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Trends in Molecular Medicine May 2021Liquid biopsies, in particular, analysis of cell-free DNA (cfDNA), have emerged as a promising noninvasive diagnostic approach in oncology. Abnormal distribution of DNA... (Review)
Review
Liquid biopsies, in particular, analysis of cell-free DNA (cfDNA), have emerged as a promising noninvasive diagnostic approach in oncology. Abnormal distribution of DNA methylation is one of the hallmarks of many cancers and methylation changes occur early during carcinogenesis. Systemic analysis of cfDNA methylation profiles is being developed for cancer early detection, monitoring for minimal residual disease (MRD), predicting treatment response and prognosis, and tracing the tissue origin. This review highlights the advantages and disadvantages of ctDNA profiling for noninvasive diagnosis of early-stage cancers and explores recent advances in the clinical application of ctDNA methylation assays. We also summarize the technologies for ctDNA methylation analysis and provide a brief overview of the bioinformatic approaches for analyzing DNA methylation sequencing data.
Topics: Biomarkers, Tumor; Cell-Free Nucleic Acids; Circulating Tumor DNA; Computational Biology; DNA Fingerprinting; DNA Methylation; Early Detection of Cancer; Humans; Liquid Biopsy; Neoplasms; Prognosis
PubMed: 33500194
DOI: 10.1016/j.molmed.2020.12.011 -
Forensic Science International. Genetics Jul 2019DNA mixture interpretation can produce opposing conclusions by qualified forensic analysts, even within the same laboratory. The long-delayed publication of the National...
DNA mixture interpretation can produce opposing conclusions by qualified forensic analysts, even within the same laboratory. The long-delayed publication of the National Institutes of Standards and Technology (NIST) study of 109 North American crime laboratories in this journal demonstrates this most clearly. This latest study supports earlier work that shows common methods such as the Combined Probability of Inclusion (CPI) have wrongly included innocent people as contributors to DNA mixtures. The 2016 President's Council of Advisors on Science and Technology report concluded, "In summary, the interpretation of complex DNA mixtures with the CPI statistic has been an inadequately specified-and thus inappropriately subjective-method. As such, the method is clearly not foundationally valid" [7]. The adoption of probabilistic genotyping by many laboratories will certainly prevent some of these errors from occurring in the future, but the same laboratories that produced past errors can also now review old cases with their new software-without additional bench work. It is critical that laboratories adopt procedures and policies to do this.
Topics: DNA; DNA Fingerprinting; Forensic Genetics; Genotype; Government Agencies; Humans; Laboratories; Microsatellite Repeats; Probability; United States
PubMed: 30947116
DOI: 10.1016/j.fsigen.2019.03.005 -
Forensic Science International Aug 2019In forensic genetics, the analysis of DNA in biological samples is a valuable tool for personal identification. There is an increasing demand in analyzing of the mixed... (Review)
Review
In forensic genetics, the analysis of DNA in biological samples is a valuable tool for personal identification. There is an increasing demand in analyzing of the mixed DNA which may provide insightful investigative instructions. With the continuous effort for the improvement of individual identification, complicated mixed stains represent a growing fraction of the samples processed by forensic laboratories. Recent technological advances have enabled quantitative analysis of DNA mixture and emerging sequencing approaches to decipher the complicated DNA mixture. Here, we describe the use of different genetic markers, typing approaches and analytical methods in mixture analysis, and how useful information can be obtained from complicated DNA mixture.
