From your eyes only: Efficiency of nuclear and mitochondrial DNA isolation from contact lenses at crime scenes

Making the Most of Lateral Flow Immunochromatographic Tests: An Efficient Protocol to Recover DNA

Lateral flow immunochromatographic (LFI) tests are widely used in both biomedical and forensic sciences for different applications. In forensic sciences, their main use is to detect body fluids at crime scenes. However, there are situations in which the amount of potential biological evidence is so low that DNA extraction is favored with respect to the identification of body fluids. Here, an efficient and quick protocol is presented to integrate the detection of body fluids through LFI with DNA extraction from a sample swab and buffer, providing a complete characterization of the biological evidence. This protocol is a modification of a general DNA extraction silica-based kit, whose main application is for blood and tissues. Thus, it could be carried out in different settings (forensic labs, hospitals, other testing labs) without the necessity of buying a specific kit for swabs. The validation of this protocol is supported by the results presented here and previous publications from our group, obtaining DNA in good quantity and with good quality. This proves the potential application of the protocol in both forensic scenarios, to fully characterize biological evidence, and biomedical settings, to molecularly confirm the results of LFI tests.

Analysis of mutational genotyping using correctable decoding sequencing with superior specificity

The ability to accurately identify SNPs or low-abundance mutations is important for early clinical diagnosis of diseases, but the existing high-throughput sequencing platforms are limited in terms of their accuracy. Here, we propose a correctable decoding sequencing strategy that may be used for high-throughput sequencing platforms. This strategy is based on adding a mixture of two types of mononucleotides, natural nucleotide and cyclic reversible termination (CRT), for cyclic sequencing. Using the synthetic characteristic of CRTs, about 75% of the calls are unambiguous for a single sequencing run, and the remaining ambiguous sequence can be accurately deduced by two parallel sequencing runs. We demonstrate the feasibility of this strategy, and its cycle efficiency can reach approximately 99.3%. This strategy is proved to be effective for correcting errors and identifying whether the sequencing information is correct or not. And its conservative theoretical error rate was determined to be 0.0009%, which is lower than that of Sanger sequencing. In addition, we establish that the information of only a single sequencing run can be used to detect samples with known mutation sites. We apply this strategy to accurately identify a mutation site in mitochondrial DNA from human cells.

Forensic DNA profiling of tears stains from commonly encountered substrates

The detection and recovery of body fluid evidence to reconstruct the involvement of people in a crime is an essential step in forensic investigation. The presence of tears is extremely rare but widely misunderstood because of its nature of secretion and low volumes found. They may be secreted in cases of sexual crimes, kidnaping, and violence among many other emotionally disturbing scenarios. It is suggestive that tears are an excellent source of epithelial cells for DNA to establish identity. They are deposited on tissue paper or handkerchief and lesser common substrates include bedding, face mask, and balaclava. Trace or touch DNA can also be retrieved from used contact lenses. Since tears can be secreted due to an emotional response, they can attract forensic analysis for identification. DNA profiling from these substrates is promising in the absence of other commonly found body fluids such as blood or saliva. The current study was done to explore the use of fresh and aged tear samples for forensic DNA analysis from three different substrates i.e., tissue paper, cotton fabric, and contact lenses. STR profiles were successfully obtained from all sample types (n = 60) with 100% allele recovery. The analysis provided consistent evidence that DNA extracted using this methodology was helpful to get reliable DNA profiles for forensics comparable with that from blood or saliva for personal identification.

A digital coding combination analysis for mutational genotyping using pyrosequencing

In the present study, we developed a novel digital coding combination analysis (DCCA) to analyze the gene mutation based on the sample combination principle. The principle is that any numerically named sample is divided into two groups, any two samples are not grouped in the same two groups, and any sample can be tested within the detection limit. Therefore, we proposed a specific combination that N samples were divided into M groups. Then N samples were analyzed, which could obtain the mutation results of M mixed groups. If only two groups showed positive (mutant type) signals, the same sample number from two positive signal groups would be the positive sample, and the remaining samples were negative (wild type). If three groups or more exhibited positive results, the same sample number from three positive signal groups would be the positive sample. If some samples remained uncertain, individual samples could be analyzed on a small scale. In the present study, we used the two genotypes of a mutation site (A5301G) to verify whether it was a useful and promising method. The results showed that we could quantitatively detect mutations and demonstrate 100% consistent results against a panel of defined mixtures with the detection limit using pyrosequencing. This method was suitable, sensitive, and reproducible for screening and analyzing low-frequency mutation samples, which could reduce reagent consumption and cost by approximately 70-80% compared with conventional clinical methods.