Human Genomics最新文献

{"title":"Integrated multiomics revealed adenosine signaling predict immunotherapy response and regulate tumor ecosystem of melanoma","authors":"Yantao Xu, Poyee Lau, Xiang Chen, Shuang Zhao, Yi He, Zixi Jiang, Xiang Chen, Guanxiong Zhang, Hong Liu","doi":"10.1186/s40246-024-00651-3","DOIUrl":"https://doi.org/10.1186/s40246-024-00651-3","url":null,"abstract":"Extracellular adenosine is extensively involved in regulating the tumor microenvironment. Given the disappointing results of adenosine-targeted therapy trials, personalized treatment might be necessary, tailored to the microenvironment status of individual patients. Here, we introduce the adenosine signaling score (ADO-score) model using non-negative matrix fraction identified patient subtypes using publicly available melanoma dataset, which aimed to profile adenosine signaling-related genes and construct a model to predict prognosis. We analyzed 580 malignant melanoma samples and demonstrated its robust value for prognosis. Further investigation in immune checkpoint inhibitor dataset suggests its potential as a stratified factor of immune checkpoint inhibitor efficacy. We validated the power of the ADO-score at the protein level immunofluorescence in a melanoma cohort from Xiangya Hospital. More importantly, single-cell and spatial transcriptomic data highlighted the cell-specific expression patterns of adenosine signaling-related genes and the existence of adenosine signaling-mediated crosstalk between tumor cells and immune cells in melanoma. Our study reveals a robust connection between adenosine signaling and clinical benefits in melanoma patients and proposes a universally applicable adenosine signaling model, the ADO-score, in gene expression profiles and histological sections. This model enables us to more precisely and conveniently select patients who are likely to benefit from immunotherapy.","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reply to correspondence by Deora et al. in Human Genomics 18, article no.: 52 (2024): critical insights on “Association of the C allele of rs479200 in the EGLN1 gene with COVID‑19 severity in Indian population: a novel finding”","authors":"Piyoosh Kumar Singh, Renuka Harit, Sajal De, Kailash C Pandey, Kapil Vashisht","doi":"10.1186/s40246-024-00671-z","DOIUrl":"https://doi.org/10.1186/s40246-024-00671-z","url":null,"abstract":"A reply to the correspondence by Deora et al.- Critical insights on “Association of the C allele of rs479200 in the EGLN1 gene with COVID‑19 severity in Indian population: a novel finding”. The reply contains point-wise rebuttal to the concerns, particularly addressing the epidemiological, statistical, and mathematical issues raised by Deora et al.","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Association of novel DNAH11 variants with asthenoteratozoospermia lead to male infertility","authors":"Senzhao Guo, Dongdong Tang, Yuge Chen, Hui Yu, Meng Gu, Hao Geng, Jiajun Fang, Baoyan Wu, Lewen Ruan, Kuokuo Li, Chuan Xu, Yang Gao, Qing Tan, Zongliu Duan, Huan Wu, Rong Hua, Rui Guo, Zhaolian Wei, Ping Zhou, Yuping Xu, Yunxia Cao, Xiaojin He, Yanwei Sha, Mingrong Lv","doi":"10.1186/s40246-024-00658-w","DOIUrl":"https://doi.org/10.1186/s40246-024-00658-w","url":null,"abstract":"Bi-allelic variants in DNAH11 have been identified as causative factors in Primary Ciliary Dyskinesia, leading to abnormal respiratory cilia. Nonetheless, the specific impact of these variants on human sperm flagellar and their involvement in male infertility remain largely unknown. A collaborative effort involving two Chinese reproductive centers conducted a study with 975 unrelated infertile men. Whole-exome sequencing was employed for variant screening, and Sanger sequencing confirmed the identified variants. Morphological and ultrastructural analyses of sperm were conducted using Scanning Electron Microscopy and Transmission Electron Microscopy. Western Blot Analysis and Immunofluorescence Analysis were utilized to assess protein levels and localization. ICSI was performed to evaluate its efficacy in achieving favorable pregnancy outcomes for individuals with DNAH11 variants. In this study, we identified seven novel variants in the DNAH11 gene in four asthenoteratozoospermia subjects. These variants led the absence of DNAH11 proteins and ultrastructure defects in sperm flagella, particularly affecting the outer dynein arms (ODAs) and adjacent structures. The levels of ODA protein DNAI2 and axoneme related proteins were down regulated, instead of inner dynein arms (IDA) proteins DNAH1 and DNAH6. Two out of four individuals with DNAH11 variants achieved clinical pregnancies through ICSI. The findings confirm the association between male infertility and bi-allelic deleterious variants in DNAH11, resulting in the aberrant assembly of sperm flagella and contributing to asthenoteratozoospermia. Importantly, ICSI emerges as an effective intervention for overcoming reproductive challenges caused by DNAH11 gene variants.","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The effect of family structure on the still-missing heritability and genomic prediction accuracy of type 2 diabetes","authors":"Mahmoud Amiri Roudbar, Seyed Milad Vahedi, Jin Jin, Mina Jahangiri, Hossein Lanjanian, Danial Habibi, Sajedeh Masjoudi, Parisa Riahi, Sahand Tehrani Fateh, Farideh Neshati, Asiyeh Sadat Zahedi, Maryam Moazzam-Jazi, Leila Najd-Hassan-Bonab, Seyedeh Fatemeh Mousavi, Sara Asgarian, Maryam Zarkesh, Mohammad Reza Moghaddas, Albert Tenesa, Anoshirvan Kazemnejad, Hassan Vahidnezhad, Hakon Hakonarson, Fereidoun Azizi, Mehdi Hedayati, Maryam Sadat Daneshpour, Mahdi Akbarzadeh","doi":"10.1186/s40246-024-00669-7","DOIUrl":"https://doi.org/10.1186/s40246-024-00669-7","url":null,"abstract":"This study aims to assess the effect of familial structures on the still-missing heritability estimate and prediction accuracy of Type 2 Diabetes (T2D) using pedigree estimated risk values (ERV) and genomic ERV. We used 11,818 individuals (T2D cases: 2,210) with genotype (649,932 SNPs) and pedigree information from the ongoing periodic cohort study of the Iranian population project. We considered three different familial structure scenarios, including (i) all families, (ii) all families with ≥ 1 generation, and (iii) families with ≥ 1 generation in which both case and control individuals are presented. Comprehensive simulation strategies were implemented to quantify the difference between estimates of $$:{text{h}}^{2}$$ and $$:{text{h}}_{text{S}text{N}text{P}}^{2}$$ . A proportion of still-missing heritability in T2D could be explained by overestimation of pedigree-based heritability due to the presence of families with individuals having only one of the two disease statuses. Our research findings underscore the significance of including families with only case/control individuals in cohort studies. The presence of such family structures (as observed in scenarios i and ii) contributes to a more accurate estimation of disease heritability, addressing the underestimation that was previously overlooked in prior research. However, when predicting disease risk, the absence of these families (as seen in scenario iii) can yield the highest prediction accuracy and the strongest correlation with Polygenic Risk Scores. Our findings represent the first evidence of the important contribution of familial structure for heritability estimations and genomic prediction studies in T2D.","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AI-derived comparative assessment of the performance of pathogenicity prediction tools on missense variants of breast cancer genes","authors":"Rahaf M. Ahmad, Bassam R. Ali, Fatma Al-Jasmi, Noura Al Dhaheri, Saeed Al Turki, Praseetha Kizhakkedath, Mohd Saberi Mohamad","doi":"10.1186/s40246-024-00667-9","DOIUrl":"https://doi.org/10.1186/s40246-024-00667-9","url":null,"abstract":"Single nucleotide variants (SNVs) can exert substantial and extremely variable impacts on various cellular functions, making accurate predictions of their consequences challenging, albeit crucial especially in clinical settings such as in oncology. Laboratory-based experimental methods for assessing these effects are time-consuming and often impractical, highlighting the importance of in-silico tools for variant impact prediction. However, the performance metrics of currently available tools on breast cancer missense variants from benchmarking databases have not been thoroughly investigated, creating a knowledge gap in the accurate prediction of pathogenicity. In this study, the benchmarking datasets ClinVar and HGMD were used to evaluate 21 Artificial Intelligence (AI)-derived in-silico tools. Missense variants in breast cancer genes were extracted from ClinVar and HGMD professional v2023.1. The HGMD dataset focused on pathogenic variants only, to ensure balance, benign variants for the same genes were included from the ClinVar database. Interestingly, our analysis of both datasets revealed variants across genes with varying penetrance levels like low and moderate in addition to high, reinforcing the