当前位置： SCI文献检索 > INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES期刊下所有文献 > Pre-Analytical Considerations for Successful Next-Generation Sequencing (NGS): Challenges and Opportunities for Formalin-Fixed and Paraffin-Embedded Tumor Tissue (FFPE) Samples.

Pre-Analytical Considerations for Successful Next-Generation Sequencing (NGS): Challenges and Opportunities for Formalin-Fixed and Paraffin-Embedded Tumor Tissue (FFPE) Samples.

Abstract：

:In cancer drug discovery, it is important to investigate the genetic determinants of response or resistance to cancer therapy as well as factors that contribute to adverse events in the course of clinical trials. Despite the emergence of new technologies and the ability to measure more diverse analytes (e.g., circulating tumor cell (CTC), circulating tumor DNA (ctDNA), etc.), tumor tissue is still the most common and reliable source for biomarker investigation. Because of its worldwide use and ability to preserve samples for many decades at ambient temperature, formalin-fixed, paraffin-embedded tumor tissue (FFPE) is likely to be the preferred choice for tissue preservation in clinical practice for the foreseeable future. Multiple analyses are routinely performed on the same FFPE samples (such as Immunohistochemistry (IHC), in situ hybridization, RNAseq, DNAseq, TILseq, Methyl-Seq, etc.). Thus, specimen prioritization and optimization of the isolation of analytes is critical to ensure successful completion of each assay. FFPE is notorious for producing suboptimal DNA quality and low DNA yield. However, commercial vendors tend to request higher DNA sample mass than what is actually required for downstream assays, which restricts the breadth of biomarker work that can be performed. We evaluated multiple genomics service laboratories to assess the current state of NGS pre-analytical processing of FFPE. Significant differences in pre-analytical capabilities were observed. Key aspects are highlighted and recommendations are made to improve the current practice in translational research.

journal_name

Int J Mol Sci

journal_title

International journal of molecular sciences

authors

Arreaza G,Qiu P,Pang L,Albright A,Hong LZ,Marton MJ,Levitan D

doi

10.3390/ijms17091579

subject

Has Abstract

pub_date

2016-09-20 00:00:00

issue

9

issn

1422-0067

pii

ijms17091579

journal_volume

17

pub_type

杂志文章

相关文献

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES文献大全
  • MT-Feeding-Induced Impermanent Sex Reversal in the Orange-Spotted Grouper during Sex Differentiation.

    abstract：:In this study, we systematically investigated the process of sex reversal induced by 17-methyltestosterone (MT) feeding and MT-feeding withdrawal at the ovary differentiation stage in orange-spotted groupers, Epinephelus coioides. Gonadal histology showed that MT feeding induced a precocious sex reversal from immature...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms19092828

    authors： Wang Q,Huang M,Peng C,Wang X,Xiao L,Wang D,Chen J,Zhao H,Zhang H,Li S,Yang H,Liu Y,Lin H,Zhang Y

    更新日期：2018-09-19 00:00:00

  • Abscisic Acid Represses Rice Lamina Joint Inclination by Antagonizing Brassinosteroid Biosynthesis and Signaling.

    abstract：:Leaf angle is a key parameter that determines plant architecture and crop yield. Hormonal crosstalk involving brassinosteroid (BR) plays an essential role in leaf angle regulation in cereals. In this study, we investigated whether abscisic acid (ABA), an important stress-responsive hormone, co-regulates lamina joint i...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms20194908

    authors： Li QF,Lu J,Zhou Y,Wu F,Tong HN,Wang JD,Yu JW,Zhang CQ,Fan XL,Liu QQ

    更新日期：2019-10-03 00:00:00

  • Structural Studies of Predicted Ligand Binding Sites and Molecular Docking Analysis of Slc2a4 as a Therapeutic Target for the Treatment of Cancer.

    abstract：:Presently, many studies have focused on exploring in silico approaches in the identification and development of alternative therapy for the treatment and management of cancer. Solute carrier family-2-member-4-gene (Slc2a4) which encodes glucose transporter 4 protein (GLUT4), has been identified as a promising therapeu...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms19020386

    authors： Aruleba RT,Adekiya TA,Oyinloye BE,Kappo AP

    更新日期：2018-01-28 00:00:00

  • Unveiling the Actual Functions of Awns in Grasses: From Yield Potential to Quality Traits.

