Human Genomics最新文献

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Development of oxidative stress- and ferroptosis-related prognostic signature in gastric cancer and identification of CDH19 as a novel biomarker. 开发胃癌氧化应激和铁蛋白沉积相关预后特征并确定 CDH19 为新型生物标记物
IF 3.8 3区 医学
Human Genomics Pub Date : 2024-11-05 DOI: 10.1186/s40246-024-00682-w
Shibo Wang, Siyi Zhang, Xiaoxuan Li, Chuanyu Leng, Xiangxue Li, Jing Lv, Shufen Zhao, Wensheng Qiu, Jing Guo
{"title":"Development of oxidative stress- and ferroptosis-related prognostic signature in gastric cancer and identification of CDH19 as a novel biomarker.","authors":"Shibo Wang, Siyi Zhang, Xiaoxuan Li, Chuanyu Leng, Xiangxue Li, Jing Lv, Shufen Zhao, Wensheng Qiu, Jing Guo","doi":"10.1186/s40246-024-00682-w","DOIUrl":"10.1186/s40246-024-00682-w","url":null,"abstract":"<p><strong>Background: </strong>Ferroptosis is a unique mode of cell death that is iron-dependent and associated with oxidative stress and lipid peroxidation. Oxidative stress and ferroptosis are essential mechanisms leading to metabolic abnormalities in cells and have been popular areas in cancer research.</p><p><strong>Methods: </strong>Initially, 76 oxidative stress and ferroptosis-related genes (OFRGs) were acquired by intersecting the gene sets from oxidative stress and ferroptosis. Afterwards, optimal OFRGs were screened using PPI networks, and individuals were separated into two OFRG subtypes (K = 2). Subsequently, we successfully constructed and verified a prognostic signature comprising SLC7A2, Cadherin 19 (CDH19), and CCN1. To further uncover potential biomarkers of gastric cancer (GC), we examined the expression level of CDH19, investigated the effects of knocking down CDH19 on the biological behavior of GC cells, and explored whether CDH19 is involved in ferroptosis and oxidative stress processes.</p><p><strong>Results: </strong>According to the findings, individuals in the low-risk scoring group have less infiltration of immune suppressive cells, fewer occurrences of immune escape and dysfunction, greater efficacy in chemotherapy and immunotherapy, and better survival outcomes. The qRT-PCR assay indicated that CDH19 expression was significantly higher in GC cells. Through experiments, we demonstrated that knocking down CDH19 can affect the transcription levels of ACSL4 and GPX4, increase intracellular iron ion concentration and accumulation of reactive oxygen species (ROS), and inhibit the proliferation and migration of GC cells.</p><p><strong>Conclusion: </strong>We developed an OFRG-related signature to predict the prognosis and treatment responsiveness of individuals with GC and identified CDH19 as a possible therapeutic target for GC.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11536560/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Best practices for germline variant and DNA methylation analysis of second- and third-generation sequencing data. 对第二代和第三代测序数据进行种系变异和 DNA 甲基化分析的最佳实践。
IF 3.8 3区 医学
Human Genomics Pub Date : 2024-11-05 DOI: 10.1186/s40246-024-00684-8
Ferdinando Bonfiglio, Andrea Legati, Vito Alessandro Lasorsa, Flavia Palombo, Giulia De Riso, Federica Isidori, Silvia Russo, Simone Furini, Giuseppe Merla, Fabio Coppedè, Marco Tartaglia, Alessandro Bruselles, Tommaso Pippucci, Andrea Ciolfi, Michele Pinelli, Mario Capasso
{"title":"Best practices for germline variant and DNA methylation analysis of second- and third-generation sequencing data.","authors":"Ferdinando Bonfiglio, Andrea Legati, Vito Alessandro Lasorsa, Flavia Palombo, Giulia De Riso, Federica Isidori, Silvia Russo, Simone Furini, Giuseppe Merla, Fabio Coppedè, Marco Tartaglia, Alessandro Bruselles, Tommaso Pippucci, Andrea Ciolfi, Michele Pinelli, Mario Capasso","doi":"10.1186/s40246-024-00684-8","DOIUrl":"10.1186/s40246-024-00684-8","url":null,"abstract":"<p><p>This comprehensive review provides insights and suggested strategies for the analysis of germline variants using second- and third-generation sequencing technologies (SGS and TGS). It addresses the critical stages of data processing, starting from alignment and preprocessing to quality control, variant calling, and the removal of artifacts. The document emphasized the importance of