JP2016536991A5 - - Google Patents
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- JP2016536991A5 JP2016536991A5 JP2016529963A JP2016529963A JP2016536991A5 JP 2016536991 A5 JP2016536991 A5 JP 2016536991A5 JP 2016529963 A JP2016529963 A JP 2016529963A JP 2016529963 A JP2016529963 A JP 2016529963A JP 2016536991 A5 JP2016536991 A5 JP 2016536991A5
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- 150000007523 nucleic acids Chemical group 0.000 claims description 14
- 239000002773 nucleotide Substances 0.000 claims description 9
- 125000003729 nucleotide group Chemical group 0.000 claims description 9
- 229920003013 deoxyribonucleic acid Polymers 0.000 claims description 6
- 229920000160 (ribonucleotides)n+m Polymers 0.000 claims description 4
- 229920002676 Complementary DNA Polymers 0.000 claims description 2
- 239000002299 complementary DNA Substances 0.000 claims description 2
- 238000000926 separation method Methods 0.000 claims description 2
- 239000000523 sample Substances 0.000 claims 4
- 230000004048 modification Effects 0.000 description 1
- 238000006011 modification reaction Methods 0.000 description 1
Description
本発明は、その具体的実施形態とともに記載されてきたが、それはさらなる改変が可能であり、本願は、一般に、本発明の原理に従って、本発明が属する技術内の公知もしくは習慣的な実施内に入るとして、本開示からのこのような逸脱を含め、そして本明細書で先に示される本質的特徴に適用され得るとおりおよび添付の特許請求の範囲に従うとおり、本発明の任意のバリエーション、使用、もしくは適合を網羅することが意図されることは、理解される。
例えば、本発明は以下の項目を提供する。
(項目1)
複製物配列決定リードをサンプル配列決定リードの集団から検出するための方法であって、前記方法は、以下:
a)アダプターを、1以上のサンプルに由来する複数の核酸フラグメントの各核酸フラグメントの5’末端にライゲーションする工程であって、ここで前記アダプターは、以下:
(i)インデックス付加プライマー結合部位;
(ii)インデックス付加部位;
(iii)識別子部位;および
(iv)標的配列プライマー結合部位
を含む、工程;
b)前記アダプター−核酸フラグメントのライゲーション生成物を増幅する工程;
c)配列決定リードの集団を、増幅されたアダプター−核酸フラグメントのライゲーション生成物から生成する工程;ならびに
d)複製物識別子部位および標的配列を有する配列決定リードを含む前記配列決定リードの集団を、検出する工程
を包含する、方法。
(項目2)
前記方法は、前記配列リードの集団から、複製物識別子部位および標的配列を有する配列決定リードを除去する工程をさらに包含する、項目1に記載の方法。
(項目3)
前記識別子部位は、前記インデックス付加部位とともに配列決定される、項目1に記載の方法。
(項目4)
前記識別子部位は、前記インデックス付加部位とは別個に配列決定される、項目1に記載の方法。
(項目5)
前記識別子部位は、前記標的配列とともに配列決定される、項目1に記載の方法。
(項目6)
前記識別子部位は、前記標的配列とは別個に配列決定される、項目1に記載の方法。
(項目7)
前記アダプターは、5’から3’へと:
(i)前記インデックス付加プライマー結合部位;
(ii)前記インデックス付加部位;
(iii)前記識別子部位;および
(iv)前記標的配列プライマー結合部位
を含む、項目1に記載の方法。
(項目8)
前記アダプターは、5’から3’へと:
(i)前記インデックス付加プライマー結合部位;
(ii)前記インデックス付加部位;
(iii)前記標的配列プライマー結合部位;および
(iv)前記識別子部位
を含む、項目1に記載の方法。
(項目9)
複数の前記核酸フラグメントは、1より多くのサンプルから生成される、項目1に記載の方法。
(項目10)
各サンプルの前記核酸フラグメントは、同じインデックス付加部位を有する、項目9に記載の方法。
(項目11)
前記配列決定リードは、前記インデックス付加部位に基づいて分離される、項目10に記載の方法。
(項目12)
前記配列決定リードの分離は、工程d)の前に行われる、項目11に記載の方法。
(項目13)
前記核酸フラグメントは、DNAフラグメント、RNAフラグメント、もしくはDNA/RNAフラグメントである、項目1に記載の方法。
(項目14)
