JP5491400B2 - 祖先データを用いるゲノム解析の方法及びシステム - Google Patents
祖先データを用いるゲノム解析の方法及びシステム Download PDFInfo
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Description
工程110では、科学文献から遺伝子型相関を取得する。遺伝子変異についての遺伝子型相関を、目的とする1又はそれ以上の表現型形質の有無について、そして遺伝子型プロファイルについて検査された個体集団の解析から決定する。次いで各々の遺伝子変異のアレル又はそのプロファイル中の多型を再検討し、特定アレルの有無が目的とする形質と関連しているかどうかを決定する。相関付けは標準的統計学的方法により実施でき、遺伝子変異及び表現型の特徴の間の統計学的に有意な相関を記録する。例えば、多型AのアレルA1の存在は心臓病と相関していることが決定づけられるかも知れない。さらなる例として、多型AにおけるアレルA1及び多型BにおけるアレルB1の共存が、癌のリスク増大に相関することが判明するかも知れない。解析結果は専門家の検討する文献に発表され、他の研究グループにより検証され、そして/又は専門家、例えば遺伝学者、統計学者、疫学者及び医師より成る委員会により解析され、さらには監督されるかも知れない。
1個の部位に或るSNPアレルを有する個体はしばしば別の部位に特定のSNPアレルを有すると予想される。SNPと、個体を疾患又は状態に陥らせ易くするアレルの相関は、連鎖不均衡によって起こり、その場合、2又はそれ以上の遺伝子座におけるアレルの非ランダムな関連性が、組換えを介したランダムな形成から予想されるよりも、程度の差はあるものの、より頻繁に集団に起こる。
ビジネス方法
本開示はさらに、祖先データを組み入れることによりゲノムプロファイルを使用して表現型を相関させる、本明細書に記載のような方法及びシステムを提供する。したがって、個体の遺伝子型相関の評価はGCIスコアとして表現又は報告され、このGCIスコアの作製に際し、祖先データを組み入れることができる。例えば、GCIスコアの決定に用いられるORは、個体の祖先又は民族性に基づいて改変され得る。
で与えられる。同様に、集団Iにおける遺伝子型Gの頻度をf(S,I,G)と表す。SNPの対S1及びS2について、或る個体がG2をS2に持つ(CEUにおいて)とすると、該個体が遺伝子型G1をSNP S1に有する確率はPCEU(S1,G1│S2,G2)と表される。同様の表記法を第二集団YRIにも使用する。
(a)被験対象及び対照についての調査に由来する遺伝子型カウント、即ち、F(P,CA,G)及びF(P,CT,G)の値はあらゆる遺伝子型Gについて既知である。
(b)或いは、遺伝子型オッズ比は、SNP P、それらの信頼区間、ならびに被験対象及び対照の総数について既知であると想定される。
(a)Pにおける頻度及びPCEUに基づきf(S,CA,G)及びf(S,CT,G)を算出する。
(b)Sにおいて抽出されたアレル頻度に基づき、F(S,CA,G)、F(S,CT,G)の例を作製する。
(c)F(S)に基づき、そしてf(S)に基づき、Sについてのp値を算出する(後者は漸近的意義におけるp値である)。
(d)測定された全てのSNP SにわたってF(S)に基づく最小p値を求める。これがPでない場合、この例を棄却する。
(e)例が棄却されない場合、その例をf(S)に基づく最小p値と共に維持し、これがその例の原因SNPということになる。
(a)この情報を、CiにおけるYRI中での該遺伝子型頻度と共に使用して、あらゆる遺伝子型Gについて頻度fYRI(Ci,CA,G)を推定する。
(b)LD情報を使用して、あらゆるSNP SについてのfYRI(S,CA,G)、fYRI(S,CT,G)を推定し、これらの頻度に基づき漸近的オッズ比を算出する。
(c)各々のSNP Sについて、全例の漸近的オッズ比を平均し、期待される漸近的オッズ比を導く。
個体に、そこからゲノムDNAが抽出される唾液試料(およそ4ml)を入れる、キット中の試料管(例えばDNA Genotekより入手可能)が提供される。この唾液試料が処理解析のためCLIA認定研究所に送付される。典型的にはこの試料は、採集キットに入って該個体に簡便に提供される輸送容器に入れて翌日配達便で該施設に送付される。
個体の遺伝子型相関の初期決定を求める依頼に応えて、ゲノムプロファイルが作製され、遺伝子型相関が作られ、そして実施例1に記載のように該個体に結果が提供される。個体の遺伝子型相関の初期決定の後、追加の遺伝子型相関が判明すると、その後の更新された相関が決定され、又は決定され得る。契約者はプレミアムレベルの契約及び自身の遺伝子型プロファイルを持っており、それは安全なデータベースに維持される。更新された相関は、この保存された遺伝子型プロファイルに関して実行される。