Topics: DNA; DNA Fingerprinting; Forensic Genetics; Genetic Markers; Haplotypes; Humans; Likelihood Functions; Microsatellite Repeats; Polymorphism, Single Nucleotide; Sequence Analysis, DNA
PubMed: 31153987
DOI: 10.1016/j.forsciint.2019.05.024 -
Forensic Science International Jan 2021Since the discovery of Deoxyribonucleic acid (DNA) capability in forensic investigation, it has been an important part of the criminal justice system. In most criminal... (Review)
Review
Since the discovery of Deoxyribonucleic acid (DNA) capability in forensic investigation, it has been an important part of the criminal justice system. In most criminal cases DNA profile originating from evidence sample collected from the crime scene is compared with the DNA profile from the reference sample. However, when a reference sample is not available for comparison, familial DNA analysis can provide important investigation leads in a criminal investigation process by identifying an individual. Moreover, this analysis is also proving effective in the identification of ethnicity and ancestry of an individual. A number of different methodologies and software are being used for familial DNA analysis. This review describes the importance of familial DNA analysis, methodologies used for familial DNA searching and identification, and its advantages in forensic. Moreover, ethical, legal and social issues associated with familial DNA analysis have also been discussed along with future directions for the proper implementation of this technology.
Topics: Chromosomes, Human, Y; DNA Fingerprinting; DNA, Mitochondrial; Databases, Genetic; Forensic Genetics; Genetic Privacy; Genotype; Humans; Microsatellite Repeats; Pedigree; Polymorphism, Single Nucleotide; Racial Groups
PubMed: 33234348
DOI: 10.1016/j.forsciint.2020.110576 -
Forensic Science International. Genetics Jul 2019The deconvolution of DNA mixtures has gathered the attention of forensic DNA scientists for over two decades. To enhance mixture deconvolution capabilities, a new... (Review)
Review
The deconvolution of DNA mixtures has gathered the attention of forensic DNA scientists for over two decades. To enhance mixture deconvolution capabilities, a new generation of sensitive DNA-typing approaches has been recently proposed. In this review, we describe novel, forensically relevant multi-SNP loci (i.e., microhaplotypes or microhaps), compound markers (i.e., DIP-STRs, SNP-STRs and DIP-SNPs) and lineage markers (i.e., rapidly mutating Y chromosome STRs) that improve the deconvolution of two and more than two-person mixtures typed using conventional STR, binary and non-binary loci. We explore the features and applications of these emerging molecular biomarkers with respect to their ability to forensically detect same-or-opposite sex donors. Finally, we discuss the impact of initial massively parallel sequencing (MPS) investigations of STR, microhaplotype and SNP/indel assays for DNA mixture profiling.
Topics: Chromosomes, Human, Y; DNA; DNA Fingerprinting; Electrophoresis, Capillary; Genetic Markers; Haplotypes; High-Throughput Nucleotide Sequencing; Humans; INDEL Mutation; Microsatellite Repeats; Polymerase Chain Reaction; Polymorphism, Single Nucleotide; Sequence Analysis, DNA
PubMed: 31071519
DOI: 10.1016/j.fsigen.2019.04.003 -
Fa Yi Xue Za Zhi Oct 2021
Topics: Chromosomes, Human, Y; DNA Fingerprinting; Humans; Male
PubMed: 35191255
DOI: 10.12116/j.issn.1004-5619.2020.500705 -
Genes Nov 2021Understanding the factors that may impact the transfer, persistence, prevalence and recovery of DNA (DNA-TPPR), and the availability of data to assign probabilities to... (Review)
Review
Understanding the factors that may impact the transfer, persistence, prevalence and recovery of DNA (DNA-TPPR), and the availability of data to assign probabilities to DNA quantities and profile types being obtained given particular scenarios and circumstances, is paramount when performing, and giving guidance on, evaluations of DNA findings given activity level propositions (activity level evaluations). In late 2018 and early 2019, three major reviews were published on aspects of DNA-TPPR, with each advocating the need for further research and other actions to support the conduct of DNA-related activity level evaluations. Here, we look at how challenges are being met, primarily by providing a synopsis of DNA-TPPR-related articles published since the conduct of these reviews and briefly exploring some of the actions taken by industry stakeholders towards addressing identified gaps. Much has been carried out in recent years, and efforts continue, to meet the challenges to continually improve the capacity of forensic experts to provide the guidance sought by the judiciary with respect to the transfer of DNA.
