Biology subjects

Ricke, D. O.

Publications and source records attributed to Ricke, D. O..

11 recordsLinked to original sources

bioRxiv2019

Rapid Generation of Medical Countermeasure Candidates Via Computational Variation Analysis

Rapid responses to emerging infectious diseases are needed for viral and bacterial pathogens. For some pathogens, no medical countermeasures (MCMs) yet exist. Pathogen heterogeneity and antigenic variation lead to immune response escape mutations for some pathogens (e.g., influenza) limiting the effectiveness of medical countermeasures. High throughput sequencing enables characterization of large numbers of pathogen isolates to which residue variation analysis can be applied to identify low variability targets. Multiple approaches are proposed that leverage these low variability targets as the first step of medical countermeasure development. Classes of MCMs informed by this approach include the following: DNA or RNA vaccines, both B-cell and T-cell vaccination strategies, anti-viral RNA targeting, antibody therapeutics, and aptamer targeting of viral protein complex interfaces as potential treatment strategies for infected individuals. Variation analysis-designed countermeasures targeting the Ebola glycoprotein are presented to illustrate the concepts for the proposed multiple targeted countermeasures.

bioinformatics↗

bioRxiv2019

SNP Identity Searching Across Ethnicities, Kinship, and Admixture

Advances in high throughput sequencing (HTS) enables application of single nucleotide polymorphism (SNP) panels for identification and mixture analysis. Large reference sets of characterized individuals with documented relationships, ethnicities, and admixture are not yet available for characterizing the impacts of different ethnicities, kinships, and admixture on identification and mixture search results for relatives and unrelated individuals. Models for the expected results are presented with comparison results on two in silico datasets spanning four ethnicities, extended kinship relationships, and also admixture between the four ethnicities.

bioinformatics↗

bioRxiv2018

Detecting HTS Barcode Contamination

DNA barcoding enables multiple samples to be characterized in parallel with high throughput sequencing (HTS) experiments for cost efficiencies. Cross-contamination of DNA barcode reagents can result in the detection of HTS sequences for barcodes that were not originally added to a particular sample. Cross-contamination of data between multiplexed samples can also occur. Avoidance and detection of contaminated barcodes is relevant for DNA forensic samples analysis, accurate cancer diagnosis, clinical research applications, metagenomic analysis, etc. We present recommendations for the avoidance of contamination and a tool, TallyBarcodes, to aid in the detection of DNA barcode contamination.

bioinformatics↗

bioRxiv2018

TranslucentID: Detecting Individuals with High Confidence in Saturated DNA SNP Mixtures

High throughput sequencing (HTS) of complex DNA mixtures with single nucleotide polymorphisms (SNPs) panels can identify multiple individuals in forensic DNA mixture samples. SNP mixture analysis relies upon the exclusion of non-contributing individuals with the subset of SNP loci with no detected minor alleles in the mixture. Few, if any, individuals are anticipated to be detectable in saturated mixtures by this mixture analysis approach because of the increased probability of matching random individuals. Being able to identify a subset of the contributors in saturated HTS SNP mixtures is valuable for forensic investigations. A desaturated mixture can be created by treating a set of SNPs with the lowest minor allele ratios as having no minor alleles. Leveraging differences in DNA contributor concentrations in saturated mixtures, we introduce TranslucentID for the identification of a subset of individuals with high confidence who contributed DNA to saturated mixtures by desaturating the mixtures.

bioinformatics↗

bioRxiv2018

11 Million SNP Reference Profiles for Identity Searching Across Ethnicities, Kinship, and Admixture

High throughput sequencing (HTS) of single nucleotide polymorphisms (SNPs) provides additional applications for DNA forensics including identification, mixture analysis, kinship prediction, and biogeographic ancestry prediction. Public repositories of human genetic data are being rapidly generated and released, but the majorities of these samples are de-identified to protect privacy, and have little or no individual metadata such as appearance (photos), ethnicity, relatives, etc. A reference in silico dataset has been generated to enable development and testing of new DNA forensics algorithms. This dataset provides 11 million SNP profiles for individuals with defined ethnicities and family relationships spanning eight generations with admixture for a panel with 39,108 SNPs.

bioinformatics↗

bioRxiv2017

The Plateau Method for Forensic DNA SNP Mixture Deconvolution

Identification of individuals in complex DNA mixtures remains a challenge for forensic analysts. Recent advances in high throughput sequencing (HTS) are enabling analysis of DNA mixtures with expanded panels of Short Tandem Repeats (STRs) and/or Single Nucleotide Polymorphisms (SNPs). We present the plateau method for direct SNP DNA mixture deconvolution into sub-profiles based on differences in contributors DNA concentrations in the mixtures in the absence of matching reference profiles. The Plateau method can detect profiles of individuals whose contribution is as low as 1/200 in a DNA mixture (patent pending)1.

