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Genome-wide association studies: inherent limitations and future challenges

null

《医学前沿（英文）》 2012年 第6卷 第4期   页码 444-450 doi: 10.1007/s11684-012-0225-3

摘要：

Genome-wide association studies (GWAS) have achieved great success in identifying genetic variants related to complex human diseases such as cancer and have provided valuable insights into their genetic architecture. Recently, GWAS is quite the fashion in China. However, there are issues related to its nature. Enormous work needs to be done in the post-GWAS era. Deep sequencing followed by functional studies will be needed to elucidate the underpinning biological mechanisms and further translate GWAS findings into medical practice. Along with pharmacogenomics, the success of GWAS in identifying genetic risk factors and genetic differences in drug response has been gradually enabling personalized medicine. In this article, we used hepatocellular carcinoma (HCC) as an example to demonstrate some of the inherent limitations and summarized future challenges of GWAS.

关键词： genome-wide association studies (GWAS)     genetic variant     cancer     limitation     challenge    

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A novel variant in the gene in a large Chinese family with a unique phenotype of Clouston syndrome

《医学前沿（英文）》 2023年 第17卷 第2期   页码 330-338 doi: 10.1007/s11684-022-0933-2

摘要： Clouston syndrome (OMIM #129500), also known as hidrotic ectodermal dysplasia type 2, is a rare autosomal dominant skin disorder. To date, four mutations in the GJB6 gene, G11R, V37E, A88V, and D50N, have been confirmed to cause this condition. In previous studies, the focus has been mainly on gene sequencing, and there has been a lack of research on clinical manifestations and pathogenesis. To confirm the diagnosis of this pedigree at the molecular level and summarize and analyse the clinical phenotype of patients and to provide a basis for further study of the pathogenesis of the disease, we performed whole-exome and Sanger sequencing on a large Chinese Clouston syndrome pedigree. Detailed clinical examination included histopathology, hair microscopy, and scanning electron microscopy. We found a novel heterozygous missense variant (c.134G>C:p.G45A) for Clouston syndrome. We identified a new clinical phenotype involving all nail needling pain in all patients and found a special honeycomb hole structure in the patients’ hair under scanning electron microscopy. Our data reveal that a novel variant (c.134G>C:p.G45A) plays a likely pathogenic role in this pedigree and highlight that genetic testing is necessary for the diagnosis of Clouston syndrome.

关键词： Clouston syndrome     whole exome sequencing     GJB6 gene     novel variant     unique phenotype    

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Potential unreliability of ALK variant allele frequency in the efficacy prediction of targeted therapy

《医学前沿（英文）》 2023年 第17卷 第3期   页码 493-502 doi: 10.1007/s11684-022-0946-x

摘要： Anaplastic lymphoma kinase (ALK) is the most common fusion gene involved in non-small cell lung cancer (NSCLC), and remarkable response has been achieved with the use of ALK tyrosine kinase inhibitors (ALK-TKIs). However, the clinical efficacy is highly variable. Pre-existing intratumoral heterogeneity (ITH) has been proven to contribute to the poor treatment response and the resistance to targeted therapies. In this work, we investigated whether the variant allele frequencies (VAFs) of ALK fusions can help assess ITH and predict targeted therapy efficacy. Through the application of next-generation sequencing (NGS), 7.2% (326/4548) of patients were detected to be ALK positive. On the basis of the adjusted VAF (adjVAF, VAF normalization for tumor purity) of four different threshold values (adjVAF < 50%, 40%, 30%, or 20%), the association of ALK subclonality with crizotinib efficacy was assessed. Nonetheless, no statistical association was observed between median progression-free survival (PFS) and ALK subclonality assessed by adjVAF, and a poor correlation of adjVAF with PFS was found among the 85 patients who received first-line crizotinib. Results suggest that the ALK VAF determined by hybrid capture-based NGS is probably unreliable for ITH assessment and targeted therapy efficacy prediction in NSCLC.

