Where to login? Do I need to register? Are there any limitations?
There’s no need to login. You don’t have to register. And there are no limitations. Nevertheless, some rules apply.
How can I enter Haplotypes to be searched?
Either provide a file containing your Haplotype(s) or enter your Haplotype manually. Enter your profile in your preferred kit format. Than Search the Database in a defined dataset.
Simply type what you are looking for in our Database Details search form.
What kind of file formats do you support?
You can trigger searches with multiple Haplotypes in the following formats
- Microsoft Office Excel 97-2004 and newer
- OpenOffice Spreadsheet Format
- Generic CSV Format
- Applied Biosystems® GeneMapper® ID/ID-X export-file
- ABI PRISM® Genotyper® export-file
Which Y-STR kits are you supporting?
We support all kits as long as all Loci are available in one of the datasets, but you will be able to select only kits that are listed here: Minimal, PowerPlex Y, Yfiler, PowerPlex Y23, Argus Y-28, GoldenEye, STRtyper-27, Yfiler Plus, PathFinder Plus, AGCU Y37, YFiler Platinum
Which datasets exist?
There are 6 datasets: Minimal, Y12, Y17, Y23, Y27, Ymax.
Which values are provided as search results?
We have structured the results in two different categories: Observed and Expected. “Observed” are counts of database matches and “Expected” are approximations/estimates of Haplotype frequencies revealed by biostatistical calculations.
Which biostatistical calculations are provided?
- Kappa method of estimation Haplotype frequencies using the frequencies of singletons within a population sample (Brenner 2010 [PubMed] [DOI]).
- Discrete Laplace
- The Discrete Laplace method to estimate Haplotype frequencies within a Metapopulation by taking allelic distribution into account (Andersen et al. 2013 [PubMed] [DOI]). Please note that “Discrete Laplace” is calculated for Minimal and Yfiler Haplotypes only and that DYS385 will be excluded. Partial haplotypes or haplotypes with intermediate alleles or Null alleles cannot be calculated with the Discrete Laplace method.
- Average Discrete Laplace
- As the Discrete Laplace method is only calculated for Metapopulations, an average over all nested Metapopulations is given in cases of higher-level repositories e.g. Eurasian or East Asian.
- Augmented Counting (n+1/N+1)
- The frequency when adding the Haplotype in question to both, the database and observations.
What method of confidence interval calculation you are using?
We are using the exact method of Clopper-Pearson (Clopper and Pearson 1934 [DOI]) for binomial confidence interval calculations. The levels are adjustable using the small carret next to the CI value (95% CI, 95% UCI, 99% CI and 99% UCI). Please see “Binomial proportion confidence interval” at Wikipedia for a detailed explanation of CI.
To validate the CI values given at YHRD using Excel or OpenOffice use the following formulas:
- α = 0.05 for 95% or 0.01 for 99%
- n = number of matches
- N = size of the database/dataset
- lower bound CI = ROUND(1 / BETA.INV(α / 2; n; N - n - 1); 0)
- upper bound CI = ROUND(1 / BETA.INV(1 - (α / 2); n + 1; N - n); 0)
- UCI = ROUND(1 / BETA.INV(1 - α; n + 1; N - n); 0)
Or use our Validation Spreadsheet.
Do I have to re-enter my Haplotype in order to search with less Loci (resolution)?
No. Simply utilize the kit- or dataset-selector at the top of the results page to switch to another dataset.
Which other features are connected to my search results?
There are three additional features
- National Database: Observed and expected frequencies.
- Metapopulations: Observed and expected frequencies.
- National Database (with Subpopulations): Observed and expected frequencies.
Is this database updated?
Sure. This database is updated regularly based on submissions of published original data.
Is there a release history or change log?
Yes. It is here.
How to contribute?
Which Y-STR loci are available?
Please see loci at “Ymax”. Each is available and searchable.
Which Y-SNPs are available?
Please see section “Y-SNPs” the latest Y-SNP tree.
Which National Databases are available?
Please see section National Databases.
What do you mean by “legacy data”?
Following the Guidelines by the German Research Foundation (Deutsche Forschungsgemeinschaft 2019 [Link] [DOI]), we keep additional meta data like informed consent forms or ethics committee approval letters for ten years (if appropriate, available and accessable). Afterwards we delete and destroy additional meta data and calling a submission “legacy data”.
How do I cite/quote YHRD.ORG?
Just quote the origin (https://yhrd.org) and cite
together with the type of information you took from YHRD.ORG in a human readable style. For reasons of confirmability, we highly recommend to include all YHRD.ORG release information (date, version etc.) as well.
Is the output of YHRD SWGDAM compliant?
We have implemented a SWGDAM compliant search for U.S. subpopulations only. Documentation/User’s Guide is available here.. Please see SWGDAM 2014 guideline for further information on the SWGDAM guideline (2014) itself.
Decommission of the U.S. Y-STR Database
U.S. Y-STR Database haplotypes have been permanently transferred to the Y-Chromosome Haplotype Reference Database (YHRD) for continuance of usage, and the U.S. Y-STR Database will be decommissioned (scheduled for June 30, 2019). Further details can be found at here, including a YHRD Users Guide to enable the user to access SWGDAM compliant data output.
What is AMOVA and what is MDS?
To measure the apportionment of variance between pairs of populations, a method called AMOVA (Analysis of Molecular Variance) can be used (Excoffier et al. 1992 [PubMed] ). In case of Y-chromosome profiles, it considers the variance in the number of STR repeat units at DYS loci within and between populations. This method takes into account the molecular relationship of alleles, rather than just their frequency. The AMOVA method can be applied to measure the genetic distance between your population sample and reference samples from the YHRD. By using the online AMOVA program it is possible to calculate FST or RST (apportionment of within/among population variance) between pairs of populations. To test for significance P values will be calculated as well (10,000 permutations). The MDS calculation is based on Kruskal’s non-metric MDS algorithm (Kruskal 1964 ).
Can I perform AMOVA and MDS?
I am an employee at a public or governmental institution; can I use the results in my reports?
Yes, you can use frequency values retrieved from this reference database for your reports. Be sure to report all relevant data, including the release date of the YHRD and to quote YHRD.ORG. Please see our Terms and/or License for further information.
I am running a commercial genealogical service and would like to include tables, maps or other results provided by this website in my reports. Can I use the results, maps etc. in my business?
I found a match! How do I contact this guy?
You can’t. This database is about haplotype frequencies not identification. We do not allow any ID number or other information relating to an identified or identifiable natural person to be submitted to us and therefore don’t store any ID or other information relating to an identified or identifiable natural person.
I’d like to have a full download of the whole database or subdatabase! Is this feasible?
You can’t download the database. However, you can contact the contributors to get information on the submissions. You also have access to the concerned publication(s).
I act on behalf of a law enforcement authority. Please deliver personal information of one donor / all donors stored in your database.
We do not allow any ID number or other information relating to an identified or identifiable natural person to be submitted to us and therefore don’t store any ID or other information relating to an identified or identifiable natural person. Thus, the haplotype cannot be traced back to a donor.
It won’t work! I have found a bug or I have further questions and/or comments. How can I contact people behind YHRD?
Please email either Sascha Willuweit (sascha[dot]willuweit[at]charite[dot]de) or Lutz Roewer (lutz[dot]roewer[at]charite[dot]de).
(Sorry, not matches were found!)