Topics: DNA; DNA Fingerprinting; Forensic Genetics; Humans; Specimen Handling
PubMed: 34828372
DOI: 10.3390/genes12111766 -
Annual Review of Genomics and Human... Aug 2020In the past few years, cases with DNA evidence that could not be solved with direct matches in DNA databases have benefited from comparing single-nucleotide polymorphism... (Review)
Review
In the past few years, cases with DNA evidence that could not be solved with direct matches in DNA databases have benefited from comparing single-nucleotide polymorphism data with private and public genomic databases. Using a combination of genome comparisons and traditional genealogical research, investigators can triangulate distant relatives to the contributor of DNA data from a crime scene, ultimately identifying perpetrators of violent crimes. This approach has also been successful in identifying unknown deceased persons and perpetrators of lesser crimes. Such advances are bringing into focus ethical questions on how much access to DNA databases should be granted to law enforcement and how best to empower public genome contributors with control over their data. The necessary policies will take time to develop but can be informed by reflection on the familial searching policies developed for searches of the federal DNA database and considerations of the anonymity and privacy interests of civilians.
Topics: Crime; DNA; DNA Fingerprinting; Databases, Nucleic Acid; Forensic Genetics; Humans; Pedigree
PubMed: 32289230
DOI: 10.1146/annurev-genom-111819-084213 -
International Journal of Molecular... Dec 2022Collection and interpretation of "touch DNA" from crime scenes represent crucial steps during criminal investigations, with clear consequences in courtrooms. Although... (Review)
Review
Collection and interpretation of "touch DNA" from crime scenes represent crucial steps during criminal investigations, with clear consequences in courtrooms. Although the main aspects of this type of evidence have been extensively studied, some controversial issues remain. For instance, there is no conclusive evidence indicating which sampling method results in the highest rate of biological material recovery. Thus, this study aimed to describe the actual considerations on touch DNA and to compare three different sampling procedures, which were "single-swab", "double-swab", and "other methods" (i.e., cutting out, adhesive tape, FTA paper scraping), based on the experimental results published in the recent literature. The data analysis performed shows the higher efficiency of the single-swab method in DNA recovery in a wide variety of experimental settings. On the contrary, the double-swab technique and other methods do not seem to improve recovery rates. Despite the apparent discrepancy with previous research, these results underline certain limitations inherent to the sampling procedures investigated. The application of this information to forensic investigations and laboratories could improve operative standard procedures and enhance this almost fundamental investigative tool's probative value.
Topics: Touch; DNA Fingerprinting; DNA; Specimen Handling
PubMed: 36555182
DOI: 10.3390/ijms232415541 -
Methods in Molecular Biology (Clifton,... 2021AFLP or amplified fragment length polymorphism is a PCR-based molecular technique that uses selective amplification of a subset of digested DNA fragments from any source... (Review)
Review
AFLP or amplified fragment length polymorphism is a PCR-based molecular technique that uses selective amplification of a subset of digested DNA fragments from any source to generate and compare unique fingerprints of genomes. It is more efficient in terms of time, economy, reproducibility, informativeness, resolution, and sensitivity, compared to other popular DNA markers. Besides, it requires very small quantities of DNA and no prior genome information. This technique is widely used in plants for taxonomy, genetic diversity, phylogenetic analysis, construction of high-resolution genetic maps, and positional cloning of genes, to determine relatedness among cultivars and varietal identity, etc. The review encompasses in detail the various applications of AFLP in plants and the major advantages and disadvantages. The review also considers various modifications of this technique and novel developments in detection of polymorphism. A wet-lab protocol is also provided.
Topics: Amplified Fragment Length Polymorphism Analysis; DNA Barcoding, Taxonomic; DNA Fingerprinting; Epigenomics; Gene Expression Profiling; Gene Expression Regulation, Plant; Genetic Variation; Plants; Transcriptome
PubMed: 33301096
DOI: 10.1007/978-1-0716-0997-2_12