JP2019509018A - 変異に基づく病気の診断および追跡 - Google Patents
変異に基づく病気の診断および追跡 Download PDFInfo
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Abstract
Description
対立遺伝子頻度= i/(nN)。
英数字入力装置(例えば、キーボード)、カーソル制御装置(例えば、マウス)、ディスクドライブ装置、信号発生装置(例えば、スピーカ)、タッチスクリーン、加速度計、マイクロフォン、セルラー無線周波数アンテナ、および、例えばネットワークインターフェースカード(NIC)、Wi-Fiカード、またはセルラーモデムであり得るネットワークインターフェースデバイスなどを含む。
特許、特許出願、特許刊行物、機関誌、書籍、論文、ウェブコンテンツなどの他の文書への参照および引用は、本開示全体にわたってなされている。そのような文献の全てが、あらゆる目的のためにその全体が参照により本明細書に援用される。
本明細書に示され、記載されたものに加えて、本発明の様々な変更および多くのさらなるそれらの実施形態は、本明細書に引用される科学文献および特許文献への言及を含めて、この文書の全内容から当業者に明らかになるであろう。本明細書の主題は、様々な実施形態およびその等価物において本発明の実施に適合させることができる重要な情報、例示および指針を含む。
下記の実施例では、以下の材料および方法を使用した。
ペアエンド配列決定と互換性のある分子のより高い収率がもたらされることを示す。断片サイズ測定では、1μlのcfDNAを投入し、ライブラリー調製前後の平均断片長を同定した。配列決定ライブラリー調製前のcfDNA分子長の分布は、平均長さμ_0が約150〜180塩基で、試料分散σ^2である正規分布X_前〜N(μ_前、σ^2)からのサンプリングとして近似することができる。ライブラリー調製後の分子長の分布X_後は、ライゲーションされた配列決定アダプターの数だけシフトした正規分布の重ね合わせとして近似することができ、各配列決定アダプターは固定長Aを持ち、それは通常、Illuminaプラットフォーム(P5およびP7アダプター)では60塩基である。配列決定され得る(配列決定可能な)分子は、cfDNA断片の各末端にライゲーションされた少なくとも1つのアダプターを有し、したがって平均μ_0、+kAを有し、ここでk≧2である。アダプターライゲーションの項で説明したように、ライブラリーをPCR増幅すると、ライゲーションされたアダプターの数kが少なくとも2の場合、配列決定可能な分子が生成される:X_後〜Σ_(k = 0)^4 Y_k×N((μ_前 + kA)、σ^2)、k∈N_0、ここで、Y_kは、k個のライゲーションされたアダプターを持つ分子の寄与の重みである。P5およびP7 PCRプライマーを用いたPCR増幅の後、集団は、集団μ_前+ 2Aが多数となる。
表1:Qiagen QIAmp Circulating Nucleic Acidキットの2回目の溶出によるcfDNA収量。6人のメラノーマ患者のcfDNA試料。溶出量は両方とも30uLのAVEであった。
表2:試料のリスト。
結腸直腸がん(CRC)患者ID番号034は、治療目的で手術を受けた。手術前後の血液試料を収集し、その中のcfDNAを上記のように配列決定した。手術前の配列決定データにより、13の検出された体細胞変異が明らかになった。13の検出された体細胞変異全ての対立遺伝子頻度は、手術後の試料では検出不可能なレベルまで減少し、腫瘍の完全切除を示した。結果を図9に示す。図9は、手術前後の体細胞突然変異を含む読み取りの割合の変化を示す。それぞれの円およびつながっている線は、個々の体細胞突然変異を表している。機能的影響を計算的に推定した突然変異を有する遺伝子を同定する。1つの同定された突然変異はTGFBR2にあり、高い機能的影響があった。研究者らは、TGF-β受容体の不活性化が、ヒト結腸がん細胞がTGF-βに対する応答性を失うことになる機構であるかどうかを調べた。例えば、非特許文献55を参照。結果は、TGFBR2遺伝子が、結腸がん細胞株のサブセットにおいて不活性化されたことを実証しており(「複製エラー陽性」を意味するRER+と呼ばれる)、マイクロサテライト不安定性を示すが、RER(-)細胞では示さない。
結腸直腸がん(CRC)患者ID番号020は、治癒目的で手術を受けた。手術前後の血液試料を収集し、その中のcfDNAを上記のように配列決定した。手術前配列決定データにより、複数の検出された体細胞変異体が明らかになった。しかし、手術後、検出された体細胞変異の対立遺伝子頻度は、検出不可能なレベルまで低下しなかった(患者034、実施例1とは対照的に)。結果を図10に示す。図10は、手術前後の体細胞突然変異を含む読み取りの数の変化を示す。それぞれの円およびつながっている線は、個々の体細胞突然変異を表している。機能的影響を計算的に推定した突然変異を有する遺伝子を同定する。
