Microarrays最新文献_第9页

Identifying Potential Regions of Copy Number Variation for Bipolar Disorder. 识别双相情感障碍拷贝数变异的潜在区域。

Microarrays Pub Date : 2014-02-28 DOI: 10.3390/microarrays3010052

Yi-Hsuan Chen, Ru-Band Lu, Hung Hung, Po-Hsiu Kuo

{"title":"Identifying Potential Regions of Copy Number Variation for Bipolar Disorder.","authors":"Yi-Hsuan Chen, Ru-Band Lu, Hung Hung, Po-Hsiu Kuo","doi":"10.3390/microarrays3010052","DOIUrl":"https://doi.org/10.3390/microarrays3010052","url":null,"abstract":"Bipolar disorder is a complex psychiatric disorder with high heritability, but its genetic determinants are still largely unknown. Copy number variation (CNV) is one of the sources to explain part of the heritability. However, it is a challenge to estimate discrete values of the copy numbers using continuous signals calling from a set of markers, and to simultaneously perform association testing between CNVs and phenotypic outcomes. The goal of the present study is to perform a series of data filtering and analysis procedures using a DNA pooling strategy to identify potential CNV regions that are related to bipolar disorder. A total of 200 normal controls and 200 clinically diagnosed bipolar patients were recruited in this study, and were randomly divided into eight control and eight case pools. Genome-wide genotyping was employed using Illumina Human Omni1-Quad array with approximately one million markers for CNV calling. We aimed at setting a series of criteria to filter out the signal noise of marker data and to reduce the chance of false-positive findings for CNV regions. We first defined CNV regions for each pool. Potential CNV regions were reported based on the different patterns of CNV status between cases and controls. Genes that were mapped into the potential CNV regions were examined with association testing, Gene Ontology enrichment analysis, and checked with existing literature for their associations with bipolar disorder. We reported several CNV regions that are related to bipolar disorder. Two CNV regions on chromosome 11 and 22 showed significant signal differences between cases and controls (p < 0.05). Another five CNV regions on chromosome 6, 9, and 19 were overlapped with results in previous CNV studies. Experimental validation of two CNV regions lent some support to our reported findings. Further experimental and replication studies could be designed for these selected regions. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"3 1","pages":"52-71"},"PeriodicalIF":0.0,"publicationDate":"2014-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays3010052","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34370658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Comparative Analysis of Biologically Relevant Response Curves in Gene Expression Experiments: Heteromorphy, Heterochrony, and Heterometry. 基因表达实验中生物学相关反应曲线的比较分析:异型、异时性和异量。

Microarrays Pub Date : 2014-02-14 DOI: 10.3390/microarrays3010039

Stuart G Baker

{"title":"Comparative Analysis of Biologically Relevant Response Curves in Gene Expression Experiments: Heteromorphy, Heterochrony, and Heterometry.","authors":"Stuart G Baker","doi":"10.3390/microarrays3010039","DOIUrl":"https://doi.org/10.3390/microarrays3010039","url":null,"abstract":"To gain biological insights, investigators sometimes compare sequences of gene expression measurements under two scenarios (such as two drugs or species). For this situation, we developed an algorithm to fit, identify, and compare biologically relevant response curves in terms of heteromorphy (different curves), heterochrony (different transition times), and heterometry (different magnitudes). The curves are flat, linear, sigmoid, hockey-stick (sigmoid missing a steady state), transient (sigmoid missing two steady states), impulse (with peak or trough), step (with intermediate-level plateau), impulse+ (impulse with an extra parameter), step+ (step with an extra parameter), further characterized by upward or downward trend. To reduce overfitting, we fit the curves to every other response, evaluated the fit in the remaining responses, and identified the most parsimonious curves that yielded a good fit. We measured goodness of fit using a statistic comparable over different genes, namely the square root of the mean squared prediction error as a percentage of the range of responses, which we call the relative prediction error (RPE). We illustrated the algorithm using data on gene expression at 14 times in the embryonic development in two species of frogs. Software written in Mathematica is freely available. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"3 1","pages":"39-51"},"PeriodicalIF":0.0,"publicationDate":"2014-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays3010039","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34370656","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Copy Number Variation in Chickens: A Review and Future Prospects. 鸡的拷贝数变异:综述和未来展望。

