scholarly journals Ancient DNAs and the Neolithic Chinese super-grandfather Y haplotypes

2018 ◽  
Author(s):  
Ye Zhang ◽  
Xiaoyun Lei ◽  
Hongyao Chen ◽  
Hui Zhou ◽  
Shi Huang
Keyword(s):  
Y Chromosome ◽  
Close Relationships ◽  
Northwest China ◽  
Han Chinese ◽  
Before Present ◽  
Central Plains ◽  
Genetic Groups ◽  
Genome Wide

AbstractPrevious studies identified 3 Neolithic Han Chinese super-grandfather Y haplotypes, O2a2b1a1a-F5, O2a2b1a2a1-F46, and O2a1b1a1a1a-F11, but their relationships with the archaeological and written records remain unexplored. We here report genome wide DNA data for 12 ancient samples (0.02x-1.28x) from China ranging from 6500 to 2500 years before present (YBP). They belonged to 4 different genetic groups, designated as Dashanqian (DSQ) of Xiajiadian Culture in the Northeast, Banpo (BP) of middle Yangshao Culture in the Central West, Zhengzhou Xishan (ZX) of Miaodigou Culture in the Central Plains, and Others. Present day F5 samples were closer in autosomal distances to the ZX and DSQ groups while F11, C, O1, and O2 samples were closer to the BP group. We also sequenced the Y chromosome of one of these ancient samples K12 from DSQ and found both K12 and a previously reported ~4000 year old sample MG48 from Northwest China to have the O2a2b1a1a1a2a-F2137 haplotype, belonging to the most prolific branch O2a2b1a1a1-F438 immediately under F5. We further found close relationships between ZX and DSQ and between ZX and ancient M117 Tibetans or present day Southwest Dai Chinese carrying the F5 subtype O2a2b1a1a6, implicating radiations of F5 subtypes from the putative place of F5 origin in ZX. These results are remarkably consistent with archaeological and written records.

scholarly journals Ancient DNAs and the Neolithic Chinese super-grandfather Y haplotypes

2019 ◽  
Author(s):  
Ye Zhang ◽  
Xiaoyun Lei ◽  
Hongyao Chen ◽  
Jiawei Li ◽  
Hui Zhou ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Close Relationships ◽  
Northwest China ◽  
Han Chinese ◽  
Before Present ◽  
Central Plains ◽  
Human Samples ◽  
Genetic Groups ◽  
Genome Wide

Abstract Background: Previous studies identified 3 Neolithic Han Chinese super-grandfather Y haplotypes, F5 (O2a2b1a1a), F46 (O2a2b1a2a1), and F11 (O2a1b1a1a1a), but their relationships with the archaeological and written records remain unexplored. Results: We here report genome wide DNA data for 11 ancient human samples (0.02x-1.28x) from China ranging from 6500 to 2500 years before present (YBP), which also includes ~11 Mb Y NRY data for one sample. The 11 ancient samples belonged to 4 different genetic groups, designated as Dashanqian (DSQ) of Xiajiadian Culture in the Northeast, Duzhong (DZ) of late Yangshao Culture in the Central Plains, Zhengzhou Xishan (ZX) of Miaodigou Culture in the Central Plains, and Others. Present day F5 samples were closer in autosomal distances to the ZX and DSQ groups while O1, O2, and C samples were closer to the DZ group. We also sequenced the Y chromosome of one of these ancient samples K12 from DSQ and found both K12 and a previously reported ~4000 year old sample MG48 from Northwest China to have the F2137 (O2a2b1a1a1a2a) haplotype, belonging to the most prolific branch F438 immediately under F5. We further found close relationships between ZX and DSQ and between ZX and ancient M117 Tibetans or present day Southwest Dai Chinese carrying the F5 subtype O2a2b1a1a6. Conclusions: The results imply radiations of F5 subtypes from the putative place of F5 origin in Henan. These results are remarkably consistent with archaeological and written records.

scholarly journals Ancient DNAs and the Neolithic Chinese super-grandfather Y haplotypes

2019 ◽  
Author(s):  
Ye Zhang ◽  
Xiaoyun Lei ◽  
Hongyao Chen ◽  
Jiawei Li ◽  
Hui Zhou ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Close Relationships ◽  
Northwest China ◽  
Han Chinese ◽  
Before Present ◽  
Central Plains ◽  
Genetic Groups ◽  
Genome Wide