关键词： ALK fusion     next-generation sequencing     fluorescence in situ hybridization     immunohistochemistry     variant allele frequency     intratumoral heterogeneity     targeted therapy    

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Effectiveness of inactivated COVID-19 vaccine against the severity of Omicron variant

《医学前沿（英文）》 2023年 第17卷 第3期   页码 576-580 doi: 10.1007/s11684-023-0991-0

摘要： Effectiveness of inactivated COVID-19 vaccine against the severity of Omicron variant

关键词： variant    

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Novel variants in LAMA3 and COL7A1 and recurrent variant in KRT5 underlying epidermolysis bullosa in

《医学前沿（英文）》 2022年 第16卷 第5期   页码 808-814 doi: 10.1007/s11684-021-0878-x

摘要： Epidermolysis bullosa (EB) is a group of clinically and genetically heterogeneous diseases characterized by trauma-induced mucocutaneous fragility and blister formation. Here, we investigated five Chinese families with EB, and eight variants including a novel nonsense variant (c.47G>A, p.W16*) in LAMA3, a known recurrent variant (c.74C>T, p.P25L) in KRT5, 2 novel (c.2531T>A, p.V844E; c.6811_6814del, p.R2271fs) and 4 known (c.6187C>T, p.R2063W; c.7097G>A, p.G2366D; c.8569G>T, p.E2857*; c.3625_3635del, p.S1209fs) variants in COL7A1 were detected. Notably, this study identified a nonsense variant in LAMA3 that causes EB within the Chinese population and revealed that this variant resulted in a reduction in LAMA3 mRNA and protein expression levels by nonsense-mediated mRNA decay. Our study expands the mutation spectra of Chinese patients with EB.

关键词： epidermolysis bullosa     LAMA3     COL7A1     KRT5     Chinese families    

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Machine learning modeling identifies hypertrophic cardiomyopathy subtypes with genetic signature

《医学前沿（英文）》 2023年 第17卷 第4期   页码 768-780 doi: 10.1007/s11684-023-0982-1

摘要： Previous studies have revealed that patients with hypertrophic cardiomyopathy (HCM) exhibit differences in symptom severity and prognosis, indicating potential HCM subtypes among these patients. Here, 793 patients with HCM were recruited at an average follow-up of 32.78 ± 27.58 months to identify potential HCM subtypes by performing consensus clustering on the basis of their echocardiography features. Furthermore, we proposed a systematic method for illustrating the relationship between the phenotype and genotype of each HCM subtype by using machine learning modeling and interactome network detection techniques based on whole-exome sequencing data. Another independent cohort that consisted of 414 patients with HCM was recruited to replicate the findings. Consequently, two subtypes characterized by different clinical outcomes were identified in HCM. Patients with subtype 2 presented asymmetric septal hypertrophy associated with a stable course, while those with subtype 1 displayed left ventricular systolic dysfunction and aggressive progression. Machine learning modeling based on personal whole-exome data identified 46 genes with mutation burden that could accurately predict subtype propensities. Furthermore, the patients in another cohort predicted as subtype 1 by the 46-gene model presented increased left ventricular end-diastolic diameter and reduced left ventricular ejection fraction. By employing echocardiography and genetic screening for the 46 genes, HCM can be classified into two subtypes with distinct clinical outcomes.

关键词： machine learning methods     hypertrophic cardiomyopathy     genetic risk    

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Antithrombin deficiency and decreased protein C activity in a young man with venous thromboembolism: a case report

null

《医学前沿（英文）》 2018年 第12卷 第3期   页码 319-323 doi: 10.1007/s11684-017-0553-4

摘要：

Antithrombin and protein C are two crucial members in the anticoagulant system and play important roles in hemostasis. Mutations in and lead to deficiency or dysfunction of the two proteins, which could result in venous thromboembolism (VTE). Here, we report a Chinese 22-year-old young man who developed recurrent and serious VTE in cerebral veins, visceral veins, and deep veins of the lower extremity. Laboratory tests and direct sequencing of and were conducted for the patient and his family members. Coagulation tests revealed that the patient presented type I antithrombin deficiency combined with decreased protein C activity resulting from a small insertion mutation c.848_849insGATGT in and a short deletion variant c.572_574delAGA in . This combination of the two mutations was absent in 400 healthy subjects each from southern and northern China. Then, we summarized all the mutations of the and gene reported in the Chinese Han population. This study demonstrates that the combination of antithrombin deficiency and decreased protein C activity can result in severe VTE and that the coexistence of different genetic factors may increase the risk of VTE.

