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Peereboom ET, Maranus AE, Timmerman LM, Geneugelijk K, Spierings E. Experimental Data on PIRCHE and T-Cell Reactivity: HLA-DPB1-Derived Peptides Identified by PIRCHE-I Show Binding to HLA-A*02:01 in vitro and T-Cell Activation in vivo. Transfus Med Hemother 2024; 51:131-139. [PMID: 38867810 PMCID: PMC11166409 DOI: 10.1159/000537789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/11/2024] [Indexed: 06/14/2024] Open
Abstract
Introduction Human leukocyte antigen (HLA)-DPB1 mismatches during hematopoietic stem cell transplantation (HSCT) with an unrelated donor result in an increased risk for the development of graft-versus-host disease (GvHD). The number of CD8+ T-cell epitopes available for indirect allorecognition as predicted by the PIRCHE algorithm has been shown to be associated with GvHD development. As a proof of principle, PIRCHE-I predictions for HLA-DPB1 mismatches were validated in vitro and in vivo. Methods PIRCHE-I analysis was performed to identify HLA-DPB1-derived peptides that could theoretically bind to HLA-A*02:01. PIRCHE-I predictions for HLA-DPB1 mismatches were validated in vitro by investigating binding affinities of HLA-DPB1-derived peptides to the HLA-A*02:01 in a competition-based binding assay. To investigate the capacity of HLA-DPB1-derived peptides to elicit a T-cell response in vivo, mice were immunized with these peptides. T-cell alloreactivity was subsequently evaluated using an interferon-gamma ELISpot assay. Results The PIRCHE-I algorithm identified five HLA-DPB1-derived peptides (RMCRHNYEL, YIYNREEFV, YIYNREELV, YIYNREEYA, and YIYNRQEYA) to be presented by HLA-A*02:01. Binding of these peptides to HLA-A*02:01 was confirmed in a competition-based peptide binding assay, all showing an IC50 value of 21 μm or lower. The peptides elicited an interferon-gamma response in vivo. Conclusion Our results indicate that the PIRCHE-I algorithm can identify potential immunogenic HLA-DPB1-derived peptides present in recipients of an HLA-DPB1-mismatched donor. These combined in vitro and in vivo observations strengthen the validity of the PIRCHE-I algorithm to identify HLA-DPB1 mismatch-related GvHD development upon HSCT.
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Affiliation(s)
- Emma T.M. Peereboom
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Anna E. Maranus
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Laura M. Timmerman
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Kirsten Geneugelijk
- Central Diagnostic Laboratory, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Eric Spierings
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Central Diagnostic Laboratory, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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Avery CN, Russell ND, Steely CJ, Hersh AO, Bohnsack JF, Prahalad S, Jorde LB. Shared genomic segments analysis identifies MHC class I and class III molecules as genetic risk factors for juvenile idiopathic arthritis. HGG ADVANCES 2024; 5:100277. [PMID: 38369753 PMCID: PMC10918567 DOI: 10.1016/j.xhgg.2024.100277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 02/13/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024] Open
Abstract
Juvenile idiopathic arthritis (JIA) is a complex rheumatic disease encompassing several clinically defined subtypes of varying severity. The etiology of JIA remains largely unknown, but genome-wide association studies (GWASs) have identified up to 22 genes associated with JIA susceptibility, including a well-established association with HLA-DRB1. Continued investigation of heritable risk factors has been hindered by disease heterogeneity and low disease prevalence. In this study, we utilized shared genomic segments (SGS) analysis on whole-genome sequencing of 40 cases from 12 multi-generational pedigrees significantly enriched for JIA. Subsets of cases are connected by a common ancestor in large extended pedigrees, increasing the power to identify disease-associated loci. SGS analysis identifies genomic segments shared among disease cases that are likely identical by descent and anchored by a disease locus. This approach revealed statistically significant signals for major histocompatibility complex (MHC) class I and class III alleles, particularly HLA-A∗02:01, which was observed at a high frequency among cases. Furthermore, we identified an additional risk locus at 12q23.2-23.3, containing genes primarily expressed by naive B cells, natural killer cells, and monocytes. The recognition of additional risk beyond HLA-DRB1 provides a new perspective on immune cell dynamics in JIA. These findings contribute to our understanding of JIA and may guide future research and therapeutic strategies.
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Affiliation(s)
- Cecile N Avery
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.
| | - Nicole D Russell
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Cody J Steely
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Aimee O Hersh
- Department of Pediatrics, University of Utah, Salt Lake City, UT 84112, USA
| | - John F Bohnsack
- Department of Pediatrics, University of Utah, Salt Lake City, UT 84112, USA
| | - Sampath Prahalad
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30307, USA
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.
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Reynolds AZ, Niedbalski SD. Sex-biased gene regulation varies across human populations as a result of adaptive evolution. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 183:e24888. [PMID: 38100225 DOI: 10.1002/ajpa.24888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 11/14/2023] [Accepted: 11/28/2023] [Indexed: 03/03/2024]
Abstract
OBJECTIVES Studies of human sexual dimorphism and gender disparities in health focus on ostensibly universal molecular sex differences, such as sex chromosomes and circulating hormone levels, while ignoring the extraordinary diversity in biology, behavior, and culture acquired by different human populations over their unique evolutionary histories. MATERIALS AND METHODS Using RNA-Seq data and whole genome sequences from 1000G and HGDP, we investigate variation in sex-biased gene expression across 11 human populations and test whether population-level variation in sex-biased expression may have resulted from adaptive evolution in regions containing sex-specific regulatory variants. RESULTS We find that sex-biased gene expression in humans is highly variable, mostly population-specific, and demonstrates between population reversals. Expression quantitative trait locus mapping reveals sex-specific regulatory regions with evidence of recent positive natural selection, suggesting that variation in sex-biased expression may have evolved as an adaptive response to ancestral environments experienced by human populations. DISCUSSION These results indicate that sex-biased gene expression is more flexible than previously thought and is not generally shared among human populations. Instead, molecular phenotypes associated with sex depend on complex interactions between population-specific molecular evolution and physiological responses to contemporary socioecologies.
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Affiliation(s)
- Adam Z Reynolds
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, USA
- Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, USA
| | - Sara D Niedbalski
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, USA
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS, Paris, France
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Kolpakov S, Yashkin A, Ukraintseva S, Yashin A, Akushevich I. Genome-Related Mechanisms Contributing to Differences in Alzheimer's Disease Incidence Between White and Black Older US Adults. J Racial Ethn Health Disparities 2024:10.1007/s40615-024-01907-3. [PMID: 38273182 DOI: 10.1007/s40615-024-01907-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/31/2023] [Accepted: 01/04/2024] [Indexed: 01/27/2024]
Abstract
In this manuscript, we leverage a modified GWAS algorithm adapted for use with multidimensional Cox models and data from the Health and Retirement Study to explore how genetic variation influences the size of the disparity in Alzheimer's disease (AD) incidence between older Black and White US adults. We identified four loci that were associated with higher AD incidence levels in older Black adults: (1) rs11077034 (hazard ratio (HR), 4.98) from the RBFOX1 gene; (2) rs7144494 (HR, 1.68) from the HISLA gene; (3) rs7660552 (HR, 3.07) from the SLC25A4 gene; and (4) rs12599485 (HR, 3.181) from the NIP30 gene. The RBFOX1, HISLA, SLC25A4, and NIP30 genes are known to be associated with AD (RBFOX1, NIP30) directly, and also influence the risk of AD risk-related morbidities such as hypertension (RBFOX1, SLC25A4), depression (SLC25A4), and certain cancers (HISLA, SLC25A4). A likely disparity-generating mechanism may lie in endocytosis and abnormal tissue growing mechanisms, depending on inherited gene mutations and the structure of proxies as well as gene-environment interactions with other risk factors such as lifestyle, education level, and access to adequate medical services.
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Affiliation(s)
- Stanislav Kolpakov
- Social Science Research Institute, Duke University, Durham, NC, 27710, USA.
| | - Arseniy Yashkin
- Social Science Research Institute, Duke University, Durham, NC, 27710, USA
| | | | - Anatoliy Yashin
- Social Science Research Institute, Duke University, Durham, NC, 27710, USA
| | - Igor Akushevich
- Social Science Research Institute, Duke University, Durham, NC, 27710, USA
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Russell ND, Jorde LB, Chow CY. Characterizing genetic variation in the regulation of the ER stress response through computational and cis-eQTL analyses. G3 (BETHESDA, MD.) 2023; 13:jkad229. [PMID: 37792690 PMCID: PMC10700025 DOI: 10.1093/g3journal/jkad229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 08/17/2023] [Accepted: 09/27/2023] [Indexed: 10/06/2023]
Abstract
Misfolded proteins in the endoplasmic reticulum (ER) elicit the ER stress response, a large transcriptional response driven by 3 well-characterized transcription factors (TFs). This transcriptional response is variable across different genetic backgrounds. One mechanism in which genetic variation can lead to transcriptional variability in the ER stress response is through altered binding and activity of the 3 main TFs: XBP1, ATF6, and ATF4. This work attempts to better understand this mechanism by first creating a computational pipeline to identify potential binding sites throughout the human genome. We utilized GTEx data sets to identify cis-eQTLs that fall within predicted TF binding sites (TFBSs). We also utilized the ClinVar database to compare the number of pathogenic vs benign variants at different positions of the binding motifs. Finally, we performed a cis-eQTL analysis on human cell lines experiencing ER stress to identify cis-eQTLs that regulate the variable ER stress response. The majority of these cis-eQTLs are unique to a given condition: control or ER stress. Some of these stress-specific cis-eQTLs fall within putative binding sites of the 3 main ER stress response TFs, providing a potential mechanism by which these cis-eQTLs might be impacting gene expression under ER stress conditions through altered TF binding. This study represents the first cis-eQTL analysis on human samples experiencing ER stress and is a vital step toward identifying the genetic components responsible for the variable ER stress response.
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Affiliation(s)
- Nikki D Russell
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Clement Y Chow
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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Shi Y, Miao BY, Ai XX, Cao P, Gao J, Xu Y, Yang Q, Fei J, Zhang Q, Mai QY, Wen YX, Qu YL, Zhou CQ, Xu YW. Identification of common genetic polymorphisms associated with down-regulated gonadotropin levels in an exome-wide association study. Fertil Steril 2023; 120:671-681. [PMID: 37001689 DOI: 10.1016/j.fertnstert.2023.03.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/17/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023]
Abstract
OBJECTIVE To investigate whether common genetic polymorphisms are associated with gonadotropin levels after down-regulation with daily gonadotropin-releasing hormone agonist and whether the polymorphisms of candidate variants influence the ovarian response to exogenous gonadotropins. DESIGN Genetic association study. SETTING University-affiliated in vitro fertilization center. PATIENTS Subjects enrolled in an exploratory exome-wide association study (n = 862), a replication exome-wide association study (n = 86), and a classifier validation study (n = 148) were recruited from September 2016 to October 2018, September 2019 to September 2020, and January 2021 to December 2021, respectively. The included patients were aged ≤40 years and had a basal follicle-stimulating hormone (FSH) ≤12 IU/L. INTERVENTIONS All participants received a luteal phase down-regulation long protocol. Genome DNA was extracted from the peripheral blood leukocytes. For the exploratory and replication cohorts, exome sequencing was conducted on a HiSeq 2500 sequencing platform. The multiplex polymerase chain reaction amplification technique and next-generation sequencing also were performed in the exploratory and replication cohorts. For the samples of the validation cohort, Sanger sequencing was performed. MAIN OUTCOME MEASURES The primary endpoint was the gonadotropin levels after down-regulation, and the secondary endpoints were hormone levels and follicle diameters during stimulation, the total dose of FSH, duration of FSH stimulation, number of oocytes retrieved, and clinical pregnancy rate. RESULTS In the exploratory cohort, we identified that FSHB rs6169 (P=2.71 × 10-24) and its single-nucleotide polymorphisms in high linkage disequilibrium were associated with the down-regulated FSH level. The same locus was confirmed in the replication cohort. Women carrying the C allele of FSHB rs6169 exhibited higher average estradiol level during stimulation (P=6.82 × 10-5), shorter duration of stimulation, and less amount of exogenous FSH (Pduration=0.0002; Pdose=0.0024). In the independent validation set, adding rs6169 genotypes into the prediction model for FSH level after down-regulation enhanced the area under the curve from 0.560 to 0.712 in a logistic regression model, and increased prediction accuracy by 41.05% when a support vector machine classifier was applied. CONCLUSION The C allele of FSHB rs6169 is a susceptibility site for the relatively high level of FSH after down-regulation, which may be associated with increased ovarian FSH sensitivity.