Abstract Background Previous studies identified 3 Neolithic Han Chinese super-grandfather Y haplotypes, O2a2b1a1a-F5, O2a2b1a2a1-F46, and O2a1b1a1a1a-F11, but their relationships with the archaeological and written records remain unexplored. Results We here report genome wide DNA data for 11 ancient samples (0.02x-1.28x) from China ranging from 6500 to 2500 years before present (YBP), which also includes ~11 Mb Y NRY data for one sample. The 11 ancient samples belonged to 4 different genetic groups, designated as Dashanqian (DSQ) of Xiajiadian Culture in the Northeast, Duzhong (DZ) of late Yangshao Culture in the Central Plains, Zhengzhou Xishan (ZX) of Miaodigou Culture in the Central Plains, and Others. Present day F5 samples were closer in autosomal distances to the ZX and DSQ groups while O1, O2, and C samples were closer to the DZ group. We also sequenced the Y chromosome of one of these ancient samples K12 from DSQ and found both K12 and a previously reported ~4000 year old sample MG48 from Northwest China to have the O2a2b1a1a1a2a-F2137 haplotype, belonging to the most prolific branch O2a2b1a1a1-F438 immediately under F5. We further found close relationships between ZX and DSQ and between ZX and ancient M117 Tibetans or present day Southwest Dai Chinese carrying the F5 subtype O2a2b1a1a6. Conclusions The results imply radiations of F5 subtypes from the putative place of F5 origin in Henan. These results are remarkably consistent with archaeological and written records.

Abstract TP134: Genome Wide Association Studies in Han Chinese Populations Identify Novel Susceptibility Loci for Specific Ischemic Stroke Subtypes

Stroke ◽  
2016 ◽  
Vol 47 (suppl_1) ◽  
Author(s):  
Tai-Ming Ko ◽  
Tsong-Hai Lee Lee ◽  
Chien-Hsiun Chen ◽  
Yuan-Tsong Chen ◽  
Jer-Yuarn Wu
Keyword(s):  
Ischemic Stroke ◽  
Chinese Population ◽  
Genetic Factors ◽  
Han Chinese ◽  
Genome Wide Association ◽  
Papillary Thyroid ◽  
Susceptibility Loci ◽  
Han Chinese Population ◽  
Chinese Populations ◽  
Genome Wide

Introduction: Although family history studies in ischemic stroke support that genetic factors may be involved in the pathogenesis of two major subtypes of ischemia stroke: large-artery atherosclerosis (LAA) and small-vessel occlusion (SVO), it is still unclear which particular genetic factors contribute to LAA or SVO. Hypothesis: Because the etiology of ischemic stroke is heterogeneous, we hypothesize that genetic factors may vary by etiologic subtypes or ethnicities. Thus, we aim to identify genetic factors that contribute to LAA or SVO based on two independent Han Chinese populations. Methods: Novel genetic variants that predispose individuals to LAA and SVO were identified by genome-wide association study comprising of 824 individuals (including 444 LAA cases and 380 SVO cases) and 1,727 controls in a Han Chinese population residing in Taiwan. The LAA study was replicated in an independent Han Chinese population comprising of an additional 319 LAA cases and 1,802 controls. Results: In LAA cases, from two independent populations, we identified five single-nucleotide polymorphisms (SNPs), including SNP-1 (P = 3.10 х 10–8), SNP-2 (P = 4.00 х 10–9), SNP-3 (P = 3.57 х 10–8), SNP-4 (P = 1.76 х 10–8), and SNP-5 (P = 2.92 х 10–8), at one novel locus on chromosome 14q13.3 within PTCSC3 (encoding papillary thyroid carcinoma susceptibility candidate 3). In SVO cases, from the discovery stage, we identified two novel candidate susceptibility loci on chromosome 3p25.3 (SNP-6, P = 3.24 х 10–5) and chromosome 14 q31.1 (SNP-7, P = 2.58 х 10–4). Conclusions: For LAA, the newly identified SNPs within PTCSC3 gene were found to have genome-wide statistical significance (P < 5 х 10–8) and were shown to be located in a risk locus correlated with papillary thyroid carcinoma. Moreover, the genetic association between PTCSC3 gene and SVO was not identified, which suggested that PTCSC3 is a specific susceptibility locus for LAA. For SVO, we identified two novel candidate genetic loci which were valuable for replication by an independent population with SVO. In conclusion, our findings provide insights into the genetic basis of LAA and SVO, which may be applicable in the study of the pathogenesis of ischemic stroke and in the development of alternative therapeutic interventions.

