Efficient DNA extraction from hair shafts

Genetic Evidence of Authenticity of a Hair Shaft Relic from the Portrait of Tsesarevich Alexei, Son of the Last Russian Emperor

To determine the value of an art piece, authenticity of the artwork must be verified. We demonstrate here a genetic approach to determine origin of a historic relic in the museum piece. We tested two hair shafts of unknown origin framed into a watercolor portrait of Tsesarevich Alexei Romanov, son of the last Russian Tzar Nicholas II, which is a unique item kept in the State Historical Museum. Genetic identification of the hair shafts was performed by analysis of mitochondrial DNA (mtDNA) markers using both massive parallel genomic sequencing and multiplex targeted PCR, followed by Sanger sequencing. In previous works, we reconstructed the complete mtDNA sequence inherited to Alexei Romanov through the Queen Victoria lineage [Rogaev et al. (2009) Proc. Natl. Acad. Sci. USA, 106, 5258-5263]. DNA extracts were obtained from the two thin hair shafts and used for comparative genetic analysis. Despite the very low quantity and quality of the DNA templates retrieved from the historical single hair shaft specimen, informative mtDNA sequences were determined. The mtDNA haplotype in the hair shafts corresponds to the mtDNA haplotype of Tsarevich Alexei, his sisters, and his mother, Empress Alexandra Feodorovna. This haplotype remains unique in the currently available mtDNA databases. Our results reveal that the hair relic from the portrait is associated with the family of the last Russian Emperor Nicholas II. The study is an example of first application of the genetic methodology for verification of the value of museum artwork items.

Human Mitochondrial Control Region and mtGenome: Design and Forensic Validation of NGS Multiplexes, Sequencing and Analytical Software

Forensic mitochondrial DNA (mtDNA) analysis conducted using next-generation sequencing (NGS), also known as massively parallel sequencing (MPS), as compared to Sanger-type sequencing brings modern advantages, such as deep coverage per base (herein referred to as read depth per base pair (bp)), simultaneous sequencing of multiple samples (libraries) and increased operational efficiencies. This report describes the design and developmental validation, according to forensic quality assurance standards, of end-to-end workflows for two multiplexes, comprised of ForenSeq mtDNA control region and mtDNA whole-genome kits the MiSeq FGx^TM instrument and ForenSeq universal analysis software (UAS) 2.0/2.1. Polymerase chain reaction (PCR) enrichment and a tiled amplicon approach target small, overlapping amplicons (60–150 bp and 60–209 bp for the control region and mtGenome, respectively). The system provides convenient access to data files that can be used outside of the UAS if desired. Studies assessed a range of environmental and situational variables, including but not limited to buccal samples, rootless hairs, dental and skeletal remains, concordance of control region typing between the two multiplexes and as compared to orthogonal data, assorted sensitivity studies, two-person DNA mixtures and PCR-based performance testing. Limitations of the system and implementation considerations are discussed. Data indicated that the two mtDNA multiplexes, MiSeq FGx and ForenSeq software, meet or exceed forensic DNA quality assurance (QA) guidelines with robust, reproducible performance on samples of various quantities and qualities.

A novel approach for visualization and localization of small amounts of DNA on swabs to improve DNA collection and recovery process

In this report, a simple and practical procedure is proposed for DNA localization on a solid matrix e.g., a collection swab. The approach is straightforward and employs spectrum decomposition using a model DNA intercalator Ethidium Bromide (EtBr). The proposed approach can detect picograms of DNA in solution and nanograms of DNA on solid surfaces (swabs) without the need for PCR amplification. The proposed technology offers the possibility for developing an inexpensive, sensitive, rapid, and practical method for localizing and recovering DNA deposited on collection swabs during routine DNA screening. Improved detection of low DNA concentrations is needed and, if feasible, will allow for better decision making in clinical medicine, biological and environmental research, and human identification in forensic investigations.

Fragmented Nuclear DNA is the Predominant Genetic Material in Human Hair Shafts

While shed hairs are one of the most commonly encountered evidence types, they are among the most limited in terms of DNA quantity and quality. As a result, nuclear DNA short tandem repeat (STR) profiling is generally unsuccessful and DNA testing of shed hair is instead performed by targeting the mitochondrial DNA control region. Although the high copy number of mitochondrial DNA relative to nuclear DNA routinely permits the recovery of mitochondrial DNA (mtDNA) data in these cases, mtDNA profiles do not offer the discriminatory power of nuclear DNA profiles. In order to better understand the total content and degradation state of DNA in single shed hairs and assess the feasibility of recovering highly discriminatory nuclear DNA data from this common evidence type, high throughput shotgun sequencing was performed on both recently collected and aged (approximately 50-year-old) hair samples. The data reflect trends that have been demonstrated previously with other technologies, namely that mtDNA quantity and quality decrease along the length of the hair shaft. In addition, the shotgun data reveal that nuclear DNA is present in shed hair and surprisingly abundant relative to mitochondrial DNA, even in the most distal fragments. Nuclear DNA comprised, at minimum, 88% of the total human reads in any given sample, and generally more than 95%. Here, we characterize both the nuclear and mitochondrial DNA content of shed hairs and discuss the implications of these data for forensic investigations.

Isolation and prominent aboriginal maternal legacy in the present-day population of La Gomera (Canary Islands)

The present-day population structure of La Gomera is outstanding in its high aboriginal heritage, the greatest in the Canary Islands. This was earlier confirmed by both mitochondrial DNA and autosomal analyses, although genetic drift due to the fifteenth century European colonization could not be excluded as the main factor responsible. The present mtDNA study of aboriginal remains and extant samples from the six municipal districts of the island indeed demonstrates that the pre-Hispanic colonization of La Gomera by North African people involved a strong founder event, shown by the high frequency of the indigenous Canarian U6b1a lineage in the aboriginal samples (65%). This value is even greater than that observed in the extant population (44%), which in turn is the highest of all the seven Canary Islands. In contrast to previous results obtained for the aboriginal populations of Tenerife and La Palma, haplogroups related to secondary waves of migration were not detected in La Gomera aborigines, indicating that isolation also had an important role in shaping the current population. The rugged relief of La Gomera divided into several distinct valleys probably promoted subsequent aboriginal intra-insular differentiation that has continued after the European colonization, as seen in the present-day population structure observed on the island.

Successful direct amplification of nuclear markers from a single hair follicle

We report on successful amplification of DNA profiles from a single hair. Direct amplification was used on the root tip of both anagen and telogen hairs using a kit to amplify 15 STR loci. All 30 anagen hairs tested from five different people gave full DNA profiles after 29 cycles with no allelic drop-in or heterozygous imbalance. Six of the 30 telogen hairs tested resulted in a full DNA profile, and a further four telogen hair samples tested produced a DNA profile of five or more complete loci that could be up-loaded to the National DNA Database (Australia). A full DNA profile was also obtained from the shaft of an anagen hair. Current practice for many laboratories is that a single hair may not be subjected to DNA testing as there is little chance of success, hence this 100 % success rate from anagen hairs is a significant advancement. A full DNA profile was obtained from a 5 year-old single hair illustrating the success when using direct PCR rather than attempting an extraction prior to the amplification step. The process described deliberately uses current DNA profiling methods with no increase in cycle number, such that the methodology can be incorporated readily into operational practice. For the first time in the field of human identification, single hairs can be analyzed with confidence that a meaningful DNA profile will be generated and the data accepted by the criminal justice system.