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Yang, Lee, Park, Yang, and Shin: Web-based Y-STR Database for Haplotype Frequency Estimation and Kinship Index Calculation
Original Article
Korean Journal of Legal Medicine

Korean Journal of Legal Medicine 2012; 36(1): 45-55.

Published online: 29 May 2012

DOI: https://doi.org/10.7580/KoreanJLegMed.2012.36.1.45

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

In Seok Yang1, Hwan Young Lee1, 2, Myung Jin Park1, Woo Ick Yang1, Kyoung-Jin Shin1, 2

1Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea.

2Human Identification Research Center, Yonsei University, Seoul, Korea.

Corresponding author (kjshin@yuhs.ac)

Received 17 April 2012       Accepted 10 May 2012

Copyright © 2012 The Korean Society for Legal Medicine

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.

Keywords: Y-chromosome, STR, database, frequency estimator, kinship index, mutation rate

Figures and Tables

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.
kjlm-36-45-g001
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.
kjlm-36-45-g002
Table 1
Information of Y-STR Haplotype Data Collected in ySTRmanager
kjlm-36-45-i001

aIf the same population data was collected from two or more different sources, the number of sources was indicated in parentheses.

bChinese 8 minor populations indicate Hui, Korean, Manchu, Naxi, Salar, Tibetan, Tuija, and Yi populations living in China.

Table 2
An Example of Kinship Test Among Alleged Father and Two Sons
kjlm-36-45-i002

aM and N indicate matched samples and population size, respectively.

bFrequency estimate was obtained by calculating upper 95% one-sided confidence interval as shown in Eq. (1).

cThe values in parentheses were calculated using the average value (0.0022) of mutation rates for the minimal haplotype.

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