The AP Runes are very important, this at early game will make you very dangerous if you time well your abilities!
The penetration runes work well against those tanky ones who build damage, they are going to be very confident, show them a Q chord to make them flee!
Progressive health runes will be absolutely important at late game, it isn't like building Armor or Magical Resistance, but at least you aren't as squishy as before (And you won't use the spaces for your AP runes!)

So... You may ask ''If I'm going AP Sona, why I would want to build Frost Quenn?''
This has two important points:
-The passive will make you VERY fast if you hit someone, if you're being chased, you can combine your E's movement speed with a good Q to run away very very very fast!
-The active will help you reveal the ones you can hit with your Q to reveal them (Remember: Your Q will only hit two enemies that are near and visible to you), also, you aren't going to waste your R!
Rylai can get you a little bit low on damage at late game, but the health it gives and the passive's slow will be very useful to not to die that fast.

If there's any doubt, here's an image:
img=http://prntscr.com/ghliq4

Pros:
-Lots of damage
-Easy poke
-No skillshots at all
-Good movement speed buff
-High healing and shield
-R can turn the tides of the battle
-Max. cooldown also scales with your R's passive (You can get up to 67% CD!)
Cons:
-Very squishy both early and late game
-Mana hungry
-Your healing isn't useful at all in early game
-Low scaling movement speed on E (Just 1% if you boost it!)

Hey there! Here's my first guide, I decided to do it about my main... Sona!
If you can send me a message or something to help me with this guide, I'd be very grateful
English isn't my main languaje, you can send me some corrections, too
Here are some of my results with my Sona build, runes and masteries:
http://prntscr.com/ghlk2e
http://prntscr.com/ghlk79
http://prntscr.com/ghlkml
Thanks for reading, bye everyone!!