meticulous data handling, highlighting advanced methodologies for annotating variants and identifying structural variations and methylated DNA sites. Special attention is given to the inspection of problematic variants, a step that is crucial for ensuring the accuracy of the analysis, particularly in clinical settings where genetic diagnostics can inform patient care. Additionally, the document covers the use of various bioinformatics tools and software that enhance the precision and reliability of these analyses. It outlines best practices for the annotation of variants, including considerations for problematic genetic alterations such as those in the human leukocyte antigen region, runs of homozygosity, and mitochondrial DNA alterations. The document also explores the complexities associated with identifying structural variants and copy number variations, underscoring the challenges posed by these large-scale genomic alterations. The objective is to offer a comprehensive framework for researchers and clinicians, ensuring that genetic analyses conducted with SGS and TGS are both accurate and reproducible. By following these best practices, the document aims to increase the diagnostic accuracy for hereditary diseases, facilitating early diagnosis, prevention, and personalized treatment strategies. This review serves as a valuable resource for both novices and experts in the field, providing insights into the latest advancements and methodologies in genetic analysis. It also aims to encourage the adoption of these practices in diverse research and clinical contexts, promoting consistency and reliability across studies.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11536923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Drosophila Toxicogenomics: genetic variation and sexual dimorphism in susceptibility to 4-Methylimidazole. 果蝇毒物基因组学:4-甲基咪唑易感性的遗传变异和性双态性。
IF 3.8 3区 医学
Human Genomics Pub Date : 2024-11-04 DOI: 10.1186/s40246-024-00689-3
Katelynne M Collins, Elisabeth Howansky, Sarah C Macon-Foley, Maria E Adonay, Vijay Shankar, Richard F Lyman, Nestor Octavio Nazario-Yepiz, Jordyn K Brooks, Rachel A Lyman, Trudy F C Mackay, Robert R H Anholt
{"title":"Drosophila Toxicogenomics: genetic variation and sexual dimorphism in susceptibility to 4-Methylimidazole.","authors":"Katelynne M Collins, Elisabeth Howansky, Sarah C Macon-Foley, Maria E Adonay, Vijay Shankar, Richard F Lyman, Nestor Octavio Nazario-Yepiz, Jordyn K Brooks, Rachel A Lyman, Trudy F C Mackay, Robert R H Anholt","doi":"10.1186/s40246-024-00689-3","DOIUrl":"10.1186/s40246-024-00689-3","url":null,"abstract":"<p><strong>Background: </strong>4-methylimidazole is a ubiquitous and potentially carcinogenic environmental toxicant. Genetic factors that contribute to variation in susceptibility to its toxic effects are challenging to assess in human populations. We used the Drosophila melanogaster Genetic Reference Panel (DGRP), a living library of natural genetic variation, to identify genes with human orthologs associated with variation in susceptibility to 4-methylimidazole.</p><p><strong>Results: </strong>We screened 204 DGRP lines for survival following 24-hour exposure to 4-methylimidazole. We found extensive genetic variation for survival, with a broad sense heritability of 0.82; as well as genetic variation in sexual dimorphism, with a cross-sex genetic correlation of 0.59. Genome-wide association analyses identified a total of 241 candidate molecular polymorphisms in or near 273 unique genes associated with survival. These polymorphisms had either sex-specific or sex-antagonistic effects, and most had putative regulatory effects. We generated interaction networks using these candidate genes as inputs and computationally recruited genes with known physical or genetic interactions. The network genes were significantly over-represented for gene ontology terms involving all aspects of development (including nervous system development) and cellular and organismal functions as well as canonical signaling pathways, and most had human orthologs.</p><p><strong>Conclusions: </strong>The genetic basis of variation in sensitivity to acute exposure to 4-methylimidazole in Drosophila is attributable to variation in genes and networks of genes known for their effects on multiple developmental and cellular processes, including possible neurotoxicity. Given evolutionary conservation of the underlying genes and pathways, these insights may be applicable to humans.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533318/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142576046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Novel FLNC variants in pediatric cardiomyopathy: an insight into disease mechanisms. 小儿心肌病中的新型 FLNC 变异:对疾病机理的深入了解。
