scholarly journals Probabilistic Genotyping of Single Cell Replicates from Complex DNA Mixtures Recovers Higher Contributor LRs than Standard Analysis

2021 ◽  
Author(s):  
Kaitlin Huffman ◽  
Erin Hanson ◽  
Jack Ballantyne
Keyword(s):  
Single Cell ◽  
Dna Typing ◽  
Complex Mixtures ◽  
Common Source ◽  
Single Source ◽  
Mixture Analysis ◽  
Likelihood Ratios ◽  
Dna Mixtures ◽  
Genotype Information ◽  
Dna Profiles

DNA mixtures are a common source of crime scene evidence and are often one of the more difficult sources of biological evidence to interpret. With the implementation of probabilistic genotyping (PG), mixture analysis has been revolutionized allowing previously unresolvable mixed profiles to be analyzed and probative genotype information from contributors to be recovered. However, due to allele overlap, artifacts, or low-level minor contributors, genotype information loss inevitably occurs. In order to reduce the potential loss of significant DNA information from donors in complex mixtures, an alternative approach is to physically separate individual cells from mixtures prior to performing DNA typing thus obtaining single source profiles from contributors. In the present work, a simplified micro-manipulation technique combined with enhanced single-cell DNA typing was used to collect one or few cells, referred to as direct single-cell subsampling (DSCS). Using this approach, single and 2-cell subsamples were collected from 2-6 person mixtures. Single-cell subsamples resulted in single source DNA profiles while the 2-cell subsamples returned either single source DNA profiles or new mini-mixtures that are less complex than the original mixture due to the presence of fewer contributors. PG (STRmixTM) was implemented, after appropriate validation, to analyze the original bulk mixtures, single source cell subsamples, and the 2-cell mini mixture subsamples from the original 2-6-person mixtures. PG further allowed replicate analysis to be employed which, in many instances, resulted in a significant gain of genotype information such that the returned donor likelihood ratios (LRs) were comparable to that seen in their single source reference profiles (i.e., the reciprocal of their random match probabilities). In every mixture, the DSCS approach gave improved results for each donor compared to standard bulk mixture analysis. With the 5- and 6- person complex mixtures, DSCS recovered highly probative LRs (> 1020) from donors that had returned non-probative LRs (<103) by standard methods.

scholarly journals Proposed Framework for Comparison of Continuous Probabilistic Genotyping Systems amongst Different Laboratories

2021 ◽  
Vol 1 (1) ◽  
pp. 33-45
Author(s):  
Dennis McNevin ◽  
Kirsty Wright ◽  
Mark Barash ◽  
Sara Gomes ◽  
Allan Jamieson ◽  
...  
Keyword(s):  
Numerical Methods ◽  
Analytical Solutions ◽  
Peak Height ◽  
Dna Profiling ◽  
Likelihood Ratios ◽  
Dna Mixtures ◽  
Individual Laboratory ◽  
Multiple Variables

Continuous probabilistic genotyping (PG) systems are becoming the default method for calculating likelihood ratios (LRs) for competing propositions about DNA mixtures. Calculation of the LR relies on numerical methods and simultaneous probabilistic simulations of multiple variables rather than on analytical solutions alone. Some also require modelling of individual laboratory processes that give rise to electropherogram artefacts and peak height variance. For these reasons, it has been argued that any LR produced by continuous PG is unique and cannot be compared with another. We challenge this assumption and demonstrate that there are a set of conditions defining specific DNA mixtures which can produce an aspirational LR and thereby provide a measure of reproducibility for DNA profiling systems incorporating PG. Such DNA mixtures could serve as the basis for inter-laboratory comparisons, even when different STR amplification kits are employed. We propose a procedure for an inter-laboratory comparison consistent with these conditions.

The Growing Role of Genetic Professionals in Forensic DNA

2009 ◽  
Vol 6 (5) ◽  
Author(s):  
Cristina Pinto
Keyword(s):  
Forensic Medicine ◽  
Tandem Repeats ◽  
Nuclear Dna ◽  
Recombinant Dna ◽  
Dna Typing ◽  
Individual Identification ◽  
Bar Code ◽  
Genomic Polymorphism ◽  
Recombinant Dna Techniques ◽  
Dna Profiles

AbstractThrough the last decade there was an enormous revolution in the field of forensic genetic.The Author reviews some of the methodologies used in the definitions of DNA profiling tackling the principles of recombinant DNA techniques. The potentiality of polymorphic DNA fragments in vertebrates is focused as well as the revolution implied in forensic medicine. The resource to DNA-DNA hybridization combined to oligonucleotide probes is emphasized leading to the production of an individual bar code with the resource of genomic polymorphism which leads to a pattern known as genetic fingerprinting. Other techniques for individual identification and paternity testing are focused as well as the use of short tandem repeats (STR's). Mitochondrial DNA sequencing use to complement nuclear DNA typing may also be profitable in certain instances. Relevant problems within the context of the use of these techniques in forensic medicine and law suits are discussed. Final considerations viewing the resource to DNA technology within the scope of the last two decades are referred regarding the resource to DNA profiles not only in the US but in Europe in general and in Portugal in special having lead to compensation and uncover of justice errors.

scholarly journals Demuxalot: scaled up genetic demultiplexing for single-cell sequencing

2021 ◽  
Author(s):  
Alex Rogozhnikov ◽  
Pavan Ramkumar ◽  
Saul Kato ◽  
Sean Escola
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Single Cell Sequencing ◽  
Additional Information ◽  
Genotype Information ◽  
Single Cell Rna Sequencing ◽  
Genotype Inference

