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I found this article on the risk of birth defects with the use of assisted reproduction.  Although there is an increase in birth defects n children conceived using ART the reason may not be due to the procedures:

“The authors demonstrate that, although patients who undergo IVF may have an increased risk of birth defects, this risk is associated with the need for IVF not necessarily the IVF technique itself.  There were very obvious differences in the patient population.” When these differences were controlled, Dr. Robins said, the risk of birth defects with IVF was no longer seen.

You can read the full article here:

Assisted Reproductive Therapies Linked to Birth Defects

Before we did IVF I was worried about the effect the procedures/medications would have on my own health as well as my future baby.  For me I researched it as much as I could and then decided the risk was worth it and hoped for the best.  Sometimes that is all you can do.