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Bougiouri K, Aninta SG, Charlton S, Harris A, Carmagnini A, Piličiauskienė G, Feuerborn TR, Scarsbrook L, Tabadda K, Blaževičius P, Parker HG, Gopalakrishnan S, Larson G, Ostrander EA, Irving-Pease EK, Frantz LA, Racimo F. Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585179. [PMID: 38903121 PMCID: PMC11188068 DOI: 10.1101/2024.03.15.585179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
The multi-millenia long history between dogs and humans has placed them at the forefront of archeological and genomic research. Despite ongoing efforts including the analysis of ancient dog and wolf genomes, many questions remain regarding their geographic and temporal origins, and the microevolutionary processes that led to the diversity of breeds today. Although ancient genomes provide valuable information, their use is hindered by low depth of coverage and post-mortem damage, which inhibits confident genotype calling. In the present study, we assess how genotype imputation of ancient dog and wolf genomes, utilising a large reference panel, can improve the resolution provided by ancient datasets. Imputation accuracy was evaluated by down-sampling high coverage dog and wolf genomes to 0.05-2x coverage and comparing concordance between imputed and high coverage genotypes. We measured the impact of imputation on principal component analyses and runs of homozygosity. Our findings show high (R2>0.9) imputation accuracy for dogs with coverage as low as 0.5x and for wolves as low as 1.0x. We then imputed a dataset of 90 ancient dog and wolf genomes, to assess changes in inbreeding during the last 10,000 years of dog evolution. Ancient dog and wolf populations generally exhibited lower inbreeding levels than present-day individuals. Interestingly, regions with low ROH density maintained across ancient and present-day samples were significantly associated with genes related to olfaction and immune response. Our study indicates that imputing ancient canine genomes is a viable strategy that allows for the use of analytical methods previously limited to high-quality genetic data.
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Affiliation(s)
- Katia Bougiouri
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Sabhrina Gita Aninta
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sophy Charlton
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Alex Harris
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alberto Carmagnini
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - Giedrė Piličiauskienė
- Department of Archeology, Faculty of History, Vilnius University, Vilnius, Lithuania
| | - Tatiana R. Feuerborn
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lachie Scarsbrook
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Kristina Tabadda
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Povilas Blaževičius
- Department of Archeology, Faculty of History, Vilnius University, Vilnius, Lithuania
- National Museum of Lithuania, Vilnius, Lithuania
| | - Heidi G. Parker
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Greger Larson
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Elaine A. Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evan K. Irving-Pease
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Laurent A.F. Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - Fernando Racimo
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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2
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Santos R, Moreno-Torres V, Pintos I, Corral O, de Mendoza C, Soriano V, Corpas M. Low-coverage whole genome sequencing for a highly selective cohort of severe COVID-19 patients. GIGABYTE 2024; 2024:gigabyte127. [PMID: 38948510 PMCID: PMC11211761 DOI: 10.46471/gigabyte.127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 06/04/2024] [Indexed: 07/02/2024] Open
Abstract
Despite the advances in genetic marker identification associated with severe COVID-19, the full genetic characterisation of the disease remains elusive. This study explores imputation in low-coverage whole genome sequencing for a severe COVID-19 patient cohort. We generated a dataset of 79 imputed variant call format files using the GLIMPSE1 tool, each containing an average of 9.5 million single nucleotide variants. Validation revealed a high imputation accuracy (squared Pearson correlation ≍0.97) across sequencing platforms, showcasing GLIMPSE1's ability to confidently impute variants with minor allele frequencies as low as 2% in individuals with Spanish ancestry. We carried out a comprehensive analysis of the patient cohort, examining hospitalisation and intensive care utilisation, sex and age-based differences, and clinical phenotypes using a standardised set of medical terms developed to characterise severe COVID-19 symptoms. The methods and findings presented here can be leveraged for future genomic projects to gain vital insights into health challenges like COVID-19.
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Affiliation(s)
- Renato Santos
- National Heart & Lung Institute, Imperial College London, London, UK
| | - Víctor Moreno-Torres
- Puerta de Hierro University Hospital & Research Institute, Majadahonda, Madrid, Spain
| | - Ilduara Pintos
- Puerta de Hierro University Hospital & Research Institute, Majadahonda, Madrid, Spain
| | - Octavio Corral
- Health Sciences School & Medical Centre, Universidad Internacional La Rioja (UNIR), Madrid, Spain
| | - Carmen de Mendoza
- Puerta de Hierro University Hospital & Research Institute, Majadahonda, Madrid, Spain
| | - Vicente Soriano
- Health Sciences School & Medical Centre, Universidad Internacional La Rioja (UNIR), Madrid, Spain
| | - Manuel Corpas
- School of Life Sciences, University of Westminster, London, UK
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3
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Childebayeva A, Zavala EI. Review: Computational analysis of human skeletal remains in ancient DNA and forensic genetics. iScience 2023; 26:108066. [PMID: 37927550 PMCID: PMC10622734 DOI: 10.1016/j.isci.2023.108066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Abstract
Degraded DNA is used to answer questions in the fields of ancient DNA (aDNA) and forensic genetics. While aDNA studies typically center around human evolution and past history, and forensic genetics is often more concerned with identifying a specific individual, scientists in both fields face similar challenges. The overlap in source material has prompted periodic discussions and studies on the advantages of collaboration between fields toward mutually beneficial methodological advancements. However, most have been centered around wet laboratory methods (sampling, DNA extraction, library preparation, etc.). In this review, we focus on the computational side of the analytical workflow. We discuss limitations and considerations to consider when working with degraded DNA. We hope this review provides a framework to researchers new to computational workflows for how to think about analyzing highly degraded DNA and prompts an increase of collaboration between the forensic genetics and aDNA fields.
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Affiliation(s)
- Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, University of Kansas, Lawrence, KS, USA
| | - Elena I. Zavala
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Biology, University of Oregon, Eugene, OR, USA
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4
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Sousa da Mota B, Rubinacci S, Cruz Dávalos DI, G Amorim CE, Sikora M, Johannsen NN, Szmyt MH, Włodarczak P, Szczepanek A, Przybyła MM, Schroeder H, Allentoft ME, Willerslev E, Malaspinas AS, Delaneau O. Imputation of ancient human genomes. Nat Commun 2023; 14:3660. [PMID: 37339987 PMCID: PMC10282092 DOI: 10.1038/s41467-023-39202-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 06/02/2023] [Indexed: 06/22/2023] Open
Abstract
Due to postmortem DNA degradation and microbial colonization, most ancient genomes have low depth of coverage, hindering genotype calling. Genotype imputation can improve genotyping accuracy for low-coverage genomes. However, it is unknown how accurate ancient DNA imputation is and whether imputation introduces bias to downstream analyses. Here we re-sequence an ancient trio (mother, father, son) and downsample and impute a total of 43 ancient genomes, including 42 high-coverage (above 10x) genomes. We assess imputation accuracy across ancestries, time, depth of coverage, and sequencing technology. We find that ancient and modern DNA imputation accuracies are comparable. When downsampled at 1x, 36 of the 42 genomes are imputed with low error rates (below 5%) while African genomes have higher error rates. We validate imputation and phasing results using the ancient trio data and an orthogonal approach based on Mendel's rules of inheritance. We further compare the downstream analysis results between imputed and high-coverage genomes, notably principal component analysis, genetic clustering, and runs of homozygosity, observing similar results starting from 0.5x coverage, except for the African genomes. These results suggest that, for most populations and depths of coverage as low as 0.5x, imputation is a reliable method that can improve ancient DNA studies.
