Background: Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate-oligonucleotide-primed PCR (DOP-PCR) and multiple annealing and looping-based amplification cycles (MALBAC). However, a comprehensive comparison of variations detection performance between these WGA methods has not yet been performed. Results: We systematically compared the advantages and disadvantages of different WGA methods, focusing particularly on variations detection. Low-coverage whole-genome sequencing revealed that DOP-PCR had the highest duplication ratio, but an even read distribution and the best reproducibility and accuracy for detection of copy-number variations (CNVs). However, MDA had significantly higher genome recovery sensitivity (~84 %) than DOP-PCR (~6 %) and MALBAC (~52 %) at high sequencing depth. MALBAC and MDA had comparable single-nucleotide variations detection efficiency, false-positive ratio, and allele drop-out ratio. We further demonstrated that SCRS data amplified by either MDA or MALBAC from a gastric cancer cell line could accurately detect gastric cancer CNVs with comparable sensitivity and specificity, including amplifications of 12p11.22 (KRAS) and 9p24.1 (JAK2, CD274, and PDCD1LG2). Conclusions: Our findings provide a comprehensive comparison of variations detection performance using SCRS amplified by different WGA methods. It will guide researchers to determine which WGA method is best suited to individual experimental needs at single-cell level.

Yong Hou;Kui Wu;Xulian Shi;Fuqiang Li;Luting Song;Hanjie Wu;Michael Dean;Guibo Li;Shirley Tsang;Runze Jiang;Xiaolong Zhang;Bo Li;Geng Liu;Niharika Bedekar;Na Lu;Guoyun Xie;Han Liang;Liao Chang;Ting Wang;Jianghao Chen;Yingrui Li;Xiuqing Zhang;焕明 杨;Xun Xu;Ling Wang;军 王

GigaScience

2015

The Xibe population originated in northeastern China, but migrated to northwestern China in 1764-6. We have used a combination of published autosomal and Y-chromosomal data, together with newly derived mtDNA HVSI sequences, to investigate the extent to which genetic data can reveal the geographical origin of this population and the level of gene flow after the migration. We find that mtDNA data are uninformative, but that both autosomal and Y-chromosomal data indicate a northeastern origin, and that the Y data suggest 28% subsequent male-mediated gene flow into the population. We thus conclude that an appropriate combination of genetic data and analytical methods can reveal even recent and local events in the history of a population. In the Chinese samples examined, the combination of a northeastern autosomal background with a northwestern Y chromosome is indicative of a Xibe individual.

Gareth T. Powell;焕明 杨;Chris Tyler-Smith;Yali Xue

Forensic Science International: Genetics

2007-6

We present the second human Y-specific minisatellite, MSY2 (DYS440). It consists of three or four copies of a 99-110 bp repeat unit and is located about 1 kb upstream of the DBY gene. The most common allele contains four units, but a three-unit allele has arisen on at least four occasions; in chimpanzees and orangutans, MSY2 contains only two units. It is therefore evolving slowly and provides a particularly useful polymorphic marker for Chinese populations. (C) 2000 Elsevier Science B.V.

Weidong Bao;Suling Zhu;Arpita Pandya;Tatiana Zerjal;Jiujin Xu;Qunfang Shu;Ruofu Du;焕明 杨;Chris Tyler-Smith

Gene

2000-2-22

Main Text (Cancer Cell 37, 21–36.e1–e13; January 13, 2020) In the original article, the surname of co-author Wouter Everaerts was spelled incorrectly as “Everaert.” It appears correctly in this Correction, and the error has been corrected online.

Jermaine Goveia;Katerina Rohlenova;Federico Taverna;Lucas Treps;Lena Christin Conradi;Andreas Pircher;Vincent Geldhof;Laura P.M.H. de Rooij;Joanna Kalucka;Liliana Sokol;Melissa García-Caballero;Yingfeng Zheng;Junbin Qian;Laure Anne Teuwen;Shawez Khan;Bram Boeckx;Els Wauters;Herbert Decaluwé;Paul De Leyn;Johan Vansteenkiste;Birgit Weynand;Xavier Sagaert;Erik Verbeken;Albert Wolthuis;Baki Topal;Wouter Everaerts;Hanibal Bohnenberger;Alexander Emmert;Dena Panovska;Frederik De Smet;Frank J.T. Staal;Rene J. Mclaughlin;Francis Impens;Vincenzo Lagani;Stefan Vinckier;Massimiliano Mazzone;Luc Schoonjans;Mieke Dewerchin;Guy Eelen;Tobias K. Karakach;焕明 杨;Jian Wang;Lars Bolund;Lin Lin;Bernard Thienpont;Xuri Li;Diether Lambrechts;Yonglun Luo;Peter Carmeliet