value of disease-specific tools. The top-performing tools on ClinVar dataset identified were MutPred (Accuracy = 0.73), Meta-RNN (Accuracy = 0.72), ClinPred (Accuracy = 0.71), Meta-SVM, REVEL, and Fathmm-XF (Accuracy = 0.70). While on HGMD dataset they were ClinPred (Accuracy = 0.72), MetaRNN (Accuracy = 0.71), CADD (Accuracy = 0.69), Fathmm-MKL (Accuracy = 0.68), and Fathmm-XF (Accuracy = 0.67). These findings offer clinicians and researchers valuable insights for selecting, improving, and developing effective in-silico tools for breast cancer pathogenicity prediction. Bridging this knowledge gap contributes to advancing precision medicine and enhancing diagnostic and therapeutic approaches for breast cancer patients with potential implications for other conditions.","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206162","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-regional genomic and transcriptomic characterization of a melanoma-associated oral cavity cancer provide evidence for CASP8 alteration-mediated field cancerization.","authors":"Shouvik Chakravarty, Arnab Ghosh, Chitrarpita Das, Subrata Das, Subrata Patra, Arindam Maitra, Sandip Ghose, Nidhan K Biswas","doi":"10.1186/s40246-024-00668-8","DOIUrl":"10.1186/s40246-024-00668-8","url":null,"abstract":"<p><strong>Background: </strong>Precancerous and malignant tumours arise within the oral cavity from a predisposed \"field\" of epithelial cells upon exposure to carcinogenic stimulus. This phenomenon is known as \"Field Cancerization\". The molecular genomic and transcriptomic alterations that lead to field cancerization and tumour progression is unknown in Indian Oral squamous cell carcinoma (OSCC) patients.</p><p><strong>Methods: </strong>We have performed whole exome sequencing, copy-number variation array and whole transcriptome sequencing from five tumours and dysplastic lesions (sampled from distinct anatomical subsites - one each from buccal anterior and posterior alveolus, dorsum of tongue-mucosal melanoma, lip and left buccal mucosa) and blood from a rare OSCC patient with field cancerization.</p><p><strong>Results: </strong>A missense CASP8 gene mutation (p.S375F) was observed to be the initiating event in oral tumour field development. APOBEC mutation signatures, arm-level copy number alterations, depletion of CD8 + T cells and activated NK cells and enrichment of pro-inflammatory mast cells were features of early-originating tumours. Pharmacological inhibition of CASP8 protein in a CASP8-wild type OSCC cell line showed enhanced levels of cellular migration and viability.</p><p><strong>Conclusion: </strong>CASP8 alterations are the earliest driving events in oral field carcinogenesis, whereas additional somatic mutational, copy number and transcriptomic alterations ultimately lead to OSCC tumour formation and progression.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11380775/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142145584","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}

{"title":"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/s40246-024-00662-0","DOIUrl":"10.1186/s40246-024-00662-0","url":null,"abstract":"<p><strong>Background: </strong>Chromosome 16p11.2 deletions and duplications were found to be the second most common copy number variation (CNV) reported in cases with clinical presentation suggestive of chromosomal syndromes. Chromosome 16p11.2 deletion syndrome shows remarkable phenotypic heterogeneity with a wide variability of presentation extending from normal development and cognition to severe phenotypes. The clinical spectrum ranges from neurocognitive and global developmental delay (GDD), intellectual disability, and language defects (dysarthria /apraxia) to neuropsychiatric and autism spectrum disorders. Other presentations include dysmorphic features, congenital malformations, insulin resistance, and a tendency for obesity. Our study aims to narrow the gap of knowledge in Saudi Arabia and the Middle Eastern and Northern African (MENA) region about genetic disorders, particularly CNV-associated disorders. Despite their rarity, genetic studies in the MENA region revealed high potential with remarkable genetic and phenotypic novelty.