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Affiliation(s)
- Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Simone Rubinacci
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Diana Ivette Cruz Dávalos
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | | | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Niels N Johannsen
- Department of Archaeology and Heritage Studies, Aarhus University, Aarhus, Denmark
| | - Marzena H Szmyt
- Institute for Eastern Research, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland
| | - Anita Szczepanek
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland
- Department of Anatomy, Jagiellonian University, Medical College, Kraków, Poland
| | | | - Hannes Schroeder
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Science, Curtin University, Bentley, WA, Australia
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- MARUM, University of Bremen, Bremen, Germany
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.
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Ancient DNA reveals admixture history and endogamy in the prehistoric Aegean. Nat Ecol Evol 2023; 7:290-303. [PMID: 36646948 PMCID: PMC9911347 DOI: 10.1038/s41559-022-01952-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 11/11/2022] [Indexed: 01/18/2023]
Abstract
The Neolithic and Bronze Ages were highly transformative periods for the genetic history of Europe but for the Aegean-a region fundamental to Europe's prehistory-the biological dimensions of cultural transitions have been elucidated only to a limited extent so far. We have analysed newly generated genome-wide data from 102 ancient individuals from Crete, the Greek mainland and the Aegean Islands, spanning from the Neolithic to the Iron Age. We found that the early farmers from Crete shared the same ancestry as other contemporaneous Neolithic Aegeans. In contrast, the end of the Neolithic period and the following Early Bronze Age were marked by 'eastern' gene flow, which was predominantly of Anatolian origin in Crete. Confirming previous findings for additional Central/Eastern European ancestry in the Greek mainland by the Middle Bronze Age, we additionally show that such genetic signatures appeared in Crete gradually from the seventeenth to twelfth centuries BC, a period when the influence of the mainland over the island intensified. Biological and cultural connectedness within the Aegean is also supported by the finding of consanguineous endogamy practiced at high frequencies, unprecedented in the global ancient DNA record. Our results highlight the potential of archaeogenomic approaches in the Aegean for unravelling the interplay of genetic admixture, marital and other cultural practices.
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Lázaro-Guevara JM, Flores-Robles BJ, Garrido-Lopez KM, McKeown RJ, Flores-Morán AE, Labrador-Sánchez E, Pinillos-Aransay V, Trasahedo EA, López-Martín JA, Soberanis LSR, Melgar MY, Téllez-Arreola JL, Thébault SC. Identification of RP1 as the genetic cause of retinitis pigmentosa in a multi-generational pedigree using Extremely Low-Coverage Whole Genome Sequencing (XLC-WGS). Gene X 2023; 851:146956. [DOI: 10.1016/j.gene.2022.146956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 09/25/2022] [Accepted: 10/03/2022] [Indexed: 11/04/2022] Open
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Wang D, Xie K, Wang Y, Hu J, Li W, Yang A, Zhang Q, Ning C, Fan X. Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing. Genet Sel Evol 2022; 54:75. [PMCID: PMC9673297 DOI: 10.1186/s12711-022-00766-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
Background Rabbit wool traits are important in fiber production and for model organism research on hair growth, but their genetic architecture remains obscure. In this study, we focused on wool characteristics in Angora rabbits, a breed well-known for the quality of its wool. Considering the cost to generate population-scale sequence data and the biased detection of variants using chip data, developing an effective genotyping strategy using low-coverage whole-genome sequencing (LCS) data is necessary to conduct genetic analyses. Results Different genotype imputation strategies (BaseVar + STITCH, Bcftools + Beagle4, and GATK + Beagle5), sequencing coverages (0.1X, 0.5X, 1.0X, 1.5X, and 2.0X), and sample sizes (100, 200, 300, 400, 500, and 600) were compared. Our results showed that using BaseVar + STITCH at a sequencing depth of 1.0X with a sample size larger than 300 resulted in the highest genotyping accuracy, with a genotype concordance higher than 98.8% and genotype accuracy higher than 0.97. We performed multivariate genome-wide association studies (GWAS), followed by conditional GWAS and estimation of the confidence intervals of quantitative trait loci (QTL) to investigate the genetic architecture of wool traits. Six QTL were detected, which explained 0.4 to 7.5% of the phenotypic variation. Gene-level mapping identified the fibroblast growth factor 10 (FGF10) gene as associated with fiber growth and diameter, which agrees with previous results from functional data analyses on the FGF gene family in other species, and is relevant for wool rabbit breeding. Conclusions We suggest that LCS followed by imputation can be a cost-effective alternative to array and high-depth sequencing for assessing common variants. GWAS combined with LCS can identify new QTL and candidate genes that are associated with quantitative traits. This study provides a cost-effective and powerful method for investigating the genetic architecture of complex traits, which will be useful for genomic breeding applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00766-y.