Microarrays Pub Date : 2014-02-05 DOI: 10.3390/microarrays3010024

Xiaofei Wang, Shannon Byers

引用次数: 21

Pigeons: A Novel GUI Software for Analysing and Parsing High Density Heterologous Oligonucleotide Microarray Probe Level Data. 鸽子:一种用于分析和解析高密度异源寡核苷酸微阵列探针级数据的新型GUI软件。

Microarrays Pub Date : 2014-01-03 DOI: 10.3390/microarrays3010001

Hung-Ming Lai, Sean T May, Sean Mayes

{"title":"Pigeons: A Novel GUI Software for Analysing and Parsing High Density Heterologous Oligonucleotide Microarray Probe Level Data.","authors":"Hung-Ming Lai, Sean T May, Sean Mayes","doi":"10.3390/microarrays3010001","DOIUrl":"https://doi.org/10.3390/microarrays3010001","url":null,"abstract":"Genomic DNA-based probe selection by using high density oligonucleotide arrays has recently been applied to heterologous species (Xspecies). With the advent of this new approach, researchers are able to study the genome and transcriptome of a non-model or an underutilised crop species through current state-of-the-art microarray platforms. However, a software package with a graphical user interface (GUI) to analyse and parse the oligonucleotide probe pair level data is still lacking when an experiment is designed on the basis of this cross species approach. A novel computer program called Pigeons has been developed for customised array data analysis to allow the user to import and analyse Affymetrix GeneChip(®) probe level data through XSpecies. One can determine empirical boundaries for removing poor probes based on genomic hybridisation of the test species to the Xspecies array, followed by making a species-specific Chip Description File (CDF) file for transcriptomics in the heterologous species, or Pigeons can be used to examine an experimental design to identify potential Single-Feature Polymorphisms (SFPs) at the DNA or RNA level. Pigeons is also focused around visualization and interactive analysis of the datasets. The software with its manual (the current release number version 1.2.1) is freely available at the website of the Nottingham Arabidopsis Stock Centre (NASC). ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"3 1","pages":"1-23"},"PeriodicalIF":0.0,"publicationDate":"2014-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays3010001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34370655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Chromosomal Microarrays in Prenatal Diagnosis: Time for a Change of Policy? 染色体微阵列产前诊断:是时候改变政策了?

Microarrays Pub Date : 2013-12-05 DOI: 10.3390/microarrays2040304

Peter Miny, Friedel Wenzel, Sevgi Tercanli, Isabel Filges

{"title":"Chromosomal Microarrays in Prenatal Diagnosis: Time for a Change of Policy?","authors":"Peter Miny, Friedel Wenzel, Sevgi Tercanli, Isabel Filges","doi":"10.3390/microarrays2040304","DOIUrl":"https://doi.org/10.3390/microarrays2040304","url":null,"abstract":"Microarrays have replaced conventional karyotyping as a first-tier test for unbalanced chromosome anomalies in postnatal cytogenetics mainly due to their unprecedented resolution facilitating the detection of submicroscopic copy number changes at a rate of 10-20% depending on indication for testing. A number of studies have addressed the performance of microarrays for chromosome analyses in high risk pregnancies due to abnormal ultrasound findings and reported an excess detection rate between 5% and 10%. In low risk pregnancies, clear pathogenic copy number changes at the submicroscopic level were encountered in 1% or less. Variants of unclear clinical significance, unsolicited findings, and copy number changes with variable phenotypic consequences are the main issues of concern in the prenatal setting posing difficult management questions. The benefit of microarray testing may be limited in pregnancies with only moderately increased risks (advanced maternal age, positive first trimester test). It is suggested to not change the current policy of microarray application in prenatal diagnosis until more data on the clinical significance of copy number changes are available. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"2 4","pages":"304-17"},"PeriodicalIF":0.0,"publicationDate":"2013-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays2040304","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34425573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