結腸直腸がん(CRC)患者ID番号187は、治療目的で手術を受けた。手術前後の血液試料を収集し、その中のcfDNAを上記のように配列決定した。患者187は、見逃された転移性結腸直腸がんにおける転移性発生の履歴を反映する手術前後の9つの体細胞変異について多様な軌跡応答を示した。結果を図11に示す。図11は、手術前後の体細胞突然変異を含む読み取りの数の変化を示す。それぞれの円およびつながっている線は、個々の体細胞突然変異を表している。機能的影響を計算的に推定した突然変異を有する遺伝子を同定する。
lobSTRプログラム(非特許文献56)を使用する、マイクロサテライト不安定性(MSI)を有する患者からのcfDNAの分析は、遺伝子座chr20:3,345,703(図12、パネルB)における2つより多くの対立遺伝子の証拠を示し、MSIがcfDNAにおいて直接観察され得ることを実証している。対照的に、MSIを有さないがん患者からの試料(陰性対照)は、cfDNAにおけるMSIの証拠を示さない。図12、パネルAの頻度の差異は、非参照反復要素の異なるハイブリダイゼーションキャプチャー効率によって引き起こすことができる。マイクロサテライト不安定性は、cfDNAの2つより多くの対立遺伝子に存在する短い縦列反復(STR)として同定される。
3つの配列決定ライブラリーを、HiSeq 2500装置で、2つのフローセルにまたがって高速ランモードで実行した。ライブラリーは、治療の開始前にがん患者ID番号009、031および045から得たcfDNA試料から調製した。SENTRYSEQライブラリー調製プロトコルでは、70ナノグラムの抽出cfDNAを使用した(上記の材料および方法の項を参照)。Qubit定量によって測定される濃度を、以下の表3に示す:
表3:試料から抽出されたcfDNAの量。
表5:8サイクルのPCR増幅後のライブラリー濃度。
表6:プルダウン後のライブラリー濃度。
表7:最終ライブラリー濃度。
治癒目的で外科的切除を受けた15人の結腸直腸がん患者について、臨床情報を収集した。3人の患者が、試験期間内に再発を臨床的に確認した。10人の患者に、転移性がんが手術後に認められた。体細胞軌跡追跡を使用し、確認された再発症例および2つの追加の予測がん再発の両方を同定した。患者情報およびcfDNA分析から予測された再発を、図20A〜Cに示す。結果は、本発明の方法による体細胞軌跡追跡を使用して、疾患の再発および/またはMRDを検出できることを実証する。
一人の転移性メラノーマ患者を、疾患進行の過程で追跡した。腫瘍の生検を疾患進行の早期に行い、ホルマリン固定パラフィン包埋(FFPE)試料を分析用に調製した。疾患が進行するにつれて、連続的な血漿収集およびCT画像化を行った。図18は、患者の疾患進行の時間経過を示し、治療、観察および試料収集の時点を示す。
Claims (35)
- 患者の健康状態を追跡する方法であって、
患者の突然変異シグネチャーを構築する工程であって、該突然変異シグネチャーが以下を含む工程:
患者の核酸試料中で観察された変異の総数;
観察された前記変異の各々についての配列関係因子;
観察された変異の各々の対立遺伝子頻度;および
変異型分類;
前記患者の前記突然変異シグネチャーを、既知の健康状態を有する患者の1つ以上のデータベースにおける突然変異シグネチャーと比較する工程;ならびに
前記患者の診断または治療を決定する工程
を含む、方法。 - 前記患者の複数の突然変異シグネチャーを含む前記患者の縦断的突然変異シグネチャーを時間をかけて決定する工程と、前記患者の縦断的突然変異シグネチャーを、診断または治療を決定する前の既知の健康状態を有する患者の1つ以上のデータベースに含まれる縦断的突然変異シグネチャーと比較する工程とをさらに含む、請求項1に記載の方法。
- 前記縦断的突然変異シグネチャーが、第1時点からの患者の第1突然変異シグネチャーおよび第2時点からの該患者の第2突然変異シグネチャーを含む、請求項2に記載の方法。
- 前記第1時点が治療の前であり、前記第2時点が前記治療の後である、請求項3に記載の方法。
- 前記治療が腫瘍切除手術を含む、請求項4に記載の方法。
- 前記治療が抗がん治療剤の投与を含む、請求項4に記載の方法。
- 前記患者の健康状態を取得する工程と、前記患者の前記健康状態および前記突然変異シグネチャーを1つ以上の前記データベースに追加する工程とをさらに含む、請求項1に記載の方法。
- 前記患者から患者情報を取得する工程と、該患者情報を、既知の健康状態を有する患者の1つ以上の前記データベースに含まれる患者情報と比較する工程とをさらに含み、前記情報が、年齢、性別、人種、民族性、家族病歴、体重、ボディマス指数、身長、以前のおよび/または重複感染、環境ばく露、および喫煙歴のうちの少なくとも1つを含む、請求項1に記載の方法。
- 前記患者のタンパク質バイオマーカーのレベルを取得する工程と、該タンパク質バイオマーカーの該レベルを、既知の健康状態を有する患者の1つ以上の前記データベースに含まれる前記タンパク質バイオマーカーのレベルと比較する工程とをさらに含む、請求項1に記載の方法。
- 前記核酸が患者試料から得られる、請求項1に記載の方法。
- 前記患者試料が、被験体の組織試料、被験体の体液、被験体の細胞試料、または被験体の糞便試料を含む、請求項1に記載の方法。
- 前記体液が、全血、唾液、涙、汗、痰、または尿から選択される、請求項11に記載の方法。
- 前記体液が全血であり、前記患者試料が前記全血の一部を含む、請求項12に記載の方法。
- 前記全血の一部が、血漿または細胞遊離核酸を含む、請求項13に記載の方法。