</p><p><strong>Results: </strong>We identified a heterozygous de novo recurrent proximal chromosome 16p11.2 microdeletion by microarray (arr[GRCh38]16p11.2(29555974_30166595)x1) [(arr[GRCh37]16p11.2(29567295_30177916)x1)] and confirmed by whole exome sequencing (arr[GRCh37]16p11.2(29635211_30199850)x1). We report a Saudi girl with severe motor and cognitive disability, myoclonic epilepsy, deafness, and visual impairment carrying the above-described deletion. Our study broadens the known phenotypic spectrum associated with recurrent proximal 16p11.2 microdeletion syndrome to include developmental dysplasia of the hip, optic atrophy, and a flat retina. Notably, the patient exhibited a rare combination of microcephaly, features consistent with the Dandy-Walker spectrum, and a thin corpus callosum (TCC), which are extremely infrequent presentations in patients with the 16p11.2 microdeletion. Additionally, the patient displayed areas of skin and hair hypopigmentation, attributed to a homozygous hypomorphic allele in the TYR gene.</p><p><strong>Conclusion: </strong>This report expands on the clinical phenotype associated with proximal 16p11.2 microdeletion syndrome, highlighting the potential of genetic research in Saudi Arabia and the MENA region. It underscores the importance of similar future studies.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11376027/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132602","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}

{"title":"The T-cell repertoire of Spanish patients with COVID-19 as a strategy to link T-cell characteristics to the severity of the disease.","authors":"Fernando Marín-Benesiu, Lucia Chica-Redecillas, Verónica Arenas-Rodríguez, Esperanza de Santiago, Silvia Martínez-Diz, Ginesa López-Torres, Ana Isabel Cortés-Valverde, Catalina Romero-Cachinero, Carmen Entrala-Bernal, Francisco Javier Fernandez-Rosado, Luis Javier Martínez-González, Maria Jesus Alvarez-Cubero","doi":"10.1186/s40246-024-00654-0","DOIUrl":"10.1186/s40246-024-00654-0","url":null,"abstract":"<p><strong>Background: </strong>The architecture and dynamics of T cell populations are critical in orchestrating the immune response to SARS-CoV-2. In our study, we used T Cell Receptor sequencing (TCRseq) to investigate TCR repertoires in 173 post-infection COVID-19 patients.</p><p><strong>Methods: </strong>The cohort included 98 mild and 75 severe cases with a median age of 53. We amplified and sequenced the TCR β chain Complementary Determining Region 3 (CDR3b) and performed bioinformatic analyses to assess repertoire diversity, clonality, and V/J allelic usage between age, sex and severity groups. CDR3b amino acid sequence inference was performed by clustering structural motifs and filtering validated reactive CDR3b to COVID-19.</p><p><strong>Results: </strong>Our results revealed a pronounced decrease in diversity and an increase in clonal expansion in the TCR repertoires of severe COVID-19 patients younger than 55 years old. These results reflect the observed trends in patients older than 55 years old (both mild and severe). In addition, we identified a significant reduction in the usage of key V alleles (TRBV14, TRBV19, TRBV15 and TRBV6-4) associated with disease severity. Notably, severe patients under 55 years old had allelic patterns that resemble those over 55 years old, accompanied by a skewed frequency of COVID-19-related motifs.</p><p><strong>Conclusions: </strong>Present results suggest that severe patients younger than 55 may have a compromised TCR repertoire contributing to a worse disease outcome.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373388/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125599","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}

{"title":"Characterizing PFAS hazards and risks: a human population-based in vitro cardiotoxicity assessment strategy.","authors":"Lucie C Ford, Hsing-Chieh Lin, Yi-Hui Zhou, Fred A Wright, Vijay K Gombar, Alexander Sedykh, Ruchir R Shah, Weihsueh A Chiu, Ivan Rusyn","doi":"10.1186/s40246-024-00665-x","DOIUrl":"10.1186/s40246-024-00665-x","url":null,"abstract":"<p><p>Per- and poly-fluoroalkyl substances (PFAS) are emerging contaminants of concern because of their wide use, persistence, and potential to be hazardous to both humans and the environment. Several PFAS have been designated as substances of concern; however, most PFAS in commerce lack toxicology and exposure data to evaluate their potential hazards and risks. Cardiotoxicity has been identified as a likely human health concern, and cell-based assays are the most sensible approach for screening and prioritization of PFAS. Human-induced pluripotent stem cell (iPSC)-derived cardiomyocytes are a widely used method to test for cardiotoxicity, and recent studies showed that many PFAS affect these cells. Because iPSC-derived cardiomyocytes are available from different