阿爾茨海默病qBiomarker拷貝數(shù)PCR芯片 Alzheimer’s Disease qBiomarker Copy Number PCR Arrays

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阿爾茨海默病qBiomarker拷貝數(shù)PCR芯片 Alzheimer’s Disease qBiomarker Copy Number PCR Arrays

阿爾茨海默病qBiomarker拷貝數(shù)PCR芯片 Alzheimer’s Disease qBiomarker Copy Number PCR Arrays
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簡介:Alzheimer’s Disease qBiomarker Copy Number PCR Arrays 阿爾茨海默病qBiomarker拷貝數(shù)PCR芯片
提供商:SABio
服務(wù)名稱:阿爾茨海默病PCR芯片
地區(qū):上海

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Alzheimer’s Disease qBiomarker Copy Number PCR Arrays


阿爾茨海默病qBiomarker拷貝數(shù)PCR芯片

 
ProductSpeciesTechnologyCat. No.
Alzheimer’s Disease qBiomarker Copy Number PCR ArraysHumanCopy NumberVAHS-0502Z
The Human Alzheimer's Disease qBiomarker Copy Number PCR Array profiles the copy number of 23 genes reported to undergo frequent genomic alterations in Alzheimer’s disease. The cause of Alzheimer’s disease, the most common form of dementia, has not determined, but it is associated with the accumulation of plaques, tangles, or deposits of amyloid beta protein. It has no treatment or cure, but early diagnosis using cognitive tests and brain scans can help in preparing for care. Several de novo genomic rearrangements, including copy number variations (CNV), have been identified at specific gene loci in patients with Alzheimer’s. The genes on this array encode cytoskeletal components, ion channels, G-protein coupled receptors, proteases, and transcription factors. These proteins regulate processes such as amyloid plaque clearance (including via an immune response), axon growth, axon guidance, central nervous system development (including dysfunction and maintenance), intracellular transport, oxidative stress responses, synaptic plasticity and synaptic transmission. Genes were chosen from the most frequently amplified or deleted genes relevant to Alzheimer’s disease based on a critical review of the primary literature and public databases. This array may serve as a useful tool to help classify samples by genotype and help verify phenotypic biomarkers. The array facilitates the analysis of each gene in each sample in quadruplicate and includes a stable multi-copy reference assay for accurate copy number determination via appropriate DNA input normalization. The simplicity of the product format and operating procedure allows routine and reliable copy number profiling in any research laboratory with access to a real-time PCR instrument.
The qBiomarker Copy Number PCR Arrays are intended for molecular biology applications. This product is not intended for the diagnosis, prevention, or treatment of a disease.
 
