Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR−/- mice

Prof. Aykut Özkul from Ankara University in Turkey performed a study to isolate SARS-CoV-2 viruses circulating in Anatolia, and to investigate virus propagation in frequently-used cells and experimental animals. Using our CleanPlex® SARS-CoV-2 panel for their amplicon-based next generation sequencing, they identified two local SARS-CoV-2 virus isolates, and investigated in vitro growth dynamics in frequently-used Vero E6 cells and identified IFNAR−/− mice as a potential animal model for SARS-CoV-2 experiments.

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Functional CRISPR dissection of gene networks controlling human regulatory T cell identity

CRISPR Regulatory T Cells Gene Network

Prof. Alexander Marson from University of California, San Francisco (UCSF), CA, USA in collaboration with researchers from University of California, Berkeley, CA, USA, Technische Universität München (TUM), Munich, Germany and multiple renowned Cancer Immunotherapy institutes in San Francisco published findings in Nature Immunology showing CRISPR–Cas9 ribonucleoprotein (RNP) technology allows dissection of complex gene modules in primary human Treg cells through targeted gene perturbation studies. Using our CleanPlex custom panels, researchers were able to perform CRISPR editing efficiency check and show pooled Cas9 RNP screens link indels with phenotypic changes in human Treg cells. The overall study resulted in functional network maps which may help to guide future development of drug targets and design of Treg cell– based immunotherapies.

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Sensitive, highly multiplexed sequencing of microhaplotypes from the Plasmodium falciparum heterozygome

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Prof. Bryan Greenhouse, Dr. Sofonias Tessema and fellow researchers from Chan Zuckerberg Biohub, University of San Francisco, USA in collaboration with researchers from University of Massachusetts, Brown University, Clinton Health Access Initiative, and Centro de Investigação em Saúde de Manhiça (CISM) of Mozambique demonstrated that targeted NGS sequencing with a custom CleanPlex Panel is a flexible, low cost, “promising tool for studying the transmission dynamics of  P. falciparum” infections (Malaria), without the need for WGA, describing that in fact, their CleanPlex approach “outperformed whole genome sequences obtained from 50 times more total reads”. They further go on to note that their custom CleanPlex Panel “demonstrated high specificity regardless of the proportions of strains in the mixture (true positive rate = 99.8)… [and] sensitivity of the method was high across a wide range of parasite densities.”

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The role of genetic mutations in intrahepatic cholestasis of pregnancy

The role of genetic mutations in intrahepatic cholestasis of pregnancy

Dr. Gültekin Adanaş Aydın, Dr. Gülten Özgen, and Dr. Orhan Görükmez from Bursa Yuksek Ihtisas Training and Research Hospital, Bursa, Turkey published a paper about the role of genetic mutations in intrahepatic cholestasis of pregnancy using a CleanPlex custom panel.

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Pediatric COVID-19 in Southern California: clinical features and viral genetic diversity

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Prof. Xiaowu Gai and Prof. Jennifer Dien Bard from Children’s Hospital Los Angeles (CHLA) recently published a paper exploring clinical features and SARS-CoV-2 genetic variation in children presenting with COVID-19. They observed diverse clinical presentations and identified association between disease severity, viral load and age. By using CleanPlex SARS-CoV-2 Research and Surveillance NGS Panel, they were able to conduct highly sensitive and full-genome interrogation of the SARS-CoV-2 virus using amplicon sequencing on Illumina platforms.

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The origin of SARS-CoV-2 in Istanbul: Sequencing findings from the epicenter of the pandemic in Turkey

The origin of SARS-CoV-2 in Istanbul: Sequencing findings from the epicenter of the pandemic in Turkey

Prof. Dinler-Doganay’s Lab at Istanbul Technical University, Prof. Doganay and his colleagues at University of Health Sciences, Istanbul, Turkey and Dr. Ilker Karacan from Science and Advanced Technology Research Center, Istanbul, Turkey reported the SARS-CoV-2 viral genomes circulating in Istanbul for the first time. By using Paragon Genomics’ CleanPlex SARS-CoV-2 Research and Surveillance Panel, amplicon-based next-generation sequencing approach was successfully applied to generate near-complete genomes with an average depth of 2616. All three viral genomes carried the D614G variant (G clade according to GISAID classification) with implications for the origin of a spread.

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Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing

Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing

Prof. Xiaowu Gai and Prof. Jennifer Dien Bard from Children’s Hospital Los Angeles (CHLA), Paragon Genomics R&D teams led by Dr. Zhitong Liu, Prof. Alexander Urban from Stanford University and scientists from MGI / BGI-ShenZhen collaborated on sequencing COVID-19 patient samples using Paragon Genomics’s CleanPlex SARS-CoV-2 Panel for highly sensitive and full-genome interrogation of the SARS-CoV-2 virus using multiplexed PCR enrichment followed by next-generation sequencing.

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Molecular assessment of pretransplant chemotherapy in the treatment of leukemia

Prof. Elliot Stieglitz‘s Lab at the UCSF Benioff Children’s Hospital developed a NGS assay powered by Paragon Genomics’ CleanPlex technology to measure the molecular burden of juvenile myelomonocytic leukemia (JMML). The researchers demonstrated that molecular testing can be helpful to distinguish between responders and nonresponders and should become an integral part of clinical care.

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Building phylogenomic data sets using highly multiplexed amplicon sequencing

Dr. Scott Geib and fellow researchers at the USDA-Agricultural Research Service developed new approach for building phylogenomic data sets using highly multiplexed amplicon sequencing powered by Paragon Genomics’ CleanPlex technology. The work provided unparalleled resolution of phylogenetic relationships in fruit flies.

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Somatic Mutations And T-Cell Clonality In Patients With Immunodeficiency

Rendering of a T Cell

Dr. Satu Mustjoki and fellow researchers from University of Helsinki, Finland, in collaboration with the University Hospital and Computer Science Department of Aalto University School of Science, report an increase in somatic mutations in CD4+ and CD8+ T cells of patients with immunodeficiency. The team used a custom CleanPlex Panel to validate the low VAF somatic mutations to gain higher confidence in their findings.

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Parkin-mediated mitophagy and autophagy flux disruption in cellular models of MERRF syndrome

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Prof. José A.Sánchez-Alcázar and fellow researchers from University of Pablo de Olavide, Spain collaborated with researchers from Department of Neurology, Uniklinikum C. G. Carus, Dresden, Germany and Instituto de Salud Carlos III, Spain and used CleanPlex Mitochondrial Disease Panel to study parkin-mediated mitophagy and autophagy flux disruption in cellular models of MERRF syndrome. 

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