ES2546230T3 - Métodos para evaluar el riesgo de cáncer de mama - Google Patents

Métodos para evaluar el riesgo de cáncer de mama Download PDF

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ES2546230T3
ES2546230T3 ES10782820.4T ES10782820T ES2546230T3 ES 2546230 T3 ES2546230 T3 ES 2546230T3 ES 10782820 T ES10782820 T ES 10782820T ES 2546230 T3 ES2546230 T3 ES 2546230T3
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breast cancer
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David A. Hinds
Bryan Walser
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Abstract

Un método para evaluar el riesgo total de un sujeto femenino humano para desarrollar un fenotipo de cáncer de mama que comprende: realizar una evaluación del riesgo clínico del sujeto femenino, realizar una evaluación del riesgo genético del sujeto femenino, en donde la evaluación del riesgo genético implica detectar, en una muestra biológica derivada del sujeto femenino, la presencia de al menos cinco polimorfismos de un solo nucleótido que se sabe que están asociados con un fenotipo de cáncer de mama, seleccionado de entre el grupo que consiste de rs2981582, rs3803662, rs889312, rs123387042, rs13281615, rs4415084, rs3817198, rs4973768, rs6504950 y rs11249433; y combinar la evaluación del riesgo clínico con la evaluación del riesgo genético para obtener el riesgo total de un sujeto femenino humano para desarrollar un fenotipo de cáncer de mama, en donde al menos cinco polimorfismos de un solo nucleótido comprenden al menos rs2981582, rs3803662, rs889312, rs13387042 y rs4415084.

Description

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Tabla 2. Marcadores sustitutos para el SNP rs2981582. Se seleccionaron marcadores con un r2 mayor a 0.05 para rs2981582 en el conjunto de datos HAPMAP (http://hapmap.ncbi.nlm.nih.gov) en un intervalo de 1 Mpb que flanquea al marcador. Se muestra el nombre del SNP correlacionado, los valores para r2 y D' para rs2981582 y el valor LOD correspondiente, así como la posición del marcador sustituto en NCB Build 36.
Identificación de los rs de la base de datos del SNP
Position SNP correlacionado Ubicación D’ r 2 LOD
rs2981582
123342307 rs3135715 123344716 1.000 0.368 15.02
rs2981582
123342307 rs7899765 123345678 1.000 0.053 2.44
rs2981582
123342307 rs1047111 123347551 0.938 0.226 9.11
rs2981582
123342307 rs1219639 123348302 1.000 0.143 6.53
rs2981582
123342307 rs10886955 123360344 0.908 0.131 5.42
rs2981582
123342307 rs1631281 123380775 0.906 0.124 5.33
rs2981582
123342307 rs3104685 123381354 0.896 0.108 4.58
rs2981582
123342307 rs1909670 123386718 1.000 0.135 6.12
rs2981582
123342307 rs7917459 123392364 1.000 0.135 6.42
rs2981582
123342307 rs17102382 123393846 1.000 0.135 6.42
rs2981582
123342307 rs10788196 123407625 1.000 0.202 9.18
rs2981582
123342307 rs2935717 123426236 0.926 0.165 7.30
rs2981582
123342307 rs3104688 123426455 0.820 0.051 2.07
rs2981582
123342307 rs4752578 123426514 1.000 0.106 5.15
rs2981582
123342307 rs1696803 123426940 0.926 0.168 7.33
rs2981582
123342307 rs12262574 123428112 1.000 0.143 7.39
rs2981582
123342307 rs4752579 123431182 1.000 0.106 5.15
rs2981582
123342307 rs12358208 123460953 0.761 0.077 2.46
rs2981582
123342307 rs17102484 123462020 0.758 0.065 2.39
rs2981582
123342307 rs2936859 123469277 0.260 0.052 1.56
rs2981582
123342307 rs10160140 123541979 0.590 0.016 0.40
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Tabla 3. Marcadores sustitutos para el SNP rs3803662. Se seleccionaron marcadores con un r2 mayor a 0.05 para rs3803662 en el conjunto de datos HAPMAP (http://hapmap.ncbi.nlm.nih.gov) en un intervalo de 1 Mpb que flanquea al marcador. Se muestra el nombre del SNP correlacionado, los valores para r2 y D' para rs3803662 y el valor LOD correspondiente, así como la posición del marcador sustituto en NCB Build 36.
