News & Updates
YHRD Release R60
YHRD has been updated to release R60. We have implemented an overview and detail pages for every “National Database” available at YHRD. Additionally, there is a table of the 10 most common haplotypes available at each metapopulation and national database page.
(posted about 1 month ago)Corrected Confidence Interval Calculation
While updating YHRD to release R59, we had migrated our Confidence Interval implementation from R package ‘binom’ to an easier and dependency-free Beta Distribution calculation (it is included in R by default). Unfortunately, we introduced a minor bug when evaluating the lower bounds in cases of no matches. Following the correct Clopper-Pearsons method by evaluating the corresponding quantiles from the beta distribution, there are two special cases which cannot be evaluated: (a) When there are no observations (successes, X = 0), and (b) When all haplotypes in the database are matching (all trials are successes, X = n). We have updated our calculations to cover those cases. The exact formulas used at YHRD are taken from Thulin, Måns (2014). “The cost of using exact confidence intervals for a binomial proportion”. Electronic Journal of Statistics. 8 (1): 817–840 formula (4) and subsequent notes.
Additionally, the Confidence Interval calculation of the expected count (n+1)/(N+1) was taken from the actual observed count. This bug has been fixed as well.
(posted about 1 month ago)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.
(posted 2 months ago)Release 59
In the course of this update we used a new tool for pairwise comparison of all 1251 population samples in order to identify possible data overlaps of high-resolution haplotypes. We identified a very small number of datasets (see release history) which were submitted twice under different names. We have erased or updated these submissions. For the US database a theta-corrected match probability calculation is now available when selecting the feature “National Database (with Subpopulations, 2014 SWGDAM-compliant)” (according to SWGDAM guidelines 2014).
(posted 4 months ago)Release 58: USYSTR database now live at YHRD
Based on the descision of the Lineage Marker Committee of SWGDAM the complete US YSTR database (release 4.2.1) is transferred from usystr.org and included in the YHRD. US colleagues can analyze Y-STR profiles according to the current SWGDAM guidelines of 2014 including theta correction und one-sided confidence interval. Please note that the new guidelines in Germany (2018) recommend the DL values to calculate match probabilities. These values are recalculated from release to release for all 33 metapopulations. Overall the YHRD database increases again drastically with now >250k haplotypes (1221 population samples from 135 countries).
(posted 5 months ago)