donors, they also can be used to quantify human variability in responses to PFAS. The primary objective of this study was to characterize potential human cardiotoxic hazard, risk, and inter-individual variability in responses to PFAS. A total of 56 PFAS from different subclasses were tested in concentration-response using human iPSC-derived cardiomyocytes from 16 donors without known heart disease. Kinetic calcium flux and high-content imaging were used to evaluate biologically-relevant phenotypes such as beat frequency, repolarization, and cytotoxicity. Of the tested PFAS, 46 showed concentration-response effects in at least one phenotype and donor; however, a wide range of sensitivities were observed across donors. Inter-individual variability in the effects could be quantified for 19 PFAS, and risk characterization could be performed for 20 PFAS based on available exposure information. For most tested PFAS, toxicodynamic variability was within a factor of 10 and the margins of exposure were above 100. This study identified PFAS that may pose cardiotoxicity risk and have high inter-individual variability. It also demonstrated the feasibility of using a population-based human in vitro method to quantify population variability and identify cardiotoxicity risks of emerging contaminants.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11368000/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142106960","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}

{"title":"Polygenic risk score portability for common diseases across genetically diverse populations.","authors":"Sonia Moreno-Grau, Manvi Vernekar, Arturo Lopez-Pineda, Daniel Mas-Montserrat, Míriam Barrabés, Consuelo D Quinto-Cortés, Babak Moatamed, Ming Ta Michael Lee, Zhenning Yu, Kensuke Numakura, Yuta Matsuda, Jeffrey D Wall, Alexander G Ioannidis, Nicholas Katsanis, Tomohiro Takano, Carlos D Bustamante","doi":"10.1186/s40246-024-00664-y","DOIUrl":"10.1186/s40246-024-00664-y","url":null,"abstract":"<p><strong>Background: </strong>Polygenic risk scores (PRS) derived from European individuals have reduced portability across global populations, limiting their clinical implementation at worldwide scale. Here, we investigate the performance of a wide range of PRS models across four ancestry groups (Africans, Europeans, East Asians, and South Asians) for 14 conditions of high-medical interest.</p><p><strong>Methods: </strong>To select the best-performing model per trait, we first compared PRS performances for publicly available scores, and constructed new models using different methods (LDpred2, PRS-CSx and SNPnet). We used 285 K European individuals from the UK Biobank (UKBB) for training and 18 K, including diverse ancestries, for testing. We then evaluated PRS portability for the best models in Europeans and compared their accuracies with respect to the best PRS per ancestry. Finally, we validated the selected PRS models using an independent set of 8,417 individuals from Biobank of the Americas-Genomelink (BbofA-GL); and performed a PRS-Phewas.</p><p><strong>Results: </strong>We confirmed a decay in PRS performances relative to Europeans when the evaluation was conducted using the best-PRS model for Europeans (51.3% for South Asians, 46.6% for East Asians and 39.4% for Africans). We observed an improvement in the PRS performances when specifically selecting ancestry specific PRS models (phenotype variance increase: 1.62 for Africans, 1.40 for South Asians and 0.96 for East Asians). Additionally, when we selected the optimal model conditional on ancestry for CAD, HDL-C and LDL-C, hypertension, hypothyroidism and T2D, PRS performance for studied populations was more comparable to what was observed in Europeans. Finally, we were able to independently validate tested models for Europeans, and conducted a PRS-Phewas, identifying cross-trait interplay between cardiometabolic conditions, and between immune-mediated components.</p><p><strong>Conclusion: </strong>Our work comprehensively evaluated PRS accuracy across a wide range of phenotypes, reducing the uncertainty with respect to which PRS model to choose and in which ancestry group. This evaluation has let us identify specific conditions where implementing risk-prioritization strategies could have practical utility across diverse ancestral groups, contributing to democratizing the implementation of PRS.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11367857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142106961","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}