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Affiliation(s)
- Yue Shi
- Reproductive Medicine Center, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China; Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong, China
| | - Ben-Yu Miao
- Reproductive Medicine Center, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China; Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong, China
| | - Xi-Xiong Ai
- Reproductive Medicine Center, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China; Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong, China; Reproductive Medicine Center, The Affiliated Shenzhen Maternity and Child Healthcare Hospital of the South Medical University, Shenzhen, Guangdong, China
| | - Ping Cao
- Reproductive Medicine Center, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China; Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong, China; Research School for Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands; Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institute, Stockholm, Sweden
| | - Jun Gao
- Reproductive Medicine Center, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China; Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong, China
| | - Yan Xu
- Reproductive Medicine Center, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China; Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong, China
| | - Qun Yang
- Peking Medriv Academy of Genetics and Reproduction, Peking, China
| | - Jia Fei
- Peking Medriv Academy of Genetics and Reproduction, Peking, China
| | - Qian Zhang
- Peking Medriv Academy of Genetics and Reproduction, Peking, China
| | - Qing-Yun Mai
- Reproductive Medicine Center, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China; Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong, China
| | - Yang-Xing Wen
- Reproductive Medicine Center, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China; Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong, China
| | - Yan-Lin Qu
- Department of Management Science and Engineering, Stanford University, Stanford, California
| | - Can-Quan Zhou
- Reproductive Medicine Center, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China; Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong, China
| | - Yan-Wen Xu
- Reproductive Medicine Center, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China; Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong, China.
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Han S, DiBlasi E, Monson ET, Shabalin A, Ferris E, Chen D, Fraser A, Yu Z, Staley M, Callor WB, Christensen ED, Crockett DK, Li QS, Willour V, Bakian AV, Keeshin B, Docherty AR, Eilbeck K, Coon H. Whole-genome sequencing analysis of suicide deaths integrating brain-regulatory eQTLs data to identify risk loci and genes. Mol Psychiatry 2023; 28:3909-3919. [PMID: 37794117 PMCID: PMC10730410 DOI: 10.1038/s41380-023-02282-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/14/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023]
Abstract
Recent large-scale genome-wide association studies (GWAS) have started to identify potential genetic risk loci associated with risk of suicide; however, a large portion of suicide-associated genetic factors affecting gene expression remain elusive. Dysregulated gene expression, not assessed by GWAS, may play a significant role in increasing the risk of suicide death. We performed the first comprehensive genomic association analysis prioritizing brain expression quantitative trait loci (eQTLs) within regulatory regions in suicide deaths from the Utah Suicide Genetic Risk Study (USGRS). 440,324 brain-regulatory eQTLs were obtained by integrating brain eQTLs, histone modification ChIP-seq, ATAC-seq, DNase-seq, and Hi-C results from publicly available data. Subsequent genomic analyses were conducted in whole-genome sequencing (WGS) data from 986 suicide deaths of non-Finnish European (NFE) ancestry and 415 ancestrally matched controls. Additional independent USGRS suicide deaths with genotyping array data (n = 4657) and controls from the Genome Aggregation Database were explored for WGS result replication. One significant eQTL locus, rs926308 (p = 3.24e-06), was identified. The rs926308-T is associated with lower expression of RFPL3S, a gene important for neocortex development and implicated in arousal. Gene-based analyses performed using Sherlock Bayesian statistical integrative analysis also detected 20 genes with expression changes that may contribute to suicide risk. From analyzing publicly available transcriptomic data, ten of these genes have previous evidence of differential expression in suicide death or in psychiatric disorders that may be associated with suicide, including schizophrenia and autism (ZNF501, ZNF502, CNN3, IGF1R, KLHL36, NBL1, PDCD6IP, SNX19, BCAP29, and ARSA). Electronic health records (EHR) data was further merged to evaluate if there were clinically relevant subsets of suicide deaths associated with genetic variants. In summary, our study identified one risk locus and ten genes associated with suicide risk via gene expression, providing new insight into possible genetic and molecular mechanisms leading to suicide.
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Affiliation(s)
- Seonggyun Han
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA.
| | - Emily DiBlasi
- Department of Psychiatry & Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Eric T Monson
- Department of Psychiatry & Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Andrey Shabalin
- Department of Psychiatry & Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Elliott Ferris
- Department of Neurobiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Danli Chen
- Department of Psychiatry & Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Alison Fraser
- Pedigree & Population Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Zhe Yu
- Pedigree & Population Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Michael Staley
- Office of the Medical Examiner, Utah Department of Health and Human Services, Salt Lake City, UT, USA
| | - W Brandon Callor
- Office of the Medical Examiner, Utah Department of Health and Human Services, Salt Lake City, UT, USA
| | - Erik D Christensen
- Office of the Medical Examiner, Utah Department of Health and Human Services, Salt Lake City, UT, USA
| | - David K Crockett
- Clinical Analytics, Intermountain Health, Salt Lake City, UT, USA
| | - Qingqin S Li
- Neuroscience Therapeutic Area, Janssen Research & Development, LLC, Titusville, NJ, USA
| | - Virginia Willour
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Amanda V Bakian
- Department of Psychiatry & Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Brooks Keeshin
- Department of Psychiatry & Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Anna R Docherty
- Department of Psychiatry & Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Hilary Coon
- Department of Psychiatry & Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
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Zeng L, He Z, Liu D, Li K, Gu K, Sun Q, Mei G, Zhang Y, Yan S, Zhang F. Genetic analysis of a large Han Chinese family line with schizoaffective psychosis. Heliyon 2023; 9:e14943. [PMID: 37025789 PMCID: PMC10070140 DOI: 10.1016/j.heliyon.2023.e14943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
To locate the specific susceptibility genes of a high incidence of schizoaffective disease (SAD) with autonomic dominant inheritance, we recruited a family group from Henan Province with a high incidence of SAD, including 19 individuals sampled from five generations. We used a genome-wide high-density SNP chip to perform genotype detection. The LINKAGE package and MENDEL programs were used for. The two-point and multipoint analyses were calculated by Merlin and SimWalk2 software to obtain the nonparametric linkage (NPL) value, corresponding P value, and parameter linkage limit of detection (LOD) value. Genome-wide linkage analysis yielded a significant linkage signal located on the short arm of chromosome 19. In the dominant genetic model, the LOD of the multipoint parametric analysis was 2.5, and the nonparametric analysis was 19.4 (P < 0.00001). Further haploid genotype analysis localized the candidate region in the 19p13.3-13.2 region, beginning at rs178414 and ending at rs11668751 with a physical length of approximately 4.9 Mb. We believe that the genes responsible for SAD are in this region.
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Affiliation(s)
- Liping Zeng
- The Clinical Laboratory of No.984 Hospital of the People's Liberation Army, Beijing, 100094, China
- Corresponding author. NO.984 Hospital of the People’s Liberation Army, Beijing, China
| | - Ziyun He
- College of Laboratory Medicine, Zunyi Medical University, Zunyi, 563006, China
| | - Di Liu
- The 3rd People's Hospital of Heilongjiang Province-Qinhuangdao Branch, Qinhuangdao, 066001,China
| | - Kai Li
- The Clinical Laboratory of No.984 Hospital of the People's Liberation Army, Beijing, 100094, China
| | - Kesheng Gu
- The Clinical Laboratory of No.984 Hospital of the People's Liberation Army, Beijing, 100094, China
| | - Qi Sun
- The Clinical Laboratory of No.984 Hospital of the People's Liberation Army, Beijing, 100094, China
| | - Guisen Mei
- The Clinical Laboratory of No.984 Hospital of the People's Liberation Army, Beijing, 100094, China
| | - Yingxue Zhang
- The Clinical Laboratory of No.984 Hospital of the People's Liberation Army, Beijing, 100094, China
| | - Shengkai Yan
- College of Laboratory Medicine, Zunyi Medical University, Zunyi, 563006, China
| | - Feng Zhang
- College of Laboratory Medicine, Zunyi Medical University, Zunyi, 563006, China
- Beijing Institute of Genomics, Chinese Academy of Sciences No. 1 Beichen West Road, Chaoyang District, Beijing, 100800, China
- Ori-Gene (ShangDong)Science and Technology Co., Ltd, 261000, China
- Corresponding author. College of Laboratory Medicine, Zunyi Medical University, Zunyi, China.
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Nicholas TJ, Cormier MJ, Quinlan AR. Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate. BMC Bioinformatics 2022; 23:490. [PMID: 36384437 PMCID: PMC9670370 DOI: 10.1186/s12859-022-05008-y] [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: 04/22/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Identification of deleterious genetic variants using DNA sequencing data relies on increasingly detailed filtering strategies to isolate the small subset of variants that are more likely to underlie a disease phenotype. Datasets reflecting population allele frequencies of different types of variants serve as powerful filtering tools, especially in the context of rare disease analysis. While such population-scale allele frequency datasets now exist for structural variants (SVs), it remains a challenge to match SV calls between multiple datasets, thereby complicating estimates of a putative SV's population allele frequency. RESULTS We introduce SVAFotate, a software tool that enables the annotation of SVs with variant allele frequency and related information from existing SV datasets. As a result, VCF files annotated by SVAFotate offer a variety of metrics to aid in the stratification of SVs as common or rare in the broader human population. CONCLUSIONS Here we demonstrate the use of SVAFotate in the classification of SVs with regards to their population frequency and illustrate how SVAFotate's annotations can be used to filter and prioritize SVs. Lastly, we detail how best to utilize these SV annotations in the analysis of genetic variation in studies of rare disease.
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Affiliation(s)
- Thomas J. Nicholas
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112 USA
| | - Michael J. Cormier
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112 USA
| | - Aaron R. Quinlan
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112 USA ,grid.223827.e0000 0001 2193 0096Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84112 USA
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10
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Huang M, Liu M, Li H, King J, Smuts A, Budowle B, Ge J. A machine learning approach for missing persons cases with high genotyping errors. Front Genet 2022; 13:971242. [PMID: 36263419 PMCID: PMC9573995 DOI: 10.3389/fgene.2022.971242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/16/2022] [Indexed: 11/22/2022] Open
Abstract
Estimating the relationships between individuals is one of the fundamental challenges in many fields. In particular, relationship.ip estimation could provide valuable information for missing persons cases. The recently developed investigative genetic genealogy approach uses high-density single nucleotide polymorphisms (SNPs) to determine close and more distant relationships, in which hundreds of thousands to tens of millions of SNPs are generated either by microarray genotyping or whole-genome sequencing. The current studies usually assume the SNP profiles were generated with minimum errors. However, in the missing person cases, the DNA samples can be highly degraded, and the SNP profiles generated from these samples usually contain lots of errors. In this study, a machine learning approach was developed for estimating the relationships with high error SNP profiles. In this approach, a hierarchical classification strategy was employed first to classify the relationships by degree and then the relationship types within each degree separately. As for each classification, feature selection was implemented to gain better performance. Both simulated and real data sets with various genotyping error rates were utilized in evaluating this approach, and the accuracies of this approach were higher than individual measures; namely, this approach was more accurate and robust than the individual measures for SNP profiles with genotyping errors. In addition, the highest accuracy could be obtained by providing the same genotyping error rates in train and test sets, and thus estimating genotyping errors of the SNP profiles is critical to obtaining high accuracy of relationship estimation.
