RU2013141237A - Способы неинвазивного пренатального установления плоидности - Google Patents

Способы неинвазивного пренатального установления плоидности Download PDF

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RU2013141237A
RU2013141237A RU2013141237/15A RU2013141237A RU2013141237A RU 2013141237 A RU2013141237 A RU 2013141237A RU 2013141237/15 A RU2013141237/15 A RU 2013141237/15A RU 2013141237 A RU2013141237 A RU 2013141237A RU 2013141237 A RU2013141237 A RU 2013141237A
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dna
chromosome
sample
polymorphic loci
ploidy
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RU2013141237/15A
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RU2671980C2 (ru
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Мэтью РАБИНОВИТЦ
Джордж ДЖЕМЕЛОС
Милена БАНДЖЕВИК
Эллисон РАЙАН
Закари ДЕМКО
Мэтью ХИЛЛ
Бернхард ЗИММЕРМАН
Йохан БАНЕР
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Натера, Инк.
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Priority claimed from US13/110,685 external-priority patent/US8825412B2/en
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Publication of RU2013141237A publication Critical patent/RU2013141237A/ru
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Abstract

1. Способ определения статуса плоидности хромосомы или сегмента хромосомы у вынашиваемого плода, предусматривающий:измерение ДНК в образце, который содержит материнскую ДНК от матери плода и плодную ДНК от плода, во множестве полиморфных локусов в хромосоме или сегменте хромосомы;вычисление на компьютере числа аллелей во множестве полиморфных локусов по измерениям ДНК, выполненным в образце;создание на компьютере множества гипотез плоидности, каждая из которых касается различного возможного состояния плоидности хромосомы или сегмента хромосомы;построение на компьютере модели совместного распределения для ожидаемого числа аллелей во множестве полиморфных локусов в хромосоме или сегменте хромосомы для каждой гипотезы плоидности;определение на компьютере относительной вероятности каждой из гипотез плоидности с использованием модели совместного распределения и числа аллелей, измеренных в образце; иустановление состояния плоидности плода путем отбора состояния плоидности, соответствующего гипотезе с наибольшей вероятностью.2. Способ по п.1, в котором ДНК в образце происходит из материнской плазмы.3. Способ по п.1, в котором способ дополнительно предусматривает предпочтительное приумножение ДНК в образце во множестве полиморфных локусов до этапа измерения.4. Способ по п.3, в котором предпочтительное приумножение ДНК в образце во множестве полиморфных локусов предусматривает:получение множества предварительно циркуляризованных зондов, где каждый зонд нацелен на один из полиморфных локусов, где 3′- и 5′-концы каждого зонда конструируют для гибридизации с областью ДНК, которая отделена от полиморфног

Claims (30)

