DOI: 10.3886/icpsr38608.v1
title: DNA Contamination, Degradation, Damage and Associated Microbiomes: A Comparative Analysis Through Massive Parallel Sequencing and Capillary Electrophoresis, United States, 2019-2021
title: Version 1

description: This project evaluated whether DNA contamination can mimic the characteristics of low copy number (LCN), aged, damaged, and degraded DNA samples. Massive Parallel Sequencing/Next Generation Sequencing (MPS/NGS) was used to see if specific patterns of nucleotide damage is present with surface DNA contamination that has been aged and/or exposed to varying concentrations of sodium hypochlorite (bleach) and ultraviolet (UV). The project included two phases.
Phase 1.0: Understand the process and rate of degradation and damage of applied touch DNA contamination on human skeletal remains and evidence tape. Five time intervals (ranging from 0 days to 1 year), three bleach treatments, and three UV treatments were tested. Two additional handlers (cumulative) created a scenario of minor contributors often encountered in forensic scenarios.
Phase 2.0: Understand the utility and degradation of the skin microbiome associated with touch DNA. This included determining if unique forensic signatures can be identified and compared, especially on bone substrates that may have their own microbiome signature.
description: This study required three individuals (two male and one female) to handle human rib fragments and leave touch DNA/contamination on the surface along with additionally providing touch DNA on evidence tape, and buccal swab samples for positive controls.
<strong>Phase 1.0:</strong> Using Massive Parallel Sequencing/Next Generation Sequencing (MPS/NGS), the research team analyzed human touch DNA from multiple donors that had been placed on two human ribs. This deposited "contamination", as well as endogenous DNA from the human remains, was analyzed over the course of a year to measure the effect of time on DNA degradation. The effect of various decontamination treatments (sodium hypochlorite and ultraviolet (UV) treatments) on DNA aged at different time intervals was also tested. For additional information, and a baseline comparison, human touch DNA from multiple donors was also extracted and analyzed from fingerprint tape and aged over the course of 1 year without treatment. The research team further evaluated whether these "degraded and damaged contamination" molecules have a performance bias or display different forms of damage/dropout/degradation between MPS/NGS (shotgun sequencing), capillary electrophoresis (CE) protocols, and newer sequencing technology.
<strong>Phase 2.0:</strong> With the experiments and samples processed in Phase 1.0, a MPS/NGS shotgun dataset was produced to allow the research team to study not only the preservation of the human DNA present but also associated skin and bone microbiomes. Positive controls from swabs of all donors' skin and a sub-set of the deposits on the bone sections were immediately extracted to create a microbiome baseline. Phase 2.0, post-MPS sequencing pipelines were optimized for analyzing microbial content and operational taxonomic units.
description: Datasets: 
DS1: DNA Contamination, Degradation, Damage and Associated Microbiomes: A Comparative Analysis Through Massive Parallel Sequencing and Capillary Electrophoresis, United States, 2019-2021
description: DNA retrieved from touched objects.
description: These data are a Fast Track Release and are distributed as they were received from the data producer. All data files have been zipped for release, but not checked or processed. Users should refer to the accompanying ICPSR README file for a brief description of the data available with this collection and consult with the investigator(s) if further information is needed.Please see the final report for additional study information.