Stanford Interpretome

Discussions concerning Autosomal DNA.

Moderator: CeCeMoore


Posts: 55
Joined: Fri May 25, 2012 8:11 pm
Location: United States of America
YDNA:
R-DF99/S11987
MtDNA:
H3ap
PostPosted: Mon Aug 26, 2013 2:45 am
Greetings, I am starting this thread for members to share their results from Stanford's Interpretome utility. I would like to compare how Interpretome stacks up against Dr. McDonald, 23andMe, etc. (mostly concerned with comparing against Dr. McDonald given the ISOGG comparisons between admix utilities - 23andMe = leader in commercial, Dr. McDonald offers a refinement over the leader in commercial).

My contribution (PCA for now using POPRES, still need to utilize the other features) -

When I ran Interpretome's PCA, using the POPRES dataset plotting PC 1 vs. PC 4 I got a picture that was consistent with Dr. McDonald's PCA. Interpretome yielded British with what seems to be a pull towards the South (& mayhaps a bit to the East as well); McDonald yielded close to the same but demonstrated a stronger Southward pull than Interpretome that put me closer to the French than British.

Screencaps (Interpretome vs. Dr. McDonald) -


V3:
Image

V2:
Image

McDonald:
Image
R-P312 clades tested for: DF99+ P312+ DF27- DF19- U152- L21- L459- Z245- L238- Z2245- Z2247-
Ysearch: VNSGW
mtDNA: H3ap
Gedmatch ID: M033622
User avatar
Posts: 542
Joined: Mon Oct 22, 2012 8:19 am
Location: Family Line Veneto ( italy ) since ~1600
YDNA:
T1a2-Z19945
MtDNA:
H95a
PostPosted: Mon Aug 26, 2013 6:45 am
Barreldriver wrote:Greetings, I am starting this thread for members to share their results from Stanford's Interpretome utility. I would like to compare how Interpretome stacks up against Dr. McDonald, 23andMe, etc. (mostly concerned with comparing against Dr. McDonald given the ISOGG comparisons between admix utilities - 23andMe = leader in commercial, Dr. McDonald offers a refinement over the leader in commercial).

My contribution (PCA for now using POPRES, still need to utilize the other features) -

When I ran Interpretome's PCA, using the POPRES dataset plotting PC 1 vs. PC 4 I got a picture that was consistent with Dr. McDonald's PCA. Interpretome yielded British with what seems to be a pull towards the South (& mayhaps a bit to the East as well); McDonald yielded close to the same but demonstrated a stronger Southward pull than Interpretome that put me closer to the French than British.

Screencaps (Interpretome vs. Dr. McDonald) -


V3:
Image

V2:
Image

McDonald:
Image


I find Interpretome poor all round except for Ancestry - HGDP European and you MUST use X-PC1 and X-PC4 - This was accurate for me

The top picture you have shown, has for me - Norwegian, Swedish and Danish ( on the fringe) ..........and I have zero association with Scandinavia as far as I know
Fathers mtdna - T2b17 ...back to 1860 Bucciol line
Grandfathers mtdna - T1a1e ...back to 1820 Mestriner line
Sons Mtdna - K1a4 ....back to 1840 Tesser line
Maternal grandfather ydna - Ild-P109

Posts: 55
Joined: Fri May 25, 2012 8:11 pm
Location: United States of America
YDNA:
R-DF99/S11987
MtDNA:
H3ap
PostPosted: Tue Aug 27, 2013 12:32 am
stoeni wrote:
I find Interpretome poor all round except for Ancestry - HGDP European and you MUST use X-PC1 and X-PC4 - This was accurate for me

The top picture you have shown, has for me - Norwegian, Swedish and Danish ( on the fringe) ..........and I have zero association with Scandinavia as far as I know


Thanks for sharing, what's your background by chance? It seems so far that the POPRES set that I had used in the OP works only with certain sorts of individuals at Interpretome just as with UCLA's SPA models (POPRES based and accurate only for Brits and nearby peoples).
R-P312 clades tested for: DF99+ P312+ DF27- DF19- U152- L21- L459- Z245- L238- Z2245- Z2247-
Ysearch: VNSGW
mtDNA: H3ap
Gedmatch ID: M033622
User avatar
Posts: 542
Joined: Mon Oct 22, 2012 8:19 am
Location: Family Line Veneto ( italy ) since ~1600
YDNA:
T1a2-Z19945
MtDNA:
H95a
PostPosted: Tue Aug 27, 2013 7:00 am
Barreldriver wrote:
stoeni wrote:
I find Interpretome poor all round except for Ancestry - HGDP European and you MUST use X-PC1 and X-PC4 - This was accurate for me

The top picture you have shown, has for me - Norwegian, Swedish and Danish ( on the fringe) ..........and I have zero association with Scandinavia as far as I know


Thanks for sharing, what's your background by chance? It seems so far that the POPRES set that I had used in the OP works only with certain sorts of individuals at Interpretome just as with UCLA's SPA models (POPRES based and accurate only for Brits and nearby peoples).


300 plus years both paternal and maternal from north-east Italy.

It plots me on your second graphic
at the -7.5, next to the swedish and Finnish flags ( right side)

I do have 50% of matches with british people , usually irish and scots, but some cornish as well.

Image

Uploaded with ImageShack.us

and this is accurate
Image

Uploaded with ImageShack.us
Fathers mtdna - T2b17 ...back to 1860 Bucciol line
Grandfathers mtdna - T1a1e ...back to 1820 Mestriner line
Sons Mtdna - K1a4 ....back to 1840 Tesser line
Maternal grandfather ydna - Ild-P109

Posts: 55
Joined: Fri May 25, 2012 8:11 pm
Location: United States of America
YDNA:
R-DF99/S11987
MtDNA:
H3ap
PostPosted: Tue Aug 27, 2013 2:15 pm
I'd take this as more support for the POPRES only being useful for certain folks - it was way way off for yours. Davidski had mentioned something about this in his Eurogenes blog when UCLA released SPA, their model files were reliant upon POPRES, - it gave wildly inaccurate results for non-British (or similar folks). It is a bit unsettling that these university teams can't correct this so that these utilities can be used by more folks - the POPRES version at Interpretome has potential in that it's more specific than the HGDP and HapMap versions, but that potential can't be actualized until the utility is relevant to a wider range of folks.

stoeni wrote:
Barreldriver wrote:
stoeni wrote:
I find Interpretome poor all round except for Ancestry - HGDP European and you MUST use X-PC1 and X-PC4 - This was accurate for me

The top picture you have shown, has for me - Norwegian, Swedish and Danish ( on the fringe) ..........and I have zero association with Scandinavia as far as I know


Thanks for sharing, what's your background by chance? It seems so far that the POPRES set that I had used in the OP works only with certain sorts of individuals at Interpretome just as with UCLA's SPA models (POPRES based and accurate only for Brits and nearby peoples).


300 plus years both paternal and maternal from north-east Italy.

It plots me on your second graphic
at the -7.5, next to the swedish and Finnish flags ( right side)

I do have 50% of matches with british people , usually irish and scots, but some cornish as well.

Image

Uploaded with ImageShack.us

and this is accurate
Image

Uploaded with ImageShack.us
R-P312 clades tested for: DF99+ P312+ DF27- DF19- U152- L21- L459- Z245- L238- Z2245- Z2247-
Ysearch: VNSGW
mtDNA: H3ap
Gedmatch ID: M033622

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