关键词： antithrombin deficiency     protein C activity     mutation     variant     venous thromboembolism     anticoagulants    

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Exergy and exergoeconomic analyses for integration of aromatics separation with aromatics upgrading

《化学科学与工程前沿（英文）》 2023年 第17卷 第2期   页码 183-193 doi: 10.1007/s11705-022-2192-9

摘要： Methanol to aromatics produces multiple products, resulting in a limited selectivity of xylene. Aromatics upgrading is an effective way to produce more valuable xylene product, and different feed ratios generate discrepant product distributions. This work integrates the aromatics separation with toluene disproportionation, transalkylation of toluene and trimethylbenzene, and isomerization of xylene and trimethylbenzene. Exergy and exergoeconomic analyses are conducted to give insights in the splitting ratios of benzene, toluene and heavy aromatics for aromatics upgrading. First, a detailed simulation model is developed in Aspen HYSYS. Then, 300 splitting ratio sets of benzene and toluene for conversion are studied to investigate the process performances. The results indicate that there are different preferences for the splitting ratios of benzene and toluene in terms of exergy and exergoeconomic performances. The process generates lower total exergy destruction when the splitting ratio of toluene varies between 0.07 and 0.18, and that of benzene fluctuates between 0.55 and 0.6. Nevertheless, the process presents lower total product unit cost with the splitting ratio of toluene less than 0.18 and that of benzene fluctuating between 0.44 and 0.89. Besides, it is found that distillation is the biggest contributor to the total exergy destruction, accounting for 94.97%.

关键词： aromatics separation and upgrading     variant splitting ratios     total exergy destruction     total product unit cost    

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Research and development of a novel subunit vaccine for the currently circulating pseudorabies virus variant

Yuzhou WANG,Tongyan WANG,He YAN,Fanli YANG,Linghua GUO,Qingyuan YANG,Xule HU,Feifei TAN,Yan XIAO,Xiangdong LI,Kegong TIAN

《农业科学与工程前沿（英文）》 2015年 第2卷 第3期   页码 216-222 doi: 10.15302/J-FASE-2015072

摘要： Pseudorabies (PR) is a devastating viral disease which leads to fatal encephalitis and respiratory disorders in pigs. Commercial gE-deleted live pseudorabies virus (PRV) vaccine has been widely used to control this disease in China. However, the new-emerging variants of PRV compromises the protection provided by current vaccines and lead to the outbreak of PR in vaccinated pig herds. Several killed and live vaccine candidates based on current PRV variants have been reported to be effective to control the disease. A subunit vaccine based on gB protein, one major PRV glycoprotein which elicits strong humoral and cellular immune responses, however, was never evaluated for protection against the current circulating PRV variants. In this study, full-length PRV gB protein was successfully expressed in baculovirus/insect cells in the soluble format and was tested on 3-week-old piglets as a subunit vaccine. Compared with unvaccinated pigs, the gB-vaccinated pigs developed specific antibody-mediated responses and were protected from the virulent PRV HN1201 challenge. All vaccinated pigs survived without showing any PRV-specific respiratory and neurological signs, but all unvaccinated pigs died within 7 days after HN1201 challenge. Hence, this novel gB-based vaccine could be applied as an effective subunit vaccine to control PRV variant in China.

关键词： pseudorabies virus     glycoprotein B protein     subunit vaccine    

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Interplay between diet and genetic susceptibility in obesity and related traits

Tiange Wang, Min Xu, Yufang Bi, Guang Ning

《医学前沿（英文）》 2018年 第12卷 第6期   页码 601-607 doi: 10.1007/s11684-018-0648-6

摘要：

The incidence of obesity has been rapidly increasing, and this condition has become a major public health threat. A substantial shift in environmental factors and lifestyle, such as unhealthy diet, is among the major driving forces of the global obesity pandemic. Longitudinal studies and randomized intervention trials have shown that genetic susceptibility to obesity may interact with dietary factors in relation to the body mass index and risk of obesity. This review summarized data from recent longitudinal studies and intervention studies on variations and diets and discussed the challenges and future prospects related to this area and public health implications.

