DNA Chip Research Inc.

Yokohama-shi, Japan

DNA Chip Research Inc.

Yokohama-shi, Japan

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Patent
DNA Chip Research Inc. and Osaka Prefectural Hospital Organization | Date: 2017-05-10

The object of the invention is to provide a method for counting the number of nucleic acid molecules in a mixture of a plurality of nucleic acid molecules more highly accurately. This is a method for highly accurately counting the number of nucleic acid molecules by detecting the read errors that occur when determining a nucleic acid base sequence, wherein the method has: a step for adding a barcode-sequence-generating oligonucleotide to a mixture of a plurality of nucleic acid molecules, thereby linking barcode sequences unique to the nucleic acid molecules to the base sequences constituting each of the nucleic acid molecules; a step for determining the base sequences of the nucleic acid molecules to which the barcode sequences have been linked; a step for detecting read errors in the barcode sequences for which the base sequences have been determined; and a step for calculating the proportion of barcode sequences free of read errors to all of the barcode sequences for which the base sequences have been determined, on the basis of the number of reads of the barcode sequences for which the base sequences have been determined, the abovementioned barcode-sequence-generating oligonucleotide comprising a maximum of five bases, and the number of barcode sequences free of read errors indicating the number of nucleic acid molecules in the mixture.


Patent
DNA Chip Research Inc. and Osaka Prefectural Hospital Organization | Date: 2015-07-02

The object of the invention is to provide a method for counting the number of nucleic acid molecules in a mixture of a plurality of nucleic acid molecules more highly accurately. This is a method for highly accurately counting the number of nucleic acid molecules by detecting the read errors that occur when determining a nucleic acid base sequence, wherein the method has: a step for adding a barcode-sequence-generating oligonucleotide to a mixture of a plurality of nucleic acid molecules, thereby linking barcode sequences unique to the nucleic acid molecules to the base sequences constituting each of the nucleic acid molecules; a step for determining the base sequences of the nucleic acid molecules to which the barcode sequences have been linked; a step for detecting read errors in the barcode sequences for which the base sequences have been determined; and a step for calculating the proportion of barcode sequences free of read errors to all of the barcode sequences for which the base sequences have been determined, on the basis of the number of reads of the barcode sequences for which the base sequences have been determined, the abovementioned barcode-sequence-generating oligonucleotide comprising a maximum of five bases, and the number of barcode sequences free of read errors indicating the number of nucleic acid molecules in the mixture.


Murakami Y.,Kyoto University | Tanaka M.,Tokyo Medical University | Toyoda H.,Ogaki Municipal Hospital | Hayashi K.,DNA Chip Research Inc. | And 3 more authors.
BMC Medical Genomics | Year: 2010

Background. HCV infection frequently induces chronic liver diseases. The current standard treatment for chronic hepatitis (CH) C combines pegylated interferon (IFN) and ribavirin, and is less than ideal due to undesirable effects. MicroRNAs (miRNAs) are endogenous small non-coding RNAs that control gene expression by degrading or suppressing the translation of target mRNAs. In this study we administered the standard combination treatment to CHC patients. We then examined their miRNA expression profiles in order to identify the miRNAs that were associated with each patient's drug response. Methods. 99 CHC patients with no anti-viral therapy history were enrolled. The expression level of 470 mature miRNAs found their biopsy specimen, obtained prior to the combination therapy, were quantified using microarray analysis. The miRNA expression pattern was classified based on the final virological response to the combination therapy. Monte Carlo Cross Validation (MCCV) was used to validate the outcome of the prediction based on the miRNA expression profile. Results. We found that the expression level of 9 miRNAs were significantly different in the sustained virological response (SVR) and non-responder (NR) groups. MCCV revealed an accuracy, sensitivity, and specificity of 70.5%, 76.5% and 63.3% in SVR and non-SVR and 70.0%, 67.5%, and 73.7% in relapse (R) and NR, respectively. Conclusions. The hepatic miRNA expression pattern that exists in CHC patients before combination therapy is associated with their therapeutic outcome. This information can be utilized as a novel biomarker to predict drug response and can also be applied to developing novel anti-viral therapy for CHC patients. © 2010 Murakami et al; licensee BioMed Central Ltd.