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Affiliation(s)
- Meng Huang
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Muyi Liu
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Hongmin Li
- Department of Computer Science, College of Science, California State University, East Bay, Hayward, CA, United States
| | - Jonathan King
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Amy Smuts
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Jianye Ge
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
- *Correspondence: Jianye Ge,
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11
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A high-throughput real-time PCR tissue-of-origin test to distinguish blood from lymphoblastoid cell line DNA for (epi)genomic studies. Sci Rep 2022; 12:4684. [PMID: 35304543 PMCID: PMC8933453 DOI: 10.1038/s41598-022-08663-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
Lymphoblastoid cell lines (LCLs) derive from blood infected in vitro by Epstein–Barr virus and were used in several genetic, transcriptomic and epigenomic studies. Although few changes were shown between LCL and blood genotypes (SNPs) validating their use in genetics, more were highlighted for other genomic features and/or in their transcriptome and epigenome. This could render them less appropriate for these studies, notably when blood DNA could still be available. Here we developed a simple, high-throughput and cost-effective real-time PCR approach allowing to distinguish blood from LCL DNA samples based on the presence of EBV relative load and rearranged T-cell receptors γ and β. Our approach was able to achieve 98.5% sensitivity and 100% specificity on DNA of known origin (458 blood and 316 LCL DNA). It was further applied to 1957 DNA samples from the CEPH Aging cohort comprising DNA of uncertain origin, identifying 784 blood and 1016 LCL DNA. A subset of these DNA was further analyzed with an epigenetic clock indicating that DNA extracted from blood should be preferred to LCL for DNA methylation-based age prediction analysis. Our approach could thereby be a powerful tool to ascertain the origin of DNA in old collections prior to (epi)genomic studies.
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12
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Ghaiyed AP, Sutherland H, Lea RA, Gardam T, Chaseling J, James K, Bernie A, Haupt LM, Christie J, Griffiths LR, Wright KM. Evaluation of an ancestry prediction strategy for historical military remains using a World War II-era sample and pedigrees with family-level admixture. AUST J FORENSIC SCI 2021. [DOI: 10.1080/00450618.2021.2005144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- A. P. Ghaiyed
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - H. Sutherland
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - R. A. Lea
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - T. Gardam
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - J. Chaseling
- School of Environment and Science, Griffith University, Nathan, Australia
| | - K. James
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - A. Bernie
- Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Canberra, Australia
| | - L. M. Haupt
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - J. Christie
- School of Environment and Science, Griffith University, Nathan, Australia
| | - L. R. Griffiths
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - K. M. Wright
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
- Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Canberra, Australia
- Royal Australian Air Force (RAAF), Williamtown, Australia
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13
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Smith G, Mathews D, Sander-Effron S, Requesens D, Turan N, Scheinfeldt L. Microsatellite Markers in Biobanking: A New Multiplexed Assay. Biopreserv Biobank 2021; 19:438-443. [PMID: 34468209 PMCID: PMC8665806 DOI: 10.1089/bio.2021.0042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microsatellites, or MSATs, offer a fast and cost-effective way for biobanks to establish a biospecimen genetic profile. Importantly, this genetic profile can be used to authenticate multiple submissions derived from the same individual as well as biospecimens derived from the same original sample submission over time. While the Certificate of Confidentiality provided by the National Institutes of Health offers some meaningful protection to prevent the disclosure of potentially identifiable information to entities within the United States, we consider, in this study, the potential to offer additional protection to participants who choose to donate to biobanks by minimizing the use of forensic Combined DNA Index System (CODIS) MSAT markers in biobanking. To this end, we report the design and validation of a new multiplexed MSAT assay that does not include CODIS markers for use in biobanking operations and quality control management.
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Affiliation(s)
- Gretchen Smith
- Coriell Institute for Medical Research, Camden, New Jersey, USA
| | - Debra Mathews
- Berman Institute of Bioethics, Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Deborah Requesens
- Coriell Institute for Medical Research, Camden, New Jersey, USA.,The Orphan Disease Center, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Nahid Turan
- Coriell Institute for Medical Research, Camden, New Jersey, USA
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14
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Goldmann JM, Hampstead JE, Wong WSW, Wilfert AB, Turner TN, Jonker MA, Bernier R, Huynen MA, Eichler EE, Veltman JA, Maxwell GL, Gilissen C. Differences in the number of de novo mutations between individuals are due to small family-specific effects and stochasticity. Genome Res 2021; 31:1513-1518. [PMID: 34301630 PMCID: PMC8415378 DOI: 10.1101/gr.271809.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 07/14/2021] [Indexed: 11/24/2022]
Abstract
The number of de novo mutations (DNMs) in the human germline is correlated with parental age at conception, but this explains only part of the observed variation. We investigated whether there is a family-specific contribution to the number of DNMs in offspring. The analysis of DNMs in 111 dizygotic twin pairs did not identify a substantial family-specific contribution. This result was corroborated by comparing DNMs of 1669 siblings to those of age-matched unrelated offspring following correction for parental age. In addition, by modeling DNM data from 1714 multi-offspring families, we estimated that the family-specific contribution explains ∼5.2% of the variation in DNM number. Furthermore, we found no substantial difference between the observed number of DNMs and those predicted by a stochastic Poisson process. We conclude that there is a small family-specific contribution to DNM number and that stochasticity explains a large proportion of variation in DNM counts.
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Affiliation(s)
- Jakob M Goldmann
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands.,Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Juliet E Hampstead
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands.,Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Wendy S W Wong
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, Virginia 22042, USA
| | - Amy B Wilfert
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Tychele N Turner
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Marianne A Jonker
- Department for Health Evidence, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Raphael Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen 6525 GA, The Netherlands
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Joris A Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - George L Maxwell
- Department of Obstetrics and Gynecology, Inova Fairfax Department and Inova Schar Cancer Institute, Falls Church, Virginia 22042, USA
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands.,Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
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15
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Antonarakis SE. History of the methodology of disease gene identification. Am J Med Genet A 2021; 185:3266-3275. [PMID: 34159713 PMCID: PMC8596769 DOI: 10.1002/ajmg.a.62400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 11/06/2022]
Abstract
The past 45 years have witnessed a triumph in the discovery of genes and genetic variation that cause Mendelian disorders due to high impact variants. Important discoveries and organized projects have provided the necessary tools and infrastructure for the identification of gene defects leading to thousands of monogenic phenotypes. This endeavor can be divided in three phases in which different laboratory strategies were employed for the discovery of disease-related genes: (i) the biochemical phase, (ii) the genetic linkage followed by positional cloning phase, and (iii) the sequence identification phase. However, much more work is needed to identify all the high impact genomic variation that substantially contributes to the phenotypic variation.
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Affiliation(s)
- Stylianos E Antonarakis
- University of Geneva Medical School, Geneva, Switzerland.,Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
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16
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Belyeu JR, Sasani TA, Pedersen BS, Quinlan AR. Unfazed: parent-of-origin detection for large and small de novo variants. Bioinformatics 2021; 37:4860-4861. [PMID: 34146087 PMCID: PMC8665740 DOI: 10.1093/bioinformatics/btab454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/25/2021] [Accepted: 06/15/2021] [Indexed: 11/12/2022] Open
Abstract
SUMMARY Unfazed is a command-line tool to determine the parental gamete of origin for de novo mutations from paired-end Illumina DNA sequencing reads. Unfazed uses variant information for a sequenced trio to identify the parental gamete of origin by linking phase-informative inherited variants to de novo mutations using read-based phasing. It achieves a high success rate by chaining reads into haplotype groups, thus increasing the search space for informative sites. Unfazed provides a simple command-line interface and scales well to large inputs, determining parent-of-origin for nearly 30,000 de novo variants in under 60 hours. AVAILABILITY Unfazed is available at https://github.com/jbelyeu/unfazed. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jonathan R Belyeu
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA.,Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, 84112
| | - Thomas A Sasani
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA.,Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, 84112.,Department of Genome Sciences, University of Washington, Seattle, WA, 98195
| | - Brent S Pedersen
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA.,Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, 84112
| | - Aaron R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA.,Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, 84112
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17
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McDonald TL, Zhou W, Castro CP, Mumm C, Switzenberg JA, Mills RE, Boyle AP. Cas9 targeted enrichment of mobile elements using nanopore sequencing. Nat Commun 2021; 12:3586. [PMID: 34117247 PMCID: PMC8196195 DOI: 10.1038/s41467-021-23918-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/25/2021] [Indexed: 02/05/2023] Open
Abstract
Mobile element insertions (MEIs) are repetitive genomic sequences that contribute to genetic variation and can lead to genetic disorders. Targeted and whole-genome approaches using short-read sequencing have been developed to identify reference and non-reference MEIs; however, the read length hampers detection of these elements in complex genomic regions. Here, we pair Cas9-targeted nanopore sequencing with computational methodologies to capture active MEIs in human genomes. We demonstrate parallel enrichment for distinct classes of MEIs, averaging 44% of reads on-targeted signals and exhibiting a 13.4-54x enrichment over whole-genome approaches. We show an individual flow cell can recover most MEIs (97% L1Hs, 93% AluYb, 51% AluYa, 99% SVA_F, and 65% SVA_E). We identify seventeen non-reference MEIs in GM12878 overlooked by modern, long-read analysis pipelines, primarily in repetitive genomic regions. This work introduces the utility of nanopore sequencing for MEI enrichment and lays the foundation for rapid discovery of elusive, repetitive genetic elements.
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Affiliation(s)
- Torrin L McDonald
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Christopher P Castro
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Camille Mumm
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Jessica A Switzenberg
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Ryan E Mills
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
| | - Alan P Boyle
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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18
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Belyeu JR, Brand H, Wang H, Zhao X, Pedersen BS, Feusier J, Gupta M, Nicholas TJ, Brown J, Baird L, Devlin B, Sanders SJ, Jorde LB, Talkowski ME, Quinlan AR. De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families. Am J Hum Genet 2021; 108:597-607. [PMID: 33675682 PMCID: PMC8059337 DOI: 10.1016/j.ajhg.2021.02.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/12/2021] [Indexed: 01/05/2023] Open
Abstract
Each human genome includes de novo mutations that arose during gametogenesis. While these germline mutations represent a fundamental source of new genetic diversity, they can also create deleterious alleles that impact fitness. Whereas the rate and patterns of point mutations in the human germline are now well understood, far less is known about the frequency and features that impact de novo structural variants (dnSVs). We report a family-based study of germline mutations among 9,599 human genomes from 33 multigenerational CEPH-Utah families and 2,384 families from the Simons Foundation Autism Research Initiative. We find that de novo structural mutations detected by alignment-based, short-read WGS occur at an overall rate of at least 0.160 events per genome in unaffected individuals, and we observe a significantly higher rate (0.206 per genome) in ASD-affected individuals. In both probands and unaffected samples, nearly 73% of de novo structural mutations arose in paternal gametes, and we predict most de novo structural mutations to be caused by mutational mechanisms that do not require sequence homology. After multiple testing correction, we did not observe a statistically significant correlation between parental age and the rate of de novo structural variation in offspring. These results highlight that a spectrum of mutational mechanisms contribute to germline structural mutations and that these mechanisms most likely have markedly different rates and selective pressures than those leading to point mutations.
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Affiliation(s)
- Jonathan R Belyeu
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02114, USA
| | - Harold Wang
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02114, USA
| | - Xuefang Zhao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02114, USA
| | - Brent S Pedersen
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Julie Feusier
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Meenal Gupta
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Thomas J Nicholas
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Joseph Brown
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Lisa Baird
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA; Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02114, USA.
| | - Aaron R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA; Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84112, USA; Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA.
