JP2012249632A - 異常なマイクロアレイの特徴部の特定 - Google Patents
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Abstract
【解決手段】a)前記核酸アレイ上の第1の特徴部との試験試料のハイブリダイゼーションの量を表す、対数変換した正規化値を取得することと、b)前記第1の特徴部に関するzスコアを算出することであって、前記対数変換した正規化値と、複数の基準アレイ上の同じ特徴部との対照試料のハイブリダイゼーションの量を表す、基準となる対数変換した正規化値の分布とを使用して前記第1の特徴部に関するzスコアを算出することと、c)前記試験特徴部が規定の閾値を上回る又は下回るzスコアを有する場合、前記試験特徴部を異常として特定する方法。
【選択図】なし
Description
「試料」という用語は、本明細書中で使用する場合、必ずしも液体形態であるという訳ではないが典型的には液体形態の、1つ又は複数の対象の核酸(DNA又はRNA)分析物を含有する材料又は材料の混合物を表す。
本発明を更に詳細に説明する前に、本発明は記載される特定の実施形態に限定されず、したがって当然のことながら変化させることができることを理解すべきである。本発明の範囲は添付の特許請求の範囲のみによって限定されるため、本明細書中で使用される専門用語は特定の実施形態を説明することのみを目的とするものであり、限定することを意図していないことも理解すべきである。
「ダークポケット」の特定
「ダークポケット」は、製造上の問題がその領域における特徴部中のプローブに損傷を与えた可能性があるアレイの領域である。これらの欠陥は、狭いシグナルダイナミックレンジを有するアレイ(例えばCGHアレイ)上では目視により認識することができるが、より広いシグナルダイナミックレンジを有するアレイ(すなわち、ほとんどの他のアレイアプリケーションタイプ)上では認識することが困難である。
zスコアマップのバイナリ「フラグマップ」への変換
スライド252665211142により、標識した部分縮重オリゴヌクレオチド(oligos)の試料とのハイブリダイゼーション後に、zスコアマップが得られた(図4)(米国特許出願公開第20060121491号を参照されたい)。
Zスコア測定基準(Z-Score Metric)と中央値のパーセントCVとの間の相関
低いzスコアを有するとして、低z近傍を占めるとして、又はその両方であるとして警告される各アレイ上の特徴部の割合(zスコア測定基準)は、緑色チャネルの加工したシグナルの中央値のパーセントCVと強く相関する(データは示していない)。
Claims (10)
- 核酸アレイ上の異常な特徴部を特定する方法であって、
a)前記核酸アレイ上の第1の特徴部との試験試料のハイブリダイゼーションの量を表す、対数変換した正規化値を取得することと、
b)前記第1の特徴部に関するzスコアを算出することであって、
i.前記対数変換した正規化値と、
ii.複数の基準アレイ上の対応する特徴部との対照試料のハイブリダイゼーションの量を表す、基準となる対数変換した正規化値の分布と
を使用して前記第1の特徴部に関するzスコアを算出することと、
c)前記試験特徴部が規定の閾値を上回る又は下回るzスコアを有する場合、前記試験特徴部を異常として特定することと
を含む、核酸アレイ上の異常な特徴部を特定する方法。 - 前記zスコアが、前記第1の特徴部に関する前記対数変換した正規化値が前記基準となる対数変換した正規化値の平均値又は中央値を、スケーリングした四分位範囲(0.74×IQR)何個分上回るか又は下回るかを表す、請求項1に記載の方法。
- 前記基準となる対数変換した正規化値を、前記特徴部を含有する基準アレイと少なくとも6個の対照試料をハイブリダイズさせることにより取得する、請求項1に記載の方法。
- 前記対照試料が前記試験試料と同じものである、請求項1に記載の方法。
- 前記対照試料及び前記試験試料が生物学的に誘導される試料である、請求項1に記載の方法。
- 前記方法が、
a)核酸アレイ上の複数の特徴部との試験試料のハイブリダイゼーションの量を表す、複数の対数変換した正規化値を取得することと、
b)前記特徴部の各々に関するzスコアを算出することであって、
i.前記対数変換した正規化値と、
ii.複数の基準アレイ上の対応する特徴部との対照試料のハイブリダイゼーションの量を表す、基準となる対数変換した正規化値の分布と
を使用して前記特徴部の各々に関するzスコアを算出することと、
c)前記複数の特徴部のうちの任意の試験特徴部が規定の閾値を上回る又は下回るzスコアを有する場合、前記複数の特徴部のうちの任意の試験特徴部を異常であるとして特定することと
を含む、請求項1に記載の方法。 - 異常な特徴部のクラスタを含有する前記核酸アレイの区域を目視により特定することができるように、前記アレイ上の前記異常な特徴部のマップを提供することを更に含む、請求項7に記載の方法。
- 前記複数の特徴部に関する最近傍解析を行うことであって、前記アレイ上の隣接する異常な特徴部のクラスタを特定する、最近傍解析を行うことを更に含む、請求項7に記載の方法。
- 請求項1に記載の方法を行うためのプログラミングを含む、有形のコンピュータ読み取り可能な媒体。
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US13/152,602 US8478545B2 (en) | 2011-06-03 | 2011-06-03 | Identification of aberrant microarray features |
US13/152,602 | 2011-06-03 |
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JP2012249632A true JP2012249632A (ja) | 2012-12-20 |
JP6055200B2 JP6055200B2 (ja) | 2016-12-27 |
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US (1) | US8478545B2 (ja) |
EP (1) | EP2530616A3 (ja) |