Patent
DNA Chip Research Inc. and Osaka Prefectural Hospital Organization | Date: 2012-05-16

The object of the invention is to provide a method for quantitatively assessing the degree of progression of a malignant neoplasm in a patient who has been medicated. Provided is a method for assessing the progression of the clinical state of a malignant neoplasm in a subject who has been administered with a medicine for treating the malignant neoplasm, the method being characterized by comprising: (1) a step of determining the ratio of DNA molecules having an activation mutation that serves as an activation marker for the medicine to DNA molecules having a normal marker gene in DNA in the blood from the subject; (2) a step of determining the ratio of DNA molecules having a resistance mutation that serves as a resistance marker for the medicine to DNA molecules having a normal marker gene in the DNA in the blood from the subject; and (3) a step of comparing a value obtained in the step (2) with a value obtained in the step (1) to thereby assess whether or not the malignant neoplasm in the subject has acquired resistance to the treatment with the medicine.


Yang D.,Hyogo College of Medicine | Yaguchi T.,Hyogo College of Medicine | Lim C.-R.,DNA Chip Research Inc. | Ishizawa Y.,DNA Chip Research Inc. | And 2 more authors.
Cancer Letters | Year: 2010

Extracellular adenosine-induced apoptosis of HepG2 cells, a human hepatoma cell line, in a concentration (0.1-20 mM)- and treatment (24-72 h)-dependent manner by activating caspase-3, -8, and -9. In the gene expression assay using a DNA microalley, adenosine upregulated mRNAs for tumor necrosis factor (TNF), TNF receptor 1-associated death domain protein (TRADD), TNF related apoptosis-inducing ligand receptor 2 (TRAIL-R2), TRADD/receptor-interacting protein kinase 1 (RIPK1), Fas-associated death domain protein (FADD), and caspase-9, involving activation of caspase-8 and -9 followed by the effector caspase-3. The results of the present study suggest that adenosine induces HepG2 cell apoptosis by activating those caspases as a result from tuning apoptosis-mediator gene transcription. © 2009 Elsevier Ireland Ltd. All rights reserved.


Narahara M.,Kyoto University | Higasa K.,Kyoto University | Nakamura S.,DNA Chip Research Inc. | Tabara Y.,Kyoto University | And 5 more authors.
PLoS ONE | Year: 2014

Profiles of sequence variants that influence gene transcription are very important for understanding mechanisms that affect phenotypic variation and disease susceptibility. Using genotypes at 1.4 million SNPs and a comprehensive transcriptional profile of 15,454 coding genes and 6,113 lincRNA genes obtained from peripheral blood cells of 298 Japanese individuals, we mapped expression quantitative trait loci (eQTLs). We identified 3,804 cis-eQTLs (within 500 kb from target genes) and 165 trans-eQTLs (>500 kb away or on different chromosomes). Cis-eQTLs were often located in transcribed or adjacent regions of genes; among these regions, 5′ untranslated regions and 5′ flanking regions had the largest effects. Epigenetic evidence for regulatory potential accumulated in public databases explained the magnitude of the effects of our eQTLs. Cis-eQTLs were often located near the respective target genes, if not within genes. Large effect sizes were observed with eQTLs near target genes, and effect sizes were obviously attenuated as the eQTL distance from the gene increased. Using a very stringent significance threshold, we identified 165 large-effect trans-eQTLs. We used our eQTL map to assess 8,069 disease-associated SNPs identified in 1,436 genome-wide association studies (GWAS). We identified genes that might be truly causative, but GWAS might have failed to identify for 148 out of the GWAS-identified SNPs; for example, TUFM (P = 3.3E-48) was identified for inflammatory bowel disease (early onset); ZFP90 (P = 4.4E-34) for ulcerative colitis; and IDUA (P = 2.2E-11) for Parkinson's disease. We identified four genes (P<2.0E-14) that might be related to three diseases and two hematological traits; each expression is regulated by trans-eQTLs on a different chromosome than the gene. © 2014 Narahara et al.