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Affiliation(s)
- Dan Wang
- grid.440622.60000 0000 9482 4676College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Kerui Xie
- grid.440622.60000 0000 9482 4676College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Yanyan Wang
- grid.440622.60000 0000 9482 4676College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Jiaqing Hu
- grid.440622.60000 0000 9482 4676College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Wenqiang Li
- grid.440622.60000 0000 9482 4676College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Aiguo Yang
- grid.440622.60000 0000 9482 4676College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Qin Zhang
- grid.440622.60000 0000 9482 4676College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Chao Ning
- grid.440622.60000 0000 9482 4676College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Xinzhong Fan
- grid.440622.60000 0000 9482 4676College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
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Song M, Greenbaum J, Luttrell J, Zhou W, Wu C, Luo Z, Qiu C, Zhao LJ, Su KJ, Tian Q, Shen H, Hong H, Gong P, Shi X, Deng HW, Zhang C. An autoencoder-based deep learning method for genotype imputation. Front Artif Intell 2022; 5:1028978. [PMID: 36406474 PMCID: PMC9671213 DOI: 10.3389/frai.2022.1028978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022] Open
Abstract
Genotype imputation has a wide range of applications in genome-wide association study (GWAS), including increasing the statistical power of association tests, discovering trait-associated loci in meta-analyses, and prioritizing causal variants with fine-mapping. In recent years, deep learning (DL) based methods, such as sparse convolutional denoising autoencoder (SCDA), have been developed for genotype imputation. However, it remains a challenging task to optimize the learning process in DL-based methods to achieve high imputation accuracy. To address this challenge, we have developed a convolutional autoencoder (AE) model for genotype imputation and implemented a customized training loop by modifying the training process with a single batch loss rather than the average loss over batches. This modified AE imputation model was evaluated using a yeast dataset, the human leukocyte antigen (HLA) data from the 1,000 Genomes Project (1KGP), and our in-house genotype data from the Louisiana Osteoporosis Study (LOS). Our modified AE imputation model has achieved comparable or better performance than the existing SCDA model in terms of evaluation metrics such as the concordance rate (CR), the Hellinger score, the scaled Euclidean norm (SEN) score, and the imputation quality score (IQS) in all three datasets. Taking the imputation results from the HLA data as an example, the AE model achieved an average CR of 0.9468 and 0.9459, Hellinger score of 0.9765 and 0.9518, SEN score of 0.9977 and 0.9953, and IQS of 0.9515 and 0.9044 at missing ratios of 10% and 20%, respectively. As for the results of LOS data, it achieved an average CR of 0.9005, Hellinger score of 0.9384, SEN score of 0.9940, and IQS of 0.8681 at the missing ratio of 20%. In summary, our proposed method for genotype imputation has a great potential to increase the statistical power of GWAS and improve downstream post-GWAS analyses.
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Affiliation(s)
- Meng Song
- School of Computing Sciences and Computer Engineering, University of Southern Mississippi, Hattiesburg, MS, United States
| | - Jonathan Greenbaum
- Tulane Center of Biomedical Informatics and Genomics, School of Medicine, Tulane University, New Orleans, LA, United States
| | - Joseph Luttrell
- School of Computing Sciences and Computer Engineering, University of Southern Mississippi, Hattiesburg, MS, United States
| | - Weihua Zhou
- College of Computing, Michigan Technological University, Houghton, MI, United States
| | - Chong Wu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Zhe Luo
- Tulane Center of Biomedical Informatics and Genomics, School of Medicine, Tulane University, New Orleans, LA, United States
| | - Chuan Qiu
- Tulane Center of Biomedical Informatics and Genomics, School of Medicine, Tulane University, New Orleans, LA, United States
| | - Lan Juan Zhao
- Tulane Center of Biomedical Informatics and Genomics, School of Medicine, Tulane University, New Orleans, LA, United States
| | - Kuan-Jui Su
- Tulane Center of Biomedical Informatics and Genomics, School of Medicine, Tulane University, New Orleans, LA, United States
| | - Qing Tian
- Tulane Center of Biomedical Informatics and Genomics, School of Medicine, Tulane University, New Orleans, LA, United States
| | - Hui Shen
- Tulane Center of Biomedical Informatics and Genomics, School of Medicine, Tulane University, New Orleans, LA, United States
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, United States
| | - Ping Gong
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, MS, United States
| | - Xinghua Shi
- Department of Computer & Information Sciences, Temple University, Philadelphia, PA, United States
| | - Hong-Wen Deng
- Tulane Center of Biomedical Informatics and Genomics, School of Medicine, Tulane University, New Orleans, LA, United States,*Correspondence: Hong-Wen Deng
| | - Chaoyang Zhang
- School of Computing Sciences and Computer Engineering, University of Southern Mississippi, Hattiesburg, MS, United States,Chaoyang Zhang
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9
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Clouard C, Ausmees K, Nettelblad C. A joint use of pooling and imputation for genotyping SNPs. BMC Bioinformatics 2022; 23:421. [PMID: 36229780 PMCID: PMC9563787 DOI: 10.1186/s12859-022-04974-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Background Despite continuing technological advances, the cost for large-scale genotyping of a high number of samples can be prohibitive. The purpose of this study is to design a cost-saving strategy for SNP genotyping. We suggest making use of pooling, a group testing technique, to drop the amount of SNP arrays needed. We believe that this will be of the greatest importance for non-model organisms with more limited resources in terms of cost-efficient large-scale chips and high-quality reference genomes, such as application in wildlife monitoring, plant and animal breeding, but it is in essence species-agnostic. The proposed approach consists in grouping and mixing individual DNA samples into pools before testing these pools on bead-chips, such that the number of pools is less than the number of individual samples. We present a statistical estimation algorithm, based on the pooling outcomes, for inferring marker-wise the most likely genotype of every sample in each pool. Finally, we input these estimated genotypes into existing imputation algorithms. We compare the imputation performance from pooled data with the Beagle algorithm, and a local likelihood-aware phasing algorithm closely modeled on MaCH that we implemented. Results We conduct simulations based on human data from the 1000 Genomes Project, to aid comparison with other imputation studies. Based on the simulated data, we find that pooling impacts the genotype frequencies of the directly identifiable markers, without imputation. We also demonstrate how a combinatorial estimation of the genotype probabilities from the pooling design can improve the prediction performance of imputation models. Our algorithm achieves 93% concordance in predicting unassayed markers from pooled data, thus it outperforms the Beagle imputation model which reaches 80% concordance. We observe that the pooling design gives higher concordance for the rare variants than traditional low-density to high-density imputation commonly used for cost-effective genotyping of large cohorts. Conclusions We present promising results for combining a pooling scheme for SNP genotyping with computational genotype imputation on human data. These results could find potential applications in any context where the genotyping costs form a limiting factor on the study size, such as in marker-assisted selection in plant breeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04974-7.
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Affiliation(s)
- Camille Clouard
- Division of Scientific Computing, Department of Information Technology, Uppsala University, Lägerhyddsvägen 1, hus 10, 75237, Uppsala, Sweden.
| | - Kristiina Ausmees
- Division of Scientific Computing, Department of Information Technology, Uppsala University, Lägerhyddsvägen 1, hus 10, 75237, Uppsala, Sweden
| | - Carl Nettelblad
- Division of Scientific Computing, Department of Information Technology, Uppsala University, Lägerhyddsvägen 1, hus 10, 75237, Uppsala, Sweden
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Genotyping, the Usefulness of Imputation to Increase SNP Density, and Imputation Methods and Tools. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2467:113-138. [PMID: 35451774 DOI: 10.1007/978-1-0716-2205-6_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Imputation has become a standard practice in modern genetic research to increase genome coverage and improve accuracy of genomic selection and genome-wide association study as a large number of samples can be genotyped at lower density (and lower cost) and, imputed up to denser marker panels or to sequence level, using information from a limited reference population. Most genotype imputation algorithms use information from relatives and population linkage disequilibrium. A number of software for imputation have been developed originally for human genetics and, more recently, for animal and plant genetics considering pedigree information and very sparse SNP arrays or genotyping-by-sequencing data. In comparison to human populations, the population structures in farmed species and their limited effective sizes allow to accurately impute high-density genotypes or sequences from very low-density SNP panels and a limited set of reference individuals. Whatever the imputation method, the imputation accuracy, measured by the correct imputation rate or the correlation between true and imputed genotypes, increased with the increasing relatedness of the individual to be imputed with its denser genotyped ancestors and as its own genotype density increased. Increasing the imputation accuracy pushes up the genomic selection accuracy whatever the genomic evaluation method. Given the marker densities, the most important factors affecting imputation accuracy are clearly the size of the reference population and the relationship between individuals in the reference and target populations.