Cancer Cell

2020-3-16

Copy number variations (CNVs) have been shown to cause numerous diseases, however, their roles in human lifespan remain elusive. In this study, we investigate the association of CNVs with longevity by comparing the Han Chinese genomes of long-lived individuals from 90 to 117 years of age and the middle-aged from 30 to 65. Our data demonstrate that the numbers of CNVs, especially deletions, increase significantly in a direct correlation with longevity. We identify eleven CNVs that strongly associate with longevity; four of them locate in the chromosome bands, 7p11.2, 20q13.33, 19p12 and 8p23.3 and overlap partially with the CNVs identified in long-lived Danish or U.S. populations, while the other seven have not been reported previously. These CNV regions encode nineteen known genes, and some of which have been shown to affect aging-related phenotypes such as the shortening of telomere length (ZNF208), the risk of cancer (FOXA1, LAMA5, ZNF716), and vascular and immune-related diseases (ARHGEF10, TOR2A, SH2D3C). In addition, we found several pathways enriched in long-lived genomes, including FOXA1 and FOXA transcription factor networks involved in regulating aging or age-dependent diseases such as cancer. Thus, our study has identified longevity-associated CNV regions and their affected genes and pathways. Our results suggest that the human genome structures such as CNVs might play an important role in determining a long life in human.

Xin Zhao;Xiaomin Liu;Aiping Zhang;Huashuai Chen;Qing Huo;Weiyang Li;Rui Ye;Zhihua Chen;Liping Liang;Qiong A. Liu;Juan Shen;Xin Jin;W. Li;Marianne Nygaard;Xiao Liu;Yong Hou;Ting Ni;Lars Bolund;William Gottschalk;Wei Tao;Jun Gu;小利 田;焕明 杨;Jian Wang;Xun Xu;Michael W. Lutz;Junxia Min;Yi Zeng;Chao Nie

Aging

2018-6-1

We investigated the in vitro developmental competence of porcine embryos produced from in vitro matured (IVM) oocytes by improved HMC and parthenogenetic activation (PA). Embryos were cultured in a modified North Carolina State University (NCSU37) medium. Firstly, we compared the developmental competence between oocytes from sows and gilts by zona-intact (ZI) and zona-free (ZF) PA. Significantly higher (p < 0.05) blastocyst rates were obtained from sow oocytes (42 ± 4% for ZF and 55 ± 6% for ZI) than gilt oocytes (20 ± 2% for ZF and 26 ± 5% for ZI). Secondly, sow oocytes were used to establish the modified HMC that was based on a modified enucleation with partial zona digestion and trisection of porcine oocytes and the use of three cytoplasts and one somatic cell for embryo reconstruction. In vitro fertilization (IVF) and in parallel ZF PA were used as the control systems. After oocyte trisection, >90% of oocyte fragments were recovered, resulting in an average of 37 reconstructed embryos from 100 oocytes. Blastocyst rates of HMC, IVF, and ZF PA embryos were 17 ± 4%, 30 ± 6%, and 47 ± 4%, respectively. Our results prove that HMC in pigs may result in high in vitro efficiency up until the blastocyst stage. In vivo developmental competence will be confirmed in embryo transfer experiments.