- 前記組織試料が、ホルマリン固定パラフィン包埋(FFPE)組織試料、新鮮凍結(FF)組織試料、およびそれらの任意の組み合わせからなる群より選択される、請求項11に記載の方法。
- 前記変異型分類が、テロメア配列のコピー数の変動、染色体不安定性、転座、逆位、挿入、欠失、ヘテロ接合性の消失、増幅、カタエギス、マイクロサテライト不安定性、およびそれらの任意の組合せからなる群より選択される、請求項1に記載の方法。
- 時間をかけて観察された変異からの腫瘍内または腫瘍間の異質性を判定する工程をさらに含む、請求項2に記載の方法。
- 時間をかけて観察された前記患者の治療前後の変異を監視することによって治療有効性を判定する工程をさらに含む、請求項17に記載の方法。
- 監視する前記工程が、微小残存病変を監視する工程を含む、請求項18に記載の方法。
- 患者の健康状態を追跡する方法であって、
患者から細胞遊離核酸を得る工程;
細胞遊離核酸についてアッセイを実施し、細胞遊離核酸中のテロメア特異的縦列反復配列を決定する工程;
患者のテロメア完全性スコアを作成する工程であって、前記スコアがテロメア縦列反復の頻度分布を含む工程;
2つ以上の時点で前記患者から得た細胞遊離核酸のテロメア完全性スコアの縦断的軌跡を生成する工程;
前記縦断的軌跡を、既知の健康状態を有する個体の1つ以上のデータベースにおける1つ以上の縦断的軌跡と比較する工程;および
前記患者の診断または治療を決定する工程
を含む、方法。 - 前記細胞遊離核酸が体液から得られる、請求項20に記載の方法。
- 前記体液が、全血、全血の一部、唾液、涙、汗、痰、または尿から選択される、請求項21に記載の方法。
- 前記患者の健康状態を取得する工程と、前記患者の前記健康状態および前記縦断的軌跡を1つ以上の前記データベースに追加する工程とをさらに含む、請求項20に記載の方法。
- 前記患者のテロメア縦列反復の頻度分布を正規化する工程をさらに含む、請求項20に記載の方法。
- 前記患者のテロメア縦列反復の頻度分布を正規化する前記工程が、前記頻度分布を、前記テロメア特異的縦列反復配列と同じ割合の個々の核酸塩基を有する制御配列と比較する工程を含む、請求項24に記載の方法。
- 前記患者のテロメア縦列反復の前記頻度分布を正規化する工程が、テロメア縦列反復の前記頻度分布を、1つ以上の前記データベースの1つ以上の頻度分布と比較する工程を含む、請求項24に記載の方法。
- 前記患者からの情報を取得する工程と、前記情報を、既知の健康状態を有する患者のデータベースと比較する工程とをさらに含み、前記情報が、患者の民族性、年齢、性別、または環境ばく露のうちの少なくとも1つを含む、請求項20に記載の方法。
- 前記患者のテロメラーゼ逆転写酵素(TERT)プロモーター突然変異プロファイルを決定する工程と、前記プロファイルを、既知の健康状態を有する個体の1つ以上の前記データベースに含まれる1つ以上のプロファイルと比較する工程とをさらに含む、請求項20に記載の方法。
- アッセイを実施する工程が、配列決定手順を実施する工程を含む、請求項20に記載の方法。
- 前記配列決定手順が全ゲノム配列決定を含む、請求項29に記載の方法。
- 前記配列決定手順が標的配列決定を含む、請求項29に記載の方法。
- 前記標的配列決定が標的PCR増幅を含む、請求項31に記載の方法。
- 前記標的配列決定が、1つ以上の選択可能なオリゴヌクレオチドを使用するハイブリッドキャプチャーを含む、請求項31に記載の方法。
- 前記テロメア特異的縦列反復配列が、テロメア参照配列へのアラインメントによって同定される、請求項20に記載の方法。
- 前記テロメア特異的縦列反復配列が、k-mer頻度の分析によって同定される、請求項20に記載の方法。
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2018
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2021
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2023
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EP3405574A1 (en) | 2018-11-28 |
CN108603234A (zh) | 2018-09-28 |
WO2017127742A1 (en) | 2017-07-27 |
US20170213008A1 (en) | 2017-07-27 |
CA3010418A1 (en) | 2017-07-27 |
AU2023204105A1 (en) | 2023-07-13 |
JP2022031683A (ja) | 2022-02-22 |
AU2017209330B2 (en) | 2023-05-04 |
JP2024009859A (ja) | 2024-01-23 |
HK1256412A1 (zh) | 2019-09-20 |
AU2017209330A1 (en) | 2018-07-19 |
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