Ultra-Fast Next Generation Human Genome Sequencing Data Processing Using DRAGEN&amp;lt;sup&amp;gt;TM&amp;lt;/sup&amp;gt; Bio-IT Processor for Precision Medicine

Goyal, Amit; Kwon, Hyuk Jung; Lee, Kichan; Garg, Reena; Yun, Seon Young; Kim, Yoon Hee; Lee, Sung-Hoon; Lee, Min Seob

doi:10.4236/ojgen.2017.71002

Cited by 35 publications

(23 citation statements)

References 16 publications

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“…RNA-seq reads were demultiplexed using the DRAGEN genome pipeline [19]. FASTQ files were aligned to hg19 reference using the STAR (v.2.6.1) aligner with default settings [20].…”

Section: Rna-seq Data Analysismentioning

confidence: 99%

Autophagy mitigates ethanol-induced mitochondrial dysfunction and oxidative stress in esophageal keratinocytes

et al. 2020

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During alcohol consumption, the esophageal mucosa is directly exposed to high concentrations of ethanol (EtOH). We therefore investigated the response of normal human esophageal epithelial cell lines EPC1, EPC2 and EPC3 to acute EtOH exposure. While these cells were able to tolerate 2% EtOH for 8 h in both three-dimensional organoids and monolayer culture conditions, RNA sequencing suggested that EtOH induced mitochondrial dysfunction. With EtOH treatment, EPC1 and EPC2 cells also demonstrated decreased mitochondrial ATPB protein expression by immunofluorescence and swollen mitochondria lacking intact cristae by transmission electron microscopy. Mitochondrial membrane potential (ΔΨm) was decreased in a subset of EPC1 and EPC2 cells stained with ΔΨm-sensitive dye MitoTracker Deep Red. In EPC2, EtOH decreased ATP level while impairing mitochondrial respiration and electron transportation chain functions, as determined by ATP fluorometric assay, respirometry, and liquid chromatography-mass spectrometry. Additionally, EPC2 cells demonstrated enhanced oxidative stress by flow cytometry for mitochondrial superoxide (MitoSOX), which was antagonized by the mitochondria-specific antioxidant MitoCP.

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“…RNA-seq reads were demultiplexed using the DRAGEN genome pipeline [19]. FASTQ files were aligned to hg19 reference using the STAR (v.2.6.1) aligner with default settings [20].…”

Section: Rna-seq Data Analysismentioning

confidence: 99%

Autophagy mitigates ethanol-induced mitochondrial dysfunction and oxidative stress in esophageal keratinocytes

et al. 2020

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“…First, a wealth of findings leaves us with little doubt that practically all human traits are influenced by genes (Collins 2010 ; Plomin et al 2016 ). Second, the cost and time taken to genotype the entire DNA sequence of an individual are continuously reducing (Goyal et al 2017 ). Third, many developed countries have already made genetic screening of newborns mandatory—for the detection and early treatment/intervention for several genetic conditions (Pourfarzam and Zadhoush 2013 ).…”

Section: Introductionmentioning

confidence: 99%

New literacy challenge for the twenty-first century: genetic knowledge is poor even among well educated

et al. 2018

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We live in an age of rapidly advancing genetic research. This research is generating new knowledge that has implications for personal health and well-being. The present study assessed the level of genetic knowledge and personal engagement with genetics in a large sample (N = 5404) of participants. Participants received secondary education in 78 countries, with the largest samples from Russia, the UK and the USA. The results showed significant group differences in genetic knowledge between different countries, professions, education levels and religious affiliations. Overall, genetic knowledge was poor. The questions were designed to assess basic genetic literacy. However, only 1.2% of participants answered all 18 questions correctly, and the average score was 65.5%. Genetic knowledge was related to peoples' attitudes towards genetics. For example, those with greater genetic knowledge were on average more willing to use genetic knowledge for their personal health management. Based on the results, the paper proposes a number of immediate steps that societies can implement to empower the public to benefit from ever-advancing genetic knowledge.

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“…725Samples were sent to CAG for sequencing. 726 727 Bulk RNA-seq analysis 728RNA-seq reads were demultiplexed using the DRAGEN genome pipeline(Goyal et al, 2017). 729 FASTQ files were aligned to hg19 reference using the STAR (v.2.6.1)(Dobin et al, 2013) aligner 730 with default settings.…”

mentioning

confidence: 99%

Neuroinflammation and EIF2 signaling persist in an HiPSC tri-culture model of HIV infection despite antiretroviral treatment

Ryan¹,

Gonzalez²,

Garifallou³

et al. 2019

Preprint

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23 HIV-Associated Neurocognitive Disorders (HAND) affect over half of HIV-infected individuals 24 worldwide, despite antiretroviral therapy (ART). Therapeutically targetable mechanisms 25 underlying HAND remain elusive. We developed a human-induced pluripotent stem cell (HiPSC) 26 based model; whereby, we independently differentiate HiPSCs into neurons, astrocytes, and 27 microglia and systematically combine to generate a tri-culture with or without HIV-infection and 28 ART. scRNAseq analysis on tri-cultures including HIV-infected microglia revealed inflammatory 29 signatures in the microglia and EIF2 signaling in all three cell types. Remarkably, EFZ alone 30 induced a similar response to infection. Treatment with the antiretroviral compound Efavirenz 31 (EFZ) mostly resolved these signatures; However, EFZ increased RhoGDI and CD40 signaling in 32 the HIV-infected microglia. This activation was associated with a persistent increase in TNFa 33 expression. This work establishes a tri-culture that recapitulates key features of HIV infection in 34 the CNS and provides a new model to examine the effects of HIV infection and its treatment with 35 antiretrovirals. 36

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Ultra-Fast Next Generation Human Genome Sequencing Data Processing Using DRAGEN<sup>TM</sup> Bio-IT Processor for Precision Medicine

Cited by 35 publications

References 16 publications

Autophagy mitigates ethanol-induced mitochondrial dysfunction and oxidative stress in esophageal keratinocytes

Autophagy mitigates ethanol-induced mitochondrial dysfunction and oxidative stress in esophageal keratinocytes

New literacy challenge for the twenty-first century: genetic knowledge is poor even among well educated

Neuroinflammation and EIF2 signaling persist in an HiPSC tri-culture model of HIV infection despite antiretroviral treatment

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