Phenomics (Cham, Switzerland)最新文献

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Prediction of Metabolic Disorders Using NMR-Based Metabolomics: The Shanghai Changfeng Study. 基于核磁共振的代谢组学预测代谢紊乱:上海长丰研究。
Phenomics (Cham, Switzerland) Pub Date : 2021-08-01 DOI: 10.1007/s43657-021-00021-2
Qi Wu, Qing-Xia Huang, Hai-Luan Zeng, Shuai Ma, Huan-Dong Lin, Ming-Feng Xia, Hui-Ru Tang, Xin Gao
{"title":"Prediction of Metabolic Disorders Using NMR-Based Metabolomics: The Shanghai Changfeng Study.","authors":"Qi Wu,&nbsp;Qing-Xia Huang,&nbsp;Hai-Luan Zeng,&nbsp;Shuai Ma,&nbsp;Huan-Dong Lin,&nbsp;Ming-Feng Xia,&nbsp;Hui-Ru Tang,&nbsp;Xin Gao","doi":"10.1007/s43657-021-00021-2","DOIUrl":"https://doi.org/10.1007/s43657-021-00021-2","url":null,"abstract":"<p><p>A metabolically healthy status, whether obese or not, is a transient stage with the potential to develop into metabolic disorders during the course of life. We investigated the incidence of metabolic disorders in 1078 metabolically healthy Chinese adults from the Shanghai Changfeng Study and looked for metabolites that discriminated the participants who would develop metabolic disorders in the future. Participants were divided into metabolically healthy overweight/obesity (MHO) and metabolically healthy normal weight (MHNW) groups according to their body mass index (BMI) and metabolic status. Their serum metabolomic profile was measured using a <sup>1</sup>H nuclear magnetic resonance spectrometer (<sup>1</sup>H-NMR). The prevalence of diabetes, hypertriglyceridemia, hypercholesterolemia and metabolic syndrome was similar between the MHNW and MHO participants at baseline. After a median of 4.2 years of follow-up, more MHO participants became metabolically unhealthy than MHNW participants. However, a subgroup of MHO participants who remained metabolically healthy (MHO → MHO) had a similar prevalence of metabolic disorders as the MHNW participants at the follow-up examination, despite a significant reduction in their serum concentrations of high-density lipoprotein (HDL) and an elevation in valine, leucine, alanine and tyrosine. Further correlation analysis indicated that serum intermediate-density lipoprotein (IDL) and very low-density lipoprotein cholesterol (VLDL-CH) might be involved in the transition from metabolically healthy to unhealthy status and could be valuable to identify the MHNW and MHO with increased metabolic risks.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"1 4","pages":"186-198"},"PeriodicalIF":0.0,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s43657-021-00021-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9500437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Random Penetrance of Mutations Among Individuals: A New Type of Genetic Drift in Molecular Evolution. 个体间突变的随机外显率:分子进化中的一种新型遗传漂变。
Phenomics (Cham, Switzerland) Pub Date : 2021-06-01 DOI: 10.1007/s43657-021-00013-2
Xun Gu
{"title":"Random Penetrance of Mutations Among Individuals: A New Type of Genetic Drift in Molecular Evolution.","authors":"Xun Gu","doi":"10.1007/s43657-021-00013-2","DOIUrl":"https://doi.org/10.1007/s43657-021-00013-2","url":null,"abstract":"<p><p>The determinative view of mutation penetrance is a fundamental assumption for the building of molecular evolutionary theory: individuals in the population with the same genotype have the same fitness effect. Since this view has been constantly challenged by experimental evidence, it is desirable to examine to what extent violation of this view could affect our understanding of molecular evolution. To this end, the author formulated a new theory of molecular evolution under a random model of penetrance: for any