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11
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Gnecchi-Ruscone GA, Szécsényi-Nagy A, Koncz I, Csiky G, Rácz Z, Rohrlach AB, Brandt G, Rohland N, Csáky V, Cheronet O, Szeifert B, Rácz TÁ, Benedek A, Bernert Z, Berta N, Czifra S, Dani J, Farkas Z, Hága T, Hajdu T, Jászberényi M, Kisjuhász V, Kolozsi B, Major P, Marcsik A, Kovacsóczy BN, Balogh C, Lezsák GM, Ódor JG, Szelekovszky M, Szeniczey T, Tárnoki J, Tóth Z, Tutkovics EK, Mende BG, Geary P, Pohl W, Vida T, Pinhasi R, Reich D, Hofmanová Z, Jeong C, Krause J. Ancient genomes reveal origin and rapid trans-Eurasian migration of 7 th century Avar elites. Cell 2022; 185:1402-1413.e21. [PMID: 35366416 PMCID: PMC9042794 DOI: 10.1016/j.cell.2022.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/28/2022] [Accepted: 03/04/2022] [Indexed: 12/12/2022]
Abstract
The Avars settled the Carpathian Basin in 567/68 CE, establishing an empire lasting over 200 years. Who they were and where they came from is highly debated. Contemporaries have disagreed about whether they were, as they claimed, the direct successors of the Mongolian Steppe Rouran empire that was destroyed by the Turks in ∼550 CE. Here, we analyze new genome-wide data from 66 pre-Avar and Avar-period Carpathian Basin individuals, including the 8 richest Avar-period burials and further elite sites from Avar's empire core region. Our results provide support for a rapid long-distance trans-Eurasian migration of Avar-period elites. These individuals carried Northeast Asian ancestry matching the profile of preceding Mongolian Steppe populations, particularly a genome available from the Rouran period. Some of the later elite individuals carried an additional non-local ancestry component broadly matching the steppe, which could point to a later migration or reflect greater genetic diversity within the initial migrant population.
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Affiliation(s)
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary
| | - István Koncz
- Institute of Archaeological Sciences, ELTE Eötvös Loránd University, 1088 Budapest, Hungary
| | - Gergely Csiky
- Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary
| | - Zsófia Rácz
- Institute of Archaeological Sciences, ELTE Eötvös Loránd University, 1088 Budapest, Hungary
| | - A B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Guido Brandt
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Veronika Csáky
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Bea Szeifert
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary
| | | | | | | | | | | | | | | | | | - Tamás Hajdu
- Dept. of Biological Anthropology, Eötvös Loránd University (ELTE), 1117 Budapest, Hungary
| | | | | | | | | | - Antónia Marcsik
- Dept. of Biological Anthropology, Szeged University, 6701 Szeged, Hungary
| | | | - Csilla Balogh
- Department of Art History, Istanbul Medeniyet University, 34720 Istanbul, Turkey
| | - Gabriella M Lezsák
- Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary
| | | | | | - Tamás Szeniczey
- Dept. of Biological Anthropology, Eötvös Loránd University (ELTE), 1117 Budapest, Hungary
| | | | | | | | - Balázs G Mende
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary
| | - Patrick Geary
- Institute for Advanced Study, Princeton, NJ 08540, USA
| | - Walter Pohl
- Institute for Medieval Research, Austrian Academy of Sciences, 1020 Vienna, Austria; Institute of Austrian Historical Research, University of Vienna, 1010 Vienna, Austria
| | - Tivadar Vida
- Institute of Archaeological Sciences, ELTE Eötvös Loránd University, 1088 Budapest, Hungary
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Human Evolutionary Biology, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Zuzana Hofmanová
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; Department of Archaeology and Museology, Faculty of Arts, Masaryk University, 60200 Brno, Czech Republic
| | - Choongwon Jeong
- School of Biological Sciences, Seoul National University, 08826 Seoul, Republic of Korea.
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
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12
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Teng J, Zhao C, Wang D, Chen Z, Tang H, Li J, Mei C, Yang Z, Ning C, Zhang Q. Assessment of the performance of different imputation methods for low-coverage sequencing in Holstein cattle. J Dairy Sci 2022; 105:3355-3366. [DOI: 10.3168/jds.2021-21360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/13/2021] [Indexed: 12/27/2022]
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13
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Joukhadar R, Daetwyler HD. Data Integration, Imputation, and Meta-analysis for Genome-Wide Association Studies. Methods Mol Biol 2022; 2481:173-183. [PMID: 35641765 DOI: 10.1007/978-1-0716-2237-7_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Growing genomic and phenotypic datasets require different groups around the world to collaborate and integrate these valuable resources to maximize their benefit and increase reference population sizes for genomic prediction and genome-wide association studies (GWAS). However, different studies use different genotyping techniques which requires a synchronizing step for the genotyped variants called "imputation" before combining them. Optimally, different GWAS datasets can be analysed within a meta-analysis, which recruits summary statistics instead of actual data. This chapter describes the general principles for genotypic imputation and meta-GWAS analysis with a description of study designs and command lines required for such analyses.
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Affiliation(s)
- Reem Joukhadar
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia.