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19
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Di Francia R, Crisci S, De Monaco A, Cafiero C, Re A, Iaccarino G, De Filippi R, Frigeri F, Corazzelli G, Micera A, Pinto A. Response and Toxicity to Cytarabine Therapy in Leukemia and Lymphoma: From Dose Puzzle to Pharmacogenomic Biomarkers. Cancers (Basel) 2021; 13:cancers13050966. [PMID: 33669053 PMCID: PMC7956511 DOI: 10.3390/cancers13050966] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 01/04/2023] Open
Abstract
Simple Summary In this review, the authors propose a crosswise examination of cytarabine-related issues ranging from the spectrum of clinical activity and severe toxicities, through updated cellular pharmacology and drug formulations, to the genetic variants associated with drug-induced phenotypes. Cytarabine (cytosine arabinoside; Ara-C) in multiagent chemotherapy regimens is often used for leukemia or lymphoma treatments, as well as neoplastic meningitis. Chemotherapy regimens can induce a suboptimal clinical outcome in a fraction of patients. The individual variability in clinical response to Leukemia & Lymphoma treatments among patients appears to be associated with intracellular accumulation of Ara-CTP due to genetic variants related to metabolic enzymes. The review provides exhaustive information on the effects of Ara-C-based therapies, the adverse drug reaction will also be provided including bone pain, ocular toxicity (corneal pain, keratoconjunctivitis, and blurred vision), maculopapular rash, and occasional chest pain. Evidence for predicting the response to cytarabine-based treatments will be highlighted, pointing at their significant impact on the routine management of blood cancers. Abstract Cytarabine is a pyrimidine nucleoside analog, commonly used in multiagent chemotherapy regimens for the treatment of leukemia and lymphoma, as well as for neoplastic meningitis. Ara-C-based chemotherapy regimens can induce a suboptimal clinical outcome in a fraction of patients. Several studies suggest that the individual variability in clinical response to Leukemia & Lymphoma treatments among patients, underlying either Ara-C mechanism resistance or toxicity, appears to be associated with the intracellular accumulation and retention of Ara-CTP due to genetic variants related to metabolic enzymes. Herein, we reported (a) the latest Pharmacogenomics biomarkers associated with the response to cytarabine and (b) the new drug formulations with optimized pharmacokinetics. The purpose of this review is to provide readers with detailed and comprehensive information on the effects of Ara-C-based therapies, from biological to clinical practice, maintaining high the interest of both researcher and clinical hematologist. This review could help clinicians in predicting the response to cytarabine-based treatments.
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Affiliation(s)
- Raffaele Di Francia
- Italian Association of Pharmacogenomics and Molecular Diagnostics, 60126 Ancona, Italy;
| | - Stefania Crisci
- Hematology-Oncology and Stem Cell transplantation Unit, National Cancer Institute, Fondazione “G. Pascale” IRCCS, 80131 Naples, Italy; (S.C.); (G.I.); (R.D.F.); (G.C.); (A.P.)
| | - Angela De Monaco
- Clinical Patology, ASL Napoli 2 Nord, “S.M. delle Grazie Hospital”, 80078 Pozzuoli, Italy;
| | - Concetta Cafiero
- Medical Oncology, S.G. Moscati, Statte, 74010 Taranto, Italy
- Correspondence: or (C.C.); (A.M.); Tel.:+39-34-0101-2002 (C.C.); +39-06-4554-1191 (A.M.)
| | - Agnese Re
- Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
| | - Giancarla Iaccarino
- Hematology-Oncology and Stem Cell transplantation Unit, National Cancer Institute, Fondazione “G. Pascale” IRCCS, 80131 Naples, Italy; (S.C.); (G.I.); (R.D.F.); (G.C.); (A.P.)
| | - Rosaria De Filippi
- Hematology-Oncology and Stem Cell transplantation Unit, National Cancer Institute, Fondazione “G. Pascale” IRCCS, 80131 Naples, Italy; (S.C.); (G.I.); (R.D.F.); (G.C.); (A.P.)
- Department of Clinical Medicine and Surgery, Federico II University, 80131 Naples, Italy
| | | | - Gaetano Corazzelli
- Hematology-Oncology and Stem Cell transplantation Unit, National Cancer Institute, Fondazione “G. Pascale” IRCCS, 80131 Naples, Italy; (S.C.); (G.I.); (R.D.F.); (G.C.); (A.P.)
| | - Alessandra Micera
- Research and Development Laboratory for Biochemical, Molecular and Cellular Applications in Ophthalmological Sciences, IRCCS—Fondazione Bietti, 00184 Rome, Italy
- Correspondence: or (C.C.); (A.M.); Tel.:+39-34-0101-2002 (C.C.); +39-06-4554-1191 (A.M.)
| | - Antonio Pinto
- Hematology-Oncology and Stem Cell transplantation Unit, National Cancer Institute, Fondazione “G. Pascale” IRCCS, 80131 Naples, Italy; (S.C.); (G.I.); (R.D.F.); (G.C.); (A.P.)
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20
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Neurexin 1 variants as risk factors for suicide death. Mol Psychiatry 2021; 26:7436-7445. [PMID: 34168285 PMCID: PMC8709873 DOI: 10.1038/s41380-021-01190-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/20/2021] [Accepted: 06/02/2021] [Indexed: 02/06/2023]
Abstract
Suicide is a significant public health concern with complex etiology. Although the genetic component of suicide is well established, the scope of gene networks and biological mechanisms underlying suicide has yet to be defined. Previously, we reported genome-wide evidence that neurexin 1 (NRXN1), a key synapse organizing molecule, is associated with familial suicide risk. Here we present new evidence for two non-synonymous variants (rs78540316; P469S and rs199784139; H885Y) associated with increased familial risk of suicide death. We tested the impact of these variants on binding interactions with known partners and assessed functionality in a hemi-synapse formation assay. Although the formation of hemi-synapses was not altered with the P469S variant relative to wild-type, both variants increased binding to the postsynaptic binding partner, leucine-rich repeat transmembrane neuronal 2 (LRRTM2) in vitro. Our findings indicate that variants in NRXN1 and related synaptic genes warrant further study as risk factors for suicide death.
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21
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Abstract
Background Pedigree files are ubiquitously used within bioinformatics and genetics studies to convey critical information about relatedness, sex and affected status of study samples. While the text based format of ped files is efficient for computational methods, it is not immediately intuitive to a bioinformatician or geneticist trying to understand family structures, many of which encode the affected status of individuals across multiple generations. The visualization of pedigrees into connected nodes with descriptive shapes and shading provides a far more interpretable format to recognize visual patterns and intuit family structures. Despite these advantages of a visual pedigree, it remains difficult to quickly and accurately visualize a pedigree given a pedigree text file. Results Here we describe ped_draw a command line and web tool as a simple and easy solution to pedigree visualization. Ped_draw is capable of drawing complex multi-generational pedigrees and conforms to the accepted standards for depicting pedigrees visually. The command line tool can be used as a simple one liner command, utilizing graphviz to generate an image file. The web tool, https://peddraw.github.io, allows the user to either: paste a pedigree file, type to construct a pedigree file in the text box or upload a pedigree file. Users can save the generated image file in various formats. Conclusions We believe ped_draw is a useful pedigree drawing tool that improves on current methods due to its ease of use and approachability. Ped_draw allows users with various levels of expertise to quickly and easily visualize pedigrees.
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22
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Identification of a tumor-specific allo-HLA-restricted γδTCR. Blood Adv 2020; 3:2870-2882. [PMID: 31585951 DOI: 10.1182/bloodadvances.2019032409] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 07/28/2019] [Indexed: 12/25/2022] Open
Abstract
γδT cells are key players in cancer immune surveillance because of their ability to recognize malignant transformed cells, which makes them promising therapeutic tools in the treatment of cancer. However, the biological mechanisms of how γδT-cell receptors (TCRs) interact with their ligands are poorly understood. Within this context, we describe the novel allo-HLA-restricted and CD8α-dependent Vγ5Vδ1TCR. In contrast to the previous assumption of the general allo-HLA reactivity of a minor fraction of γδTCRs, we show that classic anti-HLA-directed, γδTCR-mediated reactivity can selectively act on hematological and solid tumor cells, while not harming healthy tissues in vitro and in vivo. We identified the molecular interface with proximity to the peptide-binding groove of HLA-A*24:02 as the essential determinant for recognition and describe the critical role of CD8 as a coreceptor. We conclude that alloreactive γδT-cell repertoires provide therapeutic opportunities, either within the context of haplotransplantation or as individual γδTCRs for genetic engineering of tumor-reactive T cells.
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23
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Cawthon RM, Meeks HD, Sasani TA, Smith KR, Kerber RA, O'Brien E, Baird L, Dixon MM, Peiffer AP, Leppert MF, Quinlan AR, Jorde LB. Germline mutation rates in young adults predict longevity and reproductive lifespan. Sci Rep 2020; 10:10001. [PMID: 32561805 PMCID: PMC7305191 DOI: 10.1038/s41598-020-66867-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/28/2020] [Indexed: 12/22/2022] Open
Abstract
Ageing may be due to mutation accumulation across the lifespan, leading to tissue dysfunction, disease, and death. We tested whether germline autosomal mutation rates in young adults predict their remaining survival, and, for women, their reproductive lifespans. Age-adjusted mutation rates (AAMRs) in 61 women and 61 men from the Utah CEPH (Centre d’Etude du Polymorphisme Humain) families were determined. Age at death, cause of death, all-site cancer incidence, and reproductive histories were provided by the Utah Population Database, Utah Cancer Registry, and Utah Genetic Reference Project. Higher AAMRs were significantly associated with higher all-cause mortality in both sexes combined. Subjects in the top quartile of AAMRs experienced more than twice the mortality of bottom quartile subjects (hazard ratio [HR], 2.07; 95% confidence interval [CI], 1.21–3.56; p = 0.008; median survival difference = 4.7 years). Fertility analyses were restricted to women whose age at last birth (ALB) was ≥ 30 years, the age when fertility begins to decline. Women with higher AAMRs had significantly fewer live births and a younger ALB. Adult germline mutation accumulation rates are established in adolescence, and later menarche in women is associated with delayed mutation accumulation. We conclude that germline mutation rates in healthy young adults may provide a measure of both reproductive and systemic ageing. Puberty may induce the establishment of adult mutation accumulation rates, just when DNA repair systems begin their lifelong decline.
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Affiliation(s)
- Richard M Cawthon
- Department of Human Genetics, University of Utah, Salt Lake City, UT, United States.
| | - Huong D Meeks
- Population Science, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, UT, United States
| | - Thomas A Sasani
- Department of Human Genetics, University of Utah, Salt Lake City, UT, United States
| | - Ken R Smith
- Population Science, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, UT, United States
| | - Richard A Kerber
- Department of Health Management & Systems Sciences, University of Louisville, Louisville, KY, United States
| | - Elizabeth O'Brien
- Department of Health Management & Systems Sciences, University of Louisville, Louisville, KY, United States
| | - Lisa Baird
- Department of Human Genetics, University of Utah, Salt Lake City, UT, United States
| | - Melissa M Dixon
- Department of Pediatrics, University of Utah, Salt Lake City, UT, United States
| | - Andreas P Peiffer
- Department of Pediatrics, University of Utah, Salt Lake City, UT, United States
| | - Mark F Leppert
- Department of Human Genetics, University of Utah, Salt Lake City, UT, United States
| | - Aaron R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, UT, United States.,Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, United States.,USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, United States
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah, Salt Lake City, UT, United States.,USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, United States
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24
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Zhou W, Emery SB, Flasch DA, Wang Y, Kwan KY, Kidd JM, Moran JV, Mills RE. Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology. Nucleic Acids Res 2020; 48:1146-1163. [PMID: 31853540 PMCID: PMC7026601 DOI: 10.1093/nar/gkz1173] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/14/2019] [Accepted: 12/05/2019] [Indexed: 11/13/2022] Open
Abstract
Long Interspersed Element-1 (LINE-1) retrotransposition contributes to inter- and intra-individual genetic variation and occasionally can lead to human genetic disorders. Various strategies have been developed to identify human-specific LINE-1 (L1Hs) insertions from short-read whole genome sequencing (WGS) data; however, they have limitations in detecting insertions in complex repetitive genomic regions. Here, we developed a computational tool (PALMER) and used it to identify 203 non-reference L1Hs insertions in the NA12878 benchmark genome. Using PacBio long-read sequencing data, we identified L1Hs insertions that were absent in previous short-read studies (90/203). Approximately 81% (73/90) of the L1Hs insertions reside within endogenous LINE-1 sequences in the reference assembly and the analysis of unique breakpoint junction sequences revealed 63% (57/90) of these L1Hs insertions could be genotyped in 1000 Genomes Project sequences. Moreover, we observed that amplification biases encountered in single-cell WGS experiments led to a wide variation in L1Hs insertion detection rates between four individual NA12878 cells; under-amplification limited detection to 32% (65/203) of insertions, whereas over-amplification increased false positive calls. In sum, these data indicate that L1Hs insertions are often missed using standard short-read sequencing approaches and long-read sequencing approaches can significantly improve the detection of L1Hs insertions present in individual genomes.
