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Thread: DMXX's Eye Colour Project (v.2)

  1. #1
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    DMXX's Eye Colour Project (v.2)

    As mentioned in J Man's thread on hazel eyes, I am pleased to announce my project on eye colour genetics is active once more.

    For those who are unfamiliar with it, or wish to learn what happened to the project since its' inception, please view the Spoiler below.

     

    The project began in the Autosomal DNA section of the now defunct DNA-Forums in the first half of 2010. As more users became interested, the general aims of the project took shape. The initial focus was on the HER2 and OCA2 genes, both of which are browsable in a 23andMe customer's raw data. This was expanded to include additional loci, such as SLC45A2.

    At its' peak, the project contained 60 distinct genotype strings based on 16 handpicked SNP's taken from the literature of the time. These were stored on an offline spreadsheet on my hard-disk. Unfortunately, a set of computer problems resulted in the data being inaccessible in May 2011. I managed to retrieve most of the data from their original sources (PM's and posts).

    The final blow to the project came with the demise of DNA-Forums. The community scattered across various other forums and I have not encountered quite a few of them since online. As the project was entirely derived from DNA-Forums members, it was inappropriate and against my own principles to continue using personal genome data from kind participants without their continued knowledge, regardless of the small number of SNP's used.


    Several users here on Anthrogenica were participants in my project. I have listed all previous participants below. If those users could kindly inform me (publicly or privately) whether or not they are interested in remaining in the project, that would be much appreciated. All data belonging to previous users who haven't made contact will remain unused indefinitely and in their entirety.

     

    Code:
    Aaron1981
    AmandaHR
    Annihilus
    bai_xue
    BioGeek
    Cacio
    Cacio's sister
    cilldara
    Corey Reece
    David F. Reynolds
    Delcambre
    Drouhin
    Drouhin's father
    Eekhoorn
    gilljo
    Giuseppe
    Giuseppe's aunt
    Giuseppe's brother
    hamasen1
    Handschar
    Handschar's brother
    J Man
    J Man's Aunt
    J Man's Dad
    J Man's Mum
    JAFarris
    Johnserrat
    Johnserrat's daughter
    Johnserrat's son
    Jolson 1
    Jolson 2
    kvpbf's relative
    lalex
    lalex's brother
    lalex's father
    lalex's husband
    lalex's maternal grandmother
    lalex's mother
    lalex's paternal grandfather
    lalex's paternal grandmother
    Mamluk
    Mamluk's father
    Mamluk's wife
    Mmaddi
    mothdust9
    Mrwo
    Parma
    R1a1a
    R1a1a's grandfather
    Rogers5858
    romanms15
    Simranjits
    Simranjits' son
    Simranjits' wife
    Solothurn
    Solothurn's wife
    Stephen1986
    Treysl
    vadu's contribution


    I should also take this opportunity to state that, if sufficient users (at least n=50) are participating by August 15th 2013, it is my intention to formally write up and publish the results and subsequent analysis (for more information on this please view "Project Assurances and Terms" below). Participation in this project is therefore automatically taken as unwritten permission to include your eye colour SNP's for my research. This was stated toward the end of the original project and remains the case now.





    Project Aims

    Based on the 23andMe chip, ascertain...

    • Which SNP's predominantly control brown vs. light eye phenotype.
    • Which SNP's for the cohort are involved in additional variation.
    • Successfully predict the phenotype from five examples of genotype data.
    • Contrast with existing conclusions in several studies.
    • Whether 23andMe's standard v2 chip has the capacity to support more detailed eye colour prediction assays.



    How Can Users Participate?

    • Please inspect the SNP panel below.
      Code:
      rs12913832
      rs1800407
      rs12896399
      rs16891982
      rs1393350
      rs12203592
      rs7495174
      rs7183877
      rs4778232
      rs1408799
      rs8024968
      rs683
      rs4778138
      rs4778241
      rs1667394
      rs26722
      rs1015362
      rs4911414
      rs1540771
      rs12821256
      rs885479
      rs1805008
      rs1805005
      rs3829241
    • Search your 23andMe Raw Data for all the SNP's in this panel (currently accessed by logging into your profile, highlighting the cogwheel on the top left hand side, selecting "BROWSE RAW DATA").
    • List your SNP genotypes in the order shown in the panel.
    • Information on eye colour phenotype is also crucial to the project. Pictures are ideal, descriptions of phenotype are acceptable. Additional information (i.e. heritage) is welcomed but not mandatory. For a guide on how to describe your eyes, please refer to the image below (add your observations as appropriate):


