JP6141310B2 - 強固な変異体特定および検証 - Google Patents
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Description
Y.Shen他、Genome Research、vol.20、no.2、2010年2月1日、273〜280頁は、系統的配列決定エラーを明らかにするのにロジスティック回帰法および標準スコアを使用して、次世代再配列決定データにより変異体対立遺伝子確率を評価するSNP発見方法に関する。
Matukumalli L.K.他、BMC Bioinformatics、BioMed Central、London、GB、Vol.7、No.1、2006年1月6日、1〜9頁は、SNP発見における機械学習に関する。ある特定の機械学習プログラムが、決定木に基づいて使用されてきた。MLプログラムでは、配列深さ、変位型および塩基頻度などの特徴のセットに基づいて分類子を作り出すことが報告されている。
はk番目の悪いプローブのi番目の特徴である。分子は、良いプローブ・セットと悪いプローブ・セットの間の区別を示し、分母は、2つのセットそれぞれのうちの1つを示す。より高いFスコアは、その特徴がより特異的であることを示唆する。
Claims (9)
- 整列された配列決定リードを含む組み立てられた遺伝子配列中の可能性がある変異体を特定するステップと、
前記組み立てられた遺伝子配列の配列決定リードについて複数のリード特性の値を計算するステップと、
受入れ基準を満たす前記可能性がある変異体を含む前記組み立てられた遺伝子配列の配列決定リードについての、前記少なくとも1つのリード特性の前記計算された値を条件として、前記可能性がある変異体をコールするステップと、
を含む方法であって、
前記可能性がある変異体が、前記可能性がある変異体を含む前記リードについての、前記複数のリード特性の計算された値に影響を及ぼす分類子を使用して、受け入れられるもの、または拒絶されるものとして分類され、前記可能性がある変異体が、前記可能性がある変異体が受け入れられるものとして分類される場合にだけコールされ、分類が、Fスコアを使用するサポート・ベクター・マシン分類を使用して行われ、
前記特定するステップ、計算するステップ、およびコールするステップが電子データ処理デバイスによって実施され、
前記少なくとも1つのリード特性が、前記配列決定リードの物理的特性を含む、方法。 - 前記少なくとも1つのリード特性が少なくとも1つの塩基組成特性を含む、請求項1に記載の方法。
- 前記少なくとも1つのリード特性が少なくとも1つの熱力学的特性を含む、請求項1または2に記載の方法。
- 前記少なくとも1つのリード特性が、リード安定性を示す少なくとも1つのエネルギー特性を含む、請求項1〜3のいずれか1項に記載の方法。
- 前記少なくとも1つのリード特性が少なくとも1つの二次構造特性を含む、請求項1〜4のいずれか1項に記載の方法。
- 配列決定リードのセットを組み立てて、前記組み立てられた遺伝子配列を生成するステップをさらに含み、
塩基クオリティ・スコアおよびカバー度基準を満たさない配列決定リードが破棄され、前記組み立てられた遺伝子配列に含まれず、
前記組み立てられた遺伝子配列が全ゲノム配列を含む、請求項1〜5のいずれか1項に記載の方法。 - 請求項1〜6のいずれか1項に記載の方法が含む各ステップを、電子データ処理デバイスに実行させるコンピュータプログラム。
- 整列された配列決定リードを含む組み立てられた遺伝子配列を記憶する持続性記憶媒体と、
電子処理デバイスであって、
前記組み立てられた遺伝子配列中の可能性がある変異体を特定する動作、
前記組み立てられた遺伝子配列のリードについて複数のリード特性の値を計算する動作、および、
受入れ基準を満たす前記可能性がある変異体を含む前記組み立てられた遺伝子配列の配列決定リードについての、前記少なくとも1つのリード特性の前記計算された値を条件として、前記可能性がある変異体をコールする動作、
を含む動作を行うように構成された電子処理デバイスと、
を備える装置であって、
前記可能性がある変異体が、前記可能性がある変異体を含む前記リードについての、前記複数のリード特性の前記計算された値に影響を及ぼす分類子を使用して、受け入れられるもの、または拒絶されるのとして分類され、前記可能性がある変異体が、前記可能性がある変異体が受け入れられるものとして分類される場合にだけコールされ、分類が、Fスコアを使用するサポート・ベクター・マシン分類を使用して行われ、
前記少なくとも1つのリード特性が、前記配列決定リードの物理的特性を含む、装置。 - 前記少なくとも1つのリード特性が、塩基組成特性、熱力学的特性、エネルギー特性、および二次構造特性からなる群から選択された少なくとも1つのリード特性を含む、請求項8に記載の装置。
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EP11193585.4A EP2602734A1 (en) | 2011-12-08 | 2011-12-14 | Robust variant identification and validation |
PCT/IB2012/056911 WO2013084133A2 (en) | 2011-12-08 | 2012-12-03 | Robust variant identification and validation |