bioinformatics↗

bioRxiv2017

The Genetic Chain Rule for Probabilistic Kinship Estimation

Accurate kinship predictions using DNA forensic samples has utility for investigative leads, remains identification, identifying relationships between individuals of interest, etc. High throughput sequencing (HTS) of STRs and single nucleotide polymorphisms (SNPs) is enabling the characterization of larger numbers of loci. Large panels of SNP loci have been proposed for improved mixture analysis of forensic samples. While multiple kinship prediction approaches have been established, we present an approach focusing on these large HTS SNP panels for predicting degree of kinship predictions. Formulas for first degree relatives can be multiplied (chained) together to model extended kinship relationships. Predictions are made using these formulations by calculating log likelihood ratios and selecting the maximum likelihood across the possible relationships. With a panel of 30,000 SNPs evaluated on an in silico dataset, this method can resolve parents from siblings and distinguish 1st, 2nd, and 3rd degree relatives from each other and unrelated individuals.

bioinformatics↗

bioRxiv2017

A Linear Algebra Approach to Fast DNA Mixture Analysis Using GPUs

Analysis of DNA samples is an important tool in forensics, and the speed of analysis can impact investigations. Comparison of DNA sequences is based on the analysis of short tandem repeats (STRs), which are short DNA sequences of 2-5 base pairs. Current forensics approaches use 20 STR loci for analysis. The use of single nucleotide polymorphisms (SNPs) has utility for analysis of complex DNA mixtures. The use of tens of thousands of SNPs loci for analysis poses significant computational challenges because the forensic analysis scales by the product of the loci count and number of DNA samples to be analyzed. In this paper, we discuss the implementation of a DNA sequence comparison algorithm by re-casting the algorithm in terms of linear algebra primitives. By developing an overloaded matrix multiplication approach to DNA comparisons, we can leverage advances in GPU hardware and algoithms for dense matrix multiplication (DGEMM) to speed up DNA sample comparisons. We show that it is possible to compare 2048 unknown DNA samples with 20 million known samples in under 6 seconds using a NVIDIA K80 GPU.

bioinformatics↗

bioRxiv2017

FastID: Extremely Fast Forensic DNA Comparisons

Rapid analysis of DNA forensic samples can have a critical impact on time sensitive investigations. Analysis of forensic DNA samples by massively parallel sequencing is creating the next gold standard for DNA forensic analysis. This technology enables the expansion of forensic profiles from the current 20 short tandem repeat (STR) loci to tens of thousands of single nucleotide polymorphism (SNP) loci. A forensic search scales by the product of the number of loci and the number of profile comparisons. This paper introduces a method (FastID) to address the need for rapid scalable analysis of DNA forensic samples (patent pending)[1]. FastID can search a profile of 2,500 SNP loci against 20 million profiles in 5.08 seconds using a single computational thread on a laptop (Intel i7 4.0 GHz).

bioinformatics↗

bioRxiv2017

GrigoraSNPs: Optimized HTS DNA Forensic SNP Analysis

High throughput DNA sequencing technologies enable improved characterization of forensic DNA samples enabling greater insights into DNA contributor(s). Current DNA forensics techniques rely upon allele sizing of short tandem repeats by capillary electrophoresis. High throughput sequencing enables forensic sample characterizations for large numbers of single nucleotide polymorphism loci. The slowest computational component of the DNA forensics analysis pipeline is the characterization of raw sequence data. This paper optimizes the SNP calling module of the DNA analysis pipeline with runtime results that scale linearly with the number of HTS sequences (patent pending)[1]. GrigoraSNPs can analyze 100 million reads in less than 5 minutes using 3 threads on a 4.0 GHz Intel i7-6700K laptop CPU.

bioinformatics↗

bioRxiv2017

Vasomotor Symptoms Monitoring with a Commercial Activity Tracking Watch

Vasomotor Symptoms Monitoring with a Commercial Activity Tracking Watch Vasomotor Symptoms Monitoring... Disclaimer Contributors References Continuous tracking of electrodermal activity (EDA), also known as galvanic skin response (GSR), values with commercial fitness devices for individuals with vasomotor symptoms (hot flashes) provides a path forward for future studies with fine resolution monitoring. This can improve upon the current reliance on the use of personal diaries1. There are multiple conditions associated with vasomotor symptoms including menopause /early menopausal transition2, medications (Quinestrol, tramadol, etc.), chemotherapy and Tamoxifen, hyperthyroidism, infections (Inflammatory Bowel Disease - IBD, etc.), and more. Multiple studies have characterized hot flashes in preme ...

bioinformatics↗