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Affiliation(s)
- Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Diane A Flasch
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Yifan Wang
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Kenneth Y Kwan
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA.,Molecular and Behavioral Neuroscience Institute, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Jeffrey M Kidd
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA.,Department of Internal Medicine, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
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25
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Marshall C, Sturk-Andreaggi K, Ring JD, Taylor CR, Barritt-Ross S, Parson W, McMahon TP. Advancing mitochondrial genome data interpretation in missing persons casework. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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26
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Feusier J, Watkins WS, Thomas J, Farrell A, Witherspoon DJ, Baird L, Ha H, Xing J, Jorde LB. Pedigree-based estimation of human mobile element retrotransposition rates. Genome Res 2019; 29:1567-1577. [PMID: 31575651 PMCID: PMC6771411 DOI: 10.1101/gr.247965.118] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 08/14/2019] [Indexed: 12/26/2022]
Abstract
Germline mutation rates in humans have been estimated for a variety of mutation types, including single-nucleotide and large structural variants. Here, we directly measure the germline retrotransposition rate for the three active retrotransposon elements: L1, Alu, and SVA. We used three tools for calling mobile element insertions (MEIs) (MELT, RUFUS, and TranSurVeyor) on blood-derived whole-genome sequence (WGS) data from 599 CEPH individuals, comprising 33 three-generation pedigrees. We identified 26 de novo MEIs in 437 births. The retrotransposition rate estimates for Alu elements, one in 40 births, is roughly half the rate estimated using phylogenetic analyses, a difference in magnitude similar to that observed for single-nucleotide variants. The L1 retrotransposition rate is one in 63 births and is within range of previous estimates (1:20-1:200 births). The SVA retrotransposition rate, one in 63 births, is much higher than the previous estimate of one in 900 births. Our large, three-generation pedigrees allowed us to assess parent-of-origin effects and the timing of insertion events in either gametogenesis or early embryonic development. We find a statistically significant paternal bias in Alu retrotransposition. Our study represents the first in-depth analysis of the rate and dynamics of human retrotransposition from WGS data in three-generation human pedigrees.
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Affiliation(s)
- Julie Feusier
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - W Scott Watkins
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Jainy Thomas
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Andrew Farrell
- USTAR Center for Genetic Discovery, Salt Lake City, Utah 84112, USA
| | - David J Witherspoon
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Lisa Baird
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Hongseok Ha
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Jinchuan Xing
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
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27
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Sasani TA, Pedersen BS, Gao Z, Baird L, Przeworski M, Jorde LB, Quinlan AR. Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation. eLife 2019; 8:e46922. [PMID: 31549960 PMCID: PMC6759356 DOI: 10.7554/elife.46922] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 08/13/2019] [Indexed: 12/27/2022] Open
Abstract
The number of de novo mutations (DNMs) found in an offspring's genome increases with both paternal and maternal age. But does the rate of mutation accumulation in human gametes differ across families? Using sequencing data from 33 large, three-generation CEPH families, we observed significant variability in parental age effects on DNM counts across families, ranging from 0.19 to 3.24 DNMs per year. Additionally, we found that ~3% of DNMs originated following primordial germ cell specification in a parent, and differed from non-mosaic germline DNMs in their mutational spectra. We also discovered that nearly 10% of candidate DNMs in the second generation were post-zygotic, and present in both somatic and germ cells; these gonosomal mutations occurred at equivalent frequencies on both parental haplotypes. Our results demonstrate that rates of germline mutation accumulation vary among families with similar ancestry, and confirm that post-zygotic mosaicism is a substantial source of human DNM.
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Affiliation(s)
- Thomas A Sasani
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Brent S Pedersen
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Ziyue Gao
- Howard Hughes Medical Institute and Department of GeneticsStanford UniversityStanfordUnited States
| | - Lisa Baird
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Molly Przeworski
- Department of Biological SciencesColumbia UniversityNew York CityUnited States
- Department of Systems BiologyColumbia UniversityNew York CityUnited States
| | - Lynn B Jorde
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
- USTAR Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUnited States
| | - Aaron R Quinlan
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
- USTAR Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUnited States
- Department of Biomedical InformaticsUniversity of UtahSalt Lake CityUnited States
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28
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Johnston AD, Simões-Pires CA, Suzuki M, Greally JM. High-efficiency genomic editing in Epstein-Barr virus-transformed lymphoblastoid B cells using a single-stranded donor oligonucleotide strategy. Commun Biol 2019; 2:312. [PMID: 31428700 PMCID: PMC6694121 DOI: 10.1038/s42003-019-0559-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 07/29/2019] [Indexed: 12/29/2022] Open
Abstract
While human lymphoblastoid cell lines represent a valuable resource for population genetic studies, they have usually been regarded as difficult for CRISPR-mediated genomic editing because of very inefficient DNA transfection and retroviral or lentiviral transduction in these cells, which becomes a substantial problem when multiple constructs need to be co-expressed. Here we describe a protocol using a single-stranded donor oligonucleotide strategy for 'scarless' editing in lymphoblastoid cells, yielding 12/60 (20%) of clones with homology-directed recombination, when rates of <5-10% are frequently typical for many other cell types. The protocol does not require the use of lentiviruses or stable transfection, permitting lymphoblastoid cell lines to be used for CRISPR-mediated genomic targeting and screening in population genetic studies.
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Affiliation(s)
- Andrew D. Johnston
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Claudia A. Simões-Pires
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Masako Suzuki
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - John M. Greally
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
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29
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Abstract
The use of the human reference genome has shaped methods and data across modern genomics. This has offered many benefits while creating a few constraints. In the following opinion, we outline the history, properties, and pitfalls of the current human reference genome. In a few illustrative analyses, we focus on its use for variant-calling, highlighting its nearness to a 'type specimen'. We suggest that switching to a consensus reference would offer important advantages over the continued use of the current reference with few disadvantages.
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Affiliation(s)
- Sara Ballouz
- Cold Spring Harbor Laboratory, The Stanley Institute for Cognitive Genomics, Cold Spring Harbor, NY, 11724, USA
| | - Alexander Dobin
- Cold Spring Harbor Laboratory, The Stanley Institute for Cognitive Genomics, Cold Spring Harbor, NY, 11724, USA
| | - Jesse A Gillis
- Cold Spring Harbor Laboratory, The Stanley Institute for Cognitive Genomics, Cold Spring Harbor, NY, 11724, USA.
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30
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Johnston AD, Simões-Pires CA, Thompson TV, Suzuki M, Greally JM. Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding. Nat Commun 2019; 10:3472. [PMID: 31375681 PMCID: PMC6677801 DOI: 10.1038/s41467-019-11412-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 07/10/2019] [Indexed: 12/23/2022] Open
Abstract
Functional variants in the genome are usually identified by their association with local gene expression, DNA methylation or chromatin states. DNA sequence motif analysis and chromatin immunoprecipitation studies have provided indirect support for the hypothesis that functional variants alter transcription factor binding to exert their effects. In this study, we provide direct evidence that functional variants can alter transcription factor binding. We identify a multifunctional variant within the TBC1D4 gene encoding a canonical NFκB binding site, and edited it using CRISPR-Cas9 to remove this site. We show that this editing reduces TBC1D4 expression, local chromatin accessibility and binding of the p65 component of NFκB. We then used CRISPR without genomic editing to guide p65 back to the edited locus, demonstrating that this re-targeting, occurring ~182 kb from the gene promoter, is enough to restore the function of the locus, supporting the central role of transcription factors mediating the effects of functional variants.
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Affiliation(s)
- Andrew D Johnston
- Center for Epigenomics and Department of Genetics (Division of Genomics), Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Claudia A Simões-Pires
- Center for Epigenomics and Department of Genetics (Division of Genomics), Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Taylor V Thompson
- Center for Epigenomics and Department of Genetics (Division of Genomics), Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Masako Suzuki
- Center for Epigenomics and Department of Genetics (Division of Genomics), Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - John M Greally
- Center for Epigenomics and Department of Genetics (Division of Genomics), Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA.
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31
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Functional Analysis of Promoter Variants in Genes Involved in Sex Steroid Action, DNA Repair and Cell Cycle Control. Genes (Basel) 2019; 10:genes10030186. [PMID: 30823486 PMCID: PMC6470759 DOI: 10.3390/genes10030186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/09/2019] [Accepted: 02/21/2019] [Indexed: 01/16/2023] Open
Abstract
Genetic variants affecting the regulation of gene expression are among the main causes of human diversity. The potential importance of regulatory polymorphisms is underscored by results from Genome Wide Association Studies, which have already implicated such polymorphisms in the susceptibility to complex diseases such as breast cancer. In this study, we re-sequenced the promoter regions of 24 genes involved in pathways related to breast cancer including sex steroid action, DNA repair, and cell cycle control in 60 unrelated Caucasian individuals. We constructed haplotypes and assessed the functional impact of promoter variants using gene reporter assays and electrophoretic mobility shift assays. We identified putative functional variants within the promoter regions of estrogen receptor 1 (ESR1), ESR2, forkhead box A1 (FOXA1), ubiquitin interaction motif containing 1 (UIMC1) and cell division cycle 7 (CDC7). The functional polymorphism on CDC7, rs13447455, influences CDC7 transcriptional activity in an allele-specific manner and alters DNA–protein complex formation in breast cancer cell lines. Moreover, results from the Breast Cancer Association Consortium show a marginal association between rs13447455 and breast cancer risk (p = 9.3 × 10−5), thus warranting further investigation. Furthermore, our study has helped provide methodological solutions to some technical difficulties that were encountered with gene reporter assays, particularly regarding inter-clone variability and statistical consistency.
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32
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Akhtari FS, Havener TM, Fukudo M, Jack JR, McLeod HL, Wiltshire T, Motsinger-Reif AA. The influence of Neanderthal alleles on cytotoxic response. PeerJ 2018; 6:e5691. [PMID: 30386687 PMCID: PMC6202974 DOI: 10.7717/peerj.5691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 09/04/2018] [Indexed: 11/20/2022] Open
Abstract
Various studies have shown that people of Eurasian origin contain traces of DNA inherited from interbreeding with Neanderthals. Recent studies have demonstrated that these Neanderthal variants influence a range of clinically important traits and diseases. Thus, understanding the genetic factors responsible for the variability in individual response to drug or chemical exposure is a key goal of pharmacogenomics and toxicogenomics, as dose responses are clinically and epidemiologically important traits. It is well established that ethnic and racial differences are important in dose response traits, but to our knowledge the influence of Neanderthal ancestry on response to xenobiotics is unknown. Towards this aim, we examined if Neanderthal ancestry plays a role in cytotoxic response to anti-cancer drugs and toxic environmental chemicals. We identified common Neanderthal variants in lymphoblastoid cell lines (LCLs) derived from the globally diverse 1000 Genomes Project and Caucasian cell lines from the Children's Hospital of Oakland Research Institute. We analyzed the effects of these Neanderthal alleles on cytotoxic response to 29 anti-cancer drugs and 179 environmental chemicals at varying concentrations using genome-wide data. We identified and replicated single nucleotide polymorphisms (SNPs) from these association results, including a SNP in the SNORD-113 cluster. Our results also show that the Neanderthal alleles cumulatively lead to increased sensitivity to both the anti-cancer drugs and the environmental chemicals. Our results demonstrate the influence of Neanderthal ancestry-informative markers on cytotoxic response. These results could be important in identifying biomarkers for personalized medicine or in dissecting the underlying etiology of dose response traits.
