic hybridization CGH analysis for the presence of CNV at regions containing the 13 CODIS Combined DNA Index System STR, and the Amelogenin X AMELX and Amelogenin Y AMELY loci. Thirty-two individuals with CNV involving STR loci on chromosomes 2, 4, 7, 11, 12, 13, 16, and 21, and twelve with CNV involving the AMELX/AMELY loci were identified. These results were correlated with data from publicly available databases housing information on CNV identified in normal populations and additional clinical cases. These collective results demonstrate the presence of CNV in regions containing 9 of the 13 CODIS STR and AMELX/Y loci. Further characterization of STR profiles within regions of CNV, additional cataloging of these variants in multiple populations, and contributing such examples to the public domain will provide valuable information for reliable use of these loci. (Published Abstract)