JP7407193B2 - 可変の複製多重pcrを使用した配列決定方法 - Google Patents
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Description
本出願は、2018年8月8日に出願された米国仮特許出願第62/716,082号の利益を主張するものであり、その出願は参照により本明細書に組み込まれる。
本開示は以下の[1]から[21]を含む。
[1]配列分析のための方法であって、
(a)多重PCR反応に適合する複数のプライマー対を得ることと、
(b)各々、同じ試料の異なる部分を含む、少なくとも2つの多重PCR反応を設定することであって、上記プライマー対のうちの少なくともいくつかが、複数PCR反応において存在し、上記PCR反応のうちの少なくとも1つが、他の反応(複数可)の上記プライマー対のうちのいくつかを含有するが、全てを含有しない、設定することと、
(c)複数の複製アンプリコンを生成するために、上記多重PCR反応を熱循環させることと、
(d)配列リードを生成するために、上記アンプリコンを配列決定することと、
(e)選択された配列変異についてのスコアを生成するために、上記選択された配列変異について複製アンプリコンからの上記配列リードを分析することであって、上記スコアが、
i.カットオフを上回る頻度を有する配列変異を含む複製アンプリコンの数に基づいている、または
ii.上記複製物にわたる上記配列変異のための組み合わせられた証拠の強度を示す、分析することと、
(f)上記スコアに基づいて遺伝的変異として上記配列変異を呼び出すことと、を含む、方法。
[2]上記プライマー対のうちの少なくともいくつかについて、選択されたプライマー対を含む反応の数が、
i.上記選択されたプライマー対によって増幅された上記アンプリコンに見出される1つまたは複数の遺伝的変異の予期される頻度、
ii.上記試料が得られた患者の癌の種類、
iii.上記試料が得られた上記患者の治療歴、
iv.上記選択されたプライマー対によって増幅された上記アンプリコン中に見出されると予期される遺伝的変異の臨床的有意性、
v.上記試料が得られた上記患者が受けたこれまでの試験、
vi.上記選択されたプライマー対によって増幅された上記アンプリコン中に見出されると予期される1つまたは複数の遺伝子変異のエラープロファイル、および/もしくは
vii上記選択されたプライマー対によって増幅された上記アンプリコンの長さ、
またはこれらの任意の組み合わせに応じて異なる、上記[1]に記載の方法。
[3]遺伝的変異を含有する可能性がより高いアンプリコンを生成するPCRプライマー対が、遺伝的変異を含有する可能性がより低いアンプリコンを生成するPCRプライマー対よりも多くの反応において存在し、
対象となる特定の癌に関連する遺伝的変異を含有する可能性がより高いアンプリコンを生成するPCRプライマー対が、対象となる上記特定の癌に関連する遺伝的変異を含有する可能性がより低いアンプリコンを生成するPCRプライマー対よりも多くの反応において存在し、
患者が療法に対して耐性を示す遺伝的変異を含有する可能性がより高いアンプリコンを生成するPCRプライマー対が、患者が上記療法に対して耐性を示す遺伝的変異を含有する可能性がより低いアンプリコンを生成するPCRプライマー対よりも多くの反応において存在し、
臨床的に作用可能な遺伝的変異を含有する可能性がより高いアンプリコンを生成するPCRプライマー対が、臨床的に作用可能な遺伝的変異を含有する可能性がより低いアンプリコンを生成するPCRプライマー対よりも多くの反応において存在し、
高いバックグラウンドの遺伝的変異を含有する可能性がより高いアンプリコンを生成するPCRプライマー対が、低いバックグラウンドの遺伝的変異を含有する可能性がより低いアンプリコンを生成するPCRプライマー対よりも多くの反応において存在し、
より長いアンプリコンを生成するPCRプライマー対が、より短いアンプリコンを生成するPCRプライマー対よりも多くの反応において存在する、上記[1]または[2]に記載の方法。
[4]ステップ(f)において、上記呼び出しが、上記スコアを閾値と比較することによって行われ、上記閾値または閾値超で遺伝的変異を呼び出すことができる、上記[1]~[3]のいずれかに記載の方法。