    abstract：:Awns, which are either bristles or hair-like outgrowths of lemmas in the florets, are one of the typical morphological characteristics of grass species. These stiff structures contribute to grain dispersal and burial and fend off animal predators. However, their phenotypic and genetic associations with traits deciding...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章,评审

    doi：10.3390/ijms21207593

    authors： Ntakirutimana F,Xie W

    更新日期：2020-10-14 00:00:00

  • Route and Regulation of Zinc, Cadmium, and Iron Transport in Rice Plants (Oryza sativa L.) during Vegetative Growth and Grain Filling: Metal Transporters, Metal Speciation, Grain Cd Reduction and Zn and Fe Biofortification.

    abstract：:Zinc (Zn) and iron (Fe) are essential but are sometimes deficient in humans, while cadmium (Cd) is toxic if it accumulates in the liver and kidneys at high levels. All three are contained in the grains of rice, a staple cereal. Zn and Fe concentrations in rice grains harvested under different levels of soil/hydroponic...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章,评审

    doi：10.3390/ijms160819111

    authors： Yoneyama T,Ishikawa S,Fujimaki S

    更新日期：2015-08-13 00:00:00

  • Computational Methods for Modeling Aptamers and Designing Riboswitches.

    abstract：:Riboswitches, which are located within certain noncoding RNA region perform functions as genetic "switches", regulating when and where genes are expressed in response to certain ligands. Understanding the numerous functions of riboswitches requires computation models to predict structures and structural changes of the...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章,评审

    doi：10.3390/ijms18112442

    authors： Gong S,Wang Y,Wang Z,Zhang W

    更新日期：2017-11-17 00:00:00

  • Thrombocytosis and Effects of IL-6 Knock-Out in a Colitis-Associated Cancer Model.

    abstract：:There is an increasing number of studies showing that thrombocytosis-accompanying a variety of solid tumors including colorectal cancer (CRC)-is associated with shorter survival and earlier development of metastases. The mechanisms of cancer-associated thrombocytosis are not completely understood yet. The aim of our s...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms21176218

    authors： Josa V,Ferenczi S,Szalai R,Fuder E,Kuti D,Horvath K,Hegedus N,Kovacs T,Bagamery G,Juhasz B,Winkler Z,Veres DS,Zrubka Z,Mathe D,Baranyai Z

    更新日期：2020-08-27 00:00:00

  • Pigment Epithelium-Derived Factor (PEDF) Receptors Are Involved in Survival of Retinal Neurons.

    abstract：:The demise of retinal ganglion cells (RGCs) is characteristic of diseases of the retina such as glaucoma and diabetic or ischemic retinopathies. Pigment epithelium-derived factor (PEDF) is a multifunctional secreted protein that mediates neuroprotection and inhibition of angiogenesis in the retina. We have studied exp...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms22010369

    authors： Bürger S,Meng J,Zwanzig A,Beck M,Pankonin M,Wiedemann P,Eichler W,Unterlauft JD

    更新日期：2020-12-31 00:00:00

  • Aronia melanocarpa (Black Chokeberry) Reduces Ethanol-Induced Gastric Damage via Regulation of HSP-70, NF-κB, and MCP-1 Signaling.

    abstract：:Aronia melanocarpa (Michx.) Ell. belongs to the Rosaceae family. The purpose of this study is to explore the gastroprotective effect of the Aronia melanocarpa hydro-alcoholic extract (AMHAE) against ethanol-induced gastric ulcer in a rat model. Different concentrations (50, 100, and 200 mg/kg) of AMHAE, or 30 mg/kg of...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms18061195

    authors： Paulrayer A,Adithan A,Lee JH,Moon KH,Kim DG,Im SY,Kang CW,Kim NS,Kim JH

    更新日期：2017-06-05 00:00:00

  • Cannabidiol Ameliorates Monocrotaline-Induced Pulmonary Hypertension in Rats.

    abstract：:Cannabidiol (CBD) is known for its vasorelaxant (including in the human pulmonary artery), anti-proliferative and anti-inflammatory properties. The aim of our study was to examine the potential preventive effect of chronic CBD administration (10 mg/kg/day for three weeks) on monocrotaline (MCT)-induced pulmonary hyper...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms21197077

    authors： Sadowska O,Baranowska-Kuczko M,Gromotowicz-Popławska A,Biernacki M,Kicman A,Malinowska B,Kasacka I,Krzyżewska A,Kozłowska H