Demultiplexing methods have facilitated the widespread use of single-cell RNA sequencing (scRNAseq) experiments by lowering costs and reducing technical variations. Here, we present demuxalot: a method for probabilistic genotype inference from aligned reads, with no assumptions about allele ratios and efficient incorporation of prior genotype information from historical experiments in a multi-batch setting. Our method efficiently incorporates additional information across reads originating from the same transcript, enabling up to 3x more calls per read relative to naive approaches. We also propose a novel and highly performant tradeoff between methods that rely on reference genotypes and methods that learn variants from the data, by selecting a small number of highly informative variants that maximize the marginal information with respect to reference single nucleotide variants (SNVs). Our resulting improved SNV-based demultiplex method is up to 3x faster, 3x more data efficient, and achieves significantly more accurate doublet discrimination than previously published methods. This approach renders scRNAseq feasible for the kind of large multi-batch, multi-donor studies that are required to prosecute diseases with heterogeneous genetic backgrounds.

scholarly journals Lab Retriever: a software tool for calculating likelihood ratios incorporating a probability of drop-out for forensic DNA profiles

2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Keith Inman ◽  
Norah Rudin ◽  
Ken Cheng ◽  
Chris Robinson ◽  
Adam Kirschner ◽  
...  
Keyword(s):  
Software Tool ◽  
Drop Out ◽  
Forensic Dna ◽  
Likelihood Ratios ◽  
Dna Profiles

Internal validation of STRmix™ for the interpretation of single source and mixed DNA profiles

2017 ◽  
Vol 29 ◽  
pp. 126-144 ◽  
Author(s):  
Tamyra R. Moretti ◽  
Rebecca S. Just ◽  
Susannah C. Kehl ◽  
Leah E. Willis ◽  
John S. Buckleton ◽  
...  
Keyword(s):  
Single Source ◽  
Internal Validation ◽  
Dna Profiles

Principes cum Tyrannis: Two Studies on the Kaisergeschichte and its Tradition

1993 ◽  
Vol 43 (2) ◽  
pp. 491-500 ◽  
Author(s):  
R. W. Burgess
Keyword(s):  
Fourth Century ◽  
The Other ◽  
Third Century ◽  
Common Source ◽  
Single Source ◽  
Natural Assumption ◽  
Ammianus Marcellinus ◽  
The Third ◽  
Historia Augusta ◽  
Selection Of

The Kaisergeschichte (KG) was a set of short imperial biographies extending from Augustus to the death of Constantine, probably written between 337 and c. 340. It no longer exists but its existence can be deduced from other surviving works. Amongst the histories of the fourth century – Aurelius Victor, Eutropius, Festus, Jerome's Chronici canones, the Historia Augusta, the Epitome de Caesaribus, and, in places, even Ammianus Marcellinus and perhaps the Origo Constantini imperatoris (Anonymi Valesiani pars prior) – there is a common selection of facts and errors, and common wording and phrasing in their narratives between Augustus and the death of Constantine, especially in their accounts of the third century. A natural assumption is that later historians copied earlier ones, yet later historians include information not contained in earlier ones, and historians who could not have known each other's work share similarities. For example, it looks as though Aurelius Victor was copying Eutropius, yet Victor wrote before Eutropius, and Eutropius contains information not in Victor and does not reproduce Victor's peculiar style or personal biases, things which he could hardly have avoided. Therefore Eutropius cannot be copying Victor. Since neither could have copied the other, there must therefore have been a common source. In his Chronici canones Jerome appears at first to be simply copying Eutropius. Yet when he deviates from Eutropius, his deviations usually mirror other histories, such as Suetonius, Victor, Festus, even the Epitome and the Historia Augusta, two works that had not even been written when Jerome compiled his chronicle and that did not use, and would never have used, the Christian chronicle as a source. Jerome was hurriedly dictating to his secretary, he had no time to peruse four or five works at a time for his brief notices. There must have been a single source that contained both the Eutropian material and the deviations common to Jerome and the other works. That source was the KG. It is the purpose of this paper to add to the above list of authors who relied upon the KG two other writers whose work can be shown to have derived, either at first hand or later, from the KG: Polemius Silvius and Ausonius.

scholarly journals SmartCodes: functionalized barcodes that enable targeted retrieval of clonal lineages from a heterogeneous population

2018 ◽  
Author(s):  
Clare Rebbeck ◽  
Florian Raths ◽  
Bassem Ben Cheik ◽  
Kenneth Gouin ◽  
Gregory J. Hannon ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Single Cell ◽  
Tumour Progression ◽  
Complex Mixture ◽  
Heterogeneous Population ◽  
Complex Mixtures ◽  
Tumour Heterogeneity ◽  
Selectable Markers ◽  
Molecular Barcoding ◽  
Molecular Barcode

AbstractMolecular barcoding has provided means to link genotype to phenotype, to individuate cells in single-cell analyses, to enable the tracking of evolving lineages, and to facilitate the analysis of complex mixtures containing phenotypically distinct lineages. To date, all existing approaches enable retrospective associations to be made between characteristics and the lineage harbouring them, but provide no path toward isolating or manipulating those lineages within the complex mixture. Here, we describe a strategy for creating functionalized barcodes that enable straightforward manipulation of lineages within complex populations of cells, either marking and retrieval of selected lineages, or modification of their phenotype within the population, including their elimination. These “SmartCodes” rely on a simple CRISPR-based, molecular barcode reader that can switch measurable, or selectable markers, on or off in a binary fashion. While this approach could have broad impact, we envision initial approaches to the study of tumour heterogeneity, focused on issues of tumour progression, metastasis, and drug resistance.

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