阿爾茨海默病qBiomarker拷貝數(shù)PCR芯片用于檢測已報道的阿爾茨海默氏病發(fā)生頻繁突變的23個基因的拷貝數(shù)。作為最常見的癡呆癥,阿爾茨海默癥的具體病因還未發(fā)現(xiàn),但它與神經(jīng)炎性斑、神經(jīng)原纖維纏結(jié)、神經(jīng)元丟失及淀粉樣血管病等相關(guān)。阿爾茨海默病無法治療或治愈,但通過認知測試和腦部掃描進行早期診斷可以為照顧做準(zhǔn)備。一些de novo基因重組,包括拷貝數(shù)突變(CNV)已鑒定阿爾茨海默氏癥患者的特定基因位點。該芯片上的基因編碼細胞骨架元件、離子通道、g蛋白耦合的受體,蛋白酶和轉(zhuǎn)錄因子。這些蛋白調(diào)節(jié)淀粉樣斑塊間隙(包括通路和免疫反應(yīng)),軸突生長,軸突導(dǎo)向,中樞神經(jīng)系統(tǒng)發(fā)育(包括功能障礙和維護),細胞內(nèi)運輸,氧化應(yīng)激反應(yīng),突觸可塑性和突觸傳遞等過程。這些基因來自重要文獻的評論和公共數(shù)據(jù)庫中最頻繁放大或缺失的阿爾茨海默病相關(guān)基因。該芯片可成為分類樣本基因型和驗證表型生物標(biāo)記的有效工具。這個芯片上每個基因在每個樣本中有四個重復(fù),同時包含一個穩(wěn)定的多拷貝參考實驗,通過適當(dāng)?shù)腄NA插入標(biāo)準(zhǔn)化精確檢測拷貝數(shù)。簡單的產(chǎn)品格式和操作程序讓任何一個具備實時定量PCR儀的實驗室都可進行常規(guī)可靠的拷貝數(shù)檢測。
qBiomarker拷貝數(shù)PCR芯片用于分子生物學(xué)應(yīng)用。本產(chǎn)品不用于疾病的診斷、預(yù)防和治療。
Deletions:ERBB4, NRXN1.
Duplications:APP, CHRNA7, CR1, CYFIP1, NIPA1, NIPA2, OR4K2, TUBGCP5.
Behavior, Cognition, Learning & Memory:APP, ATXN1, CHRNA7, NRXN1.
Membrane Potential / Nerve Impulse:APP, ATXN1, CHRNA7, ERBB4, KLK6, NRXN1.
Amyloid Plaque Formation & Clearance:APP, CR1, CSMD1, FPR2, HLA-DPB1, KLK6.
Neurogenesis:APP, CYFIP1, NRXN1, RELN.
Central Nervous System Development:ERBB4, KLK6, NIPA1, NIPA2, RELN.
Axon Growth & Guidance:CYFIP1, RELN.
Neurotransmitter Receptor:CHRNA7.
Ion Transport:CHRNA7, NIPA1, NIPA2, SLC30A3, SLC35F2.
Immune Response:CR1, CSMD1, FPR2, HLA-DPB1.
Oxidative Stress Response:GSTT1.
Transcriptional Regulation:APP, ATXN1, ERBB4, MEOX2
G-Protein Coupled Receptors:FPR2, OR4K2.
Proteases:IMMP2L, KLK6, RELN.
Intracellular Transport:DOPEY2, IMMP2L.
Cell Adhesion & Cytoskeleton:CYFIP1, NRXN1, TUBGCP5
RNA Binding Proteins:ATXN1, HNRNPCL1.
 

How it Works

The Copy Number PCR array is a set of optimized real-time PCR primer assays on 96-well, 100-tube or 384-well plates for measuring changes in copy number. The PCR array performs copy number analysis with real-time PCR sensitivity and the multi-loci profiling capability of a microarray. Simply mix the genomic DNA sample with the appropriate ready-to-use PCR master mix, aliquot equal volumes to each well of the same plate, and then run the real-time PCR cycling program. (Download user manual)

Figure 1:How Copy Number PCR Arrays Work - Protocol Chart

 

The procedure involves isolating genomic DNA (QIAGEN QIAamp DNA Mini Kit or FFPE Tissue Kit is recommended), qPCR detection on qBiomarker Copy Number PCR Arrays or Assays, and data analysis (using the qBiomarker Copy Number Data Analysis). An optional DNA sample quality control step immediately before the detection array or assay setup allows the user to qualify the DNA samples.
To complete the Copy Number PCR Array procedure, start with 400 to1000 nanograms of genomic DNA isolated from fresh tissues, or as low as 800 nanograms of DNA from FFPE sections. Then, mix your DNA with the ready-to-use qBiomarker SYBR Green Mastermixes and aliquot the mixture into each well of the same plate containing pre-dispensed locus-specific primer assays. By performing real-time PCR, the copy number status of a particular sample is determined by comparing the CT values between your test sample and a wild-type control sample (see qBiomarker Copy Number Data Analysis section for detailed principles).

Why qBiomarker Copy Number Arrays?
     Guaranteed Performance* - ready-to-use for copy number analysis
     Time and cost saving - less than 30 minutes hands-on time for analyzing 23 loci
     Ease of data analysis using our easy-to-use Excel-based data analysis template or web-based analysis tool

Layout and Controls: The PCR Arrays are available in both 96-, 384-well plates and 100-well discs and are used to measure the copy number of 23 or 95 genes related to a disease state or pathway. Each gene/locus-specific assay is repeated in technical quadruplicate as indicated in the figure above. As an example, the first gene in the array is measured in wells A1, C1, E1 and G1. The qBiomarker Multicopy Reference Assay (MRef) is used to normalize the data for differences in the amounts of genomic DNA. The Multicopy Reference Assay is shown in purple in the above figure in wells B12, D12, F12, and H12.