アルツハイマー病(AD)のリスクは、ApoE2、ApoE3、及びApoE4と称するAPOEの3個のイソ型を生ずるアポリポ蛋白E(APOE)遺伝子の多型と相関していることが示されている。このイソ型は、APOE蛋白の残基112及び158における1又は2個のアミノ酸により、相互に異なっている。ApoE2は112/158にcys/cysを含み;ApoE3は112/158にcys/argを含み;そしてApoE2は112/158にarg/argを含む。表2に示すように、アルツハイマー病の若年発症リスクは、APOE ε4遺伝子コピーの数と共に上昇する。同様に、表3に示すように、ADの相対リスクはAPOEε4遺伝子コピーの数と共に上昇する。
以下の情報は、第V因子ライデン遺伝子の存在を示すゲノムSNPプロファイルを有する個体に提供され得る情報の例である。該個体は、この情報が初期報告で提供される基本契約を結ぶことができる。
第V因子ライデンは病気ではなく、両親から伝えられる特定の遺伝子の存在です。第V因子ライデンは、血液凝固に必要な蛋白第V(5)因子の変異体です。第V因子欠損のある人は、よりひどく出血し易く、一方第V因子ライデンを持つ人は凝固傾向の強い血液を持ちます。
第V因子の遺伝子は両親から伝えられます。多くの遺伝形質と同様、1個の遺伝子は母親から、そして1個は父親から受け継がれます。したがって、2個の正常遺伝子、又は1個の第V因子ライデン遺伝子及び1個の正常遺伝子、又は2個の第V因子ライデン遺伝子を受け継ぐことが考えられます。1個の第V因子ライデン遺伝子を持つと血栓症を発現するリスクが僅かに高くなる結果となりますが、2個の遺伝子になると、このリスクはずっと高くなります。
血栓(血栓症)のない限り、徴候はありません。
最も一般的な問題は脚の血栓です。この問題は、脚が腫れ、痛みを持ち、赤くなることで示されます。より稀な場合には、肺の血栓(肺血栓症)が発現し、呼吸を困難にします。血栓のサイズにより、これは、殆ど気付かない程度から患者が重度の呼吸困難を経験する程度までの範囲となります。さらに稀な場合には、血栓が腕又は他の身体部分に起こり得ます。これらの血栓は、血液を心臓に送る静脈で形成され、動脈(これは心臓から血液を送り出します)では形成されないので、第V因子ライデンは冠状動脈血栓症のリスクを上昇させる訳ではありません。
第V因子ライデンは血栓を作るリスクを僅かに上昇させるに過ぎず、この状態の多くの人々は血栓症を一度も経験しません。血栓ができるのを回避するためにできることは数多くあります。長時間同じ姿勢で立っていたり座っていたりすることを避けて下さい。長距離を旅行する場合には、規則的に運動することが大切です − 血液を「停滞」させてはなりません。過体重や喫煙は血栓のリスクを大幅に上昇させます。第V因子ライデン遺伝子を保有する女性は、血栓症を起こす可能性が著しく上がるため、経口避妊薬を服用してはなりません。第V因子ライデン遺伝子を保有する女性は、妊娠もまた血栓症のリスクを高めるため、妊娠する前に医師の診察を受けるべきです。
第V因子ライデンの遺伝子は血液試料中に見出すことができます。
第V因子ライデンを持つ人々は、血液が凝固し始めない限り治療を必要とせず、血液凝固が始まった場合、医師は、さらなる血栓を防止するために、ワルファリン(例えばマレバン)又はヘパリン等の血液をさらさらにする(抗凝固)薬を処方するでしょう。治療は通常3〜6ヶ月間継続させますが、血栓が幾つかある場合にはさらに長くなります。重症例では薬物治療過程を無期限に継続させ、極めて稀な例では血栓を外科的に除去する必要があるかも知れません。
第V因子ライデン遺伝子を2個持っている女性は、妊娠中ヘパリン凝固薬による治療を受ける必要があるでしょう。過去に自分自身が血栓を発現したことがある、又は血栓の家族歴を持つ、第V因子ライデン遺伝子を1個だけ持っている女性にも同じ適用を行います。
血栓の発現リスクは年齢と共に増大しますが、この遺伝子を保有する100歳を超える人々の調査では、それまでに血栓症にかかった人はごく僅かであることがわかりました。米国遺伝カウンセラー学会(NSGC)は、あなたの地域の遺伝カウンセラーの一覧表及び家族歴の創成についての情報を提供できます。www.nsgc.org/consumerでオンラインデータベースを検索して下さい。
1.リファレンスデータセットに基づきLD確率を求める
Claims (7)
- ある個体の遺伝子型を表現型と相関付けるための方法であって、
(a)或る表現型と相関を有する遺伝子変異に関連する、第一の個体集団の第一の連鎖不均衡(LD)パターンを、前記遺伝子変異に関連する、第二の個体集団の第二のLDパターンと比較し、ここで第一の個体集団及び第二の個体集団は異なる祖先を有し、
(b)工程(a)における比較から、第二の個体集団内の前記表現型が前記遺伝子変異と相関を有する確率を決定し、ここで前記確率は遺伝子型のオッズ比(OR)であり、前記遺伝子型のORは既知のORから導かれ、前記既知のORは、前記遺伝子変異が第一の個体集団の前記表現型と相関を有するORであり、
(c)高密度DNAマイクロアレイ、RT−PCR又はDNA配列決定により、前記個体のゲノムプロファイルを作成し、ここで前記個体は第二の個体集団と同じ祖先を有し、
