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ES2595373T3 - Prueba genética no invasiva mediante análisis digital - Google Patents

Prueba genética no invasiva mediante análisis digital Download PDF

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ES2595373T3
ES2595373T3 ES11175845.4T ES11175845T ES2595373T3 ES 2595373 T3 ES2595373 T3 ES 2595373T3 ES 11175845 T ES11175845 T ES 11175845T ES 2595373 T3 ES2595373 T3 ES 2595373T3
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Stephen Quake
Hei-Mun Christina Fan
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Leland Stanford Junior University
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Abstract

Un método para detectar una anormalidad genética que implica una diferencia cuantitativa entre secuencias genéticas maternas y fetales por la detección diferencial de las secuencias diana en una mezcla de material genético materno y fetal, que comprende las etapas de: a)la distribución del material genético en muestras discretas, conteniendo cada muestra en promedio no más de una secuencia diana por muestra, en el que las muestras discretas están en muestras de reacción donde se pueden analizar las secuencias diana; b)la medición de la presencia de diferentes secuencias diana en las muestras discretas, en la que la medición comprende la secuenciación directa del material genético o secuenciación de derivados amplificados de las secuencias diana en clones o amplicones del material genético; y, c) el análisis de un número de las muestras discretas, donde el número de muestras discretas analizadas y los resultados de las muestras discretas proporcionan datos suficientes para obtener resultados que distinguen dichas secuencias diana diferentes. donde una de las diferentes secuencias diana es diploide en el material genético materno y aneuploides en el material genético fetal y otra de las diferentes secuencias diana es diploide, tanto en el material genético materno como en el fetal, detectando de ese modo una anomalía genética que implica una diferencia cuantitativa entre secuencias genéticas maternas y fetales.