individual with the same mutational genotype, the coefficient of selection is a random variable. It follows that, in addition to the conventional <i>N</i> <sub>e</sub>-genetic drift (<i>N</i> <sub>e</sub> is the effective population size), the variance of penetrance among individuals (<i>ε</i> <sup>2</sup>) represents a new type of genetic drift, coined by the <i>ε</i> <sup>2</sup>-genetic drift. It has been demonstrated that these two genetic drifts together provided new insights on the nearly neutral evolution: the evolutionary rate is inversely related to the log-of-<i>N</i> <sub>e</sub> when the <i>ε</i> <sup>2</sup>-genetic drift is nontrivial. This log-of-<i>N</i> <sub>e</sub> feature of <i>ε</i> <sup>2</sup>-genetic drift did explain well why the <i>d</i> <sub>N</sub> <i>/d</i> <sub>S</sub> ratio (the nonsynonymous rate to the synonymous rate) in humans is only as twofold as that in mice, while the effective population size (<i>N</i> <sub>e</sub>) of mice is about two-magnitude larger than that of humans. It was estimated that, for the first time, the variance of random penetrance in mammalian genes was approximately <i>ε</i> <sup>2 </sup>≈ 5.89 × 10<sup>-3</sup>.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"1 3","pages":"105-112"},"PeriodicalIF":0.0,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s43657-021-00013-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9201565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Genetic Architecture of Childhood Kidney and Urological Diseases in China. 中国儿童肾脏和泌尿系统疾病的遗传结构。
Phenomics (Cham, Switzerland) Pub Date : 2021-06-01 DOI: 10.1007/s43657-021-00014-1
Ye Fang, Hua Shi, Tianchao Xiang, Jiaojiao Liu, Jialu Liu, Xiaoshan Tang, Xiaoyan Fang, Jing Chen, Yihui Zhai, Qian Shen, Guomin Li, Li Sun, Yunli Bi, Xiang Wang, Yanyan Qian, Bingbing Wu, Huijun Wang, Wenhao Zhou, Duan Ma, Jianhua Mao, Xiaoyun Jiang, Shuzhen Sun, Ying Shen, Xiaorong Liu, Aihua Zhang, Xiaowen Wang, Wenyan Huang, Qiu Li, Mo Wang, Xiaojie Gao, Yubin Wu, Fang Deng, Ruifeng Zhang, Cuihua Liu, Li Yu, Jieqiu Zhuang, Qing Sun, Xiqiang Dang, Haitao Bai, Ying Zhu, Siguang Lu, Bili Zhang, Xiaoshan Shao, Xuemei Liu, Mei Han, Lijun Zhao, Yuling Liu, Jian Gao, Ying Bao, Dongfeng Zhang, Qingshan Ma, Liping Zhao, Zhengkun Xia, Biao Lu, Yulong Wang, Mengzhun Zhao, Jianjiang Zhang, Shan Jian, Guohua He, Huifeng Zhang, Bo Zhao, Xiaohua Li, Feiyan Wang, Yufeng Li, Hongtao Zhu, Xinhui Luo, Jinghai Li, Jia Rao, Hong Xu
{"title":"Genetic Architecture of Childhood Kidney and Urological Diseases in China.","authors":"Ye Fang,&nbsp;Hua Shi,&nbsp;Tianchao Xiang,&nbsp;Jiaojiao Liu,&nbsp;Jialu Liu,&nbsp;Xiaoshan Tang,&nbsp;Xiaoyan Fang,&nbsp;Jing Chen,&nbsp;Yihui Zhai,&nbsp;Qian Shen,&nbsp;Guomin Li,&nbsp;Li Sun,&nbsp;Yunli Bi,&nbsp;Xiang Wang,&nbsp;Yanyan Qian,&nbsp;Bingbing Wu,&nbsp;Huijun Wang,&nbsp;Wenhao Zhou,&nbsp;Duan Ma,&nbsp;Jianhua Mao,&nbsp;Xiaoyun Jiang,&nbsp;Shuzhen Sun,&nbsp;Ying Shen,&nbsp;Xiaorong Liu,&nbsp;Aihua Zhang,&nbsp;Xiaowen Wang,&nbsp;Wenyan Huang,&nbsp;Qiu Li,&nbsp;Mo Wang,&nbsp;Xiaojie Gao,&nbsp;Yubin Wu,&nbsp;Fang Deng,&nbsp;Ruifeng Zhang,&nbsp;Cuihua Liu,&nbsp;Li Yu,&nbsp;Jieqiu Zhuang,&nbsp;Qing Sun,&nbsp;Xiqiang Dang,&nbsp;Haitao Bai,&nbsp;Ying Zhu,&nbsp;Siguang Lu,&nbsp;Bili Zhang,&nbsp;Xiaoshan Shao,&nbsp;Xuemei Liu,&nbsp;Mei Han,&nbsp;Lijun Zhao,&nbsp;Yuling Liu,&nbsp;Jian Gao,&nbsp;Ying Bao,&nbsp;Dongfeng Zhang,&nbsp;Qingshan Ma,&nbsp;Liping Zhao,&nbsp;Zhengkun Xia,&nbsp;Biao Lu,&nbsp;Yulong Wang,&nbsp;Mengzhun Zhao,&nbsp;Jianjiang Zhang,&nbsp;Shan Jian,&nbsp;Guohua He,&nbsp;Huifeng Zhang,&nbsp;Bo Zhao,&nbsp;Xiaohua Li,&nbsp;Feiyan Wang,&nbsp;Yufeng Li,&nbsp;Hongtao Zhu,&nbsp;Xinhui