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<DIV>Hi folks--</DIV>
<DIV> </DIV>
<DIV>I was reading the recent paper, and checking around the GET-Evidence pages,
and I have a bunch of questions that I couldn’t resolve with the documentation.
I’m sorry if I missed it, but I really did check there first—I swear <IMG
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src="cid:CAD6081862E94288AB13FEABECFADA72@MEMPC">.</DIV>
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<DIV>These could be separate items if you want to do them as separate threads. I
don’t know what the culture here is yet. But I’ll put them all in this starter
email and we can decide how to tackle them.</DIV>
<DIV> </DIV>
<DIV>Assemblies:</DIV>
<DIV>*One of the things I found really challenging was determining which
assembly a variant referred to. For example, on this page <FONT
face="Times New Roman"><A
href="http://evidence.personalgenomes.org/FLG2-S2377X">http://evidence.personalgenomes.org/FLG2-S2377X</A></FONT>
there are 2 locations for this variant. I think I might have figured it out from
some of the stuff below, but sometimes it’s not as obvious on this. How can I
tell on a report page which assembly is referred to?</DIV>
<DIV> </DIV>
<DIV>*For pages like that, with multiple entries for 1000 Genomes, what subsets
of 1000G are we talking about? I couldn’t figure out what different 1000Gs
meant. Related to this, which HapMap release are we talking about on pages
with HapMap? Are the EVS releases that matter?</DIV>
<DIV> </DIV>
<DIV>*Impact scores: I was trying to understand these and wanted to read this
page, but it was 404: <A
title=http://evidence.personalgenomes.org/guide_impact_scores
href="http://evidence.personalgenomes.org/guide_impact_scores">http://evidence.personalgenomes.org/guide_impact_scores</A></DIV>
<DIV> </DIV>
<DIV>*Everything I found was labeled by amino acid change, according to this, I
get that: <A title=http://evidence.personalgenomes.org/guide_amino_acid_calls
href="http://evidence.personalgenomes.org/guide_amino_acid_calls">http://evidence.personalgenomes.org/guide_amino_acid_calls</A>
But again, I can’t tell what coordinate system is the framework here—which
assembly? Which protein is the source of the coordinates?</DIV>
<DIV> </DIV>
<DIV>*Is there a way to locate variants that aren’t associated with a
gene/protein? I couldn’t figure that out. I understand from the documentation
that’s the focus, but I am interested in promoter regions, for example. Any way
to get there?</DIV>
<DIV> </DIV>
<DIV>So those are some initial questions. Thanks for any guidance.</DIV>
<DIV> </DIV>
<DIV>Mary</DIV>
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<DIV> </DIV>
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<DIV style="FONT-FAMILY: 'Calibri'; COLOR: #000000; FONT-SIZE: 12pt">Mary
Mangan, PhD<BR>OpenHelix LLC<BR><A
href="http://blog.openhelix.com">http://blog.openhelix.com</A><BR>twitter
@openhelix<BR></DIV></DIV></DIV></BODY></HTML>