1. Способ определения статуса плоидности хромосомы или сегмента хромосомы у вынашиваемого плода, предусматривающий:
измерение ДНК в образце, который содержит материнскую ДНК от матери плода и плодную ДНК от плода, во множестве полиморфных локусов в хромосоме или сегменте хромосомы;
вычисление на компьютере числа аллелей во множестве полиморфных локусов по измерениям ДНК, выполненным в образце;
создание на компьютере множества гипотез плоидности, каждая из которых касается различного возможного состояния плоидности хромосомы или сегмента хромосомы;
построение на компьютере модели совместного распределения для ожидаемого числа аллелей во множестве полиморфных локусов в хромосоме или сегменте хромосомы для каждой гипотезы плоидности;
определение на компьютере относительной вероятности каждой из гипотез плоидности с использованием модели совместного распределения и числа аллелей, измеренных в образце; и
установление состояния плоидности плода путем отбора состояния плоидности, соответствующего гипотезе с наибольшей вероятностью.
2. Способ по п.1, в котором ДНК в образце происходит из материнской плазмы.
3. Способ по п.1, в котором способ дополнительно предусматривает предпочтительное приумножение ДНК в образце во множестве полиморфных локусов до этапа измерения.
4. Способ по п.3, в котором предпочтительное приумножение ДНК в образце во множестве полиморфных локусов предусматривает:
получение множества предварительно циркуляризованных зондов, где каждый зонд нацелен на один из полиморфных локусов, где 3′- и 5′-концы каждого зонда конструируют для гибридизации с областью ДНК, которая отделена от полиморфного сайта локуса небольшим количеством оснований, и где небольшое количество составляет 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21-25, 26-30, 31-60 или их комбинацию;
гибридизацию предварительно циркуляризованных зондов с ДНК из образца;
заполнение гэпа между концами гибридизированных зондов с использованием ДНК-полимеразы;
циркуляризацию предварительно циркуляризованного зонда и амплификацию циркуляризованного зонда.
5. Способ по п.3, в котором предпочтительное приумножение ДНК во множестве полиморфных локусов предусматривает:
получение множества опосредованных лигированием зондов ПЦР, где каждый зонд ПЦР нацелен на один из полиморфных локусов, где соответствующие расположенные выше и ниже зонды ПЦР конструируют для гибридизации с областью ДНК на одной цепи ДНК, которая отделена от полиморфного сайта локуса небольшим количеством оснований, и где небольшое количество составляет 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21-25, 26-30, 31-60 или их комбинацию;
гибридизацию зондов опосредованной лигированием ПЦР с ДНК из образца;
заполнение гэпа между концами зонда опосредованной лигированием ПЦР с использованием ДНК-полимеразы;
лигирование зондов опосредованной лигированием ПЦР и
амплификацию дотированных зондов опосредованной лигированием ПЦР.
6. Способ по п.3, в котором предпочтительное приумножение ДНК во множестве полиморфных локусов предусматривает:
получение множества зондов гибридного захвата, которые нацелены на полиморфные локусы;
гибридизацию зондов гибридного захвата с ДНК в образце и
физическое удаление некоторой или всей негибридизированной ДНК из образца ДНК.
7. Способ по п.3, в котором предпочтительное приумножение ДНК во множестве полиморфных локусов предусматривает:
получение множества внутренних прямых праймеров, где каждый праймер нацелен на один из полиморфных локусов, где 3′-конец каждого из внутренних прямых праймеров конструируют для гибридизации с областью ДНК, расположенной выше от полиморфного сайта локуса и отделенной от полиморфного сайта небольшим количеством оснований, и где небольшое количество выбрано из группы, состоящей из 1, 2, 3, 4, 5, 6-10, 11-15, 16-20, 21-25, 26-30 и 31-60 пар оснований;
необязательно получение множества внутренних обратных праймеров, где каждый праймер нацелен на один из полиморфных локусов, где 3′-конец каждого из внутренних обратных праймеров конструируют для гибридизации с областью ДНК, расположенной выше от полиморфного сайта локуса и отделенной от полиморфного сайта небольшим количеством оснований, и где небольшое количество выбрано из группы, состоящей из 1, 2, 3, 4, 5, 6-10, 11-15, 16-20, 21-25, 26-30 и 31-60 пар оснований;
гибридизацию внутренних праймеров с ДНК и
амплификацию ДНК с использованием полимеразной цепной реакции для образования ампликонов.
8. Способ по п.7, дополнительно предусматривающий:
получение множества внешних прямых праймеров, каждый из которых нацелен на один из полиморфных локусов, где каждый из внешних прямых праймеров конструируют для гибридизации с областью ДНК, расположенной выше от соответствующего внутреннего прямого праймера;
необязательно получение множества внешних обратных праймеров, каждый из которых нацелен на один из полиморфных локусов, где каждый из внешних обратных праймеров конструируют для гибридизации с областью ДНК, расположенной непосредственно после соответствующего внутреннего обратного праймера;
гибридизацию первых праймеров с ДНК и
амплификацию ДНК с использованием полимеразной цепной реакции.
9. Способ по п.7, дополнительно предусматривающий:
получение множества внешних обратных праймеров, каждый из которых нацелен на один из полиморфных локусов, где каждый из внешних обратных праймеров конструируют для гибридизации с областью ДНК, расположенной непосредственно после соответствующего внутреннего обратного праймера;
необязательно получение множества внешних прямых праймеров, каждый из которых нацелен на один из полиморфных локусов, где каждый из внешних прямых праймеров конструируют для гибридизации с областью ДНК, расположенной выше от соответствующего внутреннего прямого праймера;
гибридизацию первых праймеров с ДНК и
амплификацию ДНК с использованием полимеразной цепной реакции.
10. Способ по п.7, дополнительно предусматривающий:
добавление универсальных адаптеров к ДНК в образце и
амплификацию ДНК в образце с использованием полимеразной цепной реакции.
11. Способ по п.7, при котором амплификацию ДНК осуществляют в одном или множестве отдельных объемов реакционной смеси, где каждый отдельный объем реакционной смеси содержит более 500 различных пар прямых и обратных праймеров.
12. Способ по п.7, дополнительно предусматривающий разделение первого образца на множество частей, и где ДНК в каждой части предпочтительно приумножают в подмножестве множества полиморфных локусов.