Luo,&nbsp;Jinghai Li,&nbsp;Jia Rao,&nbsp;Hong Xu","doi":"10.1007/s43657-021-00014-1","DOIUrl":"https://doi.org/10.1007/s43657-021-00014-1","url":null,"abstract":"<p><p>Kidney disease is manifested in a wide variety of phenotypes, many of which have an important hereditary component. To delineate the genotypic and phenotypic spectrum of pediatric nephropathy, a multicenter registration system is being implemented based on the Chinese Children Genetic Kidney Disease Database (CCGKDD). In this study, all the patients with kidney and urological diseases were recruited from 2014 to 2020. Genetic analysis was conducted using exome sequencing for families with multiple affected individuals with nephropathy or clinical suspicion of a genetic kidney disease owing to early-onset or extrarenal features. The genetic diagnosis was confirmed in 883 of 2256 (39.1%) patients from 23 provinces in China. Phenotypic profiles showed that the primary diagnosis included steroid-resistant nephrotic syndrome (SRNS, 23.5%), glomerulonephritis (GN, 32.2%), congenital anomalies of the kidney and urinary tract (CAKUT, 21.2%), cystic renal disease (3.9%), renal calcinosis/stone (3.6%), tubulopathy (9.7%), and chronic kidney disease of unknown etiology (CKDu, 5.8%). The pathogenic variants of 105 monogenetic disorders were identified. Ten distinct genomic disorders were identified as pathogenic copy number variants (CNVs) in 11 patients. The diagnostic yield differed by subgroups, and was highest in those with cystic renal disease (66.3%), followed by tubulopathy (58.4%), GN (57.7%), CKDu (43.5%), SRNS (29.2%), renal calcinosis /stone (29.3%) and CAKUT (8.6%). Reverse phenotyping permitted correct identification in 40 cases with clinical reassessment and unexpected genetic conditions. We present the results of the largest cohort of children with kidney disease in China where diagnostic exome sequencing was performed. Our data demonstrate the utility of family-based exome sequencing, and indicate that the combined analysis of genotype and phenotype based on the national patient registry is pivotal to the genetic diagnosis of kidney disease.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-021-00014-1.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"1 3","pages":"91-104"},"PeriodicalIF":0.0,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s43657-021-00014-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9500439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Comparison of Metabolic Profiling of Arabidopsis Inflorescences Between Landsberg erecta and Columbia, and Meiosis-Defective Mutants by 1H-NMR Spectroscopy. 拟南芥与哥伦比亚和减数分裂缺陷突变体花序代谢谱的1H-NMR比较
Phenomics (Cham, Switzerland) Pub Date : 2021-04-01 DOI: 10.1007/s43657-021-00012-3
Xiang Li, Hongkuan Wang, Ying Wang, Limin Zhang, Yingxiang Wang
{"title":"Comparison of Metabolic Profiling of <i>Arabidopsis</i> Inflorescences Between Landsberg <i>erecta</i> and Columbia, and Meiosis-Defective Mutants by <sup>1</sup>H-NMR Spectroscopy.","authors":"Xiang Li,&nbsp;Hongkuan Wang,&nbsp;Ying Wang,&nbsp;Limin Zhang,&nbsp;Yingxiang Wang","doi":"10.1007/s43657-021-00012-3","DOIUrl":"https://doi.org/10.1007/s43657-021-00012-3","url":null,"abstract":"<p><p>With the rapid development of omics technologies during the last several decades, genomics, transcriptomics, and proteomics have been extensively used to characterize gene or protein functions in many organisms at the cell or tissue level. However, metabolomics has not been conducted in reproductive organs, with a focus on meiosis in plants. In this study, we adopted a nuclear magnetic resonance (NMR)-based metabolomics approach to reveal the