JP (1) | JP6055200B2 (ja) |
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US20040229245A1 (en) * | 2003-01-06 | 2004-11-18 | Anton Bittner | Methods and algorithms for performing quality control during gene expression profiling on DNA microarray technology |
US20070031883A1 (en) * | 2004-03-04 | 2007-02-08 | Kincaid Robert H | Analyzing CGH data to identify aberrations |
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US5091652A (en) | 1990-01-12 | 1992-02-25 | The Regents Of The University Of California | Laser excited confocal microscope fluorescence scanner and method |
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US5888751A (en) * | 1997-07-15 | 1999-03-30 | Ludwig Institute For Cancer Research | Method for diagnosis and treating cancers, and methods for identifying pathogenic markers in a sample of normal cells |
US5948902A (en) | 1997-11-20 | 1999-09-07 | South Alabama Medical Science Foundation | Antisense oligonucleotides to human serine/threonine protein phosphatase genes |
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US6320196B1 (en) | 1999-01-28 | 2001-11-20 | Agilent Technologies, Inc. | Multichannel high dynamic range scanner |
US6355934B1 (en) | 1999-02-26 | 2002-03-12 | Packard Biochip Technologies | Imaging system for an optical scanner |
US6355431B1 (en) | 1999-04-20 | 2002-03-12 | Illumina, Inc. | Detection of nucleic acid amplification reactions using bead arrays |
US6242266B1 (en) | 1999-04-30 | 2001-06-05 | Agilent Technologies Inc. | Preparation of biopolymer arrays |
US20040203138A1 (en) | 1999-04-30 | 2004-10-14 | Caren Michael P. | Polynucleotide array fabrication |
US6323043B1 (en) | 1999-04-30 | 2001-11-27 | Agilent Technologies, Inc. | Fabricating biopolymer arrays |
US6180351B1 (en) | 1999-07-22 | 2001-01-30 | Agilent Technologies Inc. | Chemical array fabrication with identifier |
US6232072B1 (en) | 1999-10-15 | 2001-05-15 | Agilent Technologies, Inc. | Biopolymer array inspection |
US6171797B1 (en) | 1999-10-20 | 2001-01-09 | Agilent Technologies Inc. | Methods of making polymeric arrays |
US20060012491A1 (en) | 2004-07-14 | 2006-01-19 | Mahowald Peter H | Utility meter reading system |
US20060121491A1 (en) | 2004-12-02 | 2006-06-08 | Wolber Paul K | Partially degenerate oligonucleotide standards and methods for generating the same |
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US20040229245A1 (en) * | 2003-01-06 | 2004-11-18 | Anton Bittner | Methods and algorithms for performing quality control during gene expression profiling on DNA microarray technology |
US20070031883A1 (en) * | 2004-03-04 | 2007-02-08 | Kincaid Robert H | Analyzing CGH data to identify aberrations |
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