Korean J Leg Med.  2012 May;36(1):45-55. 10.7580/KoreanJLegMed.2012.36.1.45.

Web-based Y-STR Database for Haplotype Frequency Estimation and Kinship Index Calculation

Affiliations
  • 1Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea. kjshin@yuhs.ac
  • 2Human Identification Research Center, Yonsei University, Seoul, Korea.

Abstract

We developed a web-based Y chromosomal short tandem repeat (Y-STR) database (ySTRmanager, http://ystrmanager.yonsei.ac.kr) to facilitate calculation of Y-STR haplotype frequency estimates for random matches and kinship indices for various relationship levels. The ySTRmanager database provides 3 functions: (i) Y-STR haplotype search, (ii) kinship index calculation, and (iii) user database configuration. The Y-STR haplotype search function allows researchers to retrieve Y-STR haplotypes that meet queried Y-STR allele, Y-haplogroup affiliation, and/or sample information from a selected population in the open database, which consists of 12-17 Y-STR loci. The number of matches in a selected population, haplotype frequency estimator, and detailed results for matched and neighbor haplotypes are displayed as a set of search results. The kinship index calculation function provides kinship indices of 2 input Y-STR haplotypes for the relationship represented by the number of meioses, with consideration of target population and mutation rate of each Y-STR. In addition, ySTRmanager allows registered users to configure their own database to store and analyze Y-STR haplotype and/or mutation rate data. The stored Y-STR data can be used in the search function and in the analysis to obtain forensic statistical values. The ySTRmanager will be a useful system to analyze and manage Y-STR data in the practice of forensic genetics.

Keyword

Y-chromosome; STR; database; frequency estimator; kinship index; mutation rate

MeSH Terms

Alleles
Forensic Genetics
Haplotypes
Health Services Needs and Demand
Meiosis
Microsatellite Repeats
Mutation Rate

Figure

  • Fig. 1 Search setting in ySTRmanager. In order to search a particular Y-STR haplotype (Y-haplotype) from a selected population, user should provide Y-haplotype information (circled "1") and then select a target population (circled "2"). Y-STR allele values can be provided by selecting a value in list box for each Y-STR loci interested or by direct input of allele values into text box after selecting "Others" in list box. Y-haplogroup and/or sample information can be combined to Y-haplotype or used independently to search haplotypes in a selected population.

  • Fig. 2 Search results of ySTRmanager. The number of matches for the particular haplotype and its haplotype frequency estimator in a selected population are displayed in search result (the top table of a). Individual detailed information including sample name, Y-haplogroup affiliation, and sample information for matched haplotypes are shown in a table, which can be downloaded by clicking "Export" button (the bottom table of a). Neighbor haplotypes are displayed in a table only when there is at least one matched haplotype in a selected population (b). Allele values at Y-STR loci with single-step mutations (+1 repeat gain or -1 repeat loss) in neighbor haplotypes are represented by different backgrounds (dashed box in b). Detailed sample information having the neighbor haplotypes can also be appeared in a new window by clicking "View" link.


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