Hi Anna and Epsilon?,
This question of Ancestry calling a result ApoE 3/3 and 23& me calling it ApoE 3/4 or 4/4 has come up before. Here's a link to that thread from January 2018. epsilon 33, 34, 44 - whatever- what difference does it make????
By the way, it seems that Ancestry never says 3/4 when 23&me says 3/3. In fact, it seems that Ancestry rarely reports a 3/4 or 4/4 result.
From this comment by snpedia.com, it seems to be that Ancestry is not carefully checking ApoE status.
Word of caution to those with data from Ancestry.com: in our experience, based on data in OpenSNP and from Promethease users since 2006, Ancestry data always reports rs429358 as (T;T), even for people who's data from other sources indicates they are (C;T). Therefore, until Ancestry corrects this false negative problem, be aware that the ApoE genosets assigned by Promethease will be inaccurate when based on (inaccurate) Ancestry data. Specifically, some percentage of Ancestry users who are supposedly gs246 positive (Apo-ε3/ε3) are actually either gs141 (Apo-ε3/ε4) or gs216 (Apo-ε4/ε4).
For what it's worth, I and several people I know who have gotten our 3/4 or 4/4 results from 23&me had them independently verified as part of clinical trials. No one has ever been told "They got it wrong; you are a 3/3."