metabolic profile of inflorescences from two <i>Arabidopsis</i> accessions, Columbia (Col) and Landsberg <i>erecta</i> (L<i>er</i>), and several sterile mutants caused by meiosis defects. We identified 68 dominant metabolites in the samples. Col and L<i>er</i> displayed distinct metabolite profiles. Interestingly, mutants with similar meiotic defects, such as <i>Atrad51-3</i>, <i>Atrfc1-2,</i> and <i>Atpol2a-2,</i> exhibited similar alterations in metabolites, including upregulation of energy metabolites and promotion of compounds related to maintenance of genomic stability, cytoplasmic homeostasis, and membrane integrity. The collective data reveal distinct changes in metabolites in <i>Arabidopsis</i> inflorescences between the Col and L<i>er</i> wild type accessions. NMR-based metabolomics could be an effective tool for molecular phenotyping in studies of aspects of plant reproductive development such as meiosis.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-021-00012-3.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"1 2","pages":"73-89"},"PeriodicalIF":0.0,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s43657-021-00012-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9201567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
High-Throughput Phenotyping: A Platform to Accelerate Crop Improvement. 高通量表型:一个加速作物改良的平台。
Phenomics (Cham, Switzerland) Pub Date : 2021-04-01 DOI: 10.1007/s43657-020-00007-6
Sumit Jangra, Vrantika Chaudhary, Ram C Yadav, Neelam R Yadav
{"title":"High-Throughput Phenotyping: A Platform to Accelerate Crop Improvement.","authors":"Sumit Jangra,&nbsp;Vrantika Chaudhary,&nbsp;Ram C Yadav,&nbsp;Neelam R Yadav","doi":"10.1007/s43657-020-00007-6","DOIUrl":"https://doi.org/10.1007/s43657-020-00007-6","url":null,"abstract":"<p><p>Development of high-throughput phenotyping technologies has progressed considerably in the last 10 years. These technologies provide precise measurements of desired traits among thousands of field-grown plants under diversified environments; this is a critical step towards selection of better performing lines as to yield, disease resistance, and stress tolerance to accelerate crop improvement programs. High-throughput phenotyping techniques and platforms help unraveling the genetic basis of complex traits associated with plant growth and development and targeted traits. This review focuses on the advancements in technologies involved in high-throughput, field-based, aerial, and unmanned platforms. Development of user-friendly data management tools and softwares to better understand phenotyping will increase the use of field-based high-throughput techniques, which have potential to revolutionize breeding strategies and meet the future needs of stakeholders.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"1 2","pages":"31-53"},"PeriodicalIF":0.0,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s43657-020-00007-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9141114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 16
Effect of Light on Cognitive Function During a Stroop Task Using Functional Near-Infrared Spectroscopy. 利用功能近红外光谱研究Stroop任务中光对认知功能的影响。
Phenomics (Cham, Switzerland) Pub Date : 2021-04-01 DOI: 10.1007/s43657-021-00010-5
Yafei Yuan, Guanghao Li, Haoran Ren, Wei Chen