[5]上記閾値が、
(i)カットオフ頻度を上回る上記選択された配列変異を有する複製の数、および/または
(ii)複数の複製にわたる上記配列変異のための上記組み合わせられた証拠の必要な強度を示す値である、上記[4]に記載の方法。
[6]上記カットオフが、配列変異が増幅および/または配列決定エラーによってどのくらいの頻度で生成されるかを示すエラー分布に基づいている、上記[4]または[5]に記載の方法。
[7]上記エラー分布が、配列決定制御試料によって推定される、上記[6]に記載の方法。
[8]上記方法が、
i.上記選択されたプライマー対によって増幅された上記アンプリコンに見出される1つまたは複数の遺伝的変異の予期される頻度、
ii.上記試料が得られた上記患者の上記癌の種類、
iii.上記試料が得られた上記患者の治療歴、
iv.上記選択されたプライマー対によって増幅された上記アンプリコン中に見出されると予期される遺伝的変異の臨床的有意性、
v.上記試料が得られた上記患者が受けたこれまでの試験、
vi.上記選択されたプライマー対によって増幅された上記アンプリコン中に見出されると予期される遺伝子変異の上記エラープロファイル、
vi.上記試料中に見出される他の遺伝的変異、および/もしくは
vii上記配列決定の全体的なエラー率、
またはこれらの任意の組み合わせに基づいて、上記閾値または上記カットオフを増加または減少させることを含む、上記[1]~[7]のいずれかに記載の方法。
[9](b)において設定された各反応が、少なくとも5つのプライマー対を含有する、上記[1]~[8]のいずれかに記載の方法。
[10]ステップ(b)が、少なくとも3つおよび10未満の多重PCR反応を設定することを含む、上記[1]~[9]のいずれかに記載の方法。
[11]上記配列変異が、複数の変異体の置換、挿入、欠失、再配列、または組み合わせである、上記[1]~[10]のいずれかに記載の方法。
[12]上記試料が、cfDNAである、上記[1]~[11]のいずれかに記載の方法。
[13]上記複製アンプリコンが、増幅中に複製識別子でタグ付けされ、上記方法が、配列決定の前に異なる増幅反応をプールすることを含む、上記[1]~[12]のいずれかに記載の方法。
[14]各アンプリコンの長さが、独立して、50bp~500bpの範囲内である、上記[1]~[13]のいずれかに記載の方法。
[15]上記配列変異のための上記組み合わせられた証拠が、尤度値を使用して要約され、上記閾値が、尤度閾値である、上記[1]~[14]のいずれかに記載の方法。
[16]上記配列変異のための上記組み合わせられた証拠が、ベイズ統計を使用して要約され、上記閾値が、事前分布によって変化し得るベイズ因子である、上記[1]~[15]のいずれかに記載の方法。
[17]上記閾値が、機械学習を使用して確立される、上記[1]~[16]のいずれかに記載の方法。
[18]上記試料が、cfDNAであり、上記方法が、同じ対象からのcfRNAを分析することをさらに含む、上記[1]~[17]のいずれかに記載の方法。
[19]上記試料が、cfDNAであり、上記方法が、上記同じ対象からの白血球DNAを分析することをさらに含む、上記[1]~[18]のいずれかに記載の方法。
[20]上記配列変異が、特定の疾患、状態、または治療を示す、上記[1]~[19]のいずれかに記載の方法。
[21](g)上記配列変異に関する情報を含む報告書を第三者に転送することをさらに含む、上記[1]~[20]のいずれかに記載の方法。
(a)多重PCR反応に適合する複数のプライマー対を得ることと、
(b)少なくとも2つの多重PCR反応を設定することであって、各々、同じ試料の異なる部分を含有し、プライマー対のうちの少なくともいくつかが、1つを超えるPCR反応において存在し、PCR反応のうちの少なくとも1つが、他の反応(複数可)のプライマー対のうちのいくつかを含有するが、全てを含有せず、全てのPCR反応において存在しないプライマー対の少なくともいくつかについては、プライマー対を含む反応の数が、プライマー対によって増幅されたアンプリコンにおいて予期される1つ以上の配列変異の認識された重要性、尤度、および/または種類に応じて異なる、設定することと、
