Title

A Low-Cost, High-Throughput, Automated Single Nucleotide Polymorphism Assay for Forensic Human DNA Applications

Authors

Robert S. Pomeroy, University of California - San Diego
George Duncan, Broward County Sheriff's OfficeFollow
Bulbin Sunar-Reeder, Reeder Analytical Consulting
Elen Ortenberg, BioTrove
Melba Ketchum, DNA Diagnostics
Hannah Wasiluk, DNA Diagnostics
Dennis Reeder, Reeder Analytical Consulting

Document Type

Article

Publication Date

12-1-2009

Publication Title

Analytical Biochemistry

Keywords

Microarray analysis, SNP assay, Human identification, Forensic

ISSN

0003-2697

Volume

395

Issue/No.

1

First Page

61

Last Page

67

Abstract

Single nucleotide polymorphism (SNP) analysis of human DNA for the purpose of identification has some promising attributes. The question of approach is critical to the eventual adoption of this technology. The use of a low-volume open array platform was tested with a small selected set of eight SNP primers that have a low F_ST (the proportion of the total genetic variance contained in a subpopulation [S subscript] relative to the total genetic variance [T subscript]) in human populations. Because multiple SNPs must be interrogated, issues concerning DNA concentration, total DNA, and whole genome amplification were investigated. Excellent correlations were obtained for seven of the eight SNP assays on a set of DNA samples of known configuration over a broad concentration range spanning 25–150 ng/μl in blind studies. These seven SNP assays were then applied to 39 DNA samples in a population from southern India. These SNPs were sufficient to individualize each member of this sample population. In a paternity study, these same SNPs showed clear parental relationships. For low amounts of genomic DNA, the use of a commercially available whole genome amplification kit showed promise for genotyping sub-nanogram samples. Discrimination against nonhuman DNA was also demonstrated successfully. Because of the very low quantities of reagents used in the assay, the cost per test becomes reasonably inexpensive. Overall, using commercially available SNP assays, the OpenArray platform showed excellent promise as a highly automated, low-volume, high-throughput system for SNP analysis with potential applications to relevant forensic analyses such as identification and paternity.

Comments

©2009 Elsevier Inc. All rights reserved.

NSUWorks Citation

Pomeroy, Robert S.; George Duncan; Bulbin Sunar-Reeder; Elen Ortenberg; Melba Ketchum; Hannah Wasiluk; and Dennis Reeder. 2009. "A Low-Cost, High-Throughput, Automated Single Nucleotide Polymorphism Assay for Forensic Human DNA Applications." Analytical Biochemistry 395, (1): 61-67. doi:10.1016/j.ab.2009.07.041.

ORCID ID

0000-0002-4931-5316

DOI

10.1016/j.ab.2009.07.041