      Modified and taken from Beleza et al.'s Genetic Architecture of Skin and Eye Color in an African-European Admixed Population and Ruiz et al.'s Further development of forensic eye color predictive tests.
    • Share the essential data (genotype and phenotype information) with the project creator (myself, DMXX) either publicly on this thread or privately by PM.
    • Participants are sent a unique ID (IDnnn) by PM to confirm their information is stored on an offline spreadsheet.



    How Do Participants Benefit?

    • Receive deeper analysis into genotype data provided from markers validated in current scientific literature. This will be delivered via an online spreadsheet which differs from the offline hard copy. In it, user ID's are listed alongside the inferences made from their genotypes.
    • Opportunity to discuss findings or queries concerning the inheritance of eye colour via personal data.
    • Real-time updates concerning what the project has discovered and how this relates to you.



    Project Assurances and Terms

    • All communications and data between the project creator and participants (user ID's, genotypes, pictures) will remain confidential unless users choose to publicly post these.
    • At no point will user data of the sort described above be passed onto third parties.
    • Incomplete participant information (i.e. half of SNP genotypes, no picture/description) will not be included in the project.
    • If a formal report is composed, no personal genotype data or user ID's will be published. The only planned exception will be of the five predictions from genotype data. If I feel any of the pictures are worth including in the report, I will seek permission from those who provided them.
    • Updates on findings will be posted in this thread only.
    • It is worth stating that eye colour genotypes are highly unlikely to convey sensitive information concerning health traits as they tend to come from genes which regulate pigmentation. The first version of the project also revealed that a partial distinction between West Eurasians and other world groups could be gleamed from eye colour genotypes in a rudimentary and non-specific manner. Therefore, it is also highly unlikely any specific information pertaining to ancestry will be inferred.
    • As unlikely as it is, any changes made to the project's methodology or approach will be announced here.


    Updated List of Citations
    Will be completed in the next week.

  2. The Following 25 Users Say Thank You to DMXX For This Useful Post:

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  3. #2
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    Finnish
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    I1a3a1*
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    U5b2a1a1b

    Finland Sami
    Please feel free to use me and my family at your leisure.

    EDIT: Hmmm, I thought we were in it, but I don't see the names in your second spoiler. Do you want data?
    Last edited by ilmari; 07-01-2013 at 01:36 AM. Reason: to add
    Genographic Project: N52850
    GenBank: EU784076
    Z62+ Z60+ Z59+ Z58+ P38+ P30+ P19+ M307+ M258+ M253+ M170+ Z73- Z140- P37.2- P259- P109- M72- M26- M227- M223- M21- M161- L803- L573- L338- L22- L211- L1248- L1247-

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  5. #3
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    Updated with the SNP panel and a guide to use when giving your phenotype descriptions if a picture cannot be produced.

  6. #4
    Registered Users
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    Scotland
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    European
    Nationality
    English
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    R>U106>FGC3861>S1859
    mtDNA
    H2a2b [RSRS]

    England Wales Ireland Sweden
    Code:
    GG	rs12913832
    CC	rs1800407
    TT	rs12896399
    CG	rs16891982
    AG	rs1393350
    CC	rs12203592
    AA	rs7495174
    CC	rs7183877
    CC	rs4778232
    CC	rs1408799
    CC	rs8024968
    AA	rs683
    AA	rs4778138
    CC	rs4778241
    TT	rs1667394
    CC	rs26722
    CT	rs1015362
    TT	rs4911414
    CT	rs1540771
    TT	rs12821256
    GG	rs885479
    CC	rs1805008
    GT	rs1805005
    AA	rs3829241
    DSC01978_Left_Cropped_web.jpg

    Ancestry: British Isles

    Clinton P
    FullGenomes ID:FG1048A
    YFull ID:YF01371


    y-DNA.................................................. ..........................mt-DNA
    Hg: R1b1a1a1a1b3 [R-U106 > FGC3861 > L217]........Hg: H2a2b [RSRS]
    Shorthand: R-L217 or R-S1849......................................Extra Mutations: 309.1'C', 315.1'C', A16235'G', T16357'C', C16519'T'.