Description

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puede ser excluidao. Otra etapa de enriquecimiento puede ser para el tratamiento de la muestra de sangre con formaldehído, como se describe en Dhallan et al.. " Methods to Increase the Percentage of Free Fetal ADN Recovered From the Maternal Circulation," J. Am Medicina. Soc. 291 (9):1114-1119 (Marzo 2004).
2.
La distribución de las moléculas individuales de ADN de esta muestra a una serie de muestras de reacción discretas, donde se selecciona el número de muestras de reacción para dar un resultado estadísticamentesignificativo para elnúmero de copias de una diana en lasmoléculasde ADN.Además,la muestra de reacción se limita a un pequeño volumen para que las moléculas de reacción en estrecha aproximación. La cantidad de molécula de ADN por muestra de reacción es preferiblemente del orden de una copia del cromosoma de interés equivalente pormuestra de reacción.
3.
La detección de la presencia de la diana en el ADN en un gran número de muestras de reacción, preferiblemente con una técnica específica de secuencia como la secuenciación de lectura corta altamente multiplexada o una reacción de PCR en el que el producto de PCR se marca para producir una lectura cuantitativamente conveniente. La etapa de detección se denomina aquí "PCR digital" y puede ser llevada a cabo por una variedad de métodos, tales como (a) por PCR en muestras diluidas en pocillos individuales de una placa de microtitulación; (b) PCR en muestras diluidas en emulsiones que contienen cebadores inmovilizados a microesferas; o (c) PCR en muestras atrapadas en una cámara de microfluidos; y
4.
El análisis cuantitativo de la detección de las secuencias diana maternas y fetales. En algunos casos, esto puede incluir dianas a diferentes regiones, tales como sondas para un diana en un cromosoma sospechoso de estar presente en un número de copia anormal (trisonomía) en comparación con un cromosoma diploide normal, que se utiliza como control.
II.
Descripción de los Pasos
A.
Preparación de tejidos
[0038] El presente procedimiento se refiere a pruebas no invasivas. El material de partida preferido es sangre venosa periférica materna. Con el fin de obtener suficiente ADN para la prueba, se prefiere que se extraiga 10 a 20 mldesangre,afindeobteneralrededorde almenos10.000 equivalentes de genoma de ADN total.Este tamaño de la muestra se basa en una estimación de estar presente el ADN fetal como más o menos 25 equivalentes de genoma/ml de plasmamaterno en elembarazo temprano,yunaconcentración de ADN fetal de aproximadamente el 3,4% del ADN total en plasma. Sin embargo, menos sangre puede extraerse para una pantalla genética donde se requiere menos significación estadística, o la muestra de ADN se enriquece para el ADN fetal.
[0039] Cabe señalar que, aunque la presente descripción se refiere a ADN, ARN fetal encontrado en la sangre materna se puede analizar también. Como se describe en Ng et al.., "mRNA of placental origin is readily detectable in maternal plasma," Proc. Nat. Acad. Sci. 100 (8):4.748-4.753 (2003), HPL (lactógeno placentario humano) y hCG (gonadotropina coriónica humana) transcritos de ARNm eran detectables en el plasma materno, tal comose analizó mediante los ensayos en tiempo real RT-PCR respectivos. En el presente método, el ARNm que codifican genes expresados en la placenta y el presente en el cromosoma de arco de interés utilizado. Por ejemplo, DSCR4 (región crítica 4 de Síndrome de Down) se encuentra en el cromosoma 21 y se expresa principalmente en la placenta. Su secuencia de ARNm se puede encontrar en GenBank NM_005867. En este caso, se prefiere utilizar RNasa H menos (RNasa H) transcriptasas inversas (RT) para preparar cADN para la detección. RNasa H-RTs están disponibles de varios fabricantes, con SuperScriptTM II (Invitrogen), siendo el más ampliamente utilizado. La transcriptasa inversa PCR se puede usar como se describe a continuación para el ADN cromosómico.
i. Enriquecimiento de ADN o ARN a partir de plasma
[0040] La sangre materna se puede procesar para enriquecer la concentración de ADN fetal en el ADN total, como se describe en Li et al.., supra. Brevemente, el ADN circulatorio se extrae de plasma materno 5-a 10 ml utilizando la tecnología de la columna comercial (Roche High. Pure Template ADN Purification Kit; Roche, Basel, Suiza) en combinación con una bomba de vacío. Después de la extracción, el ADN se separa por electroforesis en gel de agarosa (1%) de electroforesis (Invitrogen, Basilea, Suiza), y la fracción de gel que contiene ADN circulatorio con un tamaño de aproximadamente 300 pb se escindió cuidadosamente. El ADN se extrae de esta porción de gel utilizando un kit de extracción (QIAEX II Gel Extraction Kit; Qiagen, Basilea, Suiza) y se eluyó en un volumen final de 40 µl de ácido trishidroclórico 10-mM estéril, pH 8,0 (Roche).
[0041] ADN puede ser concentrado por métodos conocidos, incluyendo centrifugación y diversos inhibidores de la enzima.El ADN se unea una membrana selectiva (porejemplo, sílice)para separarlo de contaminantes.El ADN se enriquece preferiblemente para los fragmentos que circulan en el plasma, que son menos de 1000 pares de bases de longitud, generalmente de menos de 300 pb. Esta selección de tamaño se realiza en unmedio de separación de tamaño de ADN, tal como un gel electroforético o material de cromatografía. Tal material se describe en Huber et al.., " High-resolution liquid chromatography of ADN fragments on non-porous poly(styrene-divinylbenzene) particles," Nucleic Acids Res. 1993 de marzo de 11; 21 (5):1061-1066, cromatografía de filtración en gel, gel TSK, tal como se
