Detection of Low Level Mixed Chimerism Using High Throughput SNP Genotyping

Nakorchevsky, Aleksey; Flores, Eunice

doi:10.4172/2155-9864.1000340

Cited by 2 publications

(2 citation statements)

References 13 publications

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“…The to‐date laborious and time‐consuming sample handling will be further optimised by robotic platforms for faster sample processing and to reduce risks of cross‐contamination and handling errors. Additional DNA mixture detection by Chimeric ID report generation proved not to be sensitive enough to be competitive to existing flow cytofluorimetric methods; SNP panels with higher number of assays might be more effective in this regard 35–38 . Possible contamination scenarios, for example, of female athlete's urine contamination upon sexual intercourse, 39 were not part of this study but will be addressed in future investigations.…”

Section: Discussionmentioning

confidence: 97%

“…In the described study, by Chimeric ID report generation proved not to be sensitive enough to be competitive to existing flow cytofluorimetric methods; SNP panels with higher number of assays might be more effective in this regard. [35][36][37][38] Possible contamination scenarios, for example, of female athlete's urine contamination upon sexual intercourse, 39 were not part of this study but will be addressed in future investigations.…”

Section: Discussionmentioning

confidence: 99%

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Detection of doping control sample substitutions via single nucleotide polymorphism‐based ID typing

Naumann,

Walpurgis,

Rubio

et al. 2023

Drug Testing and Analysis

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The authenticity of a doping control sample is a key element of sports drug testing programmes. Doping control sample manipulation by providing another individual's urine or blood (instead of the tested athlete's sample) has been observed in the past and is an unequivocal violation of the World Anti‐Doping Agency anti‐doping rules. To determine attempts of manipulations by sample swapping, the utility of a single nucleotide polymorphism (SNP)‐based sample authentication with a multi‐target SNP panel was assessed. The panel comprises detection assays for 44 different SNPs, 3 gender markers and 5 quality control markers for DNA‐profile determination. Sample analysis is based on a multiplex polymerase chain reaction step followed by a multiplex single base extension (SBE) reaction and subsequent SBE‐product detection by MALDI‐TOF MS. Panel performance was evaluated for urine and dried blood spot (DBS) samples. Urine (8 ml) and DBS (20 μl) test samples were reliably typed and matched to whole blood reference samples, while efficient typing of urine samples correlated with sample quality and input amounts. Robust profiling of urine doping control specimens was confirmed with an assay input of 12 ml. Samples can be processed in a high‐throughput format with an overall assay turnaround time of approximately 11 h. SNP‐based DNA typing via MALDI‐TOF MS thus represents a high throughput‐capable possibility for doping control sample authentication. SNP profiling of samples could offer the opportunity to complement existing steroid profile analytics to substantiate sample manipulations and to support quality control processes in high throughput routine settings.

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Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

Detection of doping control sample substitutions via single nucleotide polymorphism‐based ID typing

Naumann,

Walpurgis,

Rubio

et al. 2023

Drug Testing and Analysis

View full text Add to dashboard Cite

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Improving Single-Nucleotide Polymorphism-Based Fetal Fraction Estimation of Maternal Plasma Circulating Cell-Free DNA Using Bayesian Hierarchical Models

Larson

Wang

et al. 2018

Journal of Computational Biology

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The recent advances in next-generation sequencing (NGS) technologies have enabled the development of effective high-throughput noninvasive prenatal screening (NIPS) assays for fetal genetic abnormalities using maternal circulating cell-free DNA (ccfDNA). An important NIPS quality assurance is quantifying the fetal proportion of the sampled ccfDNA. For methods using allelic read count ratios from targeted sequencing of single-nucleotide polymorphisms (SNPs), systematic biases and errors may reduce accuracy and diminish assay performance. We collected ccfDNA NIPS MiSeq sequencing data from an amplicon-based 92 SNP panel along with complementary low-depth whole-genome sequencing (WGS) on 243 normal male fetus pregnancies along with additional 144 nonpregnant female donor samples. Using fetal fraction estimates based on X and Y chromosome WGS coverage as gold standard, we compared an existing SNP-based approach, FetalQuant, to a more flexible Bayesian hierarchical modeling strategy that borrows information across interrogated SNPs to character SNP-level error rates and biases to improve fetal fraction estimates. Posterior distributions for SNP-level model parameters indicate most SNPs exhibited modest to moderate extrabinomial variation and a consistent underrepresentation of fetal alleles, with some extreme outliers in both regards. Fetal fraction estimates using FetalQuant, naive to these SNP properties, were relatively poor (R = 0.14, root mean squared error [RMSE] = 0.050), particularly when the true fetal fraction was low (<5%). In contrast, by quantifying SNP-level biases and error rates, our proposed approach demonstrated improved performance by reducing the bias and variability in fetal fraction estimates (R = 0.794, RMSE = 0.025). Using high-depth targeted SNP sequencing data, we identified a high degree of variability in distributional properties across SNP allelic read counts. These results highlight the benefits of leveraging hierarchical modeling for SNP-based fetal quantification assays (FQAs) and the need to properly calibrate FQAs dependent on NGS allelic ratio data.

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Detection of Low Level Mixed Chimerism Using High Throughput SNP Genotyping

Cited by 2 publications

References 13 publications

Detection of doping control sample substitutions via single nucleotide polymorphism‐based ID typing

Detection of doping control sample substitutions via single nucleotide polymorphism‐based ID typing

Improving Single-Nucleotide Polymorphism-Based Fetal Fraction Estimation of Maternal Plasma Circulating Cell-Free DNA Using Bayesian Hierarchical Models

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