You can easily perform a Copy Number PCR Array experiment in your own laboratory, or send your samples to us and take advantage of our PCR Array Services.

*:  when using qBiomarker SYBR? Green Mastermix.

Performance Data: 
The qBiomarker Copy Number PCR Array System yields a more accurate representation of changes in copy number by using a multi-copy reference assay to normalize the raw target specific data.

qBiomarker Multicopy Reference Assay
The qBiomarker Copy Number Arrays have an integrated multi-copy reference assay for data normalization. The multi-copy reference assay  recognizes a stable sequence that appears in the human genome over 60 times, and whose copy number is not affected or minimally affected by local genomic changes. Inclusion of this reference assay during testing allows use of the ΔΔCT method to accurately make copy number calls or relative copy number change calls for specific targets.

 

qBiomarker Multicopy Reference Assay is superior to RNase P as a reference assay for copy number determination. Tumor cell line DNA (SKBR3) and reference genomic DNA were mixed in different ratios (100%, 87.5%, 75%, 50%, 25%, 12.5% and 0% SKBR3 cells respectively), and the DNA mixes were tested for GRB7 gene copy number, using either MRef assay or RNaseP assay as the reference. The GRB7 copy number in the reference genomic DNA is assumed to be 2. The "Expected" GRB7 gene copy numbers in 87.5%, 75%, 50%, 25%, 12.5% mixing ratio samples are calculated based on the GRB7 gene copy number in 100% SKBR3 genomic DNA sample, and the mixing ratio between the SKBR3 genomic DNA and Promega genomic DNA. The observed GRB7 gene copy numbers in general agree well with the expected values when using QIAGEN Multi-copy Reference Assay as the reference, while significant differences exist between the observed GRB7 gene copy numbers and the expected values when RNaseP is used as the reference assay.

RNaseP gene is not suitable as a normalizer of sample input in cancer cell line DNA samples. The absolute average copy numbers of RNaseP per normal genome copy amount of DNA were determined in two breast cancer cell line (SKBR3 and MCF7) genomic DNAs with the delta delta Ct method, using QIAGEN multi-copy reference assay as the normalization control of DNA input. The absolute copy number of RNaseP per normal genome in the genomic DNA  is assumed to be 2.

Universal Nature of Multicopy Reference Assay
The complete PCR Array System, with high quality input RNA, is guaranteed to yield single amplicons of the predicted size without primer dimers or other secondary products to ensure the most accurate real-time PCR results possible.

Stable Performance of the Multicopy Reference (MRef) Assay in 129 DNAs from 9 Major Human Populations. The qBiomarker multi-copy reference assay (MRef) and a qBiomarker copy number assay for RB1 were tested against DNAs from 129 healthy individuals from 9 major ethnic populations. Each assay and DNA sample combination was run in quadruple reactions. Delta CT between the average CT of the MRef assay and the RB1 assay was calculated for each individual DNA. The average delta Ct for samples within each ethnic population is plotted. Error bars show the standard deviation of the delta CT within each ethnic population. The RB1 gene is assumed to be present at 2 copies in all healthy individual DNAs.

Application Data

Aneuploidy Study

qBiomarker Copy Number Assays accurately identify aneuploidy. qBiomarker Copy Number Assays designed to target AR and MECP2 were tested against 4 cell line DNAs containing 1 copy (XY, Coriell NA13619), 2 copies (XX, Coriell NA01921), 3 copies (XXX, Coriell NA03623) and 4 copies (XXXX, Coriell NA11226) of X-chromosome. Chromosomal aberrations had been previously identified by cytogenetic methods. A control assay, targeting a stable, multi-copy region in the human genome, was used to normalize the amount of DNA input. ΔΔCT method was used to calculate the gene copy number, using XX (Coriell NA01921) as a 2-copy reference. Each assay was tested against each sample in quadruple replicate reactions, and a t-test was performed.


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