13. Способ по п.7, в котором внутренние праймеры выбирают путем идентификации пар праймеров, способных образовывать нежелательные дуплексы праймеров, и удаления из множества праймеров по меньшей мере одной пары праймеров, идентифицированной как способной образовывать нежелательные дуплексы праймеров.
14. Способ по п.1, дополнительно предусматривающий получение генотипических данных во множестве полиморфных локусов от одного или обоих родителей плода.
15. Способ по п.14, в котором построение модели совместного распределения для ожидаемых вероятностей числа аллелей множества полиморфных локусов в хромосоме или сегменте хромосомы осуществляют с использованием полученных генетических данных от одного или обоих родителей.
16. Способ по п.14, в котором образец выделяют из материнской плазмы, и в котором получение генотипических данных от матери осуществляют путем оценивания материнских генотипических данных по измерениям ДНК, выполненным в образце.
17. Способ по п.3, в котором предпочтительное приумножение дает среднюю степень систематической ошибки подсчета аллелей между образцом после предпочтительного приумножения и образцом перед предпочтительным приумножением с фактором не более чем 1,2.
18. Способ по п.1, в котором множеством полиморфных локусов являются однонуклеотидные полиморфизмы.
19. Способ по п.1, в котором этап измерения ДНК в образце осуществляют путем секвенирования.
20. Способ по п.1, в котором измерения ДНК в образце во множестве полиморфных локусов используют для определения того, унаследовал или не унаследовал плод один или несколько связанных с заболеванием гаплотипов.
21. Способ по п.1, в котором этап построения модели совместного распределения для вероятностей числа аллелей осуществляют с использованием данных о вероятности хромосом, обменивающихся в различных положениях в хромосоме, для моделирования зависимости между полиморфными аллелями в хромосоме.
22. Способ по п.1, в котором как этап построения модели совместного распределения для числа аллелей, так и этап определения относительной вероятности каждой гипотезы выполняют с использованием способа, для которого не требуется применение эталонной хромосомы.
23. Способ по п.1, в котором на этапе определения относительной вероятности каждой гипотезы применяют оцениваемую фракцию плодной ДНК в образце.
24. Способ по п.1, в котором этап установления состояния плоидности плода дополнительно предусматривает:
объединение относительных вероятностей каждой из гипотез плоидности, определенных с использованием модели совместного распределения и вероятностей числа аллелей, с относительными вероятностями каждой из гипотез плоидности, которые рассчитывают с использованием одной или нескольких статистических методик, выбранных из группы, состоящей из анализа подсчета считываний, сравнения степеней гетерозиготности, статистики, которая доступна только при использовании родительской генетической информации, вероятности нормализованных сигналов генотипа для определенных родительских контекстов, статистики, которая рассчитывается с использованием оцениваемой плодной фракции образца, и их комбинаций.
25. Способ по п.1, в котором оценку достоверности рассчитывают для установленного состояния плоидности.
26. Способ по п.25, в котором достоверность превышает 99% для хромосомы 13, хромосомы 18 и хромосомы 21.
27. Способ по п.1, дополнительно предусматривающий:
осуществление клинического действия на основе установленного состояния плоидности плода, где клиническое действие выбирается из прерывания беременности или сохранения беременности.
28. Отчет, показывающий определенный статус плоидности хромосомы или сегмента хромосомы у вынашиваемого плода, сгенерированный с использованием способа по п.1.
29. Набор для определения статуса плоидности целевой хромосомы или сегмента хромосомы у вынашиваемого плода, разработанный для использования со способом по п.7, содержащий:
множество внутренних прямых праймеров и необязательно множество внутренних обратных праймеров, каждый из которых конструируют для гибридизации с областью ДНК, расположенной непосредственно выше и/или ниже одного из полиморфных сайтов в целевой хромосоме или сегменте хромосомы, где область гибридизации отделена от полиморфного сайта небольшим количеством оснований, и где небольшое количество выбрано из группы, состоящей из 1, 2, 3, 4, 5, 6-10, 11-15, 16-20, 21-25, 26-30, 31-60 и их комбинаций.
30. Способ определения наличия или отсутствия анеуплоидии плода, предусматривающий:
(a) выполнение массивно-параллельного секвенирования ДНК фрагментов ДНК, произвольно выбранных из смеси плодной и материнской геномной ДНК, для определения последовательности фрагментов ДНК;
(b) идентификацию хромосом или сегментов хромосом, которым принадлежат последовательности, полученные на этапе (a);
(c) использование данных этапа (b) для определения количества по меньшей мере одной первой хромосомы или сегмента хромосомы в смеси материнской и плодной геномной ДНК, при котором предполагается, что по меньшей мере одна первая хромосома или сегмент хромосомы являются эуплоидными у плода;
(d) использование данных этапа (b) для определения количества второй хромосомы или сегмента хромосомы в смеси материнской и плодной геномной ДНК, при котором ожидается, что вторая хромосома или сегмент хромосомы являются анеуплоидными у плода;
(e) вычисление фракции плодной ДНК в смеси плодной и материнской ДНК;
(f) вычисление ожидаемого распределения количества второй хромосомы или сегмента хромосомы для случая, при котором вторая хромосома или сегмент хромосомы являются эуплоидными, с использованием количества, определенного на этапе (c);
(g) вычисление ожидаемого распределения количества второй хромосомы или сегмента хромосомы для случая, при котором вторая хромосома или сегмент хромосомы являются анеуплоидными, с использованием количества, определенного на этапе (c), и рассчитанной фракции плодной ДНК в смеси плодной и материнской ДНК на этапе (e) и
(h) использование максимального правдоподобия или максимального апостериорного подхода для определения, является ли количество второй хромосомы или сегмента хромосомы, определенное на этапе (d), с большей вероятностью частью распределения, рассчитанного на этапе (f), или распределения, рассчитанного на этапе (g); что, тем самым, указывает на наличие или отсутствие анеуплоидии у плода.
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