{"title":"Effect of Light on Cognitive Function During a Stroop Task Using Functional Near-Infrared Spectroscopy.","authors":"Yafei Yuan,&nbsp;Guanghao Li,&nbsp;Haoran Ren,&nbsp;Wei Chen","doi":"10.1007/s43657-021-00010-5","DOIUrl":"https://doi.org/10.1007/s43657-021-00010-5","url":null,"abstract":"<p><p>Light modulates human brain function through its effect on circadian rhythms, which are related to several human behavioral and physiological processes. Functional near-infrared spectroscopy (fNIRS) is a noninvasive optical neuroimaging technique used for recording brain activation during task performance. This study aimed to investigate the effects of light on cognitive function, particularly in the prefrontal cortex using fNIRS. The effect of light on cognitive modulation was analyzed using the Stroop task, which was performed on 30 participants under three different light conditions (color temperature 4500 K, 2500 K, and none). The behavioral results indicated that light conditions can easily and effectively modulate the performance of tasks based on the feedback, including the response time and accuracy. fNIRS showed hemodynamic changes in the bilateral dorsolateral prefrontal cortices, and the activated brain regions varied under different light conditions. Moreover, light may be regarded as a safe, effective, inexpensive, and accessible tool for modulating human cognitive function.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"1 2","pages":"54-61"},"PeriodicalIF":0.0,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s43657-021-00010-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9516056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Welcome to the Phenomics Journal. 欢迎来到《表型组学杂志》。
Phenomics (Cham, Switzerland) Pub Date : 2021-02-01 DOI: 10.1007/s43657-020-00009-4
Li Jin
{"title":"Welcome to the <i>Phenomics</i> Journal.","authors":"Li Jin","doi":"10.1007/s43657-020-00009-4","DOIUrl":"https://doi.org/10.1007/s43657-020-00009-4","url":null,"abstract":"","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"1 1","pages":"1-2"},"PeriodicalIF":0.0,"publicationDate":"2021-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s43657-020-00009-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9201563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 8
Using Composite Phenotypes to Reveal Hidden Physiological Heterogeneity in High-Altitude Acclimatization in a Chinese Han Longitudinal Cohort. 利用复合表型揭示中国汉族纵向队列高海拔适应中隐藏的生理异质性。
Phenomics (Cham, Switzerland) Pub Date : 2021-02-01 DOI: 10.1007/s43657-020-00005-8
Yi Li, Yanyun Ma, Kun Wang, Menghan Zhang, Yi Wang, Xiaoyu Liu, Meng Hao, Xianhong Yin, Meng Liang, Hui Zhang, Xiaofeng Wang, Xingdong Chen, Yao Zhang, Wenyuan Duan, Longli Kang, Bin Qiao, Jiucun Wang, Li Jin
{"title":"Using Composite Phenotypes to Reveal Hidden Physiological Heterogeneity in High-Altitude Acclimatization in a Chinese Han Longitudinal Cohort.","authors":"Yi Li,&nbsp;Yanyun Ma,&nbsp;Kun Wang,&nbsp;Menghan Zhang,&nbsp;Yi Wang,&nbsp;Xiaoyu Liu,&nbsp;Meng Hao,&nbsp;Xianhong Yin,&nbsp;Meng Liang,&nbsp;Hui Zhang,&nbsp;Xiaofeng Wang,&nbsp;Xingdong Chen,&nbsp;Yao Zhang,&nbsp;Wenyuan Duan,&nbsp;Longli Kang,&nbsp;Bin Qiao,&nbsp;Jiucun Wang,&nbsp;Li Jin","doi":"10.1007/s43657-020-00005-8","DOIUrl":"https://doi.org/10.1007/s43657-020-00005-8","url":null,"abstract":"<p><p>Altitude acclimatization is a human physiological process of adjusting to the decreased oxygen availability. Since several physiological processes are involved and their correlations are complicated, the analyses of single traits are insufficient in revealing the complex mechanism of high-altitude acclimatization. In this study, we examined these physiological responses as the composite phenotypes that are represented by a linear combination of physiological traits. We developed a strategy that combines both spectral clustering and partial least squares path modeling (PLSPM) to define composite phenotypes based on a cohort study of 883 Chinese Han males. In addition, we captured 14 