Rapid DNA analysis for automated processing and interpretation of low DNA content samples.

Rosemary S Turingan,Richard F Selden,Catherine Hogan,Luke Palombo,Hua Jiang,Sameer Vasantgadkar,Eugene Tan

doi:10.1186/s13323-016-0033-7

Abstract

BackgroundShort tandem repeat (STR) analysis of casework samples with low DNA content include those resulting from the transfer of epithelial cells from the skin to an object (e.g., cells on a water bottle, or brim of a cap), blood spatter stains, and small bone and tissue fragments. Low DNA content (LDC) samples are important in a wide range of settings, including disaster response teams to assist in victim identification and family reunification, military operations to identify friend or foe, criminal forensics to identify suspects and exonerate the innocent, and medical examiner and coroner offices to identify missing persons. Processing LDC samples requires experienced laboratory personnel, isolated workstations, and sophisticated equipment, requires transport time, and involves complex procedures. We present a rapid DNA analysis system designed specifically to generate STR profiles from LDC samples in field-forward settings by non-technical operators. By performing STR in the field, close to the site of collection, rapid DNA analysis has the potential to increase throughput and to provide actionable information in real time.ResultsA Low DNA Content BioChipSet (LDC BCS) was developed and manufactured by injection molding. It was designed to function in the fully integrated Accelerated Nuclear DNA Equipment (ANDE) instrument previously designed for analysis of buccal swab and other high DNA content samples (Investigative Genet. 4(1):1–15, 2013). The LDC BCS performs efficient DNA purification followed by microfluidic ultrafiltration of the purified DNA, maximizing the quantity of DNA available for subsequent amplification and electrophoretic separation and detection of amplified fragments. The system demonstrates accuracy, precision, resolution, signal strength, and peak height ratios appropriate for casework analysis.ConclusionsThe LDC rapid DNA analysis system is effective for the generation of STR profiles from a wide range of sample types. The technology broadens the range of sample types that can be processed and minimizes the time between sample collection, sample processing and analysis, and generation of actionable intelligence. The fully integrated Expert System is capable of interpreting a wide range or sample types and input DNA quantities, allowing samples to be processed and interpreted without a technical operator.

Highlights

Short tandem repeat (STR) analysis of casework samples with low DNA content include those resulting from the transfer of epithelial cells from the skin to an object, blood spatter stains, and small bone and tissue fragments
Sample concentration by integrated microfluidic ultrafiltration The High DNA Content (HDC) biochipset was initially designed for the purification and analysis of DNA prepared from buccal swabs
At 50, 5, and 1 ng of input DNA, 82, 84, and, 99 % of the DNA was recovered, respectively, indicating that the module functions appropriately across the range of DNA expected to be found in low DNA content samples

Summary

Introduction

Short tandem repeat (STR) analysis of casework samples with low DNA content include those resulting from the transfer of epithelial cells from the skin to an object (e.g., cells on a water bottle, or brim of a cap), blood spatter stains, and small bone and tissue fragments. Improvements in primers used in the core STR systems and novel multiplex polymerase chain reaction (PCR) assays [22, 23], increasing the number of PCR cycles [24, 25], and post-PCR concentration and clean-up steps [26,27,28,29] have assisted typing of LDC samples. Despite all these significant advances, processing LDC samples in the conventional laboratory is still laborious and time-consuming

Methods

Results

Conclusion