NGS-PrimerPlex: high-throughput primer design for multiplex polymerase chain reactions

Kechin, Andrey; Borobova, Viktoria; Boyarskikh, U. A.; Khrapov, E. A.; Subbotin, Sergey; Филипенко, М. Л.

doi:10.1101/2020.06.29.176834

Cited by 4 publications

(2 citation statements)

References 14 publications

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“…Most dependencies can be installed automatically in their own Conda environment through Nextflow (Di Tommaso et al, 2017). Only the optional dependencies (BaitsTools; Campana, 2018 and NGS-PrimerPlex;Kechin et al, 2020) must be installed by the end-user as no Conda recipe currently exists for these packages. We describe the pipeline briefly below.…”

Section: Mpcrselect Pipelinementioning

confidence: 99%

“…After site selection, the individual identification and ancestry assignment SNP sets are combined and the user can choose to design baits for capture-based projects using BaitsTools (Campana, 2018) or alternatively import the sites into NGS-PrimerPlex (Kechin et al, 2020) to design primers for multiplex SNP panels. Finally, as an in silico validation of the panel design, the program performs PCA (using PLINK 2) on the biallelic sites from the unfiltered input VCF, the post-filtering VCF, and the final chosen population-assignment and individual-identification sites (both separately and concatenated).…”

Section: Mpcrselect Pipelinementioning

confidence: 99%

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Recommendations for Population and Individual Diagnostic SNP Selection in Non-Model Species

Armstrong,

Li,

Campana

et al. 2024

Preprint

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Despite substantial reductions in the cost of sequencing over the last decade, genetic panels remain relevant due to their cost-effectiveness and flexibility across a variety of sample types. In particular, single nucleotide polymorphism (SNP) panels are increasingly favored for conservation applications. SNP panels are often used because of their adaptability, effectiveness with low-quality samples, and cost-efficiency for use in population monitoring and forensics. However, the selection of diagnostic SNPs for population assignment and individual identification can be challenging. The consequences of poor SNP selection are under-powered panels, inaccurate results, and monetary loss. Here, we develop a novel user-friendly SNP selection pipeline for population assignment and individual identification, mPCRselect. mPCRselect allows any researcher, who has sufficient SNP-level data, to design a successful and cost-effective SNP panel for species of conservation concern.

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Section: Mpcrselect Pipelinementioning

confidence: 99%

Section: Mpcrselect Pipelinementioning

confidence: 99%

Recommendations for Population and Individual Diagnostic SNP Selection in Non-Model Species

Armstrong,

Li,

Campana

et al. 2024

Preprint

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Detecting Microsatellite Instability in Endometrial, Colon, and Stomach Cancers Using Targeted NGS

Boyarskikh,

Kechin,

Khrapov

et al. 2023

Cancers

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Purpose: To develop a method for testing the MSI based on targeted NGS. Methods: Based on the results of previous studies, 81 microsatellite loci with high variability in MSI-H tumors were selected, and a method for calculating the MSI score was developed. Using the MSI score, we defined the MSI status in endometral (162), colon (153), and stomach (190) cancers. Accuracy of the MSI scores was evaluated by comparison with MMR immunohistochemistry for 137 endometrium (63 dMMR and 74 pMMR), 76 colon (29 dMMR and 47 pMMR), and 81 stomach (8 dMMR and 73 pMMR) cancers. Results: Classification of MSS and MSI-H tumors was performed with AUC (0.99), sensitivity (92%), and specificity (98%) for all tumors without division into types. The accuracy of MSI testing in endometrial cancer was lower than for stomach and colon cancer (0.98, 87%, and 100%, respectively). The use of 27 loci only, the most informative for endometrial cancer, increased the overall accuracy (1.00, 99%, and 99%). Comparison of MSI score values in 505 tumors showed that MSI score is significantly higher in colon (p < 10−5) and stomach (p = 0.008) cancer compared with endometrial cancer. Conclusion: The MSI score accurately determines MSI status for endometrial, colon, and stomach cancers and can be used to quantify the degree of MSI.

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Target Enrichment Approaches for Next-Generation Sequencing Applications in Oncology

Singh

2022

Diagnostics

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Screening for genomic sequence variants in genes of predictive and prognostic significance is an integral part of precision medicine. Next-generation sequencing (NGS) technologies are progressively becoming platforms of choice to facilitate this, owing to their massively parallel sequencing capability, which can be used to simultaneously screen multiple markers in multiple samples for a variety of variants (single nucleotide and multi nucleotide variants, insertions and deletions, gene copy number variations, and fusions). A crucial step in the workflow of targeted NGS is the enrichment of the genomic regions of interest to be sequenced, against the whole genomic background. This ensures that the NGS effort is focused to predominantly screen target regions of interest with minimal off-target sequencing, making it more accurate and economical. Polymerase chain reaction-based (PCR, or amplicon-based) and hybridization capture-based methodologies are the two prominent approaches employed for target enrichment. This review summarizes the basic principles of target enrichment utilized by these methods, their multiple variations that have evolved over time, automation approaches, overall comparison of their advantages and drawbacks, and commercially available choices for these methodologies.

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NGS-PrimerPlex: high-throughput primer design for multiplex polymerase chain reactions

Cited by 4 publications

References 14 publications

Recommendations for Population and Individual Diagnostic SNP Selection in Non-Model Species

Recommendations for Population and Individual Diagnostic SNP Selection in Non-Model Species

Detecting Microsatellite Instability in Endometrial, Colon, and Stomach Cancers Using Targeted NGS

Target Enrichment Approaches for Next-Generation Sequencing Applications in Oncology

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