(d)工程(b)で決定された前記確率に基づいて、工程(c)のゲノムプロファイルに対する前記表現型の相関を決定することにより、前記個体の遺伝子型を、前記個体が前記表現型を発現する尤度と相関付け、(e)工程(d)で得られた遺伝子型相関を含んでなる結果を報告する
ことを含む方法。 - 前記遺伝子型相関がGCIスコアとして報告される、請求項1に記載の方法。
- 前記遺伝子変異が未知である、請求項1又は2に記載の方法。
- 前記遺伝子変異が単一ヌクレオチド多型(SNP)である、請求項1〜3の何れか一項に記載の方法。
- 第一の個体集団及び/又は第二の個体集団が、アフリカ系アメリカ人、白色人種、アシュケナジー系ユダヤ人、スファラディー系ユダヤ人、インド人、太平洋諸島系、中東人、ドゥルーズ派、ベドウィン、南欧人、スカンジナビア人、東欧人、北アフリカ人、バスク人、西アフリカ人、及び東アフリカ人からなる群から選択されるHapMap集団(YRI、CEU、CHB、JPT、ASW、CHD、GIH、LWK、MEX、MKK、TSI)、請求項1〜4の何れか一項に記載の方法。
- ある個体の遺伝子型を表現型と相関付けるためのコンピューターシステムであって、当該システムはCPU、ディスクドライブ、及び入力装置を有し、メディア及び/又はネットワークポートからの指示を読み取り可能に構成されると共に、当該指示により、
(a)第一の個体集団の第一の連鎖不均衡(LD)パターンと第二の個体集団の第二のLDパターンとを比較し、ここで第一のLDパターン及び第二のLDパターンは、或る表現型と相関を有する同一の遺伝子変異に関連し、ここで第一の個体集団及び第二の個体集団は異なる祖先を有し、ここで前記個体は第二の個体集団と同一の祖先を有し、
(b)工程(a)における比較から、第二の個体集団内の前記表現型が前記遺伝子変異と相関を有する確率を決定し、ここで前記確率は遺伝子型のオッズ比(OR)であり、前記遺伝子型のORは既知のORから導かれ、前記既知のORは、前記遺伝子変異が第一の個体集団の前記表現型と相関を有するORであり、
(c)高密度DNAマイクロアレイ、RT−PCR、又はDNA配列決定を用いて、前記個体のゲノムプロファイルを分析し、
(d)工程(b)で決定された前記確率に基づいて、工程(c)のゲノムプロファイルに対する前記表現型の相関を決定することにより、前記個体の遺伝子型を、前記個体が前記表現型を発現する可能性と相関付け、
(e)工程(d)で得られた遺伝子型相関を含む結果を報告する
ように機能する、コンピューターシステム。 - ある個体の遺伝子型を表現型と相関付けるためのコンピューター読み取り可能メディアであって、コンピューターシステムに対し、
(a)第一の個体集団の第一の連鎖不均衡(LD)パターンと第二の個体集団の第二のLDパターンとを比較し、ここで第一のLDパターン及び第二のLDパターンは、或る表現型と相関を有する同一の遺伝子変異に関連し、ここで第一の個体集団及び第二の個体集団は異なる祖先を有し、ここで前記個体は第二の個体集団と同一の祖先を有し、
(b)工程(a)における比較から、第二の個体集団内の前記表現型が前記遺伝子変異と相関を有する確率を決定し、ここで前記確率は遺伝子型のオッズ比(OR)であり、前記遺伝子型のORは既知のORから導かれ、前記既知のORは、前記遺伝子変異が第一の個体集団の前記表現型と相関を有するORであり、
(c)高密度DNAマイクロアレイ、RT−PCR、又はDNA配列決定を用いて、前記個体のゲノムプロファイルを分析し、
(d)工程(b)で決定された前記確率に基づいて、工程(c)のゲノムプロファイルに対する前記表現型の相関を決定することにより、前記個体の遺伝子型を、前記個体が前記表現型を発現する可能性と相関付け、
(e)工程(d)で得られた遺伝子型相関を含む結果を報告する
ように機能させる指示を含む、コンピューター読み取り可能メディア。
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CA2700975A1 (en) | 2009-04-02 |
WO2009042975A1 (en) | 2009-04-02 |
US20130013217A1 (en) | 2013-01-10 |
AU2008304205B8 (en) | 2014-08-28 |
EP2215253B1 (en) | 2016-04-27 |
AU2008304205A8 (en) | 2014-08-28 |
EP2215253A4 (en) | 2011-09-07 |
CN105861664A (zh) | 2016-08-17 |
CN101842496A (zh) | 2010-09-22 |
AU2008304205B2 (en) | 2014-08-14 |
EP2215253A1 (en) | 2010-08-11 |
AU2008304205A1 (en) | 2009-04-02 |
JP2010539947A (ja) | 2010-12-24 |
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