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Affiliation(s)
- Farida S Akhtari
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States of America.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States of America
| | - Tammy M Havener
- Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | | | - John R Jack
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States of America.,Department of Statistics, North Carolina State University, Raleigh, NC, United States of America
| | - Howard L McLeod
- The DeBartolo Family Personalized Medicine Institute, Moffitt Cancer Center, Tampa, FL, United States of America
| | - Tim Wiltshire
- Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America.,Center for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Alison A Motsinger-Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States of America.,Department of Statistics, North Carolina State University, Raleigh, NC, United States of America
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33
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Alonso A, Larraga V, Alcolea PJ. The contribution of DNA microarray technology to gene expression profiling in Leishmania spp.: A retrospective view. Acta Trop 2018; 187:129-139. [PMID: 29746872 DOI: 10.1016/j.actatropica.2018.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/04/2018] [Accepted: 05/06/2018] [Indexed: 01/15/2023]
Abstract
The first completed genome project of any living organism, excluding viruses, was of the gammaproteobacteria Haemophilus influenzae in 1995. Until the last decade, genome sequencing was very tedious because genome survey sequences (GSS) and/or expressed sequence tags (ESTs) belonging to plasmid, cosmid, and artificial chromosome genome libraries had to be sequenced and assembled in silico. No genome is completely assembled because gaps and unassembled contigs are always remaining. However, most represent an organism's whole genome from a practical point of view. The first genome sequencing projects of trypanosomatid parasites Leishmania major, Trypanosoma cruzi, and T. brucei were completed in 2005 following those strategies. The functional genomics era developed on the basis of microarray technology and has been continuously evolving. In the case of the genus Leishmania, substantial information about differentiation in the digenetic life cycle of the parasite has been obtained. More recently, next generation sequencing has revolutionized genome sequencing and functional genomics, leading to more sensitive and accurate results by using much fewer resources. Though this new technology is more advantageous, it does not invalidate microarray results. In fact, promising vaccine candidates and drug targets have been found by means of microarray-based screening and preliminary proof-of-concept tests.
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34
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Sherman SL, Rao D, Keats BJ, Yee S, Spence MA, Hassold TJ, Chakravarti A, Elston RC, Crolla JA, Ennis S, Risch N. Newton E. Morton (1929-2018). Am J Hum Genet 2018; 102:1011-1017. [PMID: 33220219 DOI: 10.1016/j.ajhg.2018.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 10/14/2022] Open
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35
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Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens. Cell 2016; 167:657-669.e21. [PMID: 27768889 DOI: 10.1016/j.cell.2016.09.025] [Citation(s) in RCA: 312] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 07/28/2016] [Accepted: 09/15/2016] [Indexed: 12/31/2022]
Abstract
Individuals from different populations vary considerably in their susceptibility to immune-related diseases. To understand how genetic variation and natural selection contribute to these differences, we tested for the effects of African versus European ancestry on the transcriptional response of primary macrophages to live bacterial pathogens. A total of 9.3% of macrophage-expressed genes show ancestry-associated differences in the gene regulatory response to infection, and African ancestry specifically predicts a stronger inflammatory response and reduced intracellular bacterial growth. A large proportion of these differences are under genetic control: for 804 genes, more than 75% of ancestry effects on the immune response can be explained by a single cis- or trans-acting expression quantitative trait locus (eQTL). Finally, we show that genetic effects on the immune response are strongly enriched for recent, population-specific signatures of adaptation. Together, our results demonstrate how historical selective events continue to shape human phenotypic diversity today, including for traits that are key to controlling infection.
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36
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Eberle MA, Fritzilas E, Krusche P, Källberg M, Moore BL, Bekritsky MA, Iqbal Z, Chuang HY, Humphray SJ, Halpern AL, Kruglyak S, Margulies EH, McVean G, Bentley DR. A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree. Genome Res 2016; 27:157-164. [PMID: 27903644 PMCID: PMC5204340 DOI: 10.1101/gr.210500.116] [Citation(s) in RCA: 216] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 10/28/2016] [Indexed: 12/30/2022]
Abstract
Improvement of variant calling in next-generation sequence data requires a comprehensive, genome-wide catalog of high-confidence variants called in a set of genomes for use as a benchmark. We generated deep, whole-genome sequence data of 17 individuals in a three-generation pedigree and called variants in each genome using a range of currently available algorithms. We used haplotype transmission information to create a phased “Platinum” variant catalog of 4.7 million single-nucleotide variants (SNVs) plus 0.7 million small (1–50 bp) insertions and deletions (indels) that are consistent with the pattern of inheritance in the parents and 11 children of this pedigree. Platinum genotypes are highly concordant with the current catalog of the National Institute of Standards and Technology for both SNVs (>99.99%) and indels (99.92%) and add a validated truth catalog that has 26% more SNVs and 45% more indels. Analysis of 334,652 SNVs that were consistent between informatics pipelines yet inconsistent with haplotype transmission (“nonplatinum”) revealed that the majority of these variants are de novo and cell-line mutations or reside within previously unidentified duplications and deletions. The reference materials from this study are a resource for objective assessment of the accuracy of variant calls throughout genomes.
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Affiliation(s)
| | - Epameinondas Fritzilas
- Illumina Limited, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex, CB10 1XL, United Kingdom
| | - Peter Krusche
- Illumina Limited, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex, CB10 1XL, United Kingdom
| | - Morten Källberg
- Illumina Limited, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex, CB10 1XL, United Kingdom
| | - Benjamin L Moore
- Illumina Limited, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex, CB10 1XL, United Kingdom
| | - Mitchell A Bekritsky
- Illumina Limited, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex, CB10 1XL, United Kingdom
| | - Zamin Iqbal
- Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN, United Kingdom
| | - Han-Yu Chuang
- Illumina Incorporated, San Diego, California 92122, USA
| | - Sean J Humphray
- Illumina Limited, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex, CB10 1XL, United Kingdom
| | | | | | | | - Gil McVean
- Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN, United Kingdom.,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - David R Bentley
- Illumina Limited, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex, CB10 1XL, United Kingdom
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Gupta S, Heiman M, Duncan N, Hinckley J, Di Paola J, Shapiro AD. Variable bleeding phenotype in an Amish pedigree with von Willebrand disease. Am J Hematol 2016; 91:E431-5. [PMID: 27414491 DOI: 10.1002/ajh.24474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 07/06/2016] [Accepted: 07/12/2016] [Indexed: 01/30/2023]
Abstract
Through a cross-sectional study design, the bleeding phenotype in the Amish in Indiana (IN) and Wisconsin (WI) was described using two different bleeding scores. von Willebrand factor (VWF) testing was performed and bleeding questionnaires from Centers for Disease Control and Prevention (CDC) and European MCMDM-1 (Tosetto bleeding score (BS)) were administered to the IN and WI cohort respectively. Seven hundred and seventy nine subjects were recruited, 17% were diagnosed with VWD based on Ristocetin cofactor, VWF:RCo < 30 IU/dl. Majority of the affected (AF), 67%, were tested and had a common mutation c.4120 C > T. The WI AF were much younger at a mean age 15 years vs 26 years in IN AF cohort. The AF subjects had a median VWF:RCo of 13IU/dl with a statistically significant higher median BS 1 versus 0 in the WI AF vs WI Unaffected (UA), 2 vs 1 in the IN AF vs IN UA, P < 0.01. Adults had a higher median BS compared to children in the WI and IN cohort, 2 vs 1 and 3 vs 1 respectively (P < 0.05) but there was no statistically significant difference in the BS between males and females in either cohort. The common symptoms reported were epistaxis and gingival oozing. BS ≥ 3 and BS ≥ 4 were observed in 46% of AF IN and 16.6% of AF WI, respectively. There was significant variability in the bleeding phenotype, with an overall low BS in the affected Amish with VWD, despite a unifying mutation. Am. J. Hematol. 91:E431-E435, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Sweta Gupta
- Indiana Hemophilia and Thrombosis Center; Indianapolis
| | - Meadow Heiman
- Indiana Hemophilia and Thrombosis Center; Indianapolis
| | | | | | | | - Amy D Shapiro
- Indiana Hemophilia and Thrombosis Center; Indianapolis
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38
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Aldrup-MacDonald ME, Kuo ME, Sullivan LL, Chew K, Sullivan BA. Genomic variation within alpha satellite DNA influences centromere location on human chromosomes with metastable epialleles. Genome Res 2016; 26:1301-1311. [PMID: 27510565 PMCID: PMC5052062 DOI: 10.1101/gr.206706.116] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 08/08/2016] [Indexed: 01/27/2023]
Abstract
Alpha satellite is a tandemly organized type of repetitive DNA that comprises 5% of the genome and is found at all human centromeres. A defined number of 171-bp monomers are organized into chromosome-specific higher-order repeats (HORs) that are reiterated thousands of times. At least half of all human chromosomes have two or more distinct HOR alpha satellite arrays within their centromere regions. We previously showed that the two alpha satellite arrays of Homo sapiens Chromosome 17 (HSA17), D17Z1 and D17Z1-B, behave as centromeric epialleles, that is, the centromere, defined by chromatin containing the centromeric histone variant CENPA and recruitment of other centromere proteins, can form at either D17Z1 or D17Z1-B. Some individuals in the human population are functional heterozygotes in that D17Z1 is the active centromere on one homolog and D17Z1-B is active on the other. In this study, we aimed to understand the molecular basis for how centromere location is determined on HSA17. Specifically, we focused on D17Z1 genomic variation as a driver of epiallele formation. We found that D17Z1 arrays that are predominantly composed of HOR size and sequence variants were functionally less competent. They either recruited decreased amounts of the centromere-specific histone variant CENPA and the HSA17 was mitotically unstable, or alternatively, the centromere was assembled at D17Z1-B and the HSA17 was stable. Our study demonstrates that genomic variation within highly repetitive, noncoding DNA of human centromere regions has a pronounced impact on genome stability and basic chromosomal function.
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Affiliation(s)
- Megan E Aldrup-MacDonald
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Molly E Kuo
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Lori L Sullivan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Kimberline Chew
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Beth A Sullivan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA; Division of Human Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
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Sebestyen Z, Scheper W, Vyborova A, Gu S, Rychnavska Z, Schiffler M, Cleven A, Chéneau C, van Noorden M, Peigné CM, Olive D, Lebbink RJ, Oostvogels R, Mutis T, Schuurhuis GJ, Adams EJ, Scotet E, Kuball J. RhoB Mediates Phosphoantigen Recognition by Vγ9Vδ2 T Cell Receptor. Cell Rep 2016; 15:1973-85. [PMID: 27210746 DOI: 10.1016/j.celrep.2016.04.081] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 03/09/2016] [Accepted: 04/21/2016] [Indexed: 11/16/2022] Open
Abstract
Human Vγ9Vδ2 T cells respond to tumor cells by sensing elevated levels of phosphorylated intermediates of the dysregulated mevalonate pathway, which is translated into activating signals by the ubiquitously expressed butyrophilin A1 (BTN3A1) through yet unknown mechanisms. Here, we developed an unbiased, genome-wide screening method that identified RhoB as a critical mediator of Vγ9Vδ2 TCR activation in tumor cells. Our results show that Vγ9Vδ2 TCR activation is modulated by the GTPase activity of RhoB and its redistribution to BTN3A1. This is associated with cytoskeletal changes that directly stabilize BTN3A1 in the membrane, and the subsequent dissociation of RhoB from BTN3A1. Furthermore, phosphoantigen accumulation induces a conformational change in BTN3A1, rendering its extracellular domains recognizable by Vγ9Vδ2 TCRs. These complementary events provide further evidence for inside-out signaling as an essential step in the recognition of tumor cells by a Vγ9Vδ2 TCR.
