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https://www.readbyqxmd.com/read/28454300/single-cell-genomic-profiling-of-acute-myeloid-leukemia-for-clinical-use-a-pilot-study
#1
Benedict Yan, Yongli Hu, Kenneth H K Ban, Zenia Tiang, Christopher Ng, Joanne Lee, Wilson Tan, Lily Chiu, Tin Wee Tan, Elaine Seah, Chin Hin Ng, Wee-Joo Chng, Roger Foo
Although bulk high-throughput genomic profiling studies have led to a significant increase in the understanding of cancer biology, there is increasing awareness that bulk profiling approaches do not completely elucidate tumor heterogeneity. Single-cell genomic profiling enables the distinction of tumor heterogeneity, and may improve clinical diagnosis through the identification and characterization of putative subclonal populations. In the present study, the challenges associated with a single-cell genomics profiling workflow for clinical diagnostics were investigated...
March 2017: Oncology Letters
https://www.readbyqxmd.com/read/28453853/single-molecule-sequencing-revealing-the-presence-of-distinct-jc-polyomavirus-populations-in-patients-with-progressive-multifocal-leukoencephalopathy
#2
Hanna Seppälä, Elina Virtanen, Mika Saarela, Pia Laine, Lars Paulín, Laura Mannonen, Petri Auvinen, Eeva Auvinen
Background.: Progressive multifocal leukoencephalopathy (PML) is a fatal disease caused by reactivation of JC polyomavirus (JCPyV) in immunosuppressed individuals and lytic infection by neurotropic JCPyV in glial cells. The exact content of neurotropic mutations within individual JCPyV strains has not been studied to our knowledge. Methods.: We exploited the capacity of single-molecule real-time sequencing technology to determine the sequence of complete JCPyV genomes in single reads...
March 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28453695/genetic-variants-of-dna-repair-related-genes-predict-efficacy-of-tas-102-in-patients-with-refractory-metastatic-colorectal-cancer
#3
M Suenaga, M Schirripa, S Cao, W Zhang, D Yang, S Murgioni, D Rossini, F Marmorino, A Mennitto, Y Ning, S Okazaki, M D Berger, Y Miyamoto, R Gopez, A Barzi, T Yamaguchi, F Loupakis, H-J Lenz
Background: Tri-phosphorylated trifluridine (FTD) incorporation into DNA is TAS-102's main anti-tumor action. We tested whether genetic polymorphisms in homologous recombination (HR) and cell cycle checkpoint pathway for DNA repair is associated with outcomes in refractory metastatic colorectal cancer (mCRC) patients treated with TAS-102. Patients and methods: We analyzed genomic DNA extracted from 233 samples of three cohorts: an evaluation cohort of 52 patients receiving TAS-102, a validation cohort of 129 patients receiving TAS-102 and a control cohort of 52 patients receiving regorafenib...
May 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28453394/expression-of-mir-23a-by-apoptotic-regulators-in-human-cancer-a-review
#4
Rabih Roufayel, Seifedine Kadry
MicroRNAs play fundamental roles in mammalian development, differentiation and cellular homeostasis by regulating essential processes such as proliferation, migration, metabolism, migration and cell death. These small non-coding RNAs are also responsible in RNA silencing, and in many developmental and pathological processes. Not surprisingly, miR-23a misexpression contributes to numerous diseases including cancer where certain miRNA genes have been classified as either oncogenes or tumor suppressor genes. Since a single microRNA is capable of targeting a large number of mRNA sequences, de-regulated miRNA expression has the ability to alter various transcripts and activate a wide range of cancer-related pathways...
April 28, 2017: Cancer Biology & Therapy
https://www.readbyqxmd.com/read/28449120/sigseeker-a-peak-calling-ensemble-approach-for-constructing-epigenetic-signatures
#5
Jens Lichtenberg, Laura Elnitski, David M Bodine
Motivation: Epigenetic data are invaluable when determining the regulatory programs governing a cell. Based on use of next-generation sequencing data for characterizing epigenetic marks and transcription factor binding, numerous peak-calling approaches have been developed to determine sites of genomic significance in these data. Such analyses can produce a large number of false positive predictions, suggesting that sites supported by multiple algorithms provide a stronger foundation for inferring and characterizing regulatory programs associated with the epigenetic data...