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14
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Gusev A, Groha S, Taraszka K, Semenov YR, Zaitlen N. Constructing germline research cohorts from the discarded reads of clinical tumor sequences. Genome Med 2021; 13:179. [PMID: 34749793 PMCID: PMC8576948 DOI: 10.1186/s13073-021-00999-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 10/28/2021] [Indexed: 12/02/2022] Open
Abstract
Background Hundreds of thousands of cancer patients have had targeted (panel) tumor sequencing to identify clinically meaningful mutations. In addition to improving patient outcomes, this activity has led to significant discoveries in basic and translational domains. However, the targeted nature of clinical tumor sequencing has a limited scope, especially for germline genetics. In this work, we assess the utility of discarded, off-target reads from tumor-only panel sequencing for the recovery of genome-wide germline genotypes through imputation. Methods We developed a framework for inference of germline variants from tumor panel sequencing, including imputation, quality control, inference of genetic ancestry, germline polygenic risk scores, and HLA alleles. We benchmarked our framework on 833 individuals with tumor sequencing and matched germline SNP array data. We then applied our approach to a prospectively collected panel sequencing cohort of 25,889 tumors. Results We demonstrate high to moderate accuracy of each inferred feature relative to direct germline SNP array genotyping: individual common variants were imputed with a mean accuracy (correlation) of 0.86, genetic ancestry was inferred with a correlation of > 0.98, polygenic risk scores were inferred with a correlation of > 0.90, and individual HLA alleles were inferred with a correlation of > 0.80. We demonstrate a minimal influence on the accuracy of somatic copy number alterations and other tumor features. We showcase the feasibility and utility of our framework by analyzing 25,889 tumors and identifying the relationships between genetic ancestry, polygenic risk, and tumor characteristics that could not be studied with conventional on-target tumor data. Conclusions We conclude that targeted tumor sequencing can be leveraged to build rich germline research cohorts from existing data and make our analysis pipeline publicly available to facilitate this effort. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00999-4.
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Affiliation(s)
- Alexander Gusev
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA. .,Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA. .,The Broad Institute of MIT & Harvard, Cambridge, MA, USA.
| | - Stefan Groha
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,The Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Kodi Taraszka
- Departments of Neurology and Computational Medicine, UCLA, Los Angeles, CA, USA
| | - Yevgeniy R Semenov
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, USA
| | - Noah Zaitlen
- Departments of Neurology and Computational Medicine, UCLA, Los Angeles, CA, USA.
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15
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Fan M, Zhang Y, Fu Z, Xu M, Wang S, Xie S, Gao X, Wang Y, Li L. A deep matrix completion method for imputing missing histological data in breast cancer by integrating DCE-MRI radiomics. Med Phys 2021; 48:7685-7697. [PMID: 34724248 DOI: 10.1002/mp.15316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 02/01/2023] Open
Abstract
PURPOSE Clinical indicators of histological information are important for breast cancer treatment and operational decision making, but these histological data suffer from frequent missing values due to various experimental/clinical reasons. The limited amount of histological information from breast cancer samples impedes the accuracy of data imputation. The purpose of this study was to impute missing histological data, including Ki-67 expression level, luminal A subtype, and histological grade, by integrating tumor radiomics. METHODS To this end, a deep matrix completion (DMC) method was proposed for imputing missing histological data using nonmissing features composed of histological and tumor radiomics (termed radiohistological features). DMC finds a latent nonlinear association between radiohistological features across all samples and samples for all the features. Radiomic features of morphologic, statistical, and texture were extracted from dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) inside the tumor. Experiments on missing histological data imputation were performed with a variable number of features and missing data rates. The performance of the DMC method was compared with those of the nonnegative matrix factorization (NMF) and collaborative filtering (MCF)-based data imputation methods. The area under the curve (AUC) was used to assess the performance of missing histological data imputation. RESULTS By integrating radiomics from DCE-MRI, the DMC method showed significantly better performance in terms of AUC than that using only histological data. Additionally, DMC using 120 radiomic features showed an optimal prediction performance (AUC = 0.793), which was better than the NMF (AUC = 0.756) and MCF methods (AUC = 0.706; corrected p = 0.001). The DMC method consistently performed better than the NMF and MCF methods with a variable number of radiomic features and missing data rates. CONCLUSIONS DMC improves imputation performance by integrating tumor histological and radiomics data. This study transforms latent imaging-scale patterns for interactions with molecular-scale histological information and is promising in the tumor characterization and management of patients.
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Affiliation(s)
- Ming Fan
- Institute of Biomedical Engineering and Instrumentation, Hangzhou Dianzi University, Hangzhou, China
| | - You Zhang
- Institute of Biomedical Engineering and Instrumentation, Hangzhou Dianzi University, Hangzhou, China
| | - Zhenyu Fu
- Institute of Biomedical Engineering and Instrumentation, Hangzhou Dianzi University, Hangzhou, China
| | - Maosheng Xu
- Department of Radiology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Shiwei Wang
- Department of Radiology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Sangma Xie
- Institute of Biomedical Engineering and Instrumentation, Hangzhou Dianzi University, Hangzhou, China
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yue Wang
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, USA
| | - Lihua Li
- Institute of Biomedical Engineering and Instrumentation, Hangzhou Dianzi University, Hangzhou, China
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16
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Best practices for analyzing imputed genotypes from low-pass sequencing in dogs. Mamm Genome 2021; 33:213-229. [PMID: 34498136 PMCID: PMC8913487 DOI: 10.1007/s00335-021-09914-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/01/2021] [Indexed: 12/15/2022]
Abstract
Although DNA array-based approaches for genome-wide association studies (GWAS) permit the collection of thousands of low-cost genotypes, it is often at the expense of resolution and completeness, as SNP chip technologies are ultimately limited by SNPs chosen during array development. An alternative low-cost approach is low-pass whole genome sequencing (WGS) followed by imputation. Rather than relying on high levels of genotype confidence at a set of select loci, low-pass WGS and imputation rely on the combined information from millions of randomly sampled low-confidence genotypes. To investigate low-pass WGS and imputation in the dog, we assessed accuracy and performance by downsampling 97 high-coverage (> 15×) WGS datasets from 51 different breeds to approximately 1× coverage, simulating low-pass WGS. Using a reference panel of 676 dogs from 91 breeds, genotypes were imputed from the downsampled data and compared to a truth set of genotypes generated from high-coverage WGS. Using our truth set, we optimized a variant quality filtering strategy that retained approximately 80% of 14 M imputed sites and lowered the imputation error rate from 3.0% to 1.5%. Seven million sites remained with a MAF > 5% and an average imputation quality score of 0.95. Finally, we simulated the impact of imputation errors on outcomes for case-control GWAS, where small effect sizes were most impacted and medium-to-large effect sizes were minorly impacted. These analyses provide best practice guidelines for study design and data post-processing of low-pass WGS-imputed genotypes in dogs.