IF 3.8 3区 医学
Human Genomics Pub Date : 2024-10-29 DOI: 10.1186/s40246-024-00683-9
Rui Dong, Xin Zhou, Haiyan Zhang, Bingyi Shi, Guohua Liu, Yi Liu
{"title":"Novel FLNC variants in pediatric cardiomyopathy: an insight into disease mechanisms.","authors":"Rui Dong, Xin Zhou, Haiyan Zhang, Bingyi Shi, Guohua Liu, Yi Liu","doi":"10.1186/s40246-024-00683-9","DOIUrl":"10.1186/s40246-024-00683-9","url":null,"abstract":"<p><strong>Background: </strong>FLNC gene variants have predominantly been reported in adult populations with cardiomyopathies, and early-onset cases are less common. The genotype-phenotype relationship indicates that dilated cardiomyopathy (DCM) is often associated with FLNC truncating variants.</p><p><strong>Methods: </strong>We conducted a comprehensive genetic analysis using next generation sequencing (NGS) to identify FLNC variants in patients with cardiovascular conditions. Detailed phenotypic and variant analyses were performed to characterize the clinical features and genetic alterations. Minigene assays and structural modeling were used to investigate the pathogenicity caused by the identified variants.</p><p><strong>Results: </strong>In a cohort of 58 patients, novel heterozygous FLNC variants, c.3962A > T (p.Glu1321Val) and c.7543C > T (p.Leu2515Phe), were identified in patients presenting with dilated and mixed restrictive/hypertrophic cardiomyopathies, respectively. The c.3962A > T variant disrupted normal splicing, as demonstrated through the splicing prediction tool and minigene studies, further emphasizing its pathogenic potential.</p><p><strong>Conclusion: </strong>For missense variants of FLNC in patients with DCM, the splicing effect of the variant should be carefully checked. Early detection and intervention are crucial given the high risk of sudden cardiac death and severe cardiac complications.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11520881/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mapping the evolving trend of research on leukocyte telomere length: a text-mining study. 绘制白细胞端粒长度研究的演变趋势图:文本挖掘研究。
IF 3.8 3区 医学
Human Genomics Pub Date : 2024-10-29 DOI: 10.1186/s40246-024-00687-5
Yuanjun Lyu, Hongjie Zhao, Guiping Zeng, Jia Yang, Qipeng Shao, Haiyang Wu
{"title":"Mapping the evolving trend of research on leukocyte telomere length: a text-mining study.","authors":"Yuanjun Lyu, Hongjie Zhao, Guiping Zeng, Jia Yang, Qipeng Shao, Haiyang Wu","doi":"10.1186/s40246-024-00687-5","DOIUrl":"10.1186/s40246-024-00687-5","url":null,"abstract":"<p><strong>Background: </strong>Substantial evidence indicates that measuring leukocyte telomere length (LTL) is a useful tool that may be considered as a valuable biomarker of individual biological age, correlating with numerous chronic disorders. However, to date, there has been a lack of in-depth understanding regarding the current landscape and forthcoming developments in the LTL field. Therefore, this study aimed to utilize bibliometric methods to summarize the knowledge structure, current focus, and emerging directions in this field.</p><p><strong>Method: </strong>Scientific publications on LTL spanning the period from 2000 to 2022 were acquired from the Web of Science Core Collection database. Several bibliometric tools including CiteSpace, VOSviewer, and an online website were utilized for bibliometric analysis. The primary evaluations encompassed investigating the major contributors and their collaborative relationships among countries/regions, institutions, and authors, conducting co-citation analyses of authors, journals, as well as reference, examining reference bursts, as well as performing co-occurrence analyses of keywords.