    ySearch & mtSearch ID: Hidden Content

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  8. #5
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    IMAG0248.jpg
    American mixed McDonalds 3 top custom
    English .3815 Irish .5142 Jewish .1043
    Irish .7025 French .2116 Jewish .0858
    Irish .8118 Tuscan 0.139 Jewish .0743

    rs12913832 HERC2 28365618 rs12913832 A or G GG
    rs1800407 OCA2 28230318 rs1800407 C or T CC
    rs12896399 intergenic 92773663 rs12896399 G or T TT
    rs16891982 SLC45A2 33951693 rs16891982 C or G GG
    rs1393350 TYR 89011046 rs1393350 A or G GG
    rs12203592 IRF4 396321 rs12203592 C or T CC
    rs7495174 OCA2 28344238 rs7495174 A or G AA
    rs7183877 HERC2 28365733 rs7183877 A or C CC
    rs4778232 OCA2 28281765 rs4778232 C or T TT
    rs1408799 intergenic 12672097 rs1408799 C or T CT
    rs8024968 OCA2 28283689 rs8024968 C or T CT
    rs683 TYRP1, LOC100506267 12709305 rs683 A or C AA
    rs4778138 OCA2 28335820 rs4778138 A or G AA
    rs4778241 OCA2 28338713 rs4778241 A or C CC
    rs1667394 HERC2 28530182 rs1667394 C or T TT
    rs26722 SLC45A2 33963870 rs26722 C or T CC
    rs1015362 intergenic 32738612 rs1015362 C or T CC
    rs4911414 intergenic 32729444 rs4911414 G or T GT
    rs1540771 intergenic 466033 rs1540771 C or T CT
    rs12821256 intergenic 89328335 rs12821256 C or T CT
    rs885479 MC1R 89986154 rs885479 A or G GG
    rs1805008 MC1R 89986144 rs1805008 C or T CC
    rs1805005 MC1R 89985844 rs1805005 G or T GT
    rs3829241 TPCN2 68855363 rs3829241 A or G AG
    Last edited by cavergal; 07-06-2013 at 06:16 PM.

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  10. #6
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    Dad: U-152
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    B4a

    United States Gadsden South Korea United Kingdom Sweden
    rs12913832: AG
    rs1800407: CC
    rs12896399: GG
    rs16891982: CC
    rs1393350: AG
    rs12203592: CC
    rs7495174: AG
    rs7183877: AC
    rs4778232: CT
    rs1408799: CT
    rs8024968: CC
    rs683: AC
    rs4778138: AG
    rs4778241: AC
    rs1667394: CT
    rs26722: TT
    rs1015362: CC
    rs4911414: GG
    rs1540771: CT
    rs12821256: CT
    rs885479: AG
    rs1805008: CC
    rs1805005: GG
    rs3829241: GG




    Heritage: Korean mom, dad of mostly UK ancestry

    Eye color: Dark brown, I think. Sorry about the poor quality, but I had to take the pic in the bathroom with my cell phone.

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  12. #7
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    Quote Originally Posted by DMXX View Post
    For a guide on how to describe your eyes, please refer
    to the image below (add your observations as appropriate):
    Going by that color scheme, I guess mine counts as either Inter-light or Green-hazel?


    Code:
    rs12913832 GG
    rs1800407 CC
    rs12896399 GT
    rs16891982 GG
    rs1393350 GG
    rs12203592 CC
    rs7495174 AA
    rs7183877 CC
    rs4778232 CC
    rs1408799 CT
    rs8024968 CC
    rs683 AC
    rs4778138 AA
    rs4778241 CC
    rs1667394 TT
    rs26722 CC
    rs1015362 CT
    rs4911414 GT
    rs1540771 CT
    rs12821256 TT
    rs885479 GG
    rs1805008 CC
    rs1805005 GG
    rs3829241 AG



    My mother's:

    Code:
    rs12913832 GG
    rs1800407 CC
    rs12896399 GT
    rs16891982 GG
    rs1393350 GG
    rs12203592 CC
    rs7495174 AA
    rs7183877 CC
    rs4778232 CC
    rs1408799 CT
    rs8024968 CC
    rs683 AC
    rs4778138 AA
    rs4778241 CC
    rs1667394 TT
    rs26722 CC
    rs1015362 CT
    rs4911414 GT
    rs1540771 CC
    rs12821256 TT
    rs885479 GG
    rs1805008 CC
    rs1805005 GG
    rs3829241 AG


    My maternal grandfather (the picture is not very clear but I don't have any better photo at the moment, his eyes are just blue without any yellow flecks)

    Code:
    rs12913832 GG
    rs1800407 CC
    rs12896399 TT
    rs16891982 GG
    rs1393350 AG
    rs12203592 CC
    rs7495174 AA
    rs7183877 CC
    rs4778232 CC
    rs1408799 CC
    rs8024968 CC
    rs683 AA
    rs4778138 AA
    rs4778241 CC
    rs1667394 TT
    rs26722 CC
    rs1015362 CT
    rs4911414 GT
    rs1540771 CC
    rs12821256 TT
    rs885479 GG
    rs1805008 CC
    rs1805005 GG
    rs3829241 AG

    Ancestry: Lithuanians
    Last edited by linkus; 07-07-2013 at 01:59 AM.

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  14. #8
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    Linkus,

    I'd actually say both you and your mother belong to the "Inter-light" category because there's evidently some blue pigmentation which the "Green" category seems to lack. I imagine some of the uncertainty concerning your own eyes stems from differing resolutions; all sorts of interesting patterns can be observed in human eyes up close. Those photos provided in the study, however, clearly aren't as detailed. Even from a distance, however, your maternal grandfather's eyes are clearly a uniform blue.

    For the fun of it, I might as well post a picture of my own eyes since they provided the impetus all those years back to look into the genetics of eye colour. 23andMe determined from the couple of SNP's they currently employed I had "brown" eyes without any more definition, despite something more evidently going on phenotypically:


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  16. #9
    Senior Member
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    Cascadia
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    Finnish
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    I1a3a1*
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    U5b2a1a1b

    Finland Sami
    Mine, sorry, I know not how to make the code box like I used to know in the old forums:

    rs12913832 GG
    rs1800407 CC
    rs12896399 GG
    rs16891982 GG
    rs1393350 GG
    rs12203592 CC
    rs7495174 AA
    rs7183877 CC
    rs4778232 CC
    rs1408799 CC
    rs8024968 CC
    rs683 AA
    rs4778138 AA
    rs4778241 CC
    rs1667394 TT
    rs26722 CC
    rs1015362 CC
    rs4911414 GG
    rs1540771 CT
    rs12821256 TT
    rs885479 GG
    rs1805008 CT
    rs1805005 GG
    rs3829241 AG

    481918_10150912663666302_849124370_n.jpg

    Finnish
    Genographic Project: N52850
    GenBank: EU784076
    Z62+ Z60+ Z59+ Z58+ P38+ P30+ P19+ M307+ M258+ M253+ M170+ Z73- Z140- P37.2- P259- P109- M72- M26- M227- M223- M21- M161- L803- L573- L338- L22- L211- L1248- L1247-

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  18. #10
    Senior Member
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    Finland Sami
    My mother's data:

    rs12913832 GG
    rs1800407 CC
    rs12896399 GG
    rs16891982 GG
    rs1393350 GG
    rs12203592 CC
    rs7495174 AA
    rs7183877 CC
    rs4778232 CC
    rs1408799 CT
    rs8024968 CC
    rs683 AA
    rs4778138 AA
    rs4778241 CC
    rs1667394 TT
    rs26722 CC
    rs1015362 CT
    rs4911414 GT
    rs1540771 CC
    rs12821256 TT
    rs885479 GG
    rs1805008 CC
    rs1805005 GG
    rs3829241 AG

    moms eye a.JPG

    Finnish.
    Last edited by ilmari; 07-07-2013 at 03:46 AM. Reason: typo
    Genographic Project: N52850
    GenBank: EU784076
    Z62+ Z60+ Z59+ Z58+ P38+ P30+ P19+ M307+ M258+ M253+ M170+ Z73- Z140- P37.2- P259- P109- M72- M26- M227- M223- M21- M161- L803- L573- L338- L22- L211- L1248- L1247-

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