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17
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Davies RW, Kucka M, Su D, Shi S, Flanagan M, Cunniff CM, Chan YF, Myers S. Rapid genotype imputation from sequence with reference panels. Nat Genet 2021; 53:1104-1111. [PMID: 34083788 PMCID: PMC7611184 DOI: 10.1038/s41588-021-00877-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 04/23/2021] [Indexed: 12/30/2022]
Abstract
Inexpensive genotyping methods are essential to modern genomics. Here we present QUILT, which performs diploid genotype imputation using low-coverage whole genome sequence data. QUILT employs Gibbs sampling to partition reads into maternal and paternal sets, facilitating rapid haploid imputation using large reference panels. We show this partitioning to be accurate over many megabases, enabling highly accurate imputation close to theoretical limits and outperforming existing methods. Moreover, QUILT can impute accurately using diverse technologies, including using long reads from Oxford Nanopore Technologies, and a novel form of low-cost barcoded Illumina sequencing called haplotagging, with the latter showing improved accuracy at low coverages. Relative to DNA genotyping microarrays, QUILT offers improved accuracy at reduced cost, particularly for diverse populations that are traditionally underserved in modern genomic analyses, with accuracy nearly doubling at rare SNPs. Finally, QUILT can accurately impute (4-digit) HLA types, the first such method from low-coverage sequence data.
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Affiliation(s)
| | - Marek Kucka
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Dingwen Su
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Sinan Shi
- Department of Statistics, University of Oxford, Oxford, UK
| | - Maeve Flanagan
- Department of Pediatrics, Weill Cornell Medical College, New York, NY, USA
| | | | | | - Simon Myers
- Department of Statistics, University of Oxford, Oxford, UK.,The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
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18
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Efficient phasing and imputation of low-coverage sequencing data using large reference panels. Nat Genet 2021; 53:120-126. [PMID: 33414550 DOI: 10.1038/s41588-020-00756-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 11/20/2020] [Indexed: 01/28/2023]
Abstract
Low-coverage whole-genome sequencing followed by imputation has been proposed as a cost-effective genotyping approach for disease and population genetics studies. However, its competitiveness against SNP arrays is undermined because current imputation methods are computationally expensive and unable to leverage large reference panels. Here, we describe a method, GLIMPSE, for phasing and imputation of low-coverage sequencing datasets from modern reference panels. We demonstrate its remarkable performance across different coverages and human populations. GLIMPSE achieves imputation of a genome for less than US$1 in computational cost, considerably outperforming other methods and improving imputation accuracy over the full allele frequency range. As a proof of concept, we show that 1× coverage enables effective gene expression association studies and outperforms dense SNP arrays in rare variant burden tests. Overall, this study illustrates the promising potential of low-coverage imputation and suggests a paradigm shift in the design of future genomic studies.
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19
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Khvorykh GV, Khrunin AV. imputeqc: an R package for assessing imputation quality of genotypes and optimizing imputation parameters. BMC Bioinformatics 2020; 21:304. [PMID: 32703240 PMCID: PMC7379353 DOI: 10.1186/s12859-020-03589-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 06/08/2020] [Indexed: 11/26/2022] Open
Abstract
Background The imputation of genotypes increases the power of genome-wide association studies. However, the imputation quality should be assessed in each particular case. Nevertheless, not all imputation softwares control the error of output, e.g., the last release of fastPHASE program (1.4.8) lacks such an option. In this particular software there is also an uncertainty in choosing the model parameters. fastPHASE is based on haplotype clusters, which size should be set a priori. The parameter influences the results of imputation and downstream analysis. Results We present a software toolkit imputeqc to assess the imputation quality and/or to choose the model parameters for imputation. We demonstrate the efficacy of toolkit for evaluation of imputations made with both fastPHASE and BEAGLE software for HapMap and 1000 Genomes data. The discordance of genotypes received correlated well in both methods. Using imputeqc, we also shown how to choose the optimal number of haplotype clusters and expectation-maximization cycles for fastPHASE program. The found number of haplotype clusters of 25 was further applied for hapFLK testing that revealed signatures of selection at LCT region on chromosome 2. We also demonstrated how to decrease the computational time in the case of hapFLK testing from 3 days to 20 h. Conclusions The toolkit is implemented as an R package imputeqc and command line scripts. The code is freely available at https://github.com/inzilico/imputeqcunder the MIT license.
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Affiliation(s)
- Gennady V Khvorykh
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, 2 Kurchatov sq., Moscow, 123182, Russia.
| | - Andrey V Khrunin
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, 2 Kurchatov sq., Moscow, 123182, Russia
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20
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Yu H, Spyrou MA, Karapetian M, Shnaider S, Radzevičiūtė R, Nägele K, Neumann GU, Penske S, Zech J, Lucas M, LeRoux P, Roberts P, Pavlenok G, Buzhilova A, Posth C, Jeong C, Krause J. Paleolithic to Bronze Age Siberians Reveal Connections with First Americans and across Eurasia. Cell 2020; 181:1232-1245.e20. [DOI: 10.1016/j.cell.2020.04.037] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/16/2020] [Accepted: 04/21/2020] [Indexed: 12/30/2022]
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21
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Jiang Y, Jiang Y, Wang S, Zhang Q, Ding X. Optimal sequencing depth design for whole genome re-sequencing in pigs. BMC Bioinformatics 2019; 20:556. [PMID: 31703550 PMCID: PMC6839175 DOI: 10.1186/s12859-019-3164-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 10/16/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND As whole-genome sequencing is becoming a routine technique, it is important to identify a cost-effective depth of sequencing for such studies. However, the relationship between sequencing depth and biological results from the aspects of whole-genome coverage, variant discovery power and the quality of variants is unclear, especially in pigs. We sequenced the genomes of three Yorkshire boars at an approximately 20X depth on the Illumina HiSeq X Ten platform and downloaded whole-genome sequencing data for three Duroc and three Landrace pigs with an approximately 20X depth for each individual. Then, we downsampled the deep genome data by extracting twelve different proportions of 0.05, 0.1, 0.15, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8 and 0.9 paired reads from the original bam files to mimic the sequence data of the same individuals at sequencing depths of 1.09X, 2.18X, 3.26X, 4.35X, 6.53X, 8.70X, 10.88X, 13.05X, 15.22X, 17.40X, 19.57X and 21.75X to evaluate the influence of genome coverage, the variant discovery rate and genotyping accuracy as a function of sequencing depth. In addition, SNP chip data for Yorkshire pigs were used as a validation for the comparison of single-sample calling and multisample calling algorithms. RESULTS Our results indicated that 10X is an ideal practical depth for achieving plateau coverage and discovering accurate variants, which achieved greater than 99% genome coverage. The number of false-positive variants was increased dramatically at a depth of less than 4X, which covered 95% of the whole genome. In addition, the comparison of multi- and single-sample calling showed that multisample calling was more sensitive than single-sample calling, especially at lower depths. The number of variants discovered under multisample calling was 13-fold and 2-fold higher than that under single-sample calling at 1X and 22X, respectively. A large difference was observed when the depth was less than 4.38X. However, more false-positive variants were detected under multisample calling. CONCLUSIONS Our research will inform important study design decisions regarding whole-genome sequencing depth. Our results will be helpful for choosing the appropriate depth to achieve the same power for studies performed under limited budgets.
