Computational protocol: Patrilineal Background of Esophageal Cancer and Gastric Cardia Cancer Patients in a Chaoshan High Risk Area in China

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Protocol publication

[…] Subjects were genotyped for Y-SNP haplogroup and frequencies were compared among the 4 patient populations and She and Hakka populations (). Principal component, correlation and hierarchical cluster analyses were used to analyze the relationship among the 6 populations. Three high-risk populations from the Taihang Mountain, Fujian Minnan, and Chaoshan areas and 25 previously published Chinese populations were compared. The 25 Chinese populations were divided into 4 groups by geographic location and nationality : Northern Han (NHs) and northern minority nationalities (NMNs), southern Han (SH) and southern minority nationalities (SMNs).NH populations were Hebei , Liaoning (data provided by the State Key Laboratory of Genetic Engineering and Center for Anthropological Studies, School of Life Sciences, Fudan University), Xinjiang, Gansu, Shanxi, Neimeng, Shandong and Henan ; SH populations were Hunan, Hubei, Zhejiang, Jiangxi, Shanghai, Anhui, Jiangsu, Sichuan , Guangzhou and Guangxi (data provided by Fudan University); NMN populations were Tibetan, Mongol, Hui, Ewenki, and Shui (data provided by Fudan University); data for 3 southern minority nationalities (Yao, Zhuang and Dong and 5 northern minority nationalities (Tibetan, Mongol, Hui, Ewenki, and Shui populations were provided by Fudan University). Chaoshan patients, Henan patients, Chaoshan Hakka and Chaoshan She population belong to SHs, NHs, SHs, and SMNs, respectively. Guangzhou Han, Chaoshan Hakka, and Chaoshan patients belong to the Guangfu, Hakka, and Fulao/Helao clans, respectively, the 3 major clans in Guangdong Province. Chaoshan She people comprise the major SMNs who live in the Chaoshan area. These 4 populations are geographically proximate.STRs can be used to analyze minute genetic diversity in close populations, so on the basis of Y-SNP results, Y-STRs were used to analyze the genetic differentiation and origin among patients and high-risk populations (). We added Y-STR data for 3 high-risk populations from our previous research and for 6 previously published populations: Zhejiang , Henan , Dongbei , Tianjing , Hunan Han and Tibetan people .The extent of genetic differentiation of the populations was estimated by the Rst statistic on the basis of the Y-STR haplotypes by use of Alrequin 3.1. A neighbor-joining tree was constructed according to the Rst distance matrix with use of MEGA 5.1. A network of Y-STR data was constructed by use of Network 4.6.1.1 (www.fluxus-engineering.com). In the network map, individuals with the same mutations of Y-STRs were in the same node, and one node could generate other nodes due to gradual Y-STR mutation . […]

Pipeline specifications

Software tools CLANS, MEGA
Application Proteome data visualization
Organisms Homo sapiens
Diseases Esophageal Neoplasms, Stomach Neoplasms