News

  • Evaluation of circulating tumor DNA assays for precision oncology
    Circulating tumor DNA (ctDNA) is an accessible biomarker for cancer detection, molecular stratification, therapeutic monitoring, and post-treatment surveillance. Compared to traditional tissue biopsy, ctDNA as liquid biopsy is minimally invasive and can be performed serially to monitor tumor evolution or response to any drug therapy.  Due to these advantages, ctDNA is being rapidly adopted in precision medicine.  However, ctDNA sequencing assays face major challenges such as cell-free DNA exists as small fragments, and only a small fraction (< 0.01-0.1 %) of cell-free DNA is tumor-derived as we call ctDNA. In addition, ctDNA sequencing assays are also affected by a range of experimental variables and artifacts.
    2020-04-26
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  • RNase H-dependent PCR sequencing improving T cell receptor repertoire analysis
    T cell receptor (TCR) diversity or heterogeneity is a great measure of immune response to pathogens, cancer, and therapeutic interventions. Identification of exact pair of TCR-alpha and TCR-beta chain interacting with an antigen provides a potential vaccination therapy for cancer. Multiplex PCR amplicon sequencing is a straightforward strategy for analyzing TCR alpha and beta variables. However, non-specific amplification, primer dimers caused by multiple primers in PCR generate lots of NGS reads useless finally.
    2020-04-12
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  • CRISPR-engineered T cells in patients with refractory cancer
    CRISPR-Cas9 endonuclease is a powerful gene-editing technology. Direct editing of cells by delivering Cas9 gene typically triggers an immune response, a big challenge for CRISPR gene editing therapies. While in ex vivo, cells are treated in a dish before transplantation, Cas9 immune response can be circumvented as Cas9 transiently expresses, Cas9 is cleaned up before corrected cells are administered into patients (ref1).
    2020-04-05
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  • RNA fractionation sequencing: characterizing transcriptome regulation in developing human brain
    The brain is the most complex organ in humans, no matter in anatomy level, cell level, or molecule biology level. It has numerous types of cells that function differently, it also has enriched activity of gene expression, pre-mRNA alternative splicing. Understanding molecule mechanism regulation of the brain is vital both in human mental disorders, in high cognition of humans in primate brain evolution.
    2020-03-29
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  • Small RNA Sequencing revealed Diet affects Male Reproductive Health
    Human sperm quality declines during the past 35 years. Risk factors for low sperm quality involve environmental issues (e.g., pesticides and heavy metals), lifestyle (e.g. tobacco, alcohol drinks). Obesity with associated diabetes is another risk factor. In recent PLoS Biology, Daniel Natt and colleagues used a two-step diet intervention model to study how diet affects sperm’s motility.
    2020-03-22
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  • SHERRY: a new method for RNA-seq
    Transcriptome profiling using next generation sequencing has become routine in biological research. Typically, researchers do RNA extraction, poly(A) selection or ribosomal RNA depletion, first and second strand cDNA synthesis, sequencer adapter ligation, and final library PCR amplification.
    2020-03-15
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  • CUT&RUN: a revolutionary strategy for studying genome-wide profiles of chromatin remodelers
    CUT&RUN (cleavage under targets and release using nuclease) is an epigenomic profiling method developed by the group of Dr. Steven Henikoff at Fred Hutchinson Cancer Research Center. CUT&RUN is performed in situ on immobilized, intact cells without crosslinking. DNA fragmentation is achieved using micrococcal nuclease fused to Protein A and/or Protein G (pA/G-MNase).
    2020-03-08
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  • Nucleic acid detection of SARS-CoV-2, the novel coronavirus identified in Wuhan, China
    On Feb 23, 2020, CDC (Centers for Disease Control and Prevention) is responding to an outbreak of respiratory disease caused by a novel coronavirus, which was first detected in Wuhan, China. This virus has been officially named “SARS-CoV-2” (formerly called 2019-nCoV), which now has been detected in 32 locations internationally. This virus can be person-to-person transmitted, there are around 80,000 confirmed cases (updated Feb 24, 2020).
    2020-02-24
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  • Multiple sequencing technologies and image visualization reveal accessible chromatin structure of circular extrachromosomal DNA and its role in cancer genomics
    Extrachromosomal DNA (ecDNA) is any DNA that is found off the chromosomes. Typically, for instance, in human cells, mitochondrial DNA (mtDNA) is one type of ecDNA. Today we are going to talking about another type --- extrachromosomal circular DNA (eccDNA), which is derived directly from genomic DNA.
    2020-02-23
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  • “cP-RNA-seq” reveals New RNA molecules that may play a role in aging
    RNA plays a special role in life science. It can be as genetic materials like DNA, it can catalyze specific biochemical reactions, which is similar to the action of the protein. Due to its single strand, it forms many secondary structures, providing more variation ------ a significant evolutionary advantage compared to DNA. One specific RNA type whenever is discovered will become a fascinating research topic, such as miRNA, piRNAs, non-coding RNAs, circular RNAs.
    2020-02-16
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