前記核酸フラグメントは、ゲノムDNAフラグメントもしくはcDNAフラグメントである、項目13に記載の方法。
(項目15)
前記インデックス付加部位は、2ヌクレオチド〜8ヌクレオチドの間の長さである、項目1に記載の方法。
(項目16)
前記インデックス付加部位は、約6ヌクレオチドの長さである、項目1に記載の方法。
(項目17)
前記識別子部位は、1ヌクレオチド〜8ヌクレオチドの間の長さである、項目1に記載の方法。
(項目18)
前記識別子部位は、約8ヌクレオチドの長さである、項目1に記載の方法。
(項目19)
前記インデックス付加プライマー結合部位は、ユニバーサルインデックス付加プライマー結合部位である、項目1に記載の方法。
(項目20)
前記標的配列プライマー結合部位は、ユニバーサル標的配列プライマー結合部位である、項目1に記載の方法。
(項目21)
複数のアダプターを含むキットであって、ここで各アダプターは、以下:
(i)インデックス付加プライマー結合部位;
(ii)インデックス付加部位;
(iii)識別子部位;および
(iv)標的配列決定プライマー結合部位、
を含む、キット。
例えば、本発明は以下の項目を提供する。
(項目1)
複製物配列決定リードをサンプル配列決定リードの集団から検出するための方法であって、前記方法は、以下:
a)アダプターを、1以上のサンプルに由来する複数の核酸フラグメントの各核酸フラグメントの5’末端にライゲーションする工程であって、ここで前記アダプターは、以下:
(i)インデックス付加プライマー結合部位;
(ii)インデックス付加部位;
(iii)識別子部位;および
(iv)標的配列プライマー結合部位
を含む、工程;
b)前記アダプター−核酸フラグメントのライゲーション生成物を増幅する工程;
c)配列決定リードの集団を、増幅されたアダプター−核酸フラグメントのライゲーション生成物から生成する工程;ならびに
d)複製物識別子部位および標的配列を有する配列決定リードを含む前記配列決定リードの集団を、検出する工程
を包含する、方法。
(項目2)
前記方法は、前記配列リードの集団から、複製物識別子部位および標的配列を有する配列決定リードを除去する工程をさらに包含する、項目1に記載の方法。
(項目3)
前記識別子部位は、前記インデックス付加部位とともに配列決定される、項目1に記載の方法。
(項目4)
前記識別子部位は、前記インデックス付加部位とは別個に配列決定される、項目1に記載の方法。
(項目5)
前記識別子部位は、前記標的配列とともに配列決定される、項目1に記載の方法。
(項目6)
前記識別子部位は、前記標的配列とは別個に配列決定される、項目1に記載の方法。
(項目7)
前記アダプターは、5’から3’へと:
(i)前記インデックス付加プライマー結合部位;
(ii)前記インデックス付加部位;
(iii)前記識別子部位;および
(iv)前記標的配列プライマー結合部位
を含む、項目1に記載の方法。
(項目8)
前記アダプターは、5’から3’へと:
(i)前記インデックス付加プライマー結合部位;
(ii)前記インデックス付加部位;
(iii)前記標的配列プライマー結合部位;および
(iv)前記識別子部位
を含む、項目1に記載の方法。
(項目9)
複数の前記核酸フラグメントは、1より多くのサンプルから生成される、項目1に記載の方法。
(項目10)
各サンプルの前記核酸フラグメントは、同じインデックス付加部位を有する、項目9に記載の方法。
(項目11)
前記配列決定リードは、前記インデックス付加部位に基づいて分離される、項目10に記載の方法。
(項目12)
前記配列決定リードの分離は、工程d)の前に行われる、項目11に記載の方法。
(項目13)
前記核酸フラグメントは、DNAフラグメント、RNAフラグメント、もしくはDNA/RNAフラグメントである、項目1に記載の方法。
(項目14)
前記核酸フラグメントは、ゲノムDNAフラグメントもしくはcDNAフラグメントである、項目13に記載の方法。
(項目15)
前記インデックス付加部位は、2ヌクレオチド〜8ヌクレオチドの間の長さである、項目1に記載の方法。
(項目16)
前記インデックス付加部位は、約6ヌクレオチドの長さである、項目1に記載の方法。
(項目17)
前記識別子部位は、1ヌクレオチド〜8ヌクレオチドの間の長さである、項目1に記載の方法。
(項目18)
前記識別子部位は、約8ヌクレオチドの長さである、項目1に記載の方法。
(項目19)
前記インデックス付加プライマー結合部位は、ユニバーサルインデックス付加プライマー結合部位である、項目1に記載の方法。
(項目20)
前記標的配列プライマー結合部位は、ユニバーサル標的配列プライマー結合部位である、項目1に記載の方法。
(項目21)
複数のアダプターを含むキットであって、ここで各アダプターは、以下:
(i)インデックス付加プライマー結合部位;
(ii)インデックス付加部位;
(iii)識別子部位;および
(iv)標的配列決定プライマー結合部位、
を含む、キット。
Claims (21)
- 複製物配列決定リードをサンプル配列決定リードの集団から検出するための方法であって、前記方法は、以下:
a)アダプターを、1以上のサンプルに由来する複数の核酸フラグメントの各核酸フラグメントの5’末端にライゲーションする工程であって、ここで前記アダプターは、以下:
(i)インデックス付加プライマー結合部位;
(ii)インデックス付加部位;
(iii)1〜8ヌクレオチドからなる識別子部位;および
(iv)標的配列プライマー結合部位
を含む、工程;
b)前記アダプター−核酸フラグメントのライゲーション生成物を増幅する工程;
c)配列決定リードの集団を、増幅されたアダプター−核酸フラグメントのライゲーション生成物から生成する工程;ならびに