    更新日期：2020-09-25 00:00:00

  • Preoperative 3D FSE T1-Weighted MR Plaque Imaging for Severely Stenotic Cervical ICA: Accuracy of Predicting Emboli during Carotid Endarterectomy.

    abstract：:The aim of the present study was to determine whether preoperative three-dimensional (3D) fast spin-echo (FSE) T1-weighted magnetic resonance (MR) plaque imaging for severely stenotic cervical carotid arteries could accurately predict the development of artery-to-artery emboli during exposure of the carotid arteries i...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms17111791

    authors： Ogasawara Y,Sato Y,Narumi S,Sasaki M,Fujiwara S,Kobayashi M,Yoshida K,Terayama Y,Ogasawara K

    更新日期：2016-10-27 00:00:00

  • OsMKK3, a Stress-Responsive Protein Kinase, Positively Regulates Rice Resistance to Nilaparvata lugens via Phytohormone Dynamics.

    abstract：:Plants undergo several but very precise molecular, physiological, and biochemical modulations in response to biotic stresses. Mitogen-activated protein kinase (MAPK) cascades orchestrate multiple cellular processes including plant growth and development as well as plant responses against abiotic and biotic stresses. H...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms20123023

    authors： Zhou S,Chen M,Zhang Y,Gao Q,Noman A,Wang Q,Li H,Chen L,Zhou P,Lu J,Lou Y

    更新日期：2019-06-20 00:00:00

  • Targeted Suppression and Knockout of ASCT2 or LAT1 in Epithelial and Mesenchymal Human Liver Cancer Cells Fail to Inhibit Growth.

    abstract：:Amino acid transporters alanine-serine-cysteine transporter 2 (ASCT2) and L-Type Amino Acid Transporter 1 (LAT1) are coordinately enhanced in human cancers where among other roles, they are thought to drive mechanistic target-of-rapamycin (mTOR) growth signaling. To assess ASCT2 and LAT1 as therapeutic targets, nine u...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms19072093

    authors： Bothwell PJ,Kron CD,Wittke EF,Czerniak BN,Bode BP

    更新日期：2018-07-19 00:00:00

  • Effect of TDP2 on the Level of TOP2-DNA Complexes and SUMOylated TOP2-DNA Complexes.

    abstract：:DNA topoisomerase II (TOP2) activity involves a normally transient double-strand break intermediate in which the enzyme is coupled to DNA via a 5'-phosphotyrosyl bond. However, etoposide and other topoisomerase drugs poison the enzyme by stabilising this enzyme-bridged break, resulting in the accumulation of TOP2-DNA ...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms19072056

    authors： Lee KC,Swan RL,Sondka Z,Padget K,Cowell IG,Austin CA

    更新日期：2018-07-14 00:00:00

  • Nanosecond-Pulsed DBD Plasma-Generated Reactive Oxygen Species Trigger Immunogenic Cell Death in A549 Lung Carcinoma Cells through Intracellular Oxidative Stress.

    abstract：:A novel application for non-thermal plasma is the induction of immunogenic cancer cell death for cancer immunotherapy. Cells undergoing immunogenic death emit danger signals which facilitate anti-tumor immune responses. Although pathways leading to immunogenic cell death are not fully understood; oxidative stress is c...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms18050966

    authors： Lin A,Truong B,Patel S,Kaushik N,Choi EH,Fridman G,Fridman A,Miller V

    更新日期：2017-05-03 00:00:00

  • In Vitro Feasibility Analysis of a New Sutureless Wound-Closure System Based on a Temperature-Regulated Laser and a Transparent Collagen Membrane for Laser Tissue Soldering (LTS).

    abstract：:For the post-surgical treatment of oral wounds and mucosal defects beyond a certain size, the gold standard is still an autologous skin or mucosal graft in combination with complex suturing techniques. A variety of techniques and biomaterials has been developed for sutureless wound closure including different tissue g...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms21197104

    authors： Birkelbach MA,Smeets R,Fiedler I,Kluwe L,Wehner M,Trebst T,Hartjen P

    更新日期：2020-09-26 00:00:00

  • Resilience and Vulnerability to Pain and Inflammation in the Hippocampus.

    abstract：:Increasing evidence demonstrates the importance of hippocampal neurogenesis, a fundamental mechanism of neuroplasticity associated with cognition and emotion, in correlation to neurodegenerative and psychiatric disorders. Neuropsychiatric disorders are often a result of chronic stress or pain followed by inflammation;...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章,评审

    doi：10.3390/ijms18040739

    authors： Vasic V,Schmidt MHH

    更新日期：2017-03-31 00:00:00

  • A Tetra-Panel of Serum Circulating miRNAs for the Diagnosis of the Four Most Prevalent Tumor Types.

    abstract：:The purpose of this study is to clinically validate a series of circulating miRNAs that distinguish between the 4 most prevalent tumor types (lung cancer (LC); breast cancer (BC); colorectal cancer (CRC); and prostate cancer (PCa)) and healthy donors (HDs). A total of 18 miRNAs and 3 housekeeping miRNA genes were eval...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms21082783

    authors： Pastor-Navarro B,García-Flores M,Fernández-Serra A,Blanch-Tormo S,Martínez de Juan F,Martínez-Lapiedra C,Maia de Alcantara F,Peñalver JC,Cervera-Deval J,Rubio-Briones J,García-Rupérez J,López-Guerrero JA

    更新日期：2020-04-16 00:00:00

  • Alpha-Smooth Muscle Actin-Positive Perivascular Cells in Diabetic Retina and Choroid.

    abstract：:Structural alterations of pericytes in microvessels are important features of diabetic retinopathy. Although capillary pericytes had been known not to have α-smooth muscle actin (αSMA), a recent study revealed that a specific fixation method enabled the visualization of αSMA along retinal capillaries. In this study, w...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms21062158

    authors： Kim SJ,Kim SA,Choi YA,Park DY,Lee J

    更新日期：2020-03-20 00:00:00

  • Sod1 loss induces intrinsic superoxide accumulation leading to p53-mediated growth arrest and apoptosis.

    abstract：:Oxidative damages induced by a redox imbalance cause age-related changes in cells and tissues. Superoxide dismutase (SOD) enzymes play a major role in the antioxidant system and they also catalyze superoxide radicals (O2·-). Since the loss of cytoplasmic SOD (SOD1) resulted in aging-like phenotypes in several types of...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms140610998

    authors： Watanabe K,Shibuya S,Koyama H,Ozawa Y,Toda T,Yokote K,Shimizu T

    更新日期：2013-05-24 00:00:00

  • Burkholderia cenocepacia H111 Produces a Water-Insoluble Exopolysaccharide in Biofilm: Structural Determination and Molecular Modelling.

    abstract：:Biofilms are a multicellular way of life, where bacterial cells are close together and embedded in a hydrated macromolecular matrix which offers a number of advantages to the cells. Extracellular polysaccharides play an important role in matrix setup and maintenance. A water-insoluble polysaccharide was isolated and p...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms21051702

    authors： Bellich B,Jou IA,Caterino M,Rizzo R,Ravenscroft N,Fazli M,Tolker-Nielsen T,Brady JW,Cescutti P

    更新日期：2020-03-02 00:00:00

  • Differential Secretion of Angiopoietic Factors and Expression of MicroRNA in Umbilical Cord Blood from Healthy Appropriate-For-Gestational-Age Preterm and Term Newborns-in Search of Biomarkers of Angiogenesis-Related Processes in Preterm Birth.

    abstract：:Objectives: Premature birth, defined as less than 37 weeks gestation, affects approximately 12% of all live births around the world. Advances in neonatal care have resulted in the increased survival of infants born prematurely. Although prematurity is a known risk factor for different cardiovascular diseases, little i...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms21041305

    authors： Gródecka-Szwajkiewicz D,Ulańczyk Z,Zagrodnik E,Łuczkowska K,Rogińska D,Kawa MP,Stecewicz I,Safranow K,Machaliński B

    更新日期：2020-02-14 00:00:00

  • Examination of Adsorption Orientation of Amyloidogenic Peptides Over Nano-Gold Colloidal Particle Surfaces.

    abstract：:The adsorption of amyloidogenic peptides, amyloid beta 1-40 (Aβ1-40), alpha-synuclein (α-syn), and beta 2 microglobulin (β2m), was attempted over the surface of nano-gold colloidal particles, ranging from d = 10 to 100 nm in diameter (d). The spectroscopic inspection between pH 2 and pH 12 successfully extracted the c...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms20215354

    authors： Yokoyama K,Brown K,Shevlin P,Jenkins J,D'Ambrosio E,Ralbovsky N,Battaglia J,Deshmukh I,Ichiki A

    更新日期：2019-10-28 00:00:00

  • Development of small RNA delivery systems for lung cancer therapy.

    abstract：:RNA interference (RNAi) has emerged as a powerful tool for studying target identification and holds promise for the development of therapeutic gene silencing. Recent advances in RNAi delivery and target selection provide remarkable opportunities for translational medical research. The induction of RNAi relies on small...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章,评审

    doi：10.3390/ijms16035254

    authors： Fujita Y,Kuwano K,Ochiya T

    更新日期：2015-03-06 00:00:00

  • Polyphenolic Extract of Euphorbia supina Attenuates Manganese-Induced Neurotoxicity by Enhancing Antioxidant Activity through Regulation of ER Stress and ER Stress-Mediated Apoptosis.

    abstract：:Manganese (Mn) is an important trace element present in human body, which acts as an enzyme co-factor or activator in various metabolic reactions. While essential in trace amounts, excess levels of Mn in human brain can produce neurotoxicity, including idiopathic Parkinson's disease (PD)-like extrapyramidal manganism ...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms18020300

    authors： Bahar E,Lee GH,Bhattarai KR,Lee HY,Choi MK,Rashid HO,Kim JY,Chae HJ,Yoon H

    更新日期：2017-01-30 00:00:00

  • Salicylic Acid Induces Resistance in Rubber Tree against Phytophthora palmivora.

    abstract：:Induced resistance by elicitors is considered to be an eco-friendly strategy to stimulate plant defense against pathogen attack. In this study, we elucidated the effect of salicylic acid (SA) on induced resistance in rubber tree against Phytophthora palmivora and evaluated the possible defense mechanisms that were inv...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms19071883

    authors： Deenamo N,Kuyyogsuy A,Khompatara K,Chanwun T,Ekchaweng K,Churngchow N

    更新日期：2018-06-26 00:00:00

  • Conditioned Medium from Malignant Breast Cancer Cells Induces an EMT-Like Phenotype and an Altered N-Glycan Profile in Normal Epithelial MCF10A Cells.

    abstract：:Epithelial-mesenchymal transition (EMT) is a key process in cancer development and progression. Communication (crosstalk) between cancer cells and normal (nonmalignant) cells may facilitate cancer progression. Conditioned medium (CM) obtained from cultured cancer cells contains secreted factors capable of affecting ph...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms18081528

    authors： Guo J,Liu C,Zhou X,Xu X,Deng L,Li X,Guan F

    更新日期：2017-08-01 00:00:00

  • The NRF2 Signaling Network Defines Clinical Biomarkers and Therapeutic Opportunity in Friedreich's Ataxia.

    abstract：:Friedreich's ataxia (FA) is a trinucleotide repeats expansion neurodegenerative disorder, for which no cure or approved therapies are present. In most cases, GAA trinucleotide repetitions in the first intron of the FXN gene are the genetic trigger of FA, determining a strong reduction of frataxin, a mitochondrial prot...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章,评审

    doi：10.3390/ijms21030916

    authors： La Rosa P,Bertini ES,Piemonte F

    更新日期：2020-01-30 00:00:00

  • PD-1 and PD-L1 Expression on Circulating Lymphocytes as a Marker of Epstein-Barr Virus Reactivation-Associated Proliferative Glomerulonephritis.

    abstract：:Alterations to the programmed cell death protein-1 (PD-1) pathway were previously shown to be involved in a poorer prognosis for patients with proliferative glomerulonephritis (PGN). Here, we investigated the association between several infectious agents and the expression of PD-1 and its ligand (PD-L1) on T and B lym...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms21218001

    authors： Grywalska E,Smarz-Widelska I,Korona-Głowniak I,Mertowski S,Gosik K,Hymos A,Ludian J,Niedźwiedzka-Rystwej P,Roliński J,Załuska W

    更新日期：2020-10-27 00:00:00

  • Shielding of Hepatitis B Virus-Like Nanoparticle with Poly(2-Ethyl-2-Oxazoline).

    abstract：:Virus-like nanoparticles (VLNPs) have been studied extensively as nanocarriers for targeted drug delivery to cancer cells. However, VLNPs have intrinsic drawbacks, in particular, potential antigenicity and immunogenicity, which hamper their clinical applications. Thus, they can be eliminated easily and rapidly by host...

    journal_title：International journal of molecular sciences

    pub_type： 杂志文章

    doi：10.3390/ijms20194903

    authors： Fam SY,Chee CF,Yong CY,Ho KL,Mariatulqabtiah AR,Lau HY,Tan WS

    更新日期：2019-10-03 00:00:00