关键词： diet     genetic susceptibility     obesity     interaction    

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Optimal design of steel skeletal structures using the enhanced genetic algorithm methodology

Tugrul TALASLIOGLU

《结构与土木工程前沿（英文）》 2019年 第13卷 第4期   页码 863-889 doi: 10.1007/s11709-019-0523-9

摘要： This study concerns with the design optimization of steel skeletal structures thereby utilizing both a real-life specification provisions and ready steel profiles named hot-rolled I sections. For this purpose, the enhanced genetic algorithm methodology named EGAwMP is utilized as an optimization tool. The evolutionary search mechanism of EGAwMP is constituted on the basis of generational genetic algorithm (GGA). The exploration capacity of EGAwMP is improved in a way of dividing an entire population into sub-populations and using of a radial basis neural network for dynamically adjustment of EGAwMP’s genetic operator parameters. In order to improve the exploitation capability of EGAwMP, the proposed neural network implementation is also utilized for prediction of more accurate design variables associating with a new design strategy, design codes of which are based on the provisions of LRFD_AISC V3 specification. EGAwMP is applied to determine the real-life ready steel profiles for the optimal design of skeletal structures with 105, 200, 444, and 942 members. EGAwMP accomplishes to increase the quality degrees of optimum designations Furthermore, the importance of using the real-life steel profiles and design codes is also demonstrated. Consequently, EGAwMP is suggested as a design optimization tool for the real-life steel skeletal structures.

关键词： design optimization     genetic algorithm     multiple populations     neural network    

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Research progress on genetic improvement of

Chuanping YANG

《农业科学与工程前沿（英文）》 2017年 第4卷 第4期   页码 391-401 doi: 10.15302/J-FASE-2017183

摘要： Suk. is one of the most widely distributed species of , the fourth most valuable timber species in north-eastern China and also a common tree species for landscaping. Over the past 30 years, effective progress has been made in genetic improvement and molecular breeding of . There has been extensive research on breeding techniques, including the collection and conservation of germplasm resources, provenance trials, intensive breeding techniques, crossbreeding and asexual propagation techniques, ploidy breeding and mutation breeding technology, genome sequencing, gene cloning, transgenic and molecular mechanisms of wood formation. A germplasm resource collection has been established by collecting different provenances, and full-sib and half-sib families. In addition, the geographic variation patterns of provenances have been revealed, and the provenance division and superior provenance selections made. flowering and seeding have been improved through intensive breeding techniques. Interspecific hybridization, intraspecific hybridization and parallel crosses were made using fine parents, and intensive seed orchards have been established. Systems of asexual propagation, including cuttings, grafting and tissue culture have been established. A tetraploid was successfully constructed and a triploid seed orchard established. The growth, wood property and resistance genes of have been cloned. An efficient transgenic system mediated by was established, and genes encoding insect resistance, drought resistance and salt tolerance, lignin synthesis, flowering, hormone transport and balance obtained. molecular markers were developed and the high density genetic map constructed. All this research has provided a model and data for the foundation of forest genetic improvement and applied research.

关键词： Betula platyphylla     genetic improvement     molecular breeding     seed orchard    

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Genomics and genetic breeding in aquatic animals: progress and prospects

Wenteng XU, Songlin CHEN

《农业科学与工程前沿（英文）》 2017年 第4卷 第3期   页码 305-318 doi: 10.15302/J-FASE-2017154

摘要： Genomics focuses on dissection of genome structure and function to provide a molecular basis for understanding the genetic background. In a pivotal step, the expense of whole genome sequencing has been largely eliminated by the rapid updating of sequencing technology, leading to increasing numbers of decoded genomes of aquatic organisms, driving the aquaculture industry into the genomic era. Multiple aquatic areas have been influenced by these findings, such as accelerated generation shift in the seed industry and the process of breeding improved lines. In this article, we have summarized the latest domestic and international progress of aquatic animals in nine aspects, including WGS and fine mapping, construction of high density genetic/physical maps, trait-related marker/genes screening, as well as sex control, genome editing, and other molecular breeding technologies. Finally, the existing problems in this field have been discussed and five future counter measures have been proposed accordingly.

