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La amniocentesis detecta o descarta el síndrome de Down, el cual causa retardo mental, defectos cardíacos congénitos y características físicas tales como pliegues de piel cerca de los ojos. Igualmente detecta defectos del tubo neural, como espina bífida. Los bebés nacidos con espina bífida tienen una columna vertebral que no se cerró adecuadamente. Algunas de las complicaciones graves de la espina bífida son parálisis de las piernas, defectos de vejiga y riñones, hinchazón cerebral (hidrocefalia) y retardo mental
Si el embarazo se complica por alguna afección como la incompatibilidad Rh, el médico puede recurrir a la amniocentesis para determinar si los pulmones del bebé están lo suficientemente desarrollados para soportar un parto prematuro.
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