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[0098] La PCR digital permite la detección de aneuploidía meramente contando las transcripciones, como se ilustra mediante elsiguiente cálculo. Supongamos que el ADN fetal está presente en lasangre materna a un nivel fracción de ε, yque estamos tratando de descubriruna aneuploid ía de orden relativa a euploidía e (en el ejemplo, en relación a la detección del Síndrome de Down en los seres humanos, e=2 es euploidía y el Síndrome de Down trisomía α=3). Si cromosoma A es euploides y representa un control interno, y el cromosoma B es aneuploides y es el diana a medirse, entonces se puede amplificar segmentos representativos de ambos cromosomas mediante PCR digital. En la comparación de los amplicones de cada tipo, uno espera encontrar que por cada e amplicones de cromosoma A hay e(1-ε)+αε amplicones de cromosoma B. En el caso de una trisom ía y ε=3%, entonces para cada 2 amplicones del cromosoma A uno espera 2,03 amplicones de cromosomas B. Mientras que esta diferencia es pequeña, que se pueden medir. Por ejemplo, si uno amplifica una muestra de 1.000 equivalentes celulares, a continuación, uno espera 2.000 amplicones de cromosoma A y 2030 de cromosoma B. La diferencia de 30 amplicones es en principio detectable.
[0099] La confianza estadística requerida para resolver la diferencia en las proporciones se puede estimar de la siguiente manera. Ahí es una variación estadística aleatoria asociada con el tamaño de la muestra inicial, que va aproximadamente como la raíz cuadrada del número de muestras tomadas. De hecho, es a menudo difícil de comenzar con precisión con un número fijo de células equivalentes, y en el ejemplo anterior se espera un error estadístico de orden 32 amplicones (raíz cuadrada 32 (1000)) para la mayoría de las técnicas de preparación de muestras. Este es el mismo tamaño que la señal que estamos tratando de detectar y por lo tanto en la práctica se requiere más de 1.000 equivalentes celulares para la detección robusta. Precismante cuántos se requiere depende de la certeza estadística que se requiere. Si a uno le gustaría un resultado que es significativo para desviaciones estándar k en consecuancia
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[0100] Utilizando los valores del ejemplo anterior, si se requiere desviaciones estándar k=3, entonces el número de amplicones N debe ser de al menos 10.000 para la detección de Síndrome de Down. Sin embargo, como se discutió anteriormente, el número de secuencias diana necesarios para la confianza estadística se puede reducir mediante el uso de secuencias de control, y, además, la muestra puede ser enriquecida para el ADN fetal.
III. Aplicaciones específicas
[0101] La presente invención está particularmente adaptada para detectar anomalías genéticas que involucran diferencias cuantitativas entre las secuencias genéticas maternas y fetales. Estas anomalías genéticas incluyen mutaciones que pueden ser heterocigotos y homocigotos entre el ADN materno y fetal, y para aneuploidías. Por ejemplo, una copia que falta de cromosoma X (monosomía X) resulta en el Síndrome de Turner, mientras que una copia adicional del cromosoma 21 resulta en el Síndrome de Down. Otras enfermedades, como el síndrome de Edward y síndrome de Patau son causadas por una copia adicional del cromosoma 18 y el cromosoma 13, respectivamente. El presente método puede ser utilizado para la detección de una translocación. Además, la amplificación, transversión, inversión, aneuploidía, poliploidía, monosomía, trisomía, trisomía 21, trisomía 13, trisomía 14, trisomía 15, trisomía 16, trisomía 18, trisomía 22, triploidía, tetraploidia, y anomalías de cromosomas sexuales incluyendo, pero no limitado a XO, XXY, XYY, y XXX.
[0102] Otros cebadores específicos de cromosoma se describen en lasolicitud de patente de EE.UU. 20050164241 a Hahn, Sinuhé, et al., publicada el 28 de julio de 2005, titulada "Non-invasive detection of fetal genetic traits," aquí referenciada para la descripción de los métodos de preparación de muestras y ciertos cebadores de PCR, descritos como sigue:
Los cebadores para los genes se preparan sobre la base de secuencias de nucleótidos obtenidas a partir de bases de datos como GenBank, EMBL y similares. Los nombres de los cebadores polimórficos y las secuencias de los cebadores para los genes se muestran para los cromosomas respectivos en los siguientes ejemplos (#2, el Ejemplo 1; #4, Ejemplo 6, #14, el Ejemplo 9; #22, Ejemplo 2). Los siguientes marcadores genéticos polimórficos y fabricantes (pares de cebadores STS polimórficos: D2S207, D2S177, D2S156 y D2S159, BIOS Laboratories, Inc.) se utilizan para identificar el cromosoma #2.
[0103] Haymás de 1.000 conjuntos de cebadores de cromosoma 21 de PCR específicos que figuran en el sitio web del NIH UniSTS, que pueden estar situados en http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unists y se encuentran con la frase de búsqueda "human[organism] AND 21[chr]". UniSTS es una base de datos completa de sitios de secuencia etiquetada (STS) derivados de mapas basados en STS y otros experimentos. STS están definidasporparesde cebadoresde PCR yseasocianconinformación adicional,como posición genómica,genes y secuencias. Del mismo modo, las secuencias de cebadores para otros cromosomas humanos se pueden encontrar modificando adecuadamente la consulta de búsqueda.
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Claims (1)

  1. imagen1
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ES07763674T Active ES2429408T5 (es) 2006-02-02 2007-02-02 Examen genético fetal no invasivo mediante análisis digital
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