Your first clue should have been when he didn't remember Lestrade's name. Bit obvious now that you really think about it, didn't think about it much when it mattered, you never even gave it a second thought did you? You never even noticed how it got worse, first Graham, then Gavin then Geoff, the childish way he stumbled and mumbled over a simple four letter word, sure you laughed about it then, but no one is laughing now. You can't even imagine how many times he must have nicked the Detective Inspectors badge, which surely would have had his first name imprinted on it, but no, that never occurred to you as something of importance did it?

Because since when did he forget things?

Withdrawal?
Those frustrating times when he wouldn't speak for days on end, played the violin, my dear that's called withdrawal and if you simply took time out of your life to type it into a search engine you would see it was another symptom of a disease you refused to recognize. But no, your friends well being never seemed to concern you enough for something as difficult as that.
No one would ever say that you were a bad friend, but looking back on this, I think that a few might have changed their opinions.
Check.

Misplacing things?
He always said that Mrs Hudson took his skull, with a sneer on his face and a twinge in his voice. But my dear if you had dared to look, you could have easily found it every time in the bathroom cupboard. Because ask yourself why would Mrs Hudson ever want to touch a human skull?
Check.

Difficulty Dressing?
Spent the whole day in his pajamas? I think we know why now, maybe he had a few problems getting the right clothes on in the morning, you could've given him a hand.
Check.

Wandering off?
You remember all of the mornings you would wake up and he wouldn't be there? Gone out on a case surely? Gone to conduct some experiment? Gone to terrorize some civilians?
The hours would slowly tick pass, and yet he would still not be home, but you never worried, no you would never worry about him. Why should you? He might have the maturity of a six year old but he could handle himself. And he would march back inside like nothing happened, saying not a single word and never telling you that it had been Mycroft who had found him lost and wandering and returned him home.
Check.

"I said pass me a pen."

But here is where you, very stupidly, went wrong and the blame is entirely on you. Because you turned your back the next second and missed a most important revelation. A twinge of the brow, just the slightest twitching of your flat mates forehead should have been the second clue. That brief but brushed away flashing look of complete confusion, so utterly not the look of him, so out of place on his sure and smooth face. But you dismissed his displaced thoughts as what came along with being him, how wrong you were, it's almost sad. Almost. But no sympathy for you.

"Hadn't noticed I'd gone out then."

Because since when does he not notice something?

Trouble sleeping?
This is too easy.
Check.

Inappropriate Behavior?
And when someone says to you that inappropriate behavior is a symptom you laugh in their face and said that he was always inappropriate. But did you ever think why? Well if you had asked him about his unusual bluntness and rude nature he would have immediately rattled off high functioning sociopath and all of that other rubbish. But you know he wasn't like that, you knew that he could feel just like other people. So why did you never look into it? You could say that his brother was very similar, maybe he had learn to adopt the technique. Wrong. You might say that he was just born like that and couldn't help it. Wrong. Or you could even suggest that in his younger years he created a hard exterior, a tough shell that no one could break through as a defense mechanism. Wrong, so wrong, so very very wrong. Your friend was sick, and you didn't even see it.
Check.

Forgetting meals?
Never ate much did he? Poor child. You probably just didn't feed him enough. Maybe he might have told you that eating slows him down and diverts blood flow away from his brain and into his digestive system. He might have lied and said that he didn't need to eat much, and you would agree that he seemed to barely eat and physically appeared fine. But you are a doctor, why did you never see...
Check.

Agitation or mood swings leading to verbal or physical confrontations?
Well...
Check.

Clingy or Childlike behavior?
All of those sulks, all those temper tantrums that left you comparing him to a three year old who had been denied a sweet. When he would curl up into a little ball on his chair, and express his thoughts on your stupidity and then aim nearby items at your head.
There was always a part of you that wondered why he had chosen to put up with someone like you, seemed he didn't like people who were similar to you. Here's your explanation, you didn't dismiss him right off, you gave him a chance and he clung to that hope like a life preserver. It's all just unfolding now isn't it?
Check.

One day, a day you remember very clearly, he near shouted your name, his usually lazy drawl spiked with a fear that had your heart pounding in alarm.

"What! What! What's going on?!" Quickly scanning the empty cluttered room for what had caused such distress in his lovely voice. But there is nothing, the empty room remains empty. So your eyes drag up to the standing figure still clad in pajamas and a stained dressing gown despite the midday sun's shadow gracing the carpeted floor beneath your feet. And you know what it is by the look on his face.

"I think my memory might be deteriorating. " He mumbled out to you, tears brimming in his clear eyes as you see the cogs of his once brilliant mind turning over and over as you have many times before. His mind is all he has you remind yourself. You feel wetness prick up in your own eyes but force the emotion down for his sake, he can't see you break, not now.

"Yes, I know."

So taking his hand in the most carefree fashion you can manage, you sit him back down in the chair that has always been his. He looks up at you with a mixture of innocence and loss that makes you want to slap his perfect face, because it is so not him, where is the wit, the humor, the insults. You would give anything to have him take a crack at your "mediocre" intelligence, but that's not going to happen, it's never going to happen again.
So you explain everything, about the doctors and the hospital visits and the diagnosis that happened so many long lonely months ago. He nods numbly and accepts the information, as a logical mind does, processing it with a brain that proves to be faulty.

Less then forty minutes later you hear his shout again, and this time you can't stop your own tears.

And now you just look at him, across the room, across the dining table, across the doctors desk or across a cup of tea. And you can still see his wondrous complex mind struggling to work under the constraints and it's absolutely heartbreaking.

They tell you that it is very rare at an age like his, all you can think about is how every part of him was rare, and how it's so like him to go against the norm.

You love the fact that despite it all he still remembers your name over everyone else's, he knows you, he doesn't know his illness, or his job or who he is, but he knows you, and every time you think about that, it makes you smile and cry. Because you may have lost your best friend, but he hasn't lost you. Well at least not yet.

They explain that there is still some of his personality left in there but they don't know for how much longer, but you don't want some of him, you want everything, some of him just reminds you what you're missing.

It's the eyes, the vacant, empty, lost look they sometimes get that reminds you that the man in front of you is a ghost, a shadow of what he used to be. You remember the cases and the murders and mysteries that were a lifetime ago, you shut down the blog as soon as the doctor confirmed the diagnoses.

"John I have to say, in Sherlocks case the disease progressed unusually slow and was nearly undetectable except over a vast period of time. John?"

But all you hear is his name and unusual and a word that sounds awfully like detective and you think that sounds about right.