Hello Doctor, I Recently Was At The Hospital In August

Hello Doctor,
I recently was at the hospital in August with a missed period and horrible pregnancy symptoms which turned out I had bilateral cysts on my ovaries one side is 1cm and the next is 7.5mm. After getting these results, a few weeks after I went to my family doctor which he then prescribed me a 3 month supply of birth control pills. However, my last period was June 14th 2015 and day by day my symptoms are getting worse (nausea, back, stomach and chest pain, frequent bathroom breaks, my asthma is getting and far more symptoms) I've taken several tests for pregnancy and I'm due for another checkup in 2 months with my doctor to check for pregnancy and the growth of the cysts. However, my question for you is, could these cysts be causing my missed periods or could I actually be pregnant? My partner and I are excited for children but this whole situation is stressing us out. Thank you for your time, I look forward to what you have to say.