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US (1) | US10607719B2 (ja) |
EP (2) | EP2602734A1 (ja) |
JP (1) | JP6141310B2 (ja) |
CN (1) | CN103975329B (ja) |
BR (1) | BR112014013562A2 (ja) |
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US10424395B2 (en) * | 2015-03-27 | 2019-09-24 | Sentieon Inc. | Computation pipeline of single-pass multiple variant calls |
JP2017016665A (ja) * | 2015-07-03 | 2017-01-19 | 国立大学法人東北大学 | 配列のデータからの変異情報の選択方法、システム、及び、コンピュータプログラム |
US10600499B2 (en) | 2016-07-13 | 2020-03-24 | Seven Bridges Genomics Inc. | Systems and methods for reconciling variants in sequence data relative to reference sequence data |
CN107451428B (zh) * | 2017-08-02 | 2020-05-22 | 广东国盛医学科技有限公司 | 下一代测序中末端短串联序列的优化处理方法 |
CN107590362B (zh) * | 2017-08-21 | 2019-12-06 | 武汉菲沙基因信息有限公司 | 一种基于长读序测序判断重叠组装正误的方法 |
JP7013490B2 (ja) * | 2017-11-30 | 2022-02-15 | イルミナ インコーポレイテッド | 配列バリアントコールのためのバリデーションの方法及びシステム |
CN108959853B (zh) * | 2018-05-18 | 2020-01-17 | 广州金域医学检验中心有限公司 | 一种拷贝数变异的分析方法、分析装置、设备及存储介质 |
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FR2763600B1 (fr) * | 1997-05-20 | 1999-11-12 | Genolife | Procede de detection qualitative et quantitative d'alterations de l'adn et des ligands de ces alterations |
US6714874B1 (en) * | 2000-03-15 | 2004-03-30 | Applera Corporation | Method and system for the assembly of a whole genome using a shot-gun data set |
US6376191B1 (en) * | 2000-03-22 | 2002-04-23 | Mergen, Ltd. | Microarray-based analysis of polynucleotide sequence variations |
US8364417B2 (en) * | 2007-02-15 | 2013-01-29 | 454 Life Sciences Corporation | System and method to correct out of phase errors in DNA sequencing data by use of a recursive algorithm |
CN101131391B (zh) | 2006-08-24 | 2011-07-20 | 中国科学院上海药物研究所 | 基于分子亲电矢量和扩展支持向量机的基因毒性概率预测方法 |
EP2101275A1 (en) * | 2008-03-10 | 2009-09-16 | Koninklijke Philips Electronics N.V. | Method for polynucleotide design and selection |
US20110190657A1 (en) * | 2009-08-10 | 2011-08-04 | Carl Zeiss Meditec, Inc. | Glaucoma combinatorial analysis |
KR101952965B1 (ko) * | 2010-05-25 | 2019-02-27 | 더 리젠츠 오브 더 유니버시티 오브 캘리포니아 | Bambam:고처리율 서열분석 데이터의 병렬 비교 분석 |
US9600625B2 (en) * | 2012-04-23 | 2017-03-21 | Bina Technologies, Inc. | Systems and methods for processing nucleic acid sequence data |
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