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Shen Z, Zhang T, Twumasi G, Zhang J, Wang J, Xi Y, Wang R, Wang J, Zhang R, Liu H. Genetic analysis of a Kaijiang duck conservation population through genome-wide scan. Br Poult Sci 2024:1-9. [PMID: 38738932 DOI: 10.1080/00071668.2024.2335937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 03/08/2024] [Indexed: 05/14/2024]
Abstract
1. The Kaijiang duck is a native Chinese breed known for its excellent egg laying performance, killing-out percentage (88.57%), and disease resistance. The assessment of population genetic structure is the basis for understanding the genetics of indigenous breeds and for their protection and management.2. In this study, whole-genome sequencing was performed on 60 Kaijiang ducks to identify genetic variations and investigate the population structure. Homozygosity (ROH) analysis was conducted to assess inbreeding levels in the population.3. The study revealed a moderate level of inbreeding, indicated by an average inbreeding coefficient of 0.1043. This may impact the overall genetic diversity.4. Genomic Regions of Interest identified included 168 genomic regions exhibiting high levels of autozygosity. These regions were associated with processes including muscle growth, pigmentation, neuromodulation, and growth and reproduction.5. The significance of these pathways indicated their potential role in shaping the desirable traits of the Kaijiang duck. These findings provide insights into the genetic basis of the Kaijiang duck's desirable traits and can inform future breeding and conservation efforts.
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Affiliation(s)
- Z Shen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - T Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - G Twumasi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - J Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - J Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Y Xi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - R Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - J Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - R Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - H Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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2
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Lawson JM, Shilton CA, Lindsay-McGee V, Psifidi A, Wathes DC, Raudsepp T, de Mestre AM. Does inbreeding contribute to pregnancy loss in Thoroughbred horses? Equine Vet J 2024. [PMID: 38221707 DOI: 10.1111/evj.14057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 12/29/2023] [Indexed: 01/16/2024]
Abstract
BACKGROUND Excessive inbreeding increases the probability of uncovering homozygous recessive genotypes and has been associated with an increased risk of retained placenta and lower semen quality. No genomic analysis has investigated the association between inbreeding levels and pregnancy loss. OBJECTIVES To compare genetic inbreeding coefficients (F) of naturally occurring Thoroughbred Early Pregnancy Loss (EPLs), Mid and Late term Pregnancy Loss (MLPL) and Controls. The F value was hypothesised to be higher in cases of pregnancy loss (EPLs and MLPLs) than Controls. STUDY DESIGN Observational case-control study. METHODS Allantochorion and fetal DNA from EPL (n = 37, gestation age 14-65 days), MLPL (n = 94, gestational age 70 days-24 h post parturition) and Controls (n = 58) were genotyped on the Axiom Equine 670K SNP Genotyping Array. Inbreeding coefficients using Runs of Homozygosity (FROH) were calculated using PLINK software. ROHs were split into size categories to investigate the recency of inbreeding. RESULTS MLPLs had significantly higher median number of ROH (188 interquartile range [IQR], 180.8-197.3), length of ROH (3.10, IQR 2.93-3.33), and total number of ROH (590.8, IQR 537.3-632.3), and FROH (0.26, IQR 0.24-0.28) when compared with the Controls and the EPLs (p < 0.05). There was no significant difference in any of the inbreeding indices between the EPLs and Controls. The MLPLs had a significantly higher proportion of long (>10 Mb) ROH (2.5%, IQR 1.6-3.6) than the Controls (1.7%, IQR 0.6-2.5), p = 0.001. No unique ROHs were found in the EPL or MLPL populations. MAIN LIMITATIONS SNP-array data does not allow analysis of every base in the sequence. CONCLUSIONS This first study of the effect of genomic inbreeding levels on pregnancy loss showed that inbreeding is a contributor to MLPL, but not EPL in the UK Thoroughbred population. Mating choices remain critical, because inbreeding may predispose to MLPL by increasing the risk of homozygosity for specific lethal allele(s).
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Affiliation(s)
- Jessica M Lawson
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, UK
| | - Charlotte A Shilton
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, University of London, London, UK
| | - Victoria Lindsay-McGee
- Department of Clinical Science and Services, The Royal Veterinary College, University of London, London, UK
| | - Androniki Psifidi
- Department of Clinical Science and Services, The Royal Veterinary College, University of London, London, UK
| | - D Claire Wathes
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, UK
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
| | - Amanda M de Mestre
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, University of London, London, UK
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3
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Prem P, Muneshwar KN, Agrawal S, Jaiswal A. The Impact of Increased Homozygosity on Human Fertility: A Comprehensive Review. Cureus 2023; 15:e49000. [PMID: 38111431 PMCID: PMC10726075 DOI: 10.7759/cureus.49000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 11/18/2023] [Indexed: 12/20/2023] Open
Abstract
This comprehensive review explores the multifaceted relationship between increased homozygosity and human fertility, delving into the genetic, ethical, cultural, and public health dimensions of this complex phenomenon. Homozygosity, characterized by identical alleles at specific gene loci, can result from consanguineous marriages, