I really think you have to wait for further test results before jumping to conclusions. I have a daughter with Down Syndrome, and I have never heard of those birth defects indicating Down Syndrome. The level II ultrasound and the blood work should help in a diagnosis. I know it is very difficult to know something is wrong but not know what it is. The world of technology and the internet is wonderful, but sometimes there is just too much information out there, and we all can jump to a lot of conclusions. I know it is hard, but just try to be there to reassure your sister. It is difficult at any age to have a baby with disabilities. She will need your love and support.
Keep in mind that if the baby has Down Syndrome, it would not have been any different if she started on prenatal vitamens as soon as she knew she was pregnant. From all I have been told, Down Syndrome happens at conception as every cell in a baby's body contains the trisomy on the 21st chromasome (except in children that are Mosaic and then it affects cells at random--some have the trisome on the 21st chromasome and some don't).
I wish you all the best.