Copy Number Studies in Noisy Samples. 噪声样本中的拷贝数研究。

Microarrays Pub Date : 2013-11-06 DOI: 10.3390/microarrays2040284

Philip Ginsbach, Bowang Chen, Yanxiang Jiang, Stefan T Engelter, Caspar Grond-Ginsbach

{"title":"Copy Number Studies in Noisy Samples.","authors":"Philip Ginsbach, Bowang Chen, Yanxiang Jiang, Stefan T Engelter, Caspar Grond-Ginsbach","doi":"10.3390/microarrays2040284","DOIUrl":"https://doi.org/10.3390/microarrays2040284","url":null,"abstract":"System noise was analyzed in 77 Affymetrix 6.0 samples from a previous clinical study of copy number variation (CNV). Twenty-three samples were classified as eligible for CNV detection, 29 samples as ineligible and 25 were classified as being of intermediate quality. New software (\"noise-free-cnv\") was developed to visualize the data and reduce system noise. Fresh DNA preparations were more likely to yield eligible samples (p < 0.001). Eligible samples had higher rates of successfully genotyped SNPs (p < 0.001) and lower variance of signal intensities (p < 0.001), yielded fewer CNV findings after Birdview analysis (p < 0.001), and showed a tendency to yield fewer PennCNV calls (p = 0.053). The noise-free-cnv software visualized trend patterns of noise in the signal intensities across the ordered SNPs, including a wave pattern of noise, being co-linear with the banding pattern of metaphase chromosomes, as well as system deviations of individual probe sets (per-SNP noise). Wave noise and per-SNP noise occurred independently and could be separately removed from the samples. We recommend a two-step procedure of CNV validation, including noise reduction and visual inspection of all CNV calls, prior to molecular validation of a selected number of putative CNVs. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"2 4","pages":"284-303"},"PeriodicalIF":0.0,"publicationDate":"2013-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays2040284","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34425572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Kernel-Based Aggregation of Marker-Level Genetic Association Tests Involving Copy-Number Variation. 涉及拷贝数变异的标记水平遗传关联检测的核聚集。

Microarrays Pub Date : 2013-09-04 DOI: 10.3390/microarrays2030265

Yinglei Li, Patrick Breheny

引用次数: 1

Improving Pathological Assessment of Breast Cancer by Employing Array-Based Transcriptome Analysis. 利用基于阵列的转录组分析改善乳腺癌的病理评估。

Microarrays Pub Date : 2013-08-29 DOI: 10.3390/microarrays2030228

Zsuzsanna Mihály, Balázs Győrffy

{"title":"Improving Pathological Assessment of Breast Cancer by Employing Array-Based Transcriptome Analysis.","authors":"Zsuzsanna Mihály, Balázs Győrffy","doi":"10.3390/microarrays2030228","DOIUrl":"https://doi.org/10.3390/microarrays2030228","url":null,"abstract":"Breast cancer research has paved the way of personalized oncology with the introduction of hormonal therapy and the measurement of estrogen receptor as the first widely accepted clinical biomarker. The expression of another receptor-HER2/ERBB2/neu-was initially a sign of worse prognosis, but targeted therapy has granted improved outcome for these patients so that today HER2 positive patients have better prognosis than HER2 negative patients. Later, the introduction of multigene assays provided the pathologists with an unbiased assessment of the tumors' molecular fingerprint. The recent FDA approval of complete microarray pipelines has opened new possibilities for the objective classification of breast cancer samples. Here we review the applications of microarrays for determining ER and HER2 status, molecular subtypes as well as predicting prognosis and grade for breast cancer patients. An open question remains the role of single genes within such signatures. Openly available microarray datasets enable the execution of an independent cross-validation of new marker and signature candidates. In summary, we review the current state regarding clinical applications of microarrays in breast cancer molecular pathology. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"2 3","pages":"228-42"},"PeriodicalIF":0.0,"publicationDate":"2013-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays2030228","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34728501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 22

From High-Throughput Microarray-Based Screening to Clinical Application: The Development of a Second Generation Multigene Test for Breast Cancer Prognosis. 从高通量微阵列筛选到临床应用:第二代乳腺癌预后多基因检测的发展。

