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S1 Table. The divisions of haplogroups comprised of 22 Y-STR loci in the Jiangsu Han population (n = 916) . S2 Table. The distribution of 916 Jiangsu Han samples in prefecture-level geographic location.
Version 4 2017-06-29, 07:11
Version 3 2017-06-28, 14:43
Version 2 2017-06-28, 14:42
Version 1 2017-06-28, 03:29
dataset
posted on 2017-06-29, 07:11 authored by Tai YunchunTai YunchunSamples and DNA extraction
A total of 916 unrelated healthy male individuals of Han ancestry provided blood samples with informed consent, including 207 samples from Changzhou, 147 from Xuzhou, 111 from Suqian, 98 from Wuxi, 71 from Lianyungang, 62 from Yancheng, 55 from Huai’an, 47 from Soochow, 41 from Nanjing, 39 from Nantong, 17 from Zhenjiang, 14 from Yangzhou, and 7 from Taizhou. All individuals come from Chinese Jiangsu Han population and reside locally at least three generations. Chelex-100 protocol was adopted to extract genomic DNA. The study was conducted in accordance to the human and ethical research principles of Zhongshan City People’s Hospital and approved by the ethics committee in Zhongshan City People’s Hospital.
STR genotyping
Y-STR was typed for the PowerPlex Y23 System (Promega, USA) with GeneAmp PCR system 9700 (Thermofisher Scientific, Waltham, MA, USA). Amplified DNAs were separated on ABI3130XL DNA Genetic Analyzer (Thermofisher Scientific, Waltham, MA, USA) and analyzed using the GeneMapper ID-X software (Thermofisher Scientific, Waltham, MA, USA).
Statistical analysis
After direct count of the allele frequencies and haplotype by Arlequin 3.0, we calculated gene diversity (GD) following Nei. We also calculated several representative forensic parameters, such as haplotype diversity (HD), discrimination capacity (DC), and match probability (MP) according Sabine et al. DYS385a/b, a multi-copy locus, was analyzed as combined haplotypes. And we got the allele of DYS389II by the subtraction of DYS389I. The popular combination of computational RST values which referred to the excess similarity among alleles chosen randomly within the subgroup relative to the entire group and Multidimensional Scaling plot (MDS) was adopted as YHRD analyzed and many publications conducted. Linkage patterns and Analysis of Molecular Variance (AMOVA) which generated the pairwise RST values and according significant values were performed using Arlequin 3.0 based on detailed haplotype information of eligible individuals (samples with the null, intermediate alleles, and copy-number variations were removed). Neighbor-Joining (N-J) tree was depicted and visualized by Mega 6.0 as others conducted. Based on the matrix of RST values, we illustrated MDS as YHRD recommended and achieved values of initial stress by employing “MASS” package (https://cran.r-project.org/web/packages/MASS/index.html).
A total of 916 unrelated healthy male individuals of Han ancestry provided blood samples with informed consent, including 207 samples from Changzhou, 147 from Xuzhou, 111 from Suqian, 98 from Wuxi, 71 from Lianyungang, 62 from Yancheng, 55 from Huai’an, 47 from Soochow, 41 from Nanjing, 39 from Nantong, 17 from Zhenjiang, 14 from Yangzhou, and 7 from Taizhou. All individuals come from Chinese Jiangsu Han population and reside locally at least three generations. Chelex-100 protocol was adopted to extract genomic DNA. The study was conducted in accordance to the human and ethical research principles of Zhongshan City People’s Hospital and approved by the ethics committee in Zhongshan City People’s Hospital.
STR genotyping
Y-STR was typed for the PowerPlex Y23 System (Promega, USA) with GeneAmp PCR system 9700 (Thermofisher Scientific, Waltham, MA, USA). Amplified DNAs were separated on ABI3130XL DNA Genetic Analyzer (Thermofisher Scientific, Waltham, MA, USA) and analyzed using the GeneMapper ID-X software (Thermofisher Scientific, Waltham, MA, USA).
Statistical analysis
After direct count of the allele frequencies and haplotype by Arlequin 3.0, we calculated gene diversity (GD) following Nei. We also calculated several representative forensic parameters, such as haplotype diversity (HD), discrimination capacity (DC), and match probability (MP) according Sabine et al. DYS385a/b, a multi-copy locus, was analyzed as combined haplotypes. And we got the allele of DYS389II by the subtraction of DYS389I. The popular combination of computational RST values which referred to the excess similarity among alleles chosen randomly within the subgroup relative to the entire group and Multidimensional Scaling plot (MDS) was adopted as YHRD analyzed and many publications conducted. Linkage patterns and Analysis of Molecular Variance (AMOVA) which generated the pairwise RST values and according significant values were performed using Arlequin 3.0 based on detailed haplotype information of eligible individuals (samples with the null, intermediate alleles, and copy-number variations were removed). Neighbor-Joining (N-J) tree was depicted and visualized by Mega 6.0 as others conducted. Based on the matrix of RST values, we illustrated MDS as YHRD recommended and achieved values of initial stress by employing “MASS” package (https://cran.r-project.org/web/packages/MASS/index.html).
