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Sorry for your loss.
O.K., here's your argument for a Day 5 transfer. When cultured to the blastocyst stage, the number of stem cells present in the embryo can be assessed. This is important, because the majority of early miscarriages and biochemical pregnancies (like the one you had) are caused by embryos with too few stem cells. It is the stem cells that give rise to the fetus, while the trophectoderm (the outer "skin" of the blastocysyt stage embryo) is responsible for attaching to the endometrium, implantation and secretion of hCG into the maternal bloodstream. Embryos having too few stem cells can still attach to the endometrium (via the trophectoderm), initiate implantation and secrete hCG. In some cases they coninue to develop for a few weeks. However, the ultrasound reveals an "empty sac" (i.e. no fetal tissues because there were too few stem cells to make a baby). Your biochemical pregnancy resulted from an embryo that attached, initiated implantation, secreted hCG into your system, but, due to having too few stem cells for adequate fetal growth, failed to develop further. The demise of embryos with too few stem cells is nature's way of ensuring that a pregnancy has the best chance of going to term. In our program, embryos with too few stem cells are neither transferred or frozen. As a result of this policy, the early miscarriage and biochemical pregnancy rate in our program has been significantly reduced - fewer heartbreaks.
From the many studies that have been down comparing pregnancy rates of Day 3 and Day 5 transfers, they are both equivalent. However, "pregnancy" rates are an all-or-none endpoint. By that definition, a triplet pregnacy counts the same as a singleton pregnancy. To keep "pregnancy" rates high, clinics transfer more cell stage embryos on Day 3 in order to compensate for the develomental arrest that occurs on Day 3 (but not confirmed until Day 4). Transferring a higher number of embryos can and does result in twin, triplet and quadruplet pregnancies.
The implantation rate per blastocyst stage embryo transferred is approximately twice that of cell stage (Day 3) embryos. This means that the same pregnancy rate can be achieved by transferring fewer embryos. Ergo, fewer multiple gestations, fewer miscarriages, normal low-risk pregnancies/deliveries and less economic pressure on the patients.
The explanation for the lower pregnancy rate following blastocyst transfer in your clinic is difficult to interpret, except to infer that are not up to speed on culturing or transferring blastocysts. It may be a red flag, since, in a good program, the pregnancy rate should be equivalent with fewer blastocyst stage embryos transferred. Many RE's are not comfortable with blastocyst transfer because, in low prognosis patients (not you), there may be nothing to transfer. They don't want deal with the giving the patient the bad news or deal with the emotional fall out that follows. Its easier to transfer on Day 3 and shift the responsibility for success or failure to the patient. That may be the main reason for putting you off blastocyst transfer.
Now, about the stimulation protocol... Please understand that taking more medication does not make for eggs per se. The purpose of the medications is to sustain the growth of the follicles that begin to grow at the beginning of that cycle. The number of follicles that to begin to grow on any given cycle is not affected by the stimulation medications. If it were as easy as just taking more medication, then everybody would have tons of follicles. The medications can, however, modulate the rate of growth of the follicles (and the rate of maturation of the eggs inside the follicles). The optimal length for a stimulation is 8-11 days. If your stimulation is within this time frame, and the majority of the follicles are >16mm on the day of hCG, your RE is managing the cycle just fine. That being said, you need to find out if the low fertilization rate (<80% of mature eggs) was due to an abnormally high proportion (>20%) of immature eggs. If so, your stimulation should have been more agressive to obtain more follicles >16mm and hence more mature eggs. Risk of hyperstimulation be damned!
Best of luck.
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