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Affiliation(s)
- Yifan Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Yao Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Sheng Wang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, 271001 China
| | - Xiangdong Ding
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
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22
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Agler CS, Shungin D, Ferreira Zandoná AG, Schmadeke P, Basta PV, Luo J, Cantrell J, Pahel TD, Meyer BD, Shaffer JR, Schaefer AS, North KE, Divaris K. Protocols, Methods, and Tools for Genome-Wide Association Studies (GWAS) of Dental Traits. Methods Mol Biol 2019; 1922:493-509. [PMID: 30838596 PMCID: PMC6613560 DOI: 10.1007/978-1-4939-9012-2_38] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Oral health and disease are known to be influenced by complex interactions between environmental (e.g., social and behavioral) factors and innate susceptibility. Although the exact contribution of genomics and other layers of "omics" to oral health is an area of active research, it is well established that the susceptibility to dental caries, periodontal disease, and other oral and craniofacial traits is substantially influenced by the human genome. A comprehensive understanding of these genomic factors is necessary for the realization of precision medicine in the oral health domain. To aid in this direction, the advent and increasing affordability of high-throughput genotyping has enabled the simultaneous interrogation of millions of genetic polymorphisms for association with oral and craniofacial traits. Specifically, genome-wide association studies (GWAS) of dental caries and periodontal disease have provided initial insights into novel loci and biological processes plausibly implicated in these two common, complex, biofilm-mediated diseases. This paper presents a summary of protocols, methods, tools, and pipelines for the conduct of GWAS of dental caries, periodontal disease, and related traits. The protocol begins with the consideration of different traits for both diseases and outlines procedures for genotyping, quality control, adjustment for population stratification, heritability and association analyses, annotation, reporting, and interpretation. Methods and tools available for GWAS are being constantly updated and improved; with this in mind, the presented approaches have been successfully applied in numerous GWAS and meta-analyses among tens of thousands of individuals, including dental traits such as dental caries and periodontal disease. As such, they can serve as a guide or template for future genomic investigations of these and other traits.
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Affiliation(s)
- Cary S Agler
- Oral and Craniofacial Health Sciences, UNC School of Dentistry, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Dmitry Shungin
- Department of Odontology, Umeå University, Umeå, Sweden
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Andrea G Ferreira Zandoná
- Department of Comprehensive Dentistry, Tufts University School of Dental Medicine, Tufts University, Boston, MA, USA
| | - Paige Schmadeke
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
- Biospecimen Core Processing Facility, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Patricia V Basta
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
- Biospecimen Core Processing Facility, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Jason Luo
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
- Mammalian Genotyping Core, University of North Carolina, Chapel Hill, NC, USA
| | - John Cantrell
- Oral and Craniofacial Health Sciences, UNC School of Dentistry, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Thomas D Pahel
- Oral and Craniofacial Health Sciences, UNC School of Dentistry, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Beau D Meyer
- Department of Pediatric Dentistry, UNC School of Dentistry, CB#7450, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - John R Shaffer
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Arne S Schaefer
- Department of Periodontology, Institute of Dental, Oral and Maxillary Medicine, Charité-University Medicine Berlin, Berlin, Germany
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
- Carolina Center for Genome Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Kimon Divaris
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA.
- Department of Pediatric Dentistry, UNC School of Dentistry, CB#7450, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA.
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Malmberg MM, Barbulescu DM, Drayton MC, Shinozuka M, Thakur P, Ogaji YO, Spangenberg GC, Daetwyler HD, Cogan NOI. Evaluation and Recommendations for Routine Genotyping Using Skim Whole Genome Re-sequencing in Canola. FRONTIERS IN PLANT SCIENCE 2018; 9:1809. [PMID: 30581450 PMCID: PMC6292936 DOI: 10.3389/fpls.2018.01809] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/21/2018] [Indexed: 05/25/2023]
Abstract
Whole genome sequencing offers genome wide, unbiased markers, and inexpensive library preparation. With the cost of sequencing decreasing rapidly, many plant genomes of modest size are amenable to skim whole genome resequencing (skim WGR). The use of skim WGR in diverse sample sets without the use of imputation was evaluated in silico in 149 canola samples representative of global diversity. Fastq files with an average of 10x coverage of the reference genome were used to generate skim samples representing 0.25x, 0.5x, 1x, 2x, 3x, 4x, and 5x sequencing coverage. Applying a pre-defined list of SNPs versus de novo SNP discovery was evaluated. As skim WGR is expected to result in some degree of insufficient allele sampling, all skim coverage levels were filtered at a range of minimum read depths from a relaxed minimum read depth of 2 to a stringent read depth of 5, resulting in 28 list-based SNP sets. As a broad recommendation, genotyping pre-defined SNPs between 1x and 2x coverage with relatively stringent depth filtering is appropriate for a diverse sample set of canola due to a balance between marker number, sufficient accuracy, and sequencing cost, but depends on the intended application. This was experimentally examined in two sample sets with different genetic backgrounds: 1x coverage of 1,590 individuals from 84 Australian spring type four-parent crosses aimed at maximizing diversity as well as one commercial F1 hybrid, and 2x coverage of 379 doubled haploids (DHs) derived from a subset of the four-parent crosses. To determine optimal coverage in a simpler genetic background, the DH sample sequence coverage was further down sampled in silico. The flexible and cost-effective nature of the protocol makes it highly applicable across a range of species and purposes.
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Affiliation(s)
- M. Michelle Malmberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | | | - Michelle C. Drayton
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Maiko Shinozuka
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Preeti Thakur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Yvonne O. Ogaji
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - German C. Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Hans D. Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Noel O. I. Cogan
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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24
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Whalen A, Gorjanc G, Ros-Freixedes R, Hickey JM. Assessment of the performance of hidden Markov models for imputation in animal breeding. Genet Sel Evol 2018; 50:44. [PMID: 30223768 PMCID: PMC6142395 DOI: 10.1186/s12711-018-0416-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 09/05/2018] [Indexed: 12/31/2022] Open
Abstract
Background In this paper, we review the performance of various hidden Markov model-based imputation methods in animal breeding populations. Traditionally, pedigree and heuristic-based imputation methods have been used for imputation in large animal populations due to their computational efficiency, scalability, and accuracy. Recent advances in the area of human genetics have increased the ability of probabilistic hidden Markov model methods to perform accurate phasing and imputation in large populations. These advances may enable these methods to be useful for routine use in large animal populations, particularly in populations where pedigree information is not readily available. Methods To test the performance of hidden Markov model-based imputation, we evaluated the accuracy and computational cost of several methods in a series of simulated populations and a real animal population without using a pedigree. First, we tested single-step (diploid) imputation, which performs both phasing and imputation. Second, we tested pre-phasing followed by haploid imputation. Overall, we used four available diploid imputation methods (fastPHASE, Beagle v4.0, IMPUTE2, and MaCH), three phasing methods, (SHAPEIT2, HAPI-UR, and Eagle2), and three haploid imputation methods (IMPUTE2, Beagle v4.1, and Minimac3). Results We found that performing pre-phasing and haploid imputation was faster and more accurate than diploid imputation. In particular, among all the methods tested, pre-phasing with Eagle2 or HAPI-UR and imputing with Minimac3 or IMPUTE2 gave the highest accuracies with both simulated and real data. Conclusions The results of this study suggest that hidden Markov model-based imputation algorithms are an accurate and computationally feasible approach for performing imputation without a pedigree when pre-phasing and haploid imputation are used. Of the algorithms tested, the combination of Eagle2 and Minimac3 gave the highest accuracy across the simulated and real datasets.