Identificación de los rs de la base de datos del SNP
Position SNP correlacionado Ubicación D’ r 2 LOD
rs3803662
51143842 rs4784227 51156689 0.968 0.881 31.08
rs3803662
51143842 rs3112572 51157948 1.000 0.055 1.64
rs3803662
51143842 rs3104747 51159425 1.000 0.055 1.64
rs3803662
51143842 rs3104748 51159860 1.000 0.055 1.64
rs3803662
51143842 rs3104750 51159990 1.000 0.055 1.64
rs3803662
51143842 rs3104758 51166534 1.000 0.055 1.64
rs3803662
51143842 rs3104759 51167030 1.000 0.055 1.64
rs3803662
51143842 rs9708611 51170166 1.000 0.169 4.56
rs3803662
51143842 rs12935019 51170538 1.000 0.088 4.04
rs3803662
51143842 rs4784230 51175614 1.000 0.085 4.19
rs3803662
51143842 rs11645620 51176454 1.000 0.085 4.19
rs3803662
51143842 rs3112633 51178078 1.000 0.085 4.19
rs3803662
51143842 rs3104766 51182036 0.766 0.239 7.55
rs3803662
51143842 rs3104767 51182239 0.626 0.167 4.88
rs3803662
51143842 rs3112625 51183053 0.671 0.188 5.62
rs3803662
51143842 rs12920540 51183114 0.676 0.195 5.84
rs3803662
51143842 rs3104774 51187203 0.671 0.188 5.62
rs3803662
51143842 rs7203671 51187646 0.671 0.188 5.62
rs3803662
51143842 rs3112617 51189218 0.666 0.177 5.44
rs3803662
51143842 rs11075551 51189465 0.666 0.177 5.44
rs3803662
51143842 rs12929797 51190445 0.676 0.19 5.87
rs3803662
51143842 rs3104780 51191415 0.671 0.184 5.65
rs3803662
51143842 rs12922061 51192501 0.832 0.631 19.14
rs3803662
51143842 rs3112612 51192665 0.671 0.184 5.65
rs3803662
51143842 rs3104784 51193866 0.666 0.177 5.44
rs3803662
51143842 rs12597685 51195281 0.671 0.184 5.65
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Identificación de los rs de la base de datos del SNP
Position SNP correlacionado Ubicación D’ r 2 LOD
rs3803662
51143842 rs3104788 51196004 0.666 0.177 5.44
rs3803662
51143842 rs3104800 51203877 0.625 0.17 4.99
rs3803662
51143842 rs3112609 51206232 0.599 0.163 4.86
rs3803662
51143842 rs3112600 51214089 0.311 0.016 0.57
rs3803662
51143842 rs3104807 51215026 0.302 0.014 0.52
rs3803662
51143842 rs3112594 51229030 0.522 0.065 1.56
rs3803662
51143842 rs4288991 51230665 0.238 0.052 1.53
rs3803662
51143842 rs3104820 51233304 0.528 0.069 1.60
rs3803662
51143842 rs3104824 51236594 0.362 0.067 1.93
rs3803662
51143842 rs3104826 51237406 0.362 0.067 1.93
rs3803662
51143842 rs3112588 51238502 0.354 0.062 1.80
Tabla 4. Marcadores sustitutos para el SNP rs4415084. Se seleccionaron marcadores con un r2 mayor a 0.05 para rs4415084 en el conjunto de datos HAPMAP (http://hapmap.ncbi.nlm.nih.gov) en un intervalo de 1 Mpb que flanquea al marcador. Se muestra el nombre del SNP correlacionado, los valores para r2 y D' para rs4415084 y el valor LOD correspondiente, así como la posición del marcador sustituto en NCB Build 36
Identificación de los rs de la base de datos del SNP
Position SNP correlacionado Ubicación D’ r 2 LOD
rs4415084
44698272 rs12522626 44721455 1.000 1.0 47.37
rs4415084
44698272 rs4571480 44722945 1.000 0.976 40.54
rs4415084
44698272 rs6451770 44727152 1.000 0.978 44.88
rs4415084
44698272 rs920328 44734808 1.000 0.893 39.00
rs4415084
44698272 rs920329 44738264 1.000 1.0 47.37
rs4415084
44698272 rs2218081 44740897 1.000 1.0 47.37
rs4415084
44698272 rs16901937 44744898 1.000 0.978 45.06
rs4415084
44698272 rs11747159 44773467 0.948 0.747 28.79
rs4415084
44698272 rs2330572 44776746 0.952 0.845 34.31
rs4415084
44698272 rs994793 44779004 0.952 0.848 34.49
rs4415084
44698272 rs1438827 44787713 0.948 0.749 29.76
rs4415084
44698272 rs7712949 44806102 0.948 0.746 29.19
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Identificación de los rs de la base de datos del SNP
Position SNP correlacionado Ubicación D’ r 2 LOD
rs4415084
44698272 rs11746980 44813635 0.952 0.848 34.49
rs4415084
44698272 rs16901964 44819012 0.949 0.768 30.54
rs4415084
44698272 rs727305 44831799 0.972 0.746 27.65
rs4415084
44698272 rs10462081 44836422 0.948 0.749 29.76
rs4415084
44698272 rs13183209 44839506 0.925 0.746 28.55
rs4415084
44698272 rs13159598 44841683 0.952 0.848 34.19
rs4415084
44698272 rs3761650 44844113 0.947 0.744 28.68
rs4415084
44698272 rs13174122 44846497 0.971 0.735 26.70
rs4415084
44698272 rs11746506 44848323 0.973 0.764 29.24
rs4415084
44698272 rs7720787 44853066 0.952 0.845 34.31
rs4415084
44698272 rs9637783 44855403 0.948 0.748 29.16
rs4415084
44698272 rs4457089 44857493 0.948 0.762 29.70
rs4415084
44698272 rs6896350 44868328 0.948 0.764 29.46
rs4415084
44698272 rs1371025 44869990 0.973 0.785 30.69
rs4415084
44698272 rs4596389 44872313 0.948 0.749 29.76
rs4415084
44698272 rs6451775 44872545 0.948 0.746 29.19
rs4415084
44698272 rs729599 44878017 0.948 0.748 29.16
rs4415084
44698272 rs987394 44882135 0.948 0.749 29.76
rs4415084
44698272 rs4440370 44889109 0.948 0.748 29.16
rs4415084
44698272 rs7703497 44892785 0.948 0.749 29.76
rs4415084
44698272 rs13362132 44894017 0.952 0.827 34.09
rs4415084
44698272 rs1438821 44894208 0.951 0.844 34.52
Tabla 5. Marcadores sustitutos para el SNP rs13387042. Se seleccionaron marcadores con un r2 mayor a 0.05 para rs13387042 en el conjunto de datos HAPMAP (http://hapmap.ncbi.nlm.nih.gov) en un intervalo de 1 Mpb que flanquea al marcador. Se muestra el nombre del SNP correlacionado, los valores para r2 y D' para rs13387042 y el valor LOD correspondiente, así como la posición del marcador sustituto en NCB Build 36
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Identificación de los rs de la base de datos del SNP
Position SNP correlacionado Ubicación D’ r 2 LOD
rs13387042
217614077 rs4621152 217617230 0.865 0.364 15.30
rs13387042
217614077 rs6721996 217617708 1.000 0.979 50.46
rs13387042
217614077 rs12694403 217623659 0.955 0.33 14.24
rs13387042
217614077 rs17778427 217631258 1.000 0.351 16.12
rs13387042
217614077 rs17835044 217631850 1.000 0.351 16.12
rs13387042
217614077 rs7588345 217632061 1.000 0.193 8.93
rs13387042
217614077 rs7562029 217632506 1.000 0.413 20.33
rs13387042
217614077 rs13000023 217632639 0.949 0.287 12.20
rs13387042
217614077 rs13409592 217634573 0.933 0.192 7.69
rs13387042
217614077 rs2372957 217635302 0.855 0.168 5.97
rs13387042
217614077 rs16856888 217638914 0.363 0.101 3.31
rs13387042
217614077 rs16856890 217639976 0.371 0.101 3.29
rs13387042
217614077 rs7598926 217640464 0.382 0.109 3.60
rs13387042
217614077 rs6734010 217643676 0.543 0.217 7.90
rs13387042
217614077 rs13022815 217644369 0.800 0.319 12.94
rs13387042
217614077 rs16856893 217645298 0.739 0.109 3.45
rs13387042
217614077 rs13011060 217646422 0.956 0.352 14.71
rs13387042
217614077 rs4674132 217646764 0.802 0.327 13.10
rs13387042
217614077 rs16825211 217647249 0.912 0.326 12.95
rs13387042
217614077 rs41521045 217647581 0.903 0.112 4.70
rs13387042
217614077 rs2372960 217650960 0.678 0.058 2.12
rs13387042
217614077 rs2372967 217676158 0.326 0.052 1.97
rs13387042
217614077 rs3843337 217677680 0.326 0.052 1.97
rs13387042
217614077 rs2372972 217679386 0.375 0.062 2.28
rs13387042
217614077 rs9677455 217680497 0.375 0.062 2.28
rs13387042
217614077 rs12464728 217686802 0.478 0.073 2.54
Estrategias para amplificación del marcador
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Tabla 6. Ejemplos de cebadores oligonucleótidos útiles para la invención
Nombre
Secuencia
rs889312_for
TATGGGAAGGAGTCGTTGAG (SEQ ID NO: 1)
rs6504950_for
CTGAATCACTCCTTGCCAAC (SEQ ID NO:2)
rs4973768_for
CAAAATGATCTGACTACTCC (SEQ ID NO:3)
rs4415084_for
TGACCAGTGCTGTATGTATC (SEQ ID NO:4)
rs3817198_for
TCTCACCTGATACCAGATTC (SEQ ID NO:5)
rs3803662_for
TCTCTCCTTAATGCCTCTAT (SEQ ID NO:6)
rs2981582_for
ACTGCTGCGGGTTCCTAAAG (SEQ ID NO:7)
rs13387042_for
GGAAGATTCGATTCAACAAGG (SEQ ID NO:8)
rs13281615_for
GGTAACTATGAATCTCATC (SEQ ID NO:9)
rs11249433_for
AAAAAGCAGAGAAAGCAGGG (SEQ ID NO: 10)
rs889312_rev
AGATGATCTCTGAGATGCCC (SEQ ID NO:11)
rs6504950_rev
CCAGGGTTTGTCTACCAAAG (SEQ ID NO: 12)
rs4973768_rev
AATCACTTAAAACAAGCAG (SEQ ID NO: 13)
rs4415084_rev
CACATACCTCTACCTCTAGC (SEQ ID NO: 14)
rs3817198_rev
TTCCCTAGTGGAGCAGTGG (SEQ ID NO:15)
rs3803662_rev
CTTTCTTCGCAAATGGGTGG (SEQ ID NO:16)
rs2981582_rev
GCACTCATCGCCACTTAATG (SEQ ID NO: 17)
rs13387042_rev
GAACAGCTAAACCAGAACAG (SEQ ID NO:18)
rs13281615_rev
ATCACTCTTATTTCTCCCCC (SEQ ID NO: 19)
rs11249433_rev
TGAGTCACTGTGCTAAGGAG (SEQ ID NO:20)
Algunas técnicas para detectar marcadores genéticos utilizan la hibridación de ácido nucleico sonda con los ácidos nucleicos correspondientes al marcador genético (por ejemplo, los ácidos nucleicos amplificados producidos
5 utilizando ADN genómico como molde). Los formatos de hibridación, que incluyen, pero no se limitan a: ensayos en fase en solución, en fase sólida, en fase mixta, o in situ son útiles para la detección de alelos. Una guía amplia para la hibridación de ácidos nucleicos se encuentra en Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology--Hybridization with Nucleic Acid Probes Elsevier, Nueva York, así como en Sambrook y colaboradores (ver más arriba).
10 Por ejemplo, los marcadores que comprenden polimorfismos de longitud de fragmentos de restricción (RFLP) se detectan, por ejemplo, mediante la hibridación de una sonda que típicamente es un subfragmento (o un oligonucleótido sintético correspondiente a un subfragmento) del ácido nucleico que va a ser detectado con el ADN genómico digerido por restricción. La enzima de restricción se selecciona para proporcionar fragmentos de restricción de al menos dos longitudes alternativas (o polimórficas) en diferentes individuos o poblaciones. La
15 determinación de una o más enzimas de restricción que produzca fragmentos informativos para cada alelo de un marcador es un procedimiento simple, bien conocido en la técnica. Después de la separación por longitud en una
17
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(95% IC: -0,002 a 0,081, P empírico = 0,06). El modelo combinado tuvo un AUC de 0,571 (95% IC: 0,526 a 0,6l4). Un estimado de arranque de la diferencia en AUC para el modelo combinado versus Gail solamente también fue significativo (95% IC: 0,029 a 0,085, P <0,001).
La métrica de reclasificación en el subconjunto de biopsias indicó que el NRI es 0,18, lo cual es muy significativo a
5 pesar del menor número de casos (Z = 3,9, P = 4.9 x 10-5). Aquí, la clasificación mejoró para el 14.8% de los controles (P = 1.5 x 10-5), pero solamente el 2.8% de los casos (p = 0.16; Tablas 7 y 8). El nuevo muestreo de arranque indicó que la diferencia en NRI entre la cohorte completa y el subconjunto de la biopsia fue estadísticamente significativo. Con base en 1000 replicas de arranque, un intervalo de confianza del 95% para la mejora en NRI en el subgrupo de biopsia se extendió de 0.02 hasta 0.16, con un P empírico = 0.03.
10 Tabla 7. Pruebas de regresión logística de asociación con subtipos de receptores de cáncer de mama
Tumores positivos para ER Tumores negativos para ER
Predictor
β (95% de IC) P β (95% de IC) P
log( riesgo de 5 años de Gail)
0.55 (0.37 a 0.72) 1.1x10 -9 -0.03 (-0.37 a 0.32) 0.89
log( riesgo de SNP)
1.20 (0.92 a 1.47) 1.7x10 -18 0.56 (0.03 a 1.09) 0.04
log(riesgo de SNP X Gail)
0.72 (0.57 a 0.87) 2.4 x 10 -22 0.14 (-0.14 a 0.43) 0.32
Tabla 8. Índice de probabilidad combinado para el panel de 7-SNP que indica un valor predictivo mejorado para el cáncer de mama ER+ por oposición al cáncer de mama ER-
Identificación de los rs de la base de datos del SNP
Gen Frecuencia del alelo de riesgo Índice de probabilidad de cáncer de mama
Todo
ER+ ER
rs2981582
FGFR2 0.38 1.26 1.3 1.035
rs3803662
TNRC9 0.25 1.2 1.275 1.105
rs889312
MAP3K1 0.28 1.13 1.12 1.07
rs13387042
(ninguno) 0.5 1.2 1.22 1.06
rs13281615
(ninguno) 0.4 1.08 1.13 1.03
rs4415084
FGF10 0.44 1.16 1.23 0.98
rs3817198
LSP1-H19 0.3 1.07 1.07 1.04
Índice de probabilidad combinado
2.7484 3.3682 1.2939
15 Discusión
Una estrategia que combina tanto los factores de riesgo clínico (riesgo de Gail) como los factores de riesgo genético comunes bien validados (panel 7-SNP) da como resultado una mejora en la clasificación de los riesgos BCa en mujeres blancas posmenopáusicas. Esto puede tener implicaciones significativas para informar las estrategias primarias de prevención y/o detección.
20 Ejemplo 2 -Uso de los SNP para la evaluación del riesgo de cáncer de mama : modelo 10-SNP
Determinación del genotipo de SNP
28
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