Microarrays Pub Date : 2013-08-29 DOI: 10.3390/microarrays2030243

Jan C Brase, Ralf Kronenwett, Christoph Petry, Carsten Denkert, Marcus Schmidt

{"title":"From High-Throughput Microarray-Based Screening to Clinical Application: The Development of a Second Generation Multigene Test for Breast Cancer Prognosis.","authors":"Jan C Brase, Ralf Kronenwett, Christoph Petry, Carsten Denkert, Marcus Schmidt","doi":"10.3390/microarrays2030243","DOIUrl":"https://doi.org/10.3390/microarrays2030243","url":null,"abstract":"Several multigene tests have been developed for breast cancer patients to predict the individual risk of recurrence. Most of the first generation tests rely on proliferation-associated genes and are commonly carried out in central reference laboratories. Here, we describe the development of a second generation multigene assay, the EndoPredict test, a prognostic multigene expression test for estrogen receptor (ER) positive, human epidermal growth factor receptor (HER2) negative (ER+/HER2-) breast cancer patients. The EndoPredict gene signature was initially established in a large high-throughput microarray-based screening study. The key steps for biomarker identification are discussed in detail, in comparison to the establishment of other multigene signatures. After biomarker selection, genes and algorithms were transferred to a diagnostic platform (reverse transcription quantitative PCR (RT-qPCR)) to allow for assaying formalin-fixed, paraffin-embedded (FFPE) samples. A comprehensive analytical validation was performed and a prospective proficiency testing study with seven pathological laboratories finally proved that EndoPredict can be reliably used in the decentralized setting. Three independent large clinical validation studies (n = 2,257) demonstrated that EndoPredict offers independent prognostic information beyond current clinicopathological parameters and clinical guidelines. The review article summarizes several important steps that should be considered for the development process of a second generation multigene test and offers a means for transferring a microarray signature from the research laboratory to clinical practice. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"2 3","pages":"243-64"},"PeriodicalIF":0.0,"publicationDate":"2013-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays2030243","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34425570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Hydrogel Microwell Arrays Allow the Assessment of Protease-Associated Enhancement of Cancer Cell Aggregation and Survival. 水凝胶微孔阵列允许评估蛋白酶相关的癌细胞聚集和生存增强。

Microarrays Pub Date : 2013-08-22 DOI: 10.3390/microarrays2030208

Daniela Loessner, Stefan Kobel, Judith A Clements, Matthias P Lutolf, Dietmar W Hutmacher

{"title":"Hydrogel Microwell Arrays Allow the Assessment of Protease-Associated Enhancement of Cancer Cell Aggregation and Survival.","authors":"Daniela Loessner, Stefan Kobel, Judith A Clements, Matthias P Lutolf, Dietmar W Hutmacher","doi":"10.3390/microarrays2030208","DOIUrl":"https://doi.org/10.3390/microarrays2030208","url":null,"abstract":"Current routine cell culture techniques are only poorly suited to capture the physiological complexity of tumor microenvironments, wherein tumor cell function is affected by intricate three-dimensional (3D), integrin-dependent cell-cell and cell-extracellular matrix (ECM) interactions. 3D cell cultures allow the investigation of cancer-associated proteases like kallikreins as they degrade ECM proteins and alter integrin signaling, promoting malignant cell behaviors. Here, we employed a hydrogel microwell array platform to probe using a high-throughput mode how ovarian cancer cell aggregates of defined size form and survive in response to the expression of kallikreins and treatment with paclitaxel, by performing microscopic, quantitative image, gene and protein analyses dependent on the varying microwell and aggregate sizes. Paclitaxel treatment increased aggregate formation and survival of kallikrein-expressing cancer cells and levels of integrins and integrin-related factors. Cancer cell aggregate formation was improved with increasing aggregate size, thereby reducing cell death and enhancing integrin expression upon paclitaxel treatment. Therefore, hydrogel microwell arrays are a powerful tool to screen the viability of cancer cell aggregates upon modulation of protease expression, integrin engagement and anti-cancer treatment providing a micro-scaled yet high-throughput technique to assess malignant progression and drug-resistance. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"2 3","pages":"208-27"},"PeriodicalIF":0.0,"publicationDate":"2013-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays2030208","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34728500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 12