composite phenotypes from 28 physiological traits of high-altitude acclimatization. Using these composite phenotypes, we applied k-means clustering to reveal hidden population physiological heterogeneity in high-altitude acclimatization. Furthermore, we employed multivariate linear regression to systematically model (Models 1 and 2) oxygen saturation (SpO<sub>2</sub>) changes in high-altitude acclimatization and evaluated model fitness performance. Composite phenotypes based on Model 2 fit better than single trait-based Model 1 in all measurement indices. This new strategy of using composite phenotypes may be potentially employed as a general strategy for complex traits research such as genetic loci discovery and analyses of phenomics.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"1 1","pages":"3-14"},"PeriodicalIF":0.0,"publicationDate":"2021-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s43657-020-00005-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9141115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
The Ultrafast and Accurate Mapping Algorithm FANSe3: Mapping a Human Whole-Genome Sequencing Dataset Within 30 Minutes. 超快速和精确的绘图算法FANSe3:在30分钟内绘制人类全基因组测序数据集。
Phenomics (Cham, Switzerland) Pub Date : 2021-02-01 DOI: 10.1007/s43657-020-00008-5
Gong Zhang, Yongjian Zhang, Jingjie Jin
{"title":"The Ultrafast and Accurate Mapping Algorithm FANSe3: Mapping a Human Whole-Genome Sequencing Dataset Within 30 Minutes.","authors":"Gong Zhang,&nbsp;Yongjian Zhang,&nbsp;Jingjie Jin","doi":"10.1007/s43657-020-00008-5","DOIUrl":"https://doi.org/10.1007/s43657-020-00008-5","url":null,"abstract":"<p><p>Aligning billions of reads generated by the next-generation sequencing (NGS) to reference sequences, termed \"mapping\", is the time-consuming and computationally-intensive process in most NGS applications. A Fast, accurate and robust mapping algorithm is highly needed. Therefore, we developed the FANSe3 mapping algorithm, which can map a 30 × human whole-genome sequencing (WGS) dataset within 30 min, a 50 × human whole exome sequencing (WES) dataset within 30 s, and a typical mRNA-seq dataset within seconds in a single-server node without the need for any hardware acceleration feature. Like its predecessor FANSe2, the error rate of FANSe3 can be kept as low as 10<sup>-9</sup> in most cases, this is more robust than the Burrows-Wheeler transform-based algorithms. Error allowance hardly affected the identification of a driver somatic mutation in clinically relevant WGS data and provided robust gene expression profiles regardless of the parameter settings and sequencer used. The novel algorithm, designed for high-performance cloud-computing after infrastructures, will break the bottleneck of speed and accuracy in NGS data analysis and promote NGS applications in various fields. The FANSe3 algorithm can be downloaded from the website: http://www.chi-biotech.com/fanse3/.</p>","PeriodicalId":74435,"journal":{"name":"Phenomics (Cham, Switzerland)","volume":"1 1","pages":"22-30"},"PeriodicalIF":0.0,"publicationDate":"2021-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s43657-020-00008-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9145061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 12
In Situ Saturating Mutagenesis Screening Identifies a Functional Genomic Locus that Regulates Ucp1 Expression. 原位饱和诱变筛选鉴定了一个调节Ucp1表达的功能性基因组位点。
Phenomics (Cham, Switzerland) Pub Date : 2021-02-01 DOI: 10.1007/s43657-020-00006-7
Yan Qiu, Xiaojian Liu, Yingmin Sun, Shuang Li, Yuda Wei, Cheng Tian, Qiurong Ding
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引用次数: 3
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