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Affiliation(s)
- Zsolt Sebestyen
- Department of Hematology and Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht 3508, the Netherlands
| | - Wouter Scheper
- Department of Hematology and Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht 3508, the Netherlands
| | - Anna Vyborova
- Department of Hematology and Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht 3508, the Netherlands
| | - Siyi Gu
- Department of Clinical Chemistry and Hematology, University Medical Center, Utrecht 3508 GA, the Netherlands
| | - Zuzana Rychnavska
- Department of Hematology and Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht 3508, the Netherlands
| | - Marleen Schiffler
- Department of Hematology and Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht 3508, the Netherlands
| | - Astrid Cleven
- Department of Hematology and Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht 3508, the Netherlands
| | - Coraline Chéneau
- Department of Hematology and Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht 3508, the Netherlands
| | - Martje van Noorden
- Department of Hematology and Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht 3508, the Netherlands
| | - Cassie-Marie Peigné
- INSERM, Unité Mixte de Recherche 892, Centre de Recherche en Cancérologie Nantes Angers, 44000 Nantes, France; University of Nantes, 44000 Nantes, France; Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 6299, 44000 Nantes, France
| | - Daniel Olive
- INSERM, Centre de Recherche en Cancérologie Marseille, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht 3584, the Netherlands
| | - Rimke Oostvogels
- Department of Clinical Chemistry and Hematology, University Medical Center, Utrecht 3508 GA, the Netherlands
| | - Tuna Mutis
- Department of Clinical Chemistry and Hematology, University Medical Center, Utrecht 3508 GA, the Netherlands
| | - Gerrit Jan Schuurhuis
- Department of Hematology, VU University Medical Center, Amsterdam 1081, the Netherlands
| | - Erin J Adams
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57(th) Street, Chicago, IL 60615, USA
| | - Emmanuel Scotet
- INSERM, Unité Mixte de Recherche 892, Centre de Recherche en Cancérologie Nantes Angers, 44000 Nantes, France; University of Nantes, 44000 Nantes, France; Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 6299, 44000 Nantes, France
| | - Jürgen Kuball
- Department of Hematology and Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht 3508, the Netherlands.
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40
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Gall BJ, Wilson A, Schroer AB, Gross JD, Stoilov P, Setola V, Watkins CM, Siderovski DP. Genetic variations in GPSM3 associated with protection from rheumatoid arthritis affect its transcript abundance. Genes Immun 2016; 17:139-47. [PMID: 26821282 PMCID: PMC4777669 DOI: 10.1038/gene.2016.3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/21/2015] [Accepted: 12/22/2015] [Indexed: 12/16/2022]
Abstract
G protein signaling modulator 3 (GPSM3) is a regulator of G protein-coupled receptor signaling, with expression restricted to leukocytes and lymphoid organs. Previous genome-wide association studies have highlighted single-nucleotide polymorphisms (SNPs; rs204989 and rs204991) in a region upstream of the GPSM3 transcription start site as being inversely correlated to the prevalence of rheumatoid arthritis (RA)-this association is supported by the protection afforded to Gpsm3-deficient mice in models of inflammatory arthritis. Here, we assessed the functional consequences of these polymorphisms. We collected biospecimens from 50 volunteers with RA diagnoses, 50 RA-free volunteers matched to the aforementioned group and 100 unmatched healthy young volunteers. We genotyped these individuals for GPSM3 (rs204989, rs204991), CCL21 (rs2812378) and HLA gene region (rs6457620) polymorphisms, and found no significant differences in minor allele frequencies between the RA and disease-free cohorts. However, we identified that individuals homozygous for SNPs rs204989 and rs204991 had decreased GPSM3 transcript abundance relative to individuals homozygous for the major allele. In vitro promoter activity studies suggest that SNP rs204989 is the primary cause of this decrease in transcript levels. Knockdown of GPSM3 in THP-1 cells, a human monocytic cell line, was found to disrupt ex vivo migration to the chemokine MCP-1.
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Affiliation(s)
- BJ Gall
- Department of Physiology & Pharmacology, West Virginia University School of Medicine, Morgantown, WV, USA 26506-9229
| | - A Wilson
- Department of Orthopaedics, West Virginia University School of Medicine, Morgantown, WV, USA 26506-9229
| | - AB Schroer
- Department of Physiology & Pharmacology, West Virginia University School of Medicine, Morgantown, WV, USA 26506-9229
| | - JD Gross
- Department of Physiology & Pharmacology, West Virginia University School of Medicine, Morgantown, WV, USA 26506-9229
| | - P Stoilov
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, WV, USA 26506-9229
| | - V Setola
- Department of Physiology & Pharmacology, West Virginia University School of Medicine, Morgantown, WV, USA 26506-9229
- Department of Behavioral Medicine & Psychiatry, West Virginia University School of Medicine, Morgantown, WV, USA 26506-9229
| | - CM Watkins
- Department of Orthopaedics, West Virginia University School of Medicine, Morgantown, WV, USA 26506-9229
| | - DP Siderovski
- Department of Physiology & Pharmacology, West Virginia University School of Medicine, Morgantown, WV, USA 26506-9229
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41
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Whole-cell biosensor for label-free detection of GPCR-mediated drug responses in personal cell lines. Biosens Bioelectron 2015; 74:233-42. [DOI: 10.1016/j.bios.2015.06.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/09/2015] [Accepted: 06/15/2015] [Indexed: 01/08/2023]
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42
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Oostvogels R, Lokhorst HM, Mutis T. Minor histocompatibility Ags: identification strategies, clinical results and translational perspectives. Bone Marrow Transplant 2015; 51:163-71. [PMID: 26501766 DOI: 10.1038/bmt.2015.256] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 08/11/2015] [Accepted: 08/15/2015] [Indexed: 12/14/2022]
Abstract
Allogeneic stem cell transplantation (allo-SCT) and donor lymphocyte infusion are effective treatment modalities for various hematological malignancies. Their therapeutic effect, the graft-versus-tumor (GvT) effect, is based mainly on an alloimmune response of donor T cells directed at tumor cells, in which differences in the expression of minor histocompatibility Ags (mHags) on the cells of the patient and donor have a crucial role. However, these differences are also responsible for induction of sometimes detrimental GvHD. As relapse and development of GvHD pose major threats for a large proportion of allotransplanted patients, additional therapeutic strategies are required. To augment the GvT response without increasing the risk of GvHD, specific mHag-directed immunotherapeutic strategies have been developed. Over the past years, much effort has been put into the identification of therapeutically relevant mHags to enable these strategies for a substantial proportion of patients. Currently, the concept of mHag-directed immunotherapy is tested in clinical trials on feasibility, safety and efficacy. In this review, we will summarize the recent developments in mHag identification and the clinical data on mHag-specific immune responses and mHag-directed therapies in patients with hematological malignancies. Finally, we will outline the current challenges and future prospectives in the field.
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Affiliation(s)
- R Oostvogels
- Department of Clinical Chemistry and Hematology, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Hematology, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Hematology, VU University Medical Center, Amsterdam, The Netherlands
| | - H M Lokhorst
- Department of Hematology, VU University Medical Center, Amsterdam, The Netherlands
| | - T Mutis
- Department of Clinical Chemistry and Hematology, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Hematology, VU University Medical Center, Amsterdam, The Netherlands
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43
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Spierings E. Minor histocompatibility antigens: past, present, and future. ACTA ACUST UNITED AC 2015; 84:374-60. [PMID: 25262921 DOI: 10.1111/tan.12445] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Indexed: 01/02/2023]
Abstract
Minor histocompatibility (H) antigens are key molecules driving allo-immune responses in both graft-versus-host-disease (GvHD) and in graft-versus-leukemia (GvL) reactivity in human leukocyte antigen (HLA)-matched hematopoietic stem-cell transplantation (HSCT). Dissection of the dual function of minor H antigens became evident through their different modes of tissue and cell expression, i.e. hematopoietic system-restricted or broad. Broadly expressed minor H antigens can cause both GvHD and GvL effects, while hematopoietic system-restricted minor H antigens are more prone to induce GvL responses. This phenomenon renders the latter group of minor H antigens as curative tools for HSCT-based immunotherapy of hematological malignancies and disorders, in which minor H antigen-specific responses are enhanced in order to eradicate the malignant cells. This article describes the immunogenetics of minor H antigens and methods that have been developed to identify them. Moreover, it summarizes the clinical relevance of minor H antigens in transplantation, with special regards to allogeneic HSCT and solid-organ transplantation.
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Affiliation(s)
- Eric Spierings
- Laboratory for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
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44
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Evaluating intra- and inter-individual variation in the human placental transcriptome. Genome Biol 2015; 16:54. [PMID: 25887593 PMCID: PMC4404591 DOI: 10.1186/s13059-015-0627-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/10/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene expression variation is a phenotypic trait of particular interest as it represents the initial link between genotype and other phenotypes. Analyzing how such variation apportions among and within groups allows for the evaluation of how genetic and environmental factors influence such traits. It also provides opportunities to identify genes and pathways that may have been influenced by non-neutral processes. Here we use a population genetics framework and next generation sequencing to evaluate how gene expression variation is apportioned among four human groups in a natural biological tissue, the placenta. RESULTS We estimate that on average, 33.2%, 58.9%, and 7.8% of the placental transcriptome is explained by variation within individuals, among individuals, and among human groups, respectively. Additionally, when technical and biological traits are included in models of gene expression they each account for roughly 2% of total gene expression variation. Notably, the variation that is significantly different among groups is enriched in biological pathways associated with immune response, cell signaling, and metabolism. Many biological traits demonstrate correlated changes in expression in numerous pathways of potential interest to clinicians and evolutionary biologists. Finally, we estimate that the majority of the human placental transcriptome exhibits expression profiles consistent with neutrality; the remainder are consistent with stabilizing selection, directional selection, or diversifying selection. CONCLUSIONS We apportion placental gene expression variation into individual, population, and biological trait factors and identify how each influence the transcriptome. Additionally, we advance methods to associate expression profiles with different forms of selection.
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45
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Brown CC, Havener TM, Medina MW, Jack JR, Krauss RM, McLeod HL, Motsinger-Reif AA. Genome-wide association and pharmacological profiling of 29 anticancer agents using lymphoblastoid cell lines. Pharmacogenomics 2015; 15:137-46. [PMID: 24444404 DOI: 10.2217/pgs.13.213] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Association mapping with lymphoblastoid cell lines (LCLs) is a promising approach in pharmacogenomics research, and in the current study we utilized LCLs to perform association mapping for 29 chemotherapy drugs. MATERIALS & METHODS Currently, we use LCLs to perform genome-wide association mapping of the cytotoxic response of 520 European-Americans to 29 different anticancer drugs; the largest LCL study to date. A novel association approach using a multivariate analysis of covariance design was employed with the software program MAGWAS, testing for differences in the dose-response profiles between genotypes without making assumptions about the response curve or the biologic mode of association. Additionally, by classifying 25 of the 29 drugs into eight families according to structural and mechanistic relationships, MAGWAS was used to test for associations that were shared across each drug family. Finally, a unique algorithm using multivariate responses and multiple linear regressions across pairs of response curves was used for unsupervised clustering of drugs. RESULTS Among the single-drug studies, suggestive associations were obtained for 18 loci, 12 within/near genes. Three of these, MED12L, CHN2 and MGMT, have been previously implicated in cancer pharmacogenomics. The drug family associations resulted in four additional suggestive loci (three contained within/near genes). One of these genes, HDAC4, associated with the DNA alkylating agents, shows possible clinical interactions with temozolomide. For the drug clustering analysis, 18 of 25 drugs clustered into the appropriate family. CONCLUSION This study demonstrates the utility of LCLs in identifying genes that have clinical importance in drug response and for assigning unclassified agents to specific drug families, and proposes new candidate genes for follow-up in a large number of chemotherapy drugs.
