JP6630672B2 - Ngsシステム用の対照及びそれを用いる方法 - Google Patents
Ngsシステム用の対照及びそれを用いる方法 Download PDFInfo
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- JP6630672B2 JP6630672B2 JP2016544852A JP2016544852A JP6630672B2 JP 6630672 B2 JP6630672 B2 JP 6630672B2 JP 2016544852 A JP2016544852 A JP 2016544852A JP 2016544852 A JP2016544852 A JP 2016544852A JP 6630672 B2 JP6630672 B2 JP 6630672B2
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- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6869—Methods for sequencing
- C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
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- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
- C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
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- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/166—Oligonucleotides used as internal standards, controls or normalisation probes
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Description
本明細書及び特許請求の範囲で使用される場合、単数形(the singular forms of "a" and "an")は文脈により特に明確に指定のない限り、対応する複数形も包含する。
本発明は、好ましくは核酸検出法の感度に影響を及ぼさない、システム対照、すなわち陽性対照及び/又は陰性対照を使用する、次世代シークエンシングを含むサンプルにおける標的配列を含む核酸の存在を検出する新たな方法を提供する。
FFPE samples FFPEサンプル
Workflow ワークフロー
Coverage カバレージ
図2
SC coveragevs SC amounts in AmpliSeq AmpliSeqにおけるSC量に対するSCカバレージ
SC coverage SCカバレージ
SC per AmpliSeq reaction AmpliSeq反応当たりのSC
Normalized SCcoverage vs SC amount SC量に対する正規化SCカバレージ
Normalized SCcoverage 正規化SCカバレージ
図3
Ave ampliconscov 平均アンプリコンカバレージ
Ave coverage 平均カバレージ
SC per AmpliSeq reaction AmpliSeq反応当たりのSC
Spiked 100fg 100 fgスパイク
図4
SC coverage SCカバレージ
SC cov (normalized) SCカバレージ(正規化)
DNA input DNAインプット
SC coverage(norm) SCカバレージ(正規化)
図5
AmpliconCoverage Distribution (summary) アンプリコンカバレージ分布(概要)
Coverage カバレージ
Expected 予想
Target 標的
Mutation 突然変異
35_1_ExtractedNTC 35_1_抽出NTC
MEDIAN 中央値
図6
Table 1 表1
Spike-in SC スパイクインSC
Standalone SC 独立SC
no TMVamplicon TMVアンプリコンなし
variant callerrors 変異コールエラー
humanamplicons ヒトアンプリコン
Sample サンプル
someamplicons 一部のアンプリコン
all amplicons 全てのアンプリコン
Conclusion 結論
Successfulrun ランの成功
Deletions intumor DNA, PCR inhibition in sample. Variant calling in successful amlicons is possible. 腫瘍DNAの欠失、サンプルにおけるPCR阻害。奏功するアンプリコン(amplicons)の変異コーリングが可能である。
Low qualitysample 低品質のサンプル
Strong PCRinhibition in sample サンプルにおけるPCRの強い阻害
Generalworkflow failure 全体的なワークフローの失敗
Possibleworkflow failure, results are not reliable ワークフローの失敗の可能性、結果の信頼性は高くない
Possiblefalse positive / false negative variant calls 偽陽性/偽陰性の変異コールの可能性
Possiblecontamination 汚染の可能性
Claims (12)
- サンプル及び抽出前に調製された少なくとも1つの対照サンプルから核酸材料を抽出することを含み、抽出された該核酸材料を次世代シークエンシング法に供することを更に含み、前記対照サンプルが核酸対照を添加したサンプル材料を含み、前記核酸対照が標的核酸配列とは異なる少なくとも1つの核酸対照配列を含み、前記核酸対照配列が少なくとも1つの野生型核酸配列と該野生型核酸配列の少なくとも1つの突然変異体とを含み、前記核酸対照配列が標的核酸配列とは異なる遺伝子に由来する、次世代シークエンシングベースの診断補助方法。
- 前記核酸対照が非ヒト由来の核酸から選択されるか、又はウイルス核酸から選択される、請求項1に記載の次世代シークエンシングベースの診断補助方法。
- 前記核酸対照がタバコモザイクウイルスに由来する核酸から選択される、請求項1又は2に記載の次世代シークエンシングベースの診断補助方法。