Y. Du;P. M. Kragh;X. Zhang;S. Purup;焕明 杨;L. Bolund;G. Vajta

Cloning and Stem Cells

2005

Aging has been one of the several topics intensely investigated during recent decades. More scientists have been scrutinizing mechanisms behind the human aging process. Ultra-weak photon emission is known as one type of spontaneous photon emission that can be detected with a highly sensitive single photon counting photomultiplier tube (PMT) from the surface of human bodies. It may reflect the body's oxidative damage. Our aim was to examine whether ultra-weak photon emission from a human hand is able to predict one's chronological age. Sixty subjects were recruited and grouped by age. We examined four areas of each hand: palm side of fingers, palm side of hand, dorsum side of fingers, and dorsum side of hand. Left and right hand were measured synchronously with two independent PMTs. Mean strength and Fano factor values of photon counts were utilized to compare the UPE patterns of males and females of different age groups. Subsequently, we utilized UPE data from the most sensitive PMT to develop an age prediction model. We randomly picked 49 subjects to construct the model, whereas the remaining 11 subjects were utilized for validation. The results demonstrated that the model was a good regression compared to the observed values (Pearson's r = 0.6, adjusted R square = 0.4, p = 9.4E − 7, accuracy = 49/60). Further analysis revealed that the average difference between the chronological age and predicted age was only 7.6 ± 0.8 years. It was concluded that this fast and non-invasive photon technology is sufficiently promising to be developed for the estimation of biological aging.

Xin Zhao;Eduard van Wijk;Yu Yan;Roeland van Wijk;焕明 杨;Yan Zhang;Jian Wang

Journal of Photochemistry and Photobiology B: Biology

2016-9-1

The YH database is a server that allows the user to easily browse and download data from the first Asian diploid genome. The aim of this platform is to facilitate the study of this Asian genome and to enable improved organization and presentation large-scale personal genome data. Powered by GBrowse, we illustrate here the genome sequences, SNPs, and sequencing reads in the MapView. The relationships between phenotype and genotype can be searched by location, dbSNP ID, HGMD ID, gene symbol and disease name. A BLAST web service is also provided for the purpose of aligning query sequence against YH genome consensus. The YH database is currently one of the three personal genome database, organizing the original data and analysis results in a user-friendly interface, which is an endeavor to achieve fundamental goals for establishing personal medicine. The database is available at http://yh.genomics.org.

Guoqing Li;Lijia Ma;Chao Song;Zhentao Yang;Xiulan Wang;Hui Huang;Yingrui Li;Ruiqiang Li;Xiuqing Zhang;焕明 杨;Jian Wang;军 王

Nucleic Acids Research

2009

Choroideremia is an X-linked hereditary retinal dystrophy leading to blindness in early adulthood. RFLP analyses in three Danish families were consistent with close linkage between choroideremia and the locus DXYS1, located at Xq13-Xq21. Measurable linkage was found between choroideremia and DXS17, at Xq22. Furthermore, choroideremia was diagnosed in a boy with an interstitial deletion at Xq13-Xq21, strongly suggesting the assignment of the locus for choroideremia to this region of the X chromosome. The deletion also covered DXYS1, but did not include DXS17.

Marianne Schwartz;T. Rosenberg;E. Niebuhr;C. Lundsteen;H. Sardemann;O. Andersen;焕明 杨;L. U. Lamm

Human Genetics

1986-12

Schistosomiasis is a neglected tropical disease caused by blood flukes (genus Schistosoma; schistosomes) and affecting 200 million people worldwide. No vaccines are available, and treatment relies on one drug, praziquantel. Schistosoma haematobium has come into the spotlight as a major cause of urogenital disease, as an agent linked to bladder cancer and as a predisposing factor for HIV/AIDS. The parasite is transmitted to humans from freshwater snails. Worms dwell in blood vessels and release eggs that become embedded in the bladder wall to elicit chronic immune-mediated disease and induce squamous cell carcinoma. Here we sequenced the 385-Mb genome of S. haematobium using Illumina-based technology at 74-fold coverage and compared it to sequences from related parasites. We included genome annotation based on function, gene ontology, networking and pathway mapping. This genome now provides an unprecedented resource for many fundamental research areas and shows great promise for the design of new disease interventions.

Neil D. Young;Aaron R. Jex;Bo Li;Shiping Liu;Linfeng Yang;Zijun Xiong;Yingrui Li;Cinzia Cantacessi;Ross S. Hall;Xun Xu;Fangyuan Chen;Xuan Wu;Adhemar Zerlotini;Guilherme Oliveira;Andreas Hofmann;Guojie Zhang;Xiaodong Fang;Yi Kang;Bronwyn E. Campbell;Alex Loukas;Shoba Ranganathan;David Rollinson;Gabriel Rinaldi;Paul J. Brindley;焕明 杨;军 王;Jian Wang;Robin B. Gasser

Nature Genetics

2012-2