(c)複数の複製アンプリコンを生成するために、多重PCR反応を熱循環させることと、
(d)配列リードを生成するために、アンプリコンを配列決定することと、
(e)選択された配列変異についてのスコアを生成するために、選択された配列変異について複製アンプリコンからの配列リードを分析することであって、スコアが、i.カットオフを上回る頻度を有する配列変異を含む複製アンプリコンの数に基づいている、またはii.複製物にわたる配列変異のために組み合わせられた証拠の強度を示す、分析することと
(f)スコアに基づいて配列変異を呼び出すことと、を含み得る。
別段の定義がない限り、本明細書で使用される全ての技術用語および科学用語は、本発明が属する技術分野の当業者が一般的に理解するのと同じ意味を有する。さらに、参照を明確かつ容易にするために、ある特定の要素が、定義される。
Claims (15)
- 最小限の残存疾患の分析のための方法であって、
(a)腫瘍物質を配列決定することを介して患者の腫瘍において以前に同定された配列変異を含有する配列を増幅するように設計され、多重PCR反応に適合する複数のプライマー対を得るステップと、
(b)各々、(a)の患者由来のcfDNAの試料の異なるアリコートを含む、少なくとも2つの複製多重PCR反応を設定するステップと、
(c)複数の複製アンプリコンを生成するために、前記複製多重PCR反応を熱循環させるステップと、
(d)配列リードを生成するために、前記アンプリコンを配列決定するステップと、
(e)前記患者の腫瘍に以前に同定された選択された配列変異についてのスコアを生成するために、前記選択された配列変異について複製アンプリコンからの前記配列リードを分析するステップであって、前記スコアが、
i.カットオフを上回る頻度を有する配列変異を含む複製アンプリコンの数に基づいている、または
ii.前記複製アンプリコンにわたる前記患者特異的配列変異のための組み合わせられた証拠の強度を示す、分析するステップと、
(f)前記スコアに基づいて遺伝的変異として前記配列変異を呼び出すステップと、を含む、方法。 - 前記プライマー対のうちの少なくともいくつかが、1より多いPCR反応中にあり、前記PCR反応の少なくとも1つが、いくつかではあるが全部ではない他の反応のプライマーを含む、請求項1に記載の方法。
- 異なる反応が同じプライマーを含む、請求項1に記載の方法。
- (b)のcfDNAの前記試料が、処置後の患者から収集されたものである、請求項1に記載の方法。
- (b)のcfDNAの前記試料が、癌治療後の患者から収集されたものである、請求項4に記載の方法。
- ステップ(b)から(f)が、同じ患者から異なる時間に収集されたcfDNAの第1および第2の試料に対して行われる、請求項1に記載の方法。
- ステップ(b)において、前記試料が、3または4つの複製多重PCR反応に分割される、請求項1に記載の方法。
- (b)の前記多重PCR反応の各々が、少なくとも5つのプライマー対を含む、請求項1に記載の方法。
- (c)の各アンプリコンの長さが、独立して50bpから500bpの範囲内にある、請求項1に記載の方法。
- ステップ(f)において、前記呼び出しが、前記スコアを閾値と比較することによって行われ、前記閾値または閾値超で遺伝的変異を呼び出すことができる、請求項1に記載の方法。
- 前記カットオフが、配列変異が増幅および/または配列決定エラーによってどのくらいの頻度で生成されるかを示すエラー分布に基づいている、請求項1に記載の方法。
- 前記エラー分布が、配列決定制御試料によって推定される、請求項11に記載の方法。
- (e)iiの前記配列変異のための前記組み合わせられた証拠が、尤度値を使用して要約され、前記閾値が、尤度閾値である、請求項10に記載の方法。
- (e)iiの前記配列変異のための前記組み合わせられた証拠が、ベイズ統計を使用して要約され、前記閾値が、事前分布によって変化し得るベイズ因子である、請求項10に記載の方法。
- 前記配列変異に関する情報を含む報告書を第三者に転送することをさらに含む、請求項1に記載の方法。
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