News & Updates
Contributions to the YHRD
We have updated the requirements for first-submitters of population data to the YHRD. Please note that we have stopped sending QC samples, since Y-STR typing methods are sufficiently established and standardized. Please note that we now request original epg’s of positive and negative controls and allelic ladders of the kit. Please consult help pages for further information.
(posted about 2 months ago)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 3 months 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 4 months 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 5 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 6 months ago)