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Affiliation(s)
- Chad C Brown
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC 27607, USA
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46
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Yuan Y, Tian L, Lu D, Xu S. Analysis of genome-wide RNA-sequencing data suggests age of the CEPH/Utah (CEU) lymphoblastoid cell lines systematically biases gene expression profiles. Sci Rep 2015; 5:7960. [PMID: 25609584 PMCID: PMC4302305 DOI: 10.1038/srep07960] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/29/2014] [Indexed: 01/19/2023] Open
Abstract
In human, Lymphoblastoid cell lines (LCLs) from the CEPH/CEU (Centre d'Etude du Polymorphisme Humain – Utah) family resource have been extensively used for examining the genetics of gene expression levels. However, we noted that CEU/CEPH cell lines were collected and transformed approximately thirty years ago, much earlier than the other cell lines from the pertaining individuals, which we suspected could potentially affect gene expression, data analysis and results interpretation. In this study, by analyzing RNA sequencing data of CEU and the other three European populations as well as an African population, we systematically examined and evaluated the potential confounding effect of LCL age on gene expression levels and patterns. Our results indicated that gene expression profiles of CEU samples have been biased by the older age of CEU cell lines. Interestingly, most of CEU-specific expressions are associated with functions related to cell proliferation, which are more likely due to older age of cell lines than intrinsic characters of the population. We suggested the results be carefully explained when CEU LCLs are used for transcriptomic data analysis in future studies.
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Affiliation(s)
- Yuan Yuan
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max-Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lei Tian
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max-Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Dongsheng Lu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max-Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shuhua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max-Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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47
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Kuiper JJW, Van Setten J, Ripke S, Van 'T Slot R, Mulder F, Missotten T, Baarsma GS, Francioli LC, Pulit SL, De Kovel CGF, Ten Dam-Van Loon N, Den Hollander AI, Huis in het Veld P, Hoyng CB, Cordero-Coma M, Martín J, Llorenç V, Arya B, Thomas D, Bakker SC, Ophoff RA, Rothova A, De Bakker PIW, Mutis T, Koeleman BPC. A genome-wide association study identifies a functional ERAP2 haplotype associated with birdshot chorioretinopathy. Hum Mol Genet 2014; 23:6081-7. [PMID: 24957906 PMCID: PMC4204766 DOI: 10.1093/hmg/ddu307] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 06/05/2014] [Accepted: 06/12/2014] [Indexed: 12/19/2022] Open
Abstract
Birdshot chorioretinopathy (BSCR) is a rare form of autoimmune uveitis that can lead to severe visual impairment. Intriguingly, >95% of cases carry the HLA-A29 allele, which defines the strongest documented HLA association for a human disease. We have conducted a genome-wide association study in 96 Dutch and 27 Spanish cases, and 398 unrelated Dutch and 380 Spanish controls. Fine-mapping the primary MHC association through high-resolution imputation at classical HLA loci, identified HLA-A*29:02 as the principal MHC association (odds ratio (OR) = 157.5, 95% CI 91.6-272.6, P = 6.6 × 10(-74)). We also identified two novel susceptibility loci at 5q15 near ERAP2 (rs7705093; OR = 2.3, 95% CI 1.7-3.1, for the T allele, P = 8.6 × 10(-8)) and at 14q32.31 in the TECPR2 gene (rs150571175; OR = 6.1, 95% CI 3.2-11.7, for the A allele, P = 3.2 × 10(-8)). The association near ERAP2 was confirmed in an independent British case-control samples (combined meta-analysis P = 1.7 × 10(-9)). Functional analyses revealed that the risk allele of the polymorphism near ERAP2 is strongly associated with high mRNA and protein expression of ERAP2 in B cells. This study further defined an extremely strong MHC risk component in BSCR, and detected evidence for a novel disease mechanism that affects peptide processing in the endoplasmic reticulum.
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Affiliation(s)
- Jonas J W Kuiper
- Department of Ophthalmology, Department of Clinical Chemistry and Hematology
| | | | - Stephan Ripke
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA, Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Tom Missotten
- The Rotterdam Eye Hospital, Rotterdam, The Netherlands
| | | | | | | | | | | | - Anneke I Den Hollander
- Department of Ophthalmology and Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | | | | | - Miguel Cordero-Coma
- Unidad de Uveitis. Servicio de Oftalmología, Hospital Universitario de León, León, Spain
| | - Javier Martín
- Instituto de Parasitología y Biomedicina López-Neyra, IPBLN, CSIC, Granada, Spain
| | - Victor Llorenç
- Institut Clinic d'Oftalmologia (ICOF), Hospital Clinic de Barcelona, Barcelona, Spain
| | - Bharti Arya
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Dhanes Thomas
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Steven C Bakker
- Department of Psychiatry, Rudolph Magnus Institute of Neuroscience
| | - Roel A Ophoff
- Department of Psychiatry, Rudolph Magnus Institute of Neuroscience, Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA and
| | - Aniki Rothova
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Paul I W De Bakker
- Department of Medical Genetics, Department of Epidemiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tuna Mutis
- Department of Clinical Chemistry and Hematology
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Hodges LM, Fyer AJ, Weissman MM, Logue MW, Haghighi F, Evgrafov O, Rotondo A, Knowles JA, Hamilton SP. Evidence for linkage and association of GABRB3 and GABRA5 to panic disorder. Neuropsychopharmacology 2014; 39:2423-31. [PMID: 24755890 PMCID: PMC4138754 DOI: 10.1038/npp.2014.92] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 02/23/2014] [Accepted: 02/24/2014] [Indexed: 01/04/2023]
Abstract
Panic disorder (PD) is a debilitating anxiety disorder characterized by episodes of intense fear with autonomic and psychological symptoms that lead to behavioral impairment. A convergence of genetic and biological evidence implicates gamma-aminobutyric acid type A receptor subunits on chromosome 15q12 as candidate genes for PD. This study investigated 120 Caucasian, multiplex PD pedigrees using regional microsatellites (chr15q11-13) and found support for linkage (logarithm of odds (LOD) ⩾2), with a prominent parent-of-origin effect. Genotyping with 10 single-nucleotide polymorphisms (SNPs) showed linkage to GABRB3 (rs11631421, LOD=4.6) and GABRA5 (rs2075716, LOD=2.2), and allelic association to GABRB3 (rs8024564, p=0.005; rs8025575, p=0.02) and GABRA5 (rs35399885, p=0.05). Genotyping of an independent Sardinian PD trio sample also supported association in the region, again with a parent-of-origin effect. These findings provide genetic evidence for the involvement of the genes GABRB3 and GABRA5 in the susceptibility to PD.
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Affiliation(s)
- Laura M Hodges
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Abby J Fyer
- Department of Psychiatry, Columbia University College of Physicians and Surgeons and the New York State Psychiatric Institute, New York, NY, USA,Department of Psychiatry, Columbia University College of Physicians and Surgeons and the New York State Psychiatric Institute, 1050 Riverside Drive, Unit 82, New York, NY 10032, USA, Tel: +1 212 543 5372, Fax: +1 212 543 6609, E-mail:
| | - Myrna M Weissman
- Department of Psychiatry, Columbia University College of Physicians and Surgeons and the New York State Psychiatric Institute, New York, NY, USA
| | - Mark W Logue
- Biomedical Genetics, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Fatemeh Haghighi
- Department of Psychiatry, Icahn School of Medicine, New York, NY, USA
| | - Oleg Evgrafov
- Department of Psychiatry and Behavioral Sciences, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - James A Knowles
- Department of Psychiatry and Behavioral Sciences, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Steven P Hamilton
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, CA, USA,Department of Psychiatry, Kaiser Permanente Medical Center, San Francisco, CA, USA,Department of Psychiatry, Kaiser Permanente Medical Center, 4141 Geary Boulevard, 3rd Floor, San Francisco, CA 94118, USA, Tel: +1 415 833 2034, Fax: +1 415 833 2034, E-mail:
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Hariani GD, Lam EJ, Havener T, Kwok PY, McLeod HL, Wagner MJ, Motsinger-Reif AA. Application of next generation sequencing to CEPH cell lines to discover variants associated with FDA approved chemotherapeutics. BMC Res Notes 2014; 7:360. [PMID: 24924344 PMCID: PMC4068968 DOI: 10.1186/1756-0500-7-360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 05/30/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The goal of this study was to perform candidate gene association with cytotoxicity of chemotherapeutics in cell line models through resequencing and discovery of rare and low frequency variants along with common variations. Here, an association study of cytotoxicity response to 30 FDA approved drugs was conducted and we applied next generation targeted sequencing technology to discover variants from 103 candidate genes in 95 lymphoblastoid cell lines from 14 CEPH pedigrees. In this article, we called variants across 95 cell lines and performed association analysis for cytotoxic response using the Family Based Association Testing method and software. RESULTS We called 2281 variable SNP genotypes across the 103 genes for these cell lines and identified three genes of significant association within this marker set. Specifically, ATP-binding cassette, sub-family C, member 5 (ABCC5), metallothionein 1A (MT1A) and NAD(P)H dehydrogenase quinone1 (NQO1) were significantly associated with oxaliplatin drug response. The significant SNP on NQO1 (rs1800566) has been linked with poor survival rates in patients with non-small cell lung cancer treated with cisplatin (which belongs to the same class of drugs as oxaliplatin). A SNP (rs1846692) near the 5' region of MT1A was associated with arsenic trioxide. CONCLUSIONS The results from this study are promising and this serves as a proof-of-principle demonstration of the use of sequencing data in the cytotoxicity models of human cell lines. With increased sample sizes, such studies will be a fast and powerful way to associate common and rare variants with drug response; while overcoming the cost and time limitations to recruit cohorts for association study.
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Affiliation(s)
- Gunjan D Hariani
- Bioinformatics Research Center, North Carolina State University, 307 Ricks Hall, 1 Lampe Dr, Raleigh, NC 27695 CB7566, USA
| | - Ernest J Lam
- Cardiovascular Research Institute, UCSF School of Medicine, San Francisco, CA, USA
| | - Tammy Havener
- Center for Institute of Pharmacogenomics and Individualized Therapy, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, UCSF School of Medicine, San Francisco, CA, USA
| | - Howard L McLeod
- Center for Institute of Pharmacogenomics and Individualized Therapy, UNC Chapel Hill, Chapel Hill, NC, USA
- Moffitt Cancer Center, Tampa, FL, USA
| | - Michael J Wagner
- Center for Institute of Pharmacogenomics and Individualized Therapy, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Alison A Motsinger-Reif
- Bioinformatics Research Center, North Carolina State University, 307 Ricks Hall, 1 Lampe Dr, Raleigh, NC 27695 CB7566, USA
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
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50
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Abstract
The existence of BRCA1 was proven in 1990 by mapping predisposition to young-onset breast cancer in families to chromosome 17q21. Knowing that such a gene existed and approximately where it lay triggered efforts by public and private groups to clone and sequence it. The press baptized the competition "the race" and reported on it in detail for the next 4 years. BRCA1 was positionally cloned in September 1994. Twenty years later, I reflect on "the race" and its consequences for breast cancer prevention and treatment.
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Affiliation(s)
- Mary-Claire King
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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