April 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28449065/a-homozygous-missense-mutation-in-eral1-encoding-a-mitochondrial-rrna-chaperone-causes-perrault-syndrome
#6
Iliana A Chatzispyrou, Marielle Alders, Sergio Guerrero-Castillo, Ruben Zapata Perez, Martin A Haagmans, Laurent Mouchiroud, Janet Koster, Rob Ofman, Frank Baas, Hans R Waterham, Johannes N Spelbrink, Johan Auwerx, Marcel M Mannens, Riekelt H Houtkooper, Astrid S Plomp
Perrault syndrome (PS) is a rare recessive disorder characterized by ovarian dysgenesis and sensorineural deafness. It is clinically and genetically heterogeneous, and previously mutations have been described in different genes, mostly related to mitochondrial proteostasis. We diagnosed three unrelated females with PS and set out to identify the underlying genetic cause using exome sequencing. We excluded mutations in the known PS genes, but identified a single homozygous mutation in the ERAL1 gene (c.707A>T; p...
April 25, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28448765/digital-assays-part-i-partitioning-statistics-and-digital-pcr
#7
Amar S Basu
A digital assay is one in which the sample is partitioned into many small containers such that each partition contains a discrete number of biological entities (0, 1, 2, 3, …). A powerful technique in the biologist's toolkit, digital assays bring a new level of precision in quantifying nucleic acids, measuring proteins and their enzymatic activity, and probing single-cell genotypes and phenotypes. Part I of this review begins with the benefits and Poisson statistics of partitioning, including sources of error...
April 1, 2017: SLAS Technology
https://www.readbyqxmd.com/read/28448556/a-highly-specific-and-sensitive-massive-parallel-sequencer-based-test-for-somatic-mutations-in-non-small-cell-lung-cancer
#8
Yoshiaki Inoue, Jun Shiihara, Hitoshi Miyazawa, Hiromitsu Ohta, Megumi Higo, Yoshiaki Nagai, Kunihiko Kobayashi, Yasuo Saijo, Masanori Tsuchida, Mitsuo Nakayama, Koichi Hagiwara
Molecular targeting therapy for non-small cell lung cancer (NSCLC) has clarified the importance of mutation testing when selecting treatment regimens. As a result, multiple-gene mutation tests are urgently needed. We developed a next-generation sequencer (NGS)-based, multi-gene test named the MINtS for investigating driver mutations in both cytological specimens and snap-frozen tissue samples. The MINtS was used to investigate the EGFR, KRAS, BRAF genes from DNA, and the ERBB2, and the ALK, ROS1, and RET fusion genes from RNA...
2017: PloS One
https://www.readbyqxmd.com/read/28448066/structural-basis-of-crispr-spycas9-inhibition-by-an-anti-crispr-protein
#9
De Dong, Minghui Guo, Sihan Wang, Yuwei Zhu, Shuo Wang, Zhi Xiong, Jianzheng Yang, Zengliang Xu, Zhiwei Huang
The CRISPR-Cas9 systems are bacterial encoded adaptive immune systems to defend against phages infection, through RNA-guided endonuclease activity of Cas9 to degrade double-stranded DNA bearing a protospacer adjacent motif (PAM) and complementary sequences to the guide RNA1,2,3,4,5. Recently, two anti-CRISPR proteins AcrIIA2 and AcrIIA4 from Listeria monocytogenes (Lmo) prophages have been identified, both of which potently inhibit Streptococcus pyogenes Cas9 (SpyCas9) and LmoCas9 activity in bacteria and human cells6...
