Where to login? Do I need to register? Are there any limitations?
There’s no need to login anymore. 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. Both using Search the Database.
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 databases.
Which databases exist?
There are 6 databases: Minimal (YHRD Core Loci), PowerPlex Y (Promega PowerPlex® Y), Yfiler (Applied Biosystems AmpFLSTR® Yfiler®), PowerPlex Y23 (Promega PowerPlex® Y23), Yfiler Plus (Applied Biosystems AmpFLSTR® Yfiler® Plus), Maximal (YHRD Max Loci).
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 (see reference).
- Discrete Laplace
- The Discrete Laplace method to estimate Haplotype frequencies within a Metapopulation by taking allelic distribution into account (see reference). 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 (see reference) for binomial confidence interval calculations.
Do I have to re-enter my Haplotype in order to search with less Loci (resolution)?
No. Simply utilize the kit-“bar” at the top of the results page to switch to another database.
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.
- Ancestry Information: Matches in the Minimal Haplotype database grouped by Nations, Metapopulations and Y-SNPs. A heat map with markers of all matching populations/geo-positions is provided as well.
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?
There are some items disabled in the menu. Are those features available?
No, those features are not yet available. There’s a platform to add missing and/or new features to our list of todos.
Which Y-STR loci are available?
Please see section “Loci” the latest database composition overview.
Which Y-SNPs are available?
Please see section “Y-SNPs” the latest database composition overview.
Which National Databases are available?
Please see section “National” the latest database composition overview.
How do I cite/quote YHRD.ORG?
Just quote the origin (https://yhrd.org) and cite Willuweit S., Roewer L. (2015), ‘The new Y Chromosome Haplotype Reference Database.’, Forensic Sci Int Genet 15, 43-8 [Pubmed] [DOI] 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.
Decommision 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 L., Smouse PE., Quattro JM. (1992), ‘Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data.’, Genetics 131(2), 479-91 [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 , J. B. (1964), ‘Nonmetric Multidimensional Scaling: A Numerical Method’, Psychometrika 29(2), 115-129).
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 ancestry information provided by the 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.
I act on behalf of an law enforcement authority. Please deliver personal information of one donor / all donors stored in your database.
We do not have any identification key connected with the haplotype. Thus the haplotype cannot be traced back to a donor.
It won’t work! I have found a bug!
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!)