Biology subjects

Koeppel, A. F.

Publications and source records attributed to Koeppel, A. F..

5 recordsLinked to original sources

bioRxiv2022

Internal Validation of the ForenSeq Kintelligence Kit for Application to Forensic Genetic Genealogy

Forensic Genetic Genealogy (FGG) requires high density single nucleotide polymorphism (SNP) profiles to infer distant relationships. The ForenSeq Kintelligence kit is a recently developed method targeting approximately 10,000 SNPs that were selected to be compatible with genetic genealogy databases, while avoiding medically relevant SNPs. The targeted PCR method is ideal for low input and degraded samples, which are particularly challenging for microarray analysis. We made modifications to library preparation and sample pooling to further enhance the performance of low input samples. To align this FGG method with forensic laboratory standards, we performed an internal validation study in accordance with the Scientific Working Group on DNA Analysis Methods Validation Guidelines for DNA Analysis Methods. The sensitivity and precision and accuracy studies produced accurate and reliable profiles down to 0.05 ng of DNA. The mixture and contamination studies demonstrated that the method could detect the presence of a minor contributor down to 0.02 ng, while system wide contamination was negligible. Nonprobative bone, fired shell casing, and adhesive tape samples performed well with inputs ranging from 0.05 to 1.0 ng of DNA. A bone with a high degradation index and tested at 0.1 ng DNA input resulted in a call rate of 92.9% and a heterozygosity rate of 0.387. We demonstrated the importance of both call rate and heterozygosity rate to assess profile performance. Validating FGG methods is critical to ensuring the reliability and utility of SNP profiles that will be uploaded to genetic genealogy databases for the purpose of generating investigative leads.

genomics↗

bioRxiv2022

Developmental Validation of the Illumina Infinium Assay using the Global Screening Array (GSA) on the iScan System for use in Forensic Laboratories

Microarray processing, which interrogates hundreds of thousands of single nucleotide polymorphisms (SNPs) across the human genome, has recently gained traction in forensics due to its use in forensic genetic genealogy, which is based on analysis using SNPs to compare distant relatives in publicly curated databases for the purposes of developing investigative leads or identifying human remains. To date, there has been no published developmental validation of microarray processing using the Scientific Working Group on DNA Analysis Methods (SWGDAM) Validation Guidelines for DNA Analysis Methods and Federal Bureau of Investigation Quality Assurance Standards. Validation of these methods are warranted to identify samples suitable for microarray analysis and to assess the quality of the data obtained prior to upload to genealogical databases. In this study, we validated the Global Screening Array (GSA) for use in forensic investigations according to SWGDAM guidelines, including the following studies: precision and accuracy, sensitivity, contamination, degradation, species specificity, mock case-type samples, mixtures, repeatability and reproducibility, and stability. Results indicated accurate genotype calls with SNP call rates >95% at DNA input as low as 0.20 ng. In addition to SNP call rate, we developed interpretation thresholds for signal intensity and heterozygosity to allow for sample quality assessment and identification of highly degraded and/or non-human DNA. This study demonstrates that high quality data can be generated from multiple sample types, including mock forensic evidence that simulated the challenges that are often encountered in forensic cold cases.

genomics↗

bioRxiv2022

Environmental DNA sequencing data from algal blooms in Lake Erie using Oxford Nanopore MinION

Harmful Algal Blooms (HABs) pose a significant and increasing risk, both to human health and to the Blue Economy. Genomics approaches to early detection promise to help mitigate these risks. We have developed and prototyped HABSSED (HAB Surveillance by Sequencing of Environmental DNA), a portable, reliable, rapid, low-cost pipeline for detecting HABs in the field using 3rd generation sequencing with the Oxford Nanopore MinION device. We demonstrated the efficacy of our approach by sequencing existing samples collected from a National Oceanic and Atmospheric Administration (NOAA) Great Lakes Environmental Research Laboratory (GLERL) on Lake Erie. We sequenced environmental DNA (eDNA) from samples drawn before, during, and after a Microcystis bloom, and estimate the abundanced of HAB-associated taxa. While sequencing results showed some evidence of human and E. coli contamination, we find that the abundance of Mycrocystis and other HAB-associated orgnisms significantly differs between pre- and post-bloom environments. Here we describe the publicly available sequencing data that was generated as part of this research, which is available in the Sequence Read Archive (SRA) under accession number PRJNA812770.

genomics↗

bioRxiv2019

The maternal-fetal interface of successful pregnancies and impact of fetal sex using single cell sequencing

The first trimester is a critical window of maternal-fetal communication for pregnancy. Therefore, we characterized crosstalk in ongoing human pregnancies at 11-13 weeks gestation. RNA-sequencing of matched maternal decidua and placenta identified 818 receptors and 3502 ligands, including 126 differentially expressed receptor-ligand pairs. Using single cell RNA-sequencing to further dissect placenta heterogeneity, we identified five major cell types (trophoblasts, stromal cells, hofbauer cells, antigen presenting cells and endothelial cells) with unique crosstalk at the maternal-fetal interface. We identified seven unique trophoblast subclusters, including new subtypes that transition into the terminal cell types, extra-villous trophoblasts and syncytiotrophoblasts. As fetal sex impacts pregnancy, we analyzed sex differences in each cell type and identified differences in immune cell function. TGF{beta}1, {beta}-estradiol, and dihydrotestosterone emerge as upstream regulators of sexually dimorphic genes in a cell type specific manner. Thus, the fetal contribution at the maternal-fetal interface is cell and sex specific.

developmental biology↗

bioRxiv2018

In situ 10-cell RNA sequencing in tissue and tumor biopsy samples

Single-cell transcriptomic methods classify new and existing cell types very effectively, but alternative approaches are needed to quantify the individual regulatory states of cells in their native tissue context. We combined the tissue preservation and single-cell resolution of laser capture with an improved preamplification procedure enabling RNA sequencing of 10 microdissected cells. This in situ 10-cell RNA sequencing (10cRNA-seq) can exploit fluorescent reporters of cell type in genetically engineered mice and is compatible with freshly cryoembedded clinical biopsies from patients. Through recombinant RNA spike-ins, we estimate dropout-free technical reliability as low as ~250 copies and a 50% detection sensitivity of ~45 copies per 10-cell reaction. By using small pools of microdissected cells, 10cRNA-seq improves per-cell reliability and sensitivity beyond existing approaches for single-cell RNA sequencing (scRNA-seq). Accordingly, in multiple tissue and tumor settings, we observe 1.5-2-fold increases in genes detected and overall alignment rates compared to scRNA-seq. Combined with existing approaches to deconvolve small pools of cells, 10cRNA-seq offers a reliable, unbiased, and sensitive way to measure cell-state heterogeneity in tissues and tumors.

systems biology↗