April 27, 2017: Nature
https://www.readbyqxmd.com/read/28447726/a-three-caller-pipeline-for-variant-analysis-of-cancer-whole-exome-sequencing-data
#10
Ze-Kun Liu, Yu-Kui Shang, Zhi-Nan Chen, Huijie Bian
Rapid advancements in next generation sequencing (NGS) technologies, coupled with the dramatic decrease in cost, have made NGS one of the leading approaches applied in cancer research. In addition, it is increasingly used in clinical practice for cancer diagnosis and treatment. Somatic (cancer‑only) single nucleotide variants and small insertions and deletions (indels) are the simplest classes of mutation, however, their identification in whole exome sequencing data is complicated by germline polymorphisms, tumor heterogeneity and errors in sequencing and analysis...
March 16, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28447043/comparative-genomics-of-human-stem-cell-factor-scf
#11
Moein Dehbashi, Elahe Kamali, Sadeq Vallian
Stem cell factor (SCF) is a critical protein with key roles in the cell such as hematopoiesis, gametogenesis and melanogenesis. In the present study a comparative analysis on nucleotide sequences of SCF was performed in Humanoids using bioinformatics tools including NCBI-BLAST, MEGA6, and JBrowse. Our analysis of nucleotide sequences to find closely evolved organisms with high similarity by NCBI-BLAST tools and MEGA6 showed that human and Chimpanzee (Pan troglodytes) were placed into the same cluster. By using JBrowse, we found that SCF in Neanderthal had a single copy number similar to modern human and partly conserved nucleotide sequences...
March 2017: Molecular Biology Research Communications
https://www.readbyqxmd.com/read/28446964/strategies-for-the-acquisition-of-transcriptional-and-epigenetic-information-in-single-cells
#12
REVIEW
Guang Li, Elda Dzilic, Nick Flores, Alice Shieh, Sean M Wu
As the basic unit of living organisms, each single cell has unique molecular signatures and functions. Our ability to uncover the transcriptional and epigenetic signature of single cells has been hampered by the lack of tools to explore this area of research. The advent of microfluidic single cell technology along with single cell genome-wide DNA amplification methods had greatly improved our understanding of the expression variation in single cells. Transcriptional expression profile by multiplex qPCR or genome-wide RNA sequencing has enabled us to examine genes expression in single cells in different tissues...
March 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28446707/deterministic-versus-stochastic-model-of-reprogramming-new-evidence-from-cellular-barcoding-technique
#13
Anastasia M Yunusova, Veniamin S Fishman, Gennady V Vasiliev, Nariman R Battulin
Factor-mediated reprogramming of somatic cells towards pluripotency is a low-efficiency process during which only small subsets of cells are successfully reprogrammed. Previous analyses of the determinants of the reprogramming potential are based on average measurements across a large population of cells or on monitoring a relatively small number of single cells with live imaging. Here, we applied lentiviral genetic barcoding, a powerful tool enabling the identification of familiar relationships in thousands of cells...
April 2017: Open Biology
https://www.readbyqxmd.com/read/28446532/next-generation-sequencing-ngs-analysis-on-single-circulating-tumor-cells-ctcs-with-no-need-of-whole-genome-amplification-wga
#14
Raffaele Palmirotta, Domenica Lovero, Erica Silvestris, Claudia Felici, Davide Quaresmini, Paola Cafforio, Franco Silvestris
BACKGROUND: Isolation and genotyping of circulating tumor cells (CTCs) is gaining an increasing interest by clinical researchers in oncology not only for investigative purposes, but also for concrete application in clinical practice in terms of diagnosis, prognosis and decision treatment with targeted therapies. For the mutational analysis of single CTCs, the most advanced biotechnology methodology currently available includes the combination of whole genome amplification (WGA) followed by next-generation sequencing (NGS)...
May 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28446220/scale-modeling-allele-specific-gene-expression-by-single-cell-rna-sequencing
#15
Yuchao Jiang, Nancy R Zhang, Mingyao Li
Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing allows the comparison of expression distribution between the two alleles of a diploid organism and the characterization of allele-specific bursting. Here, we propose SCALE to analyze genome-wide allele-specific bursting, with adjustment of technical variability. SCALE detects genes exhibiting allelic differences in bursting parameters and genes whose alleles burst non-independently...