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Affiliation(s)
- Andrew Whalen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, Scotland, UK.
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, Scotland, UK
| | - Roger Ros-Freixedes
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, Scotland, UK
| | - John M Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, Scotland, UK
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25
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Taylor JC, Bongartz T, Massey J, Mifsud B, Spiliopoulou A, Scott IC, Wang J, Morgan M, Plant D, Colombo M, Orchard P, Twigg S, McInnes IB, Porter D, Freeston JE, Nam JL, Cordell HJ, Isaacs JD, Strathdee JL, Arnett D, de Hair MJH, Tak PP, Aslibekyan S, van Vollenhoven RF, Padyukov L, Bridges SL, Pitzalis C, Cope AP, Verstappen SMM, Emery P, Barnes MR, Agakov F, McKeigue P, Mushiroda T, Kubo M, Weinshilboum R, Barton A, Morgan AW, Barrett JH. Genome-wide association study of response to methotrexate in early rheumatoid arthritis patients. THE PHARMACOGENOMICS JOURNAL 2018; 18:528-538. [PMID: 29795407 DOI: 10.1038/s41397-018-0025-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 10/10/2017] [Accepted: 02/09/2018] [Indexed: 11/09/2022]
Abstract
Methotrexate (MTX) monotherapy is a common first treatment for rheumatoid arthritis (RA), but many patients do not respond adequately. In order to identify genetic predictors of response, we have combined data from two consortia to carry out a genome-wide study of response to MTX in 1424 early RA patients of European ancestry. Clinical endpoints were change from baseline to 6 months after starting treatment in swollen 28-joint count, tender 28-joint count, C-reactive protein and the overall 3-component disease activity score (DAS28). No single nucleotide polymorphism (SNP) reached genome-wide statistical significance for any outcome measure. The strongest evidence for association was with rs168201 in NRG3 (p = 10-7 for change in DAS28). Some support was also seen for association with ZMIZ1, previously highlighted in a study of response to MTX in juvenile idiopathic arthritis. Follow-up in two smaller cohorts of 429 and 177 RA patients did not support these findings, although these cohorts were more heterogeneous.
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Affiliation(s)
- John C Taylor
- Leeds Institute of Cancer and Pathology, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | | | - Jonathan Massey
- Arthritis Research UK Centre for Genetics and Genomics, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.,NIHR Manchester BRC, Central Manchester Foundation Trust, Manchester, UK
| | - Borbala Mifsud
- Clinical Pharmacology, William Harvey Research Institute, Queen Mary University, London, UK
| | - Athina Spiliopoulou
- Centre for Population Health Sciences, Usher Institute, University of Edinburgh Old Medical School, Teviot Place, Edinburgh, UK.,Pharmatics Ltd., 9, Little France Road, Edinburgh, UK
| | - Ian C Scott
- Research Institute for Primary Care and Health Sciences, Primary Care Sciences, Keele University and Department of Rheumatology, Haywood Hospital, High Lane, Burslem, Staffordshire, UK.,Department of Medical and Molecular Genetics, King's College London, London, UK
| | | | - Michael Morgan
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK.,Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
| | - Darren Plant
- Arthritis Research UK Centre for Genetics and Genomics, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.,NIHR Manchester BRC, Central Manchester Foundation Trust, Manchester, UK
| | - Marco Colombo
- Centre for Population Health Sciences, Usher Institute, University of Edinburgh Old Medical School, Teviot Place, Edinburgh, UK
| | - Peter Orchard
- Pharmatics Ltd., 9, Little France Road, Edinburgh, UK
| | - Sarah Twigg
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Iain B McInnes
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Duncan Porter
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Jane E Freeston
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Jackie L Nam
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | | | - John D Isaacs
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University and NIHR Newcastle Biomedical Research Centre in Ageing and Long Term Conditions, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Jenna L Strathdee
- Leeds Institute of Cancer and Pathology, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Donna Arnett
- University of Kentucky College of Public Health, Lexington, KY, 40536, USA
| | | | - Paul P Tak
- Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands.,GlaxoSmithKline, Stevenage, UK.,Cambridge University, Cambridge, UK.,Ghent University, Ghent, Belgium
| | - Stella Aslibekyan
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ronald F van Vollenhoven
- Rheumatology Unit, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - S Louis Bridges
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Costantino Pitzalis
- Barts and The London School of Medicine & Dentistry, William Harvey Research Institute, Queen Mary University, London, UK
| | - Andrew P Cope
- Academic Department of Rheumatology, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Suzanne M M Verstappen
- Arthritis Research UK Centre for Genetics and Genomics, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.,NIHR Manchester BRC, Central Manchester Foundation Trust, Manchester, UK
| | - Paul Emery
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Michael R Barnes
- Barts and The London School of Medicine & Dentistry, William Harvey Research Institute, Queen Mary University, London, UK
| | - Felix Agakov
- Pharmatics Ltd., 9, Little France Road, Edinburgh, UK
| | - Paul McKeigue
- Centre for Population Health Sciences, Usher Institute, University of Edinburgh Old Medical School, Teviot Place, Edinburgh, UK
| | | | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | | | - Anne Barton
- Arthritis Research UK Centre for Genetics and Genomics, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.,NIHR Manchester BRC, Central Manchester Foundation Trust, Manchester, UK
| | - Ann W Morgan
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK.
| | - Jennifer H Barrett
- Leeds Institute of Cancer and Pathology, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
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26
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Ameen R, Shemmari SA, Askar M. Next-generation sequencing characterization of HLA in multi-generation families of Kuwaiti descent. Hum Immunol 2018; 79:137-142. [DOI: 10.1016/j.humimm.2017.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 12/22/2017] [Accepted: 12/26/2017] [Indexed: 10/18/2022]
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