d)前記配列決定リードの集団における他の配列決定リードと同一である識別子部位および核酸フラグメントを含む配列決定リードとして、複製物配列決定リードを同定する工程
を包含する、方法。 - 前記方法は、前記配列リードの集団から、複製物識別子部位および標的配列を有する配列決定リードを除去する工程をさらに包含する、請求項1に記載の方法。
- 前記識別子部位は、前記インデックス付加部位とともに配列決定される、請求項1に記載の方法。
- 前記識別子部位は、前記インデックス付加部位とは別個に配列決定される、請求項1に記載の方法。
- 前記識別子部位は、前記標的配列とともに配列決定される、請求項1に記載の方法。
- 前記識別子部位は、前記標的配列とは別個に配列決定される、請求項1に記載の方法。
- 前記アダプターは、5’から3’へと:
(i)前記インデックス付加プライマー結合部位;
(ii)前記インデックス付加部位;
(iii)前記識別子部位;および
(iv)前記標的配列プライマー結合部位
を含む、請求項1に記載の方法。 - 前記アダプターは、5’から3’へと:
(i)前記インデックス付加プライマー結合部位;
(ii)前記インデックス付加部位;
(iii)前記標的配列プライマー結合部位;および
(iv)前記識別子部位
を含む、請求項1に記載の方法。 - 複数の前記核酸フラグメントは、1より多くのサンプルから生成される、請求項1に記載の方法。
- 各サンプルの前記核酸フラグメントは、同じインデックス付加部位を有し、異なるサンプルの前記核酸フラグメントは異なるインデックス付加部位を有する、請求項9に記載の方法。
- 前記配列決定リードは、前記インデックス付加部位に基づいて分離される、請求項10に記載の方法。
- 前記配列決定リードの分離は、工程d)の前に行われる、請求項11に記載の方法。
- 前記核酸フラグメントは、DNAフラグメント、RNAフラグメント、もしくはDNA/RNAフラグメントである、請求項1に記載の方法。
- 前記核酸フラグメントは、ゲノムDNAフラグメントもしくはcDNAフラグメントである、請求項13に記載の方法。
- 前記インデックス付加部位は、2ヌクレオチド〜8ヌクレオチドの間の長さである、請求項1に記載の方法。
- 前記インデックス付加部位は、約6ヌクレオチドの長さである、請求項1に記載の方法。
- 前記識別子部位は、6ヌクレオチドの長さである、請求項1に記載の方法。
- 前記識別子部位は、8ヌクレオチドの長さである、請求項1に記載の方法。
- 前記インデックス付加プライマー結合部位は、ユニバーサルインデックス付加プライマー結合部位である、請求項1に記載の方法。
- 前記標的配列プライマー結合部位は、ユニバーサル標的配列プライマー結合部位である、請求項1に記載の方法。
- インデックス付加部位に基づいてフラグメントまたは配列決定リードを分離する工程をさらに含む、請求項10に記載の方法。
Applications Claiming Priority (3)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US201361903826P | 2013-11-13 | 2013-11-13 | |
US61/903,826 | 2013-11-13 | ||
PCT/US2014/065530 WO2015073711A1 (en) | 2013-11-13 | 2014-11-13 | Compositions and methods for identification of a duplicate sequencing read |
Publications (3)
Publication Number | Publication Date |
---|---|
JP2016536991A JP2016536991A (ja) | 2016-12-01 |
JP2016536991A5 true JP2016536991A5 (ja) | 2017-12-21 |
JP6525473B2 JP6525473B2 (ja) | 2019-06-05 |
Family
ID=53044101
Family Applications (1)
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JP2016529963A Active JP6525473B2 (ja) | 2013-11-13 | 2014-11-13 | 複製物配列決定リードを同定するための組成物および方法 |
Country Status (6)
Country | Link |
---|---|
US (5) | US9546399B2 (ja) |
EP (1) | EP3068883B1 (ja) |
JP (1) | JP6525473B2 (ja) |
CN (1) | CN105849264B (ja) |
CA (1) | CA2929596C (ja) |
WO (1) | WO2015073711A1 (ja) |
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EP3068883B1 (en) | 2013-11-13 | 2020-04-29 | Nugen Technologies, Inc. | Compositions and methods for identification of a duplicate sequencing read |
US10450597B2 (en) | 2014-01-27 | 2019-10-22 | The General Hospital Corporation | Methods of preparing nucleic acids for sequencing |
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