Dear All, Another follow up question regarding the family structure of HCP data. The S1200 reference manual mentioned (quote below) a Pedigree_ID field which seems to be missing from the current "Restricted Data" csv file or is it somewhere else ?
In addition, apart from this field is there any other field to confirm the individuals share the same household environment ? Best regards, Yann "With the S1200 release, we have now verified the self reports for subjects for which we have GWAS genetic data. We have updated these measures to Twin_Stat (original self report), ZygositySR (orginal self-reported zygosity), ZygosityGT (twin zygosity verified by genotyping), Pedigree_ID (new, family ID based on original, self-reported Mother_ID and Father_ID), Mother_ID (verified by genotyping, if available), and Father_ID (verified by genotyping, if available). Therefore, for some subjects, Mother_ID or Father_ID has changed from what they were in previous releases based on the genotyping data." https://www.humanconnectome.org/documentation/S1200/HCP_S1200_Release_Reference_Manual.pdf 2017-03-03 16:37 GMT+01:00 Elam, Jennifer <e...@wustl.edu>: > Hi Ben, > > As described in the S1200 Reference Manual > <https://www.humanconnectome.org/documentation/S1200/HCP_S1200_Release_Reference_Manual.pdf>, > if the column ZygosityGT is blank for a set of twins we are missing genetic > material/GWAS data on one or both of the twin pair, so unfortunately we > don't have more data to share on the 64 twin pairs that do not have that > measure. > > > Best, > > Jenn > > > Jennifer Elam, Ph.D. > Scientific Outreach, Human Connectome Project > Washington University School of Medicine > Department of Neuroscience, Box 8108 > 660 South Euclid Avenue > St. Louis, MO 63110 > 314-362-9387 > e...@wustl.edu > www.humanconnectome.org > > ------------------------------ > *From:* Benjamin Risk <bb...@cornell.edu> > *Sent:* Friday, March 3, 2017 9:16:56 AM > *To:* Elam, Jennifer > *Cc:* D. van der Linden; hcp-users@humanconnectome.org > *Subject:* Re: [HCP-Users] Question regarding Twins in HCP > > I have a follow-up question on ZygosityGT. In the new data release, there > appear to be 64 twin pairs without zygosity verified by genotyping data > (and 244 with ZygosityGT). Are there plans to make genotyping-based > zygosity available for these individuals? > > Thank you, > Ben > > On Tue, Feb 28, 2017 at 11:56 AM, Elam, Jennifer <e...@wustl.edu> wrote: > >> Hi Dimitri, >> >> Since your message was in response to an offline thread, for the benefit >> of the HCP-Users list, let me explain what you are referencing regarding >> dizygotic (DZ) twins that were "mislabeled" as monozygotic (MZ). Zygosity >> and other family structure information currently available in ConnectomeDB >> (S900 release data) is based on self report. In the upcoming 1200 Subjects >> Release (S1200), we will be introducing a new measure, ZygosityGT, which is >> zygosity verified by the genotyping data available. >> >> >> When we compare self-reported zygosity (the ZygositySR measure in the >> S1200) of the 244 HCP twin pairs that have with ZygosityGT, we find that 36 >> twin pairs that self-reported to be DZ, were verified by genetics to be, in >> fact, MZ. Researchers with experience from other twin studies tell us that >> it is common in these studies to find MZ twins that think they are DZ twins >> based on what their family was told by hospital staff at birth before the >> recent age of routine genetic testing of fetuses/newborns. >> >> >> To access twin and other family structure measures in ConnectomeDB you >> must first apply for restricted data access by filling out and sending us >> this form: https://store.humanconnectome.org/data/data-use-terms/DataUs >> eTerms_HCP_RestrictedAccess_26Jan2016.pdf >> >> When you are approved for restricted data access (usually takes 1-2 >> weeks), you will be able to select to view and download Open Access, >> Restricted, or Sensitive data in ConnectomeDB with the pulldown at the top >> left of the interface: >> >> >> Others on the list can discuss this part of your message: >> >> I also wondered whether this discrepancy in labels may play a large role >> in the very high correlations between DZ twins on variables such as >> intelligence and height. Because of this, the heritability coefficients for >> such variables often comes out very low. >> >> For many important variables, the magnitude of the correlations between >> DZ twins is very high in this sample (compared to the literature). >> >> >> Best, >> >> Jenn >> >> >> Jennifer Elam, Ph.D. >> Scientific Outreach, Human Connectome Project >> Washington University School of Medicine >> Department of Neuroscience, Box 8108 >> 660 South Euclid Avenue >> St. Louis, MO 63110 >> 314-362-9387 >> e...@wustl.edu >> www.humanconnectome.org >> >> ------------------------------ >> *From:* hcp-users-boun...@humanconnectome.org < >> hcp-users-boun...@humanconnectome.org> on behalf of D. van der Linden < >> vanderlin...@fsw.eur.nl> >> *Sent:* Tuesday, February 28, 2017 6:38:50 AM >> *To:* hcp-users@humanconnectome.org >> *Subject:* [HCP-Users] Question regarding Twins in HCP >> >> Dear HCP team, >> >> I have a question regarding the data. The topic is rather important >> because it may strongly affect the outcomes of our analyses. It involves >> the following: >> >> If I understood it correctly, in the 900 dataset there were subjects who >> were classified as dizygotic twins but were actually monozygotic twins. I >> think there were around 36 twin pairs that were incorrectly labeled. If >> this is true this may affect estimates of heritability. >> >> >> Therefore, I wonder where I can find the information which twin pairs >> were incorrectly labelled so that I can make the corrections. >> >> >> I also wondered whether this discrepancy in labels may play a large role >> in the very high correlations between DZ twins on variables such as >> intelligence and height. Because of this, the heritability coefficients for >> such variables often comes out very low. >> >> For many important variables, the magnitude of the correlations between >> DZ twins is very high in this sample (compared to the literature). >> >> >> Kind regards, >> >> Dimitri van der Linden >> Associate Professor Psychology >> >> Erasmus University Rotterdam >> Tel: +31 10 408 2454 <+31%2010%20408%202454> >> Email: vanderlin...@fsw.eur.nl >> >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
