CGH

比較基因組雜交晶片服務 CGH Microarray Service

以微陣列技術為基礎的比較基因組雜交 (array-based Comparative Genomic Hybridization --aCGH) 是一個功能強大的技術,可用來偵測染色體 DNA 拷貝數變異。以已知的正常染色體套數為基準,來檢測染色體的獲得和損失的變異。 多樣化的晶片規格及可自由調整探針佈放密度的客製化晶片,使得 CGH Microarray 工具能有高靈活度的應用。

Agilent 比較基因組雜交晶片是一高解析度工具,僅需少量 DNA 即可對全基因組 DNA 拷貝數變異進行檢測。探針序列的設計除了考慮 Tm 值、二級結構、序列特異性等,還要求需具有高敏感性和高特異性。國際期刊 PNAS 曾針對其效能進行實驗驗證 ,以 GM50122 18q- cell line 測試,所得結果和已知 deletion 位置相符。 CGH Microarray 應用範圍包含:Cancer genome、Genetic disease 及 Assessment of genome instability 等。


詳細規格

目前有 244K 規格目錄晶片及 SurePrint G3 製程高密度晶片兩種類型。

1. 244K 規格目錄晶片

Agilent aCGH 晶片種類 Human 244A Human 105A Mouse 244A Mouse105A
Agilent Product Number G4411B G4412A G4415A G4416A
Design ID 014693 014698 014695 014699
Format 1 x 244K 2 x 105K 1 x 244K 2 x 105K
Arrays/Slide 1 2 1 2
Slides/Kit 5 5 5 5
Distinct Biological Features 236,381 99,026 235,402 98,797
Replicated Biological Features (X5) 1,000 525 1,400 760
Internal Quality Control Features 5,045 4,626 5,099 4,712
Composition Content sourced from
- UCSC hg18 (NCBI Build 36), March 2006
Content sourced from
- UCSC mm8 (NCBI Build 36), February 2006
Probe Spacing 8.9 KB overall median probe spacing (7.4 KB in Refseq genes) 22 KB overall median probe spacing (19 KB in Refseq genes) 7.8 KB overall median probe spacing (6.2 KB in Refseq genes) 19.3 KB overall median probe spacing (15.7 KB in Refseq genes)

2. SurePrint G3 製程高密度晶片
若客戶希望以更高解析度偵測變異,可使用以更高密度打點的 Agilent SurePrint G3 製程晶片,晶片解析度最高可達 1M,本類晶片需搭配新款可掃描 2u 的 scanner 。SurePrint G3 製程晶片各種規格如下:

Agilent aCGH 晶片種類 Human 1M Human 2x400K Human 4x180K Mouse105A
Agilent Product Number G4447A G4448A G4449A G4450A
Design ID 21529 021850 022060 021924
Format 1 x 1M 2 x 400K 4 x 180K 8 x 60K
Arrays/Slide 1 2 4 8
Slides/Kit 5 5 3 3
Distinct Biological Features 963,029 411,056 170,334 55,077
Replicated Biological Features (X5) 1,000 1,000 1,000 1,000
Internal Quality Control Features 6,685 5,126 6,539 3,886
Composition Content sourced from
- UCSC hg18 (NCBI Build 36), March 2006
Probe Spacing 2.1 KB overall median probe spacing (1.8 KB in Refseq genes) 5.3 KB overall median probe spacing (4.6 KB in Refseq genes) 13 KB overall median probe spacing (11 KB in Refseq genes) 41 KB overall median probe spacing (33 KB in Refseq genes)

Mouse 等其他熱門物種也已經有相當規格之目錄晶片,如有需求可與當區業務討論。若以上晶片規格無法滿足研究人員的需要,威健另外提供客制化晶片,詳細介紹請見客制化晶片的製作。

樣品條件

檢體類別:DNA、Tissue、Cell line、Blood

DNA QC 標準:
DNA 濃度 DNA 總量 OD260/280
≧ 50 ng/μL 500 ng - 3 μg ≧1.7
Note: DNA 量影響訊號強度,最好大於 500 ng,請盡量不要太低量。

其他檢體 (Tissue、Cell line、Blood) :
檢體條件請參考核酸萃取的檢體條件

對照組樣品 :
CGH Microarray 為比較基因組雜合實驗,需有參考 genomic DNA 以茲對照。CNV 相關研究建議採用國際常用之 NA10851 cell line 樣品,一般癌症實驗建議使用該癌症之 normal part ,此種樣本在取樣時須特別注意,不要與實驗部分混雜。此二種樣品需由客戶自行準備,若客戶無適當的對照 DNA 時,可採用威健提供之 Promega normal male/ female genomic DNA ,對照 DNA 樣品不另外計費。

其他檢體(組織、血液、細胞):檢體條件請參考核酸萃取的檢體條件

實驗流程

流程說明
DNA QC 檢查
晶片實驗:DNA 片斷化
片斷化 DNA 進行螢光標定,實驗組的 DNA 標定 Cy5 螢光,對照組 DNA 標定 Cy3
晶片實驗:實驗組 DNA 與對照組 DNA 雜交反應,Wash 晶片後進行晶片掃描。
資料輸出,整理 DATA。初次委託者由專責人員到場做資料解說。

報告內容

Gene expression microarray 服務及報告內容 (雙光)

報告產出 說明 格式
報告內容
(Raw data)
Scanning image Combined Cy3, Cy5 Image TIFF
Raw data Feature Extraction 軟體輸出 txt
Design file 所用晶片原始 design file xml
報告內容
(以圖形化資料輸出軟體輸出之 data)
Cytoreport DNA analytics 輸出 pdf
text aberration summary DNA analytics 輸出 excel
重要染色體變異位置貼圖 DNA analytics 輸出 ppt
檔案說明 文件檔案之說明 ppt, word

Cytoreport


重要染色體變異位置貼圖



Reference

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  6. A Novel Translocation Breakpoint within the BPTF Gene Is Associated with a Pre-Malignant Phenotype.PLoS One. 2010 Mar 11;5(3):e9657. Buganim Y, Goldstein I, Lipson D, Milyavsky M, Polak-Charcon S, Mardoukh C, Solomon H, Kalo E, Madar S, Brosh R, Perelman M, Navon R, Goldfinger N, Barshack I, Yakhini Z, Rotter V
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  8. A Systematic Comparison of Microarray Platforms for DNA Copy Number Profiling. Genomic copy number aberrations (CNAs) frequently occur in cancers and microarray-based comparative genomic hybridization (CGH) is a key technology for copy number profiling. Considering the diversity.
  9. Accelerated carcinogenesis following liver regeneration is associated with chronic inflammation-induced double-strand DNA breaks. Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):2207-12. Epub 2010 Jan 25. Barash H, R Gross E, Edrei Y, Ella E, Israel A, Cohen I, Corchia N, Ben-Moshe T, Pappo O, Pikarsky E, Goldenberg D, Shiloh Y, Galun E, Abramovitch R
  10. An 8.35 Mb overlapping interstitial deletion of 8q24 in two patients with coloboma, congenital heart defect, limb abnormalities, psychomotor retardation and convulsions. Eur J Med Genet. 2009 Sep-Oct;52(5):353-7. Epub 2009 May 21. Verheij JB, de Munnik SA, Dijkhuizen T, de Leeuw N, Olde Weghuis D, van den Hoek GJ, Rijlaarsdam RS, Thomasse YE, Dikkers FG, Marcelis CL, van Ravenswaaij-Arts CM
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