Patent
DNA Chip Research Inc., Keio University and Saitama University | Date: 2014-12-31

The object of the invention is to find a simple biomarker with high reproducibility with regard to a method for evaluating the activity of the condition and progression of rheumatoid arthritis disease and provide an effective evaluation method therefor. The invention is to provide a method for determining the value of a rheumatoid arthritis-linked indicator in a subject, the method being characterized by comprising a step for measuring the amount of expression of the FAM20A gene in blood collected from the subject, a step for analyzing the measured amount of expression using a gene expression profile that is prepared in advance and correlates with the indicator and a step for estimating the value of the indicator in the subject on the basis of the analysis results.


Patent
DNA Chip Research Inc., Saitama University and Keio University | Date: 2011-11-17

The object of the invention is to find a simple biomarker with high reproducibility with regard to a method for evaluating the activity of the condition and progression of rheumatoid arthritis disease and provide an effective evaluation method therefor. The invention is to provide a method for determining the value of a rheumatoid arthritis-linked indicator in a subject, the method being characterized by comprising a step for measuring the amount of expression of the FAM20A gene in blood collected from the subject, a step for analyzing the measured amount of expression using a gene expression profile that is prepared in advance and correlates with the indicator and a step for estimating the value of the indicator in the subject on the basis of the analysis results.


Yamashita D.,Ehime University | Yamashita D.,Hokkaido University | Kondo T.,Hokkaido University | Ohue S.,Ehime University | And 8 more authors.
Cancer Research | Year: 2015

Glioma-initiating cells (GIC) have stem-like cell properties thought to be sufficient for recurrence, progression, and drug resistance in glioblastomas. In the present study, we defined miRNA (miR)-340 as a differentially expressed miRNA in human GICs that inhibit GIC-mediated tumorigenesis. Furthermore, we defined tissue plasminogen activator (PLAT) as a critical direct target of miR340 for inhibition. Among miRNAs screened, we found that miR340 expression was decreased in all human GICs and in human glioblastoma tissues, compared with human neural stem cells and normal brain tissues. miR340 overexpression in GICs suppressed their proliferative, invasive, and migratory properties in vitro, triggering cell senescence in vitro and inhibiting GIC-induced tumorigenesis in mouse brains. shRNA-mediated silencing of PLAT in GICs phenocopied the effects of miR340 overexpression in vitro and in vivo, suggesting a potential role for tissue factor in stem-like cell function. Taken together, our results identified miR340 as a tumor suppressor that functions in GIC to enforce PLAT blockade and ablate their stem-like functions. ©2015 AACR.


Nakamura S.,DNA Chip Research Inc. | Kobayashi M.,DNA Chip Research Inc. | Sugino T.,Soiken Inc. | Kajimoto O.,Soiken Inc. | And 2 more authors.
Biochemical and Biophysical Research Communications | Year: 2010

A 4-h bout of exercise induces immunomodulatory effects. Peripheral blood was withdrawn before, and at 4, 8 and 24 h after the start of exercise. RNA from the unfractionated white blood cells was analyzed using Agilent human 44 K microarray. The expression profiles were sorted into seven clusters based on their unique time-dependent kinetics. In a separate experiment, cell-specific markers were collected and compared among the members in each cluster. Two clusters were assigned as representing neutrophils, one as NK cells, and another mostly as T cells. Three clusters seemed to be mixtures of several cell types. Extension of this approach to other systems is discussed. © 2009 Elsevier Inc. All rights reserved.

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