</p><p><strong>Results: </strong>There are 1818 papers with 66,668 citations identified. Both the annual publication and citation counts on LTL exhibited significant upward trends. The United States emerged as the most prominent contributor, as evidenced by the greatest volume of papers and the highest H-index value. University of California San Francisco and Aviv A were identified as the most productive institution and author in this domain, respectively. Reference analysis revealed that longitudinal study and mendelian randomization study are the most concerned research method in this field recently. Keywords analysis showed that the most concerned diseases in LTL fields were aging, inflammation, cardiovascular diseases, endocrine diseases, neurological and psychiatric diseases, and cancers. In addition, the following research directions such as \"COPD\", \"mendelian randomization\", \"adiposity\", \"colorectal cancer\", \"National Health and Nutrition Examination Survey (NHNES)\", \"telomerase reverse transcriptase\", \"pregnancy\" have garnered increasing attention in recent times and hold the potential to evolve into research foci in the foreseeable future.</p><p><strong>Conclusion: </strong>This is the first bibliometric study that provides comprehensive overview of LTL research. The findings of this study could become valuable references for investigators to explore and address the current and emerging challenges in LTL research.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11520877/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142521802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Computational approaches to investigate the relationship between periodontitis and cardiovascular diseases for precision medicine. 用计算方法研究牙周炎与心血管疾病之间的关系,实现精准医疗。
IF 3.8 3区 医学
Human Genomics Pub Date : 2024-10-19 DOI: 10.1186/s40246-024-00685-7
Sophia Duenas, Zachary McGee, Ishani Mhatre, Karthikeyan Mayilvahanan, Kush Ketan Patel, Habiba Abdelhalim, Atharv Jayprakash, Uzayr Wasif, Oluchi Nwankwo, William Degroat, Naveena Yanamala, Partho P Sengupta, Daniel Fine, Zeeshan Ahmed
{"title":"Computational approaches to investigate the relationship between periodontitis and cardiovascular diseases for precision medicine.","authors":"Sophia Duenas, Zachary McGee, Ishani Mhatre, Karthikeyan Mayilvahanan, Kush Ketan Patel, Habiba Abdelhalim, Atharv Jayprakash, Uzayr Wasif, Oluchi Nwankwo, William Degroat, Naveena Yanamala, Partho P Sengupta, Daniel Fine, Zeeshan Ahmed","doi":"10.1186/s40246-024-00685-7","DOIUrl":"10.1186/s40246-024-00685-7","url":null,"abstract":"<p><p>Periodontitis is a highly prevalent inflammatory illness that leads to the destruction of tooth supporting tissue structures and has been associated with an increased risk of cardiovascular disease (CVD). Precision medicine, an emerging branch of medical treatment, aims can further improve current traditional treatment by personalizing care based on one's environment, genetic makeup, and lifestyle. Genomic databases have paved the way for precision medicine by elucidating the pathophysiology of complex, heritable diseases. Therefore, the investigation of novel periodontitis-linked genes associated with CVD will enhance our understanding of their linkage and related biochemical pathways for targeted therapies. In this article, we highlight possible mechanisms of actions connecting PD and CVD. Furthermore, we delve deeper into certain heritable inflammatory-associated pathways linking the two. The goal is to gather, compare, and assess high-quality scientific literature alongside genomic datasets that seek to establish a link between periodontitis and CVD. The scope is focused on the most up to date and authentic literature published within the last 10 years, indexed and available from PubMed Central, that analyzes periodontitis-associated genes linked to CVD. Based on the comparative analysis criteria, fifty-one genes associated with both periodontitis and CVD were identified and reported. The prevalence of genes associated with both CVD and periodontitis warrants investigation to assess the validity of a potential linkage between the pathophysiology of both diseases.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11491019/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142464155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Correction: Chromosome 16p11.2 microdeletion syndrome with microcephaly and Dandy-Walker malformation spectrum: expanding the known phenotype. 更正:染色体 16p11.2 微缺失综合征伴小头畸形和 Dandy-Walker 畸形谱系:扩展已知表型。