April 26, 2017: Genome Biology
https://www.readbyqxmd.com/read/28445990/prognostic-value-of-tumor-mutations-in-radically-treated-locally-advanced-non-small-cell-lung-cancer-patients
#16
Angela Boros, Ludovic Lacroix, Benjamin Lacas, Julien Adam, Jean-Pierre Pignon, Caroline Caramella, David Planchard, Vincent de Montpreville, Eric Deutsch, Antonin Levy, Benjamin Besse, Cécile Le Pechoux
INTRODUCTION: Chemo-radiation is standard treatment in locally advanced non-small cell lung cancers (NSCLC). The prognostic value of mutations has been poorly explored in this population. RESULTS: Clinical data were collected from 190 patients and mutational profiles were obtained in 78 of them; 58 (74%) were males, 31 (40%) current smokers, 47/31 stage IIIA/IIIB and 40 (51%) adenocarcinoma. The following mutations were identified: EGFR 12% (9/78), KRAS 15% (12/78), BRAF 5% (3/65), PI3KCA 2% (1/57), NRAS 3% (1/32), and ALK+ (FISH) 4% (2/51)...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445759/pulsatile-lipid-vesicles-under-osmotic-stress
#17
Morgan Chabanon, James C S Ho, Bo Liedberg, Atul N Parikh, Padmini Rangamani
The response of lipid bilayers to osmotic stress is an important part of cellular function. Recent experimental studies showed that when cell-sized giant unilamellar vesicles (GUVs) are exposed to hypotonic media, they respond to the osmotic assault by undergoing a cyclical sequence of swelling and bursting events, coupled to the membrane's compositional degrees of freedom. Here, we establish a fundamental and quantitative understanding of the essential pulsatile behavior of GUVs under hypotonic conditions by advancing a comprehensive theoretical model of vesicle dynamics...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28445510/whole-genome-re-sequencing-to-identify-suppressor-mutations-of-mutant-and-foreign-escherichia-coli-ftsz
#18
Kiani A J Arkus Gardner, Masaki Osawa, Harold P Erickson
FtsZ is an essential protein for bacterial cell division, where it forms the cytoskeletal scaffold and may generate the constriction force. We have found previously that some mutant and foreign FtsZ that do not complement an ftsZ null can function for cell division in E. coli upon acquisition of a suppressor mutation somewhere in the genome. We have now identified, via whole genome re-sequencing, single nucleotide polymorphisms in 11 different suppressor strains. Most of the mutations are in genes of various metabolic pathways, which may modulate cell division indirectly...
2017: PloS One
https://www.readbyqxmd.com/read/28443228/genome-sequencing-analysis-of-atypical-shigella-flexneri-isolated-in-korea
#19
Nan-Ok Kim, Hae-Young Na, Su-Mi Jung, Gyung Tae Chung, Hyo Sun Kawk, Sahyun Hong
OBJECTIVES: An atypical Shigella flexneri strain with a plural agglutination pattern [i.e., reacting not only with serum samples containing type antigen II but also with serum samples containing group antigens (3)4 and 7(8)] was selected for genome sequencing, with the aim of obtaining additional comparative information about such strains. METHODS: The genomic DNA of atypical S. flexneri strain NCCP 15744 was sequenced using an Ion Torrent PGM sequencing machine (Life Technologies, USA)...
February 2017: Osong Public Health and Research Perspectives
https://www.readbyqxmd.com/read/28443105/identification-of-microrna-targets-of-capsicum-spp-using-mirtrans-a-trans-omics-approach
#20
Lu Zhang, Cheng Qin, Junpu Mei, Xiaocui Chen, Zhiming Wu, Xirong Luo, Jiaowen Cheng, Xiangqun Tang, Kailin Hu, Shuai C Li
The microRNA (miRNA) can regulate the transcripts that are involved in eukaryotic cell proliferation, differentiation, and metabolism. Especially for plants, our understanding of miRNA targets, is still limited. Early attempts of prediction on sequence alignments have been plagued by enormous false positives. It is helpful to improve target prediction specificity by incorporating the other data sources such as the dependency between miRNA and transcript expression or even cleaved transcripts by miRNA regulations, which are referred to as trans-omics data...
2017: Frontiers in Plant Science
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