关键词： aquaculture     genomics     genetic breeding     progress    

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Search-and-replace editing of genetic information

Yao LIU, Xingxu HUANG, Xiaolong WANG

《农业科学与工程前沿（英文）》 2020年 第7卷 第2期   页码 231-232 doi: 10.15302/J-FASE-2020322

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Age-related trends in genetic parameters for wood properties in

Chao SUN, Meng LAI, Shougong ZHANG, Xiaomei SUN

《农业科学与工程前沿（英文）》 2017年 第4卷 第4期   页码 482-492 doi: 10.15302/J-FASE-2017184

摘要： Wood properties are important traits that determine quality of structural wood. With the aim of performing efficient early selection for wood properties, we investigated genetic variation in 20 clones aged from 4 to 15 years for four quality traits: wood density, wall thickness to lumen area, microfibrillar angle (MFA) and modulus of elasticity (MOE). We observed that age-related trends in overall means varied for different traits: MFA decreased with the age, while the others generally increased with the age. Phenotypic variance always showed significant differences from the age of 8 years onward, with CVG ranging from 4% to 25%. Also, clonal repeatability increased steadily until 9 years old and then kept medium or higher intensity (0.4–0.8). After the age of 6, genetic correlations were generally higher than phenotypic correlations. Estimates of early selection efficiency suggested that the optimal selection age for wood density was at age 5–6 years, while it was 9–10 years for the other traits. In combination with previous results, we proposed a comprehensive early selection strategy for larch clonal breeding that involved selection based on nursery rooting ability, phenology, growth traits, and wood properties.

关键词： early selection     genetic variation     wood properties     SilviScan     Larix kaempferi    

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标题 作者 时间 类型 操作

Genome-wide association studies: inherent limitations and future challenges

null

期刊论文

A novel variant in the gene in a large Chinese family with a unique phenotype of Clouston syndrome

期刊论文

Potential unreliability of ALK variant allele frequency in the efficacy prediction of targeted therapy

期刊论文

Effectiveness of inactivated COVID-19 vaccine against the severity of Omicron variant

期刊论文

Novel variants in LAMA3 and COL7A1 and recurrent variant in KRT5 underlying epidermolysis bullosa in

期刊论文

Machine learning modeling identifies hypertrophic cardiomyopathy subtypes with genetic signature

期刊论文

Antithrombin deficiency and decreased protein C activity in a young man with venous thromboembolism: a case report

null

期刊论文

Exergy and exergoeconomic analyses for integration of aromatics separation with aromatics upgrading

期刊论文

Research and development of a novel subunit vaccine for the currently circulating pseudorabies virus variant

Yuzhou WANG,Tongyan WANG,He YAN,Fanli YANG,Linghua GUO,Qingyuan YANG,Xule HU,Feifei TAN,Yan XIAO,Xiangdong LI,Kegong TIAN

期刊论文

Interplay between diet and genetic susceptibility in obesity and related traits

Tiange Wang, Min Xu, Yufang Bi, Guang Ning

期刊论文

Optimal design of steel skeletal structures using the enhanced genetic algorithm methodology

Tugrul TALASLIOGLU

期刊论文

Research progress on genetic improvement of

Chuanping YANG

期刊论文

Genomics and genetic breeding in aquatic animals: progress and prospects

Wenteng XU, Songlin CHEN

期刊论文

Search-and-replace editing of genetic information

Yao LIU, Xingxu HUANG, Xiaolong WANG

期刊论文

Age-related trends in genetic parameters for wood properties in

Chao SUN, Meng LAI, Shougong ZHANG, Xiaomei SUN

期刊论文