IF 3.8 3区 医学
Human Genomics Pub Date : 2024-10-15 DOI: 10.1186/s40246-024-00681-x
Liena Elbaghir Omer Elsayed, Norah Ayed AlHarbi, Ashwaq Mohammed Alqarni, Huda Hussein Elwasila Eltayeb, Noura Mostafa Mohamed Mostafa, Maha Mohammed Abdulrahim, Hadeel Ibrahim Bin Zaid, Latifah Mansour Alanzi, Sarah Abdullah Ababtain, Khawlah Aldulaijan, Sheka Yagub Aloyouni, Moneeb Abdullah Kassem Othman, Mohammad Abdullah Alkheilewi, Adel Mohammed Binduraihem, Hadeel Abdollah Alrukban, Hiba Yousif Ahmed, Faten Abdullah AlRadini, Hadil Mohammad Alahdal, Aziza Mufareh Mushiba, Omaima Abdulazeem Alzaher
{"title":"Correction: Chromosome 16p11.2 microdeletion syndrome with microcephaly and Dandy-Walker malformation spectrum: expanding the known phenotype.","authors":"Liena Elbaghir Omer Elsayed, Norah Ayed AlHarbi, Ashwaq Mohammed Alqarni, Huda Hussein Elwasila Eltayeb, Noura Mostafa Mohamed Mostafa, Maha Mohammed Abdulrahim, Hadeel Ibrahim Bin Zaid, Latifah Mansour Alanzi, Sarah Abdullah Ababtain, Khawlah Aldulaijan, Sheka Yagub Aloyouni, Moneeb Abdullah Kassem Othman, Mohammad Abdullah Alkheilewi, Adel Mohammed Binduraihem, Hadeel Abdollah Alrukban, Hiba Yousif Ahmed, Faten Abdullah AlRadini, Hadil Mohammad Alahdal, Aziza Mufareh Mushiba, Omaima Abdulazeem Alzaher","doi":"10.1186/s40246-024-00681-x","DOIUrl":"10.1186/s40246-024-00681-x","url":null,"abstract":"","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11475645/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142464156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Fast and accurate DNASeq variant calling workflow composed of LUSH toolkit. 快速准确的 DNASeq 变异调用工作流程由 LUSH 工具包组成。
IF 3.8 3区 医学
Human Genomics Pub Date : 2024-10-10 DOI: 10.1186/s40246-024-00666-w
Taifu Wang, Youjin Zhang, Haoling Wang, Qiwen Zheng, Jiaobo Yang, Tiefeng Zhang, Geng Sun, Weicong Liu, Longhui Yin, Xinqiu He, Rui You, Chu Wang, Zhencheng Liu, Zhijian Liu, Jin'an Wang, Xiangqian Jin, Zengquan He
{"title":"Fast and accurate DNASeq variant calling workflow composed of LUSH toolkit.","authors":"Taifu Wang, Youjin Zhang, Haoling Wang, Qiwen Zheng, Jiaobo Yang, Tiefeng Zhang, Geng Sun, Weicong Liu, Longhui Yin, Xinqiu He, Rui You, Chu Wang, Zhencheng Liu, Zhijian Liu, Jin'an Wang, Xiangqian Jin, Zengquan He","doi":"10.1186/s40246-024-00666-w","DOIUrl":"10.1186/s40246-024-00666-w","url":null,"abstract":"<p><strong>Background: </strong>Whole genome sequencing (WGS) is becoming increasingly prevalent for molecular diagnosis, staging and prognosis because of its declining costs and the ability to detect nearly all genes associated with a patient's disease. The currently widely accepted variant calling pipeline, GATK, is limited in terms of its computational speed and efficiency, which cannot meet the growing analysis needs.</p><p><strong>Results: </strong>Here, we propose a fast and accurate DNASeq variant calling workflow that is purely composed of tools from LUSH toolkit. The precision and recall measurements indicate that both the LUSH and GATK pipelines exhibit high levels of consistency, with precision and recall rates exceeding 99% on the 30x NA12878 dataset. In terms of processing speed, the LUSH pipeline outperforms the GATK pipeline, completing 30x WGS data analysis in just 1.6 h, which is approximately 17 times faster than GATK. Notably, the LUSH_HC tool completes the processing from BAM to VCF in just 12 min, which is around 76 times faster than GATK.</p><p><strong>Conclusion: </strong>These findings suggest that the LUSH pipeline is a highly promising alternative to the GATK pipeline for WGS data analysis, with the potential to significantly improve bedside analysis of acutely ill patients, large-scale cohort data analysis, and high-throughput variant calling in crop breeding programs. Furthermore, the LUSH pipeline is highly scalable and easily deployable, allowing it to be readily applied to various scenarios such as clinical diagnosis and genomic research.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11465951/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142400199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Implementing differentially pigmented skin models for predicting drug response variability across human ancestries. 实施不同色素皮肤模型,预测不同人类祖先对药物反应的差异。
IF 3.8 3区 医学
Human Genomics Pub Date : 2024-10-09 DOI: 10.1186/s40246-024-00677-7
Sophie Zaaijer, Simon C Groen
{"title":"Implementing differentially pigmented skin models for predicting drug response variability across human ancestries.","authors":"Sophie Zaaijer, Simon C Groen","doi":"10.1186/s40246-024-00677-7","DOIUrl":"10.1186/s40246-024-00677-7","url":null,"abstract":"<p><p>Persistent racial disparities in health outcomes have catalyzed legislative reforms and heightened scientific focus recently. However, despite the well-documented properties of skin pigments in binding drug compounds, their impact on therapeutic efficacy and adverse drug responses remains insufficiently explored. This perspective examines the intricate relationships between variation in melanin-based skin pigmentation and pharmacokinetics and -dynamics, highlighting the need for considering diversity in skin pigmentation as a variable to advance the equitability of pharmacological interventions. The article provides guidelines on the selection of New Approach Methods (NAMs) to foster inclusive study designs in preclinical drug development pipelines, leading to an improved level of translatability to the clinic.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11465898/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comprehensive analysis of NGS-based expanded carrier screening and follow-up in southern and southwestern China: results from 3024 Chinese individuals. 中国华南和西南地区基于 NGS 的扩大携带者筛查和随访的综合分析:3024 名中国人的结果。
IF 3.8 3区 医学
Human Genomics Pub Date : 2024-10-08 DOI: 10.1186/s40246-024-00680-y
Qinlin Huang, Juan Wen, Hongyun Zhang, Yanling Teng, Wen Zhang, Huimin Zhu, Desheng Liang, Lingqian Wu, Zhuo Li
{"title":"Comprehensive analysis of NGS-based expanded carrier screening and follow-up in southern and southwestern China: results from 3024 Chinese individuals.","authors":"Qinlin Huang, Juan Wen, Hongyun Zhang, Yanling Teng, Wen Zhang, Huimin Zhu, Desheng Liang, Lingqian Wu, Zhuo Li","doi":"10.1186/s40246-024-00680-y","DOIUrl":"10.1186/s40246-024-00680-y","url":null,"abstract":"<p><strong>Background: </strong>This study aimed to screen southern and southwestern Chinese individuals using expanded carrier screening (ECS), which explores the carrier status of recessively inherited diseases in southern and southwestern China, evaluates the clinical effectiveness of ECS application, and helps recognize high-risk fetuses that may have genetic disorders early in pregnancy, to provide better reproductive guidance.</p><p><strong>Methods: </strong>ECS for 220 diseases based on next-generation sequencing was performed on 3024 southern and southwestern Chinese individuals (1512 couples). Carrier status was analyzed; genes and loci with high frequencies of variants and on high-risk couples (ARCs) were focused to evaluate the clinical utility of our ECS technology and provide them precise fertility guidance.</p><p><strong>Results: </strong>In total, Pathogenic/likely pathogenic(P/LP) variants were found in 1885 individuals, so the carrier frequency was 62.3%, and 23.2% of the individuals were carriers of multiple diseases. furthermore, 2837 variants were detected, and the average number of P/LP variants carried per subject was 0.938. Additionally, 128 ARCs carried P/LP variants of the same gene, and the theoretical incidence rate in their offspring was as high as 2.12%.</p><p><strong>Conclusion: </strong>This study validated the application of our ECS technique for carrier screening in southern China, identifying carrier status and providing accurate carrier frequencies for hundreds of genetic diseases.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11462907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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