scholarly journals Global genome diversity of the Leishmania donovani complex

2019 ◽  
Author(s):  
Susanne U. Franssen ◽  
Caroline Durrant ◽  
Olivia Stark ◽  
Bettina Moser ◽  
Tim Downing ◽  
...  
Keyword(s):  
Structural Variation ◽  
Leishmania Donovani ◽  
Geographical Origin ◽  
Genomic Variation ◽  
Protozoan Parasites ◽  
Suspected Drug ◽  
Genetic Groups ◽  
Genome Wide ◽  
Future Work ◽  
Globally Distributed

AbstractProtozoan parasites of the Leishmania donovani complex – L. donovani and L. infantum – cause the fatal disease visceral leishmaniasis. We present the first comprehensive genome-wide global study, with 151 cultured field isolates representing most of the geographical distribution. L. donovani isolates separated into five groups that largely coincide with geographical origin but vary greatly in diversity. In contrast, the majority of L. infantum samples fell into one globally-distributed group with little diversity. This picture is complicated by several hybrid lineages. Identified genetic groups vary in heterozygosity and levels of linkage, suggesting different recombination histories. We characterise chromosome-specific patterns of aneuploidy and identified extensive structural variation, including known and suspected drug resistance loci. This study reveals greater genetic diversity than suggested by geographically-focused studies, provides a resource of genomic variation for future work and sets the scene for a new understanding of the evolution and genetics of the Leishmania donovani complex.

scholarly journals Genome-wide association study of antipsychotic-induced sinus bradycardia in Chinese schizophrenia patients

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0249997
Author(s):  
Saizheng Weng ◽  
Bo Wang ◽  
Mo Li ◽  
Shan Chao ◽  
Ruiqian Lin ◽  
...  
Keyword(s):  
Adverse Drug Reaction ◽  
Drug Reaction ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Sinus Bradycardia ◽  
Susceptibility Gene ◽  
Han Chinese ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

Second-generation antipsychotics (SGAs) play a critical role in current treatment of schizophrenia (SCZ). It has been observed that sinus bradycardia, rare but in certain situations life threatening adverse drug reaction, can be induced by SGAs across different schizophrenia populations. However, the roles of genetic factors in this phenomenon have not been studied yet. In the present study, a genome-wide association study of single nucleotide polymorphisms (SNPs) was performed on Chinese Han SCZ patients to identify susceptibility loci that were associated with sinus bradycardia induced by SGAs. This study applied microarray to obtain genotype profiles of 88 Han Chinese SCZ patients. Our results found that there were no SNPs had genome-wide significant association with sinus bradycardia induced by SGAs. The top GWAS hit located in gene KIAA0247, which mainly regulated by the tumor suppressor P53 and thus plays a role in carcinogenesis based on resent research and it should not be a susceptibility locus to sinus bradycardia induced by SGAs. Using gene-set functional analysis, we tested that if top 500 SNPs mapped genes were relevant to sinus bradycardia. The result of gene prioritization analysis showed CTNNA3 was strongly correlated with sinus bradycardia, hinting it was a susceptibility gene of this ADR. Our study provides a preliminary study of genetic variants associated with sinus bradycardia induced by SGAs in Han Chinese SCZ patients. The discovery of a possible susceptibility gene shed light on further study of this adverse drug reaction in Han Chinese SCZ patients.

scholarly journals Inferring the population history of Tai-Kadai-speaking people and southernmost Han Chinese on Hainan Island by genome-wide array genotyping

2020 ◽  
Vol 28 (8) ◽  
pp. 1111-1123 ◽  
Author(s):  
Guanglin He ◽  
Zheng Wang ◽  
Jianxin Guo ◽  
Mengge Wang ◽  
Xing Zou ◽  
...  
Keyword(s):  
Hainan Island ◽  
Han Chinese ◽  
Population History ◽  
Genome Wide ◽  
History Of
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