- 請求項1〜3のいずれか一項に記載の核酸対照を所定の比率で少なくとも2つ含む、請求項1〜3のいずれか一項に記載の次世代シークエンシングベースの診断補助方法。
- 感染因子又は癌遺伝子に由来する配列の有無の検出に好適である、請求項1〜4のいずれか一項に記載の次世代シークエンシングベースの診断補助方法。
- シークエンシング反応後の感染因子又は癌遺伝子に由来する標的配列の存在又は非存在及び少なくとも1つの核酸対照配列の存在が、前記サンプルからの核酸抽出の達成を示す、請求項1〜5のいずれか一項に記載の次世代シークエンシングベースの診断補助方法。
- 陰性対照を更に含む、請求項1〜6のいずれか一項に記載の次世代シークエンシングベースの診断補助方法。
- 前記陰性対照が少なくとも1つの請求項1〜3のいずれか一項に記載の核酸対照を含み、前記陰性対照がサンプル材料を含まない、請求項7に記載の次世代シークエンシングベースの診断補助方法。
- 前記陰性対照を標的核酸に特異的なシークエンシング反応に供することを含む、請求項7又は8に記載の次世代シークエンシングベースの診断補助方法。
- 前記陰性対照を標的核酸に特異的なシークエンシング反応に供することを含み、該陰性対照における標的核酸に特異的な配列の不検出、及び対照核酸に特異的な配列の存在の検出が無汚染を示す、請求項7〜9のいずれか一項に記載の次世代シークエンシングベースの診断補助方法。
- 前記対照核酸が前記サンプルからの核酸の抽出後に0.1 fg〜10 fgの量で存在する、請求項10に記載の次世代シークエンシングベースの診断補助方法。
- 前記サンプルがヒト対象に由来する臨床サンプルであり、前記対照核酸がヒトに感染しない動物ウイルス、植物ウイルスから選択される非ヒトウイルスの野生型及び/又は突然変異配列を含むプラスミドであるか、又は前記対照核酸が人工的に設計されたものであり、相当物が自然に見られない、請求項10又は11に記載の次世代シークエンシングベースの診断補助方法。
Applications Claiming Priority (3)
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GB201402249A GB201402249D0 (en) | 2014-02-10 | 2014-02-10 | NGS systems control and methods involving the same |
GB1402249.5 | 2014-02-10 | ||
PCT/IB2015/050990 WO2015118513A1 (en) | 2014-02-10 | 2015-02-10 | Ngs systems control and methods involving the same |
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JP2017505120A JP2017505120A (ja) | 2017-02-16 |
JP6630672B2 true JP6630672B2 (ja) | 2020-01-15 |
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US (1) | US11104948B2 (ja) |
EP (1) | EP3105324B1 (ja) |
JP (1) | JP6630672B2 (ja) |
CN (1) | CN106257989B (ja) |
AU (1) | AU2015213570B2 (ja) |
DK (1) | DK3105324T3 (ja) |
ES (1) | ES2719412T3 (ja) |
GB (1) | GB201402249D0 (ja) |
PT (1) | PT3105324T (ja) |
TR (1) | TR201903795T4 (ja) |
WO (1) | WO2015118513A1 (ja) |
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GB201411603D0 (en) * | 2014-06-30 | 2014-08-13 | Vela Operations Pte Ltd | Compositions for quantitative and/or semiquantitative mutation detection methods |
DK3384054T3 (en) * | 2015-12-01 | 2024-01-08 | Lgc Clinical Diagnostics Inc | Multiplex cellular reference materials |
DK3354746T3 (da) | 2017-01-30 | 2019-09-02 | Gmi Gregor Mendel Inst Fuer Molekulare Pflanzenbiologie Gmbh | Nye spike-in-nukleotider til normalisering af sekvensdata |
WO2020041449A1 (en) * | 2018-08-21 | 2020-02-27 | Zymo Research Corporation | Methods and compositions for tracking sample quality |
US20220090204A1 (en) * | 2018-11-21 | 2022-03-24 | Guangzhou Igene Biotechnology Co., Ltd. | Dna reference standard and use thereof |
CN111944806A (zh) * | 2020-07-30 | 2020-11-17 | 上海韦翰斯生物医药科技有限公司 | 一种高通量测序污染检测用分子标签组及其应用 |
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GB8608850D0 (en) | 1986-04-11 | 1986-05-14 | Diatech Ltd | Packaging system |
US5596132A (en) | 1990-03-12 | 1997-01-21 | Cornell Research Foundation, Inc. | Induction of resistance to virus diseases by transformation of plants with a portion of a plant virus genome involving a read-through replicase gene |
US5955647A (en) | 1994-02-03 | 1999-09-21 | The Scripps Research Institute | Method for using tobacco mosaic virus to overproduce peptides and proteins |
EP1157131A2 (en) | 1999-02-22 | 2001-11-28 | Lynx Therapeutics, Inc. | Polymorphic dna fragments and uses thereof |
US7863430B2 (en) | 2000-03-28 | 2011-01-04 | Queensland University Of Technology | Construct capable of release in closed circular form from a larger nucleotide sequence permitting site specific expression and/or developmentally regulated expression of selected genetic sequences |
AU2003291893A1 (en) * | 2002-12-13 | 2004-07-09 | Infectio Diagnostic (I.D.I.) Inc. | Biological reagents and methods to verify the efficiency of sample preparation and nucleic acid amplification and/or detection |
US9169515B2 (en) | 2010-02-19 | 2015-10-27 | Life Technologies Corporation | Methods and systems for nucleic acid sequencing validation, calibration and normalization |
WO2012125848A2 (en) | 2011-03-16 | 2012-09-20 | Baylor College Of Medicine | A method for comprehensive sequence analysis using deep sequencing technology |
EP2825675B1 (en) * | 2012-03-13 | 2017-12-27 | Patel, Abhijit Ajit | Measurement of nucleic acid variants using highly-multiplexed error-suppressed deep sequencing |
US9512477B2 (en) * | 2012-05-04 | 2016-12-06 | Boreal Genomics Inc. | Biomarker anaylsis using scodaphoresis |
GB201208942D0 (en) * | 2012-05-21 | 2012-07-04 | Vela Operations Pte Ltd | Extraction control for RNA |
JP6009096B2 (ja) | 2012-11-26 | 2016-10-19 | ザ・ユニバーシティ・オブ・トレド | 核酸の標準化された配列決定のための方法およびその使用 |
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- 2015-02-10 DK DK15709555.5T patent/DK3105324T3/en active
- 2015-02-10 TR TR2019/03795T patent/TR201903795T4/tr unknown
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- 2015-02-10 EP EP15709555.5A patent/EP3105324B1/en active Active
- 2015-02-10 US US15/117,656 patent/US11104948B2/en active Active
- 2015-02-10 JP JP2016544852A patent/JP6630672B2/ja active Active
- 2015-02-10 ES ES15709555T patent/ES2719412T3/es active Active
- 2015-02-10 WO PCT/IB2015/050990 patent/WO2015118513A1/en active Application Filing
- 2015-02-10 AU AU2015213570A patent/AU2015213570B2/en active Active
- 2015-02-10 CN CN201580008082.7A patent/CN106257989B/zh active Active
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Publication number | Publication date |
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US11104948B2 (en) | 2021-08-31 |
AU2015213570A1 (en) | 2016-06-16 |
CN106257989A (zh) | 2016-12-28 |
EP3105324B1 (en) | 2018-12-19 |
WO2015118513A1 (en) | 2015-08-13 |
US20180037949A1 (en) | 2018-02-08 |
GB201402249D0 (en) | 2014-03-26 |
ES2719412T3 (es) | 2019-07-10 |
AU2015213570B2 (en) | 2020-12-24 |
PT3105324T (pt) | 2019-04-01 |
DK3105324T3 (en) | 2019-04-08 |
CN106257989B (zh) | 2020-04-28 |
EP3105324A1 (en) | 2016-12-21 |
JP2017505120A (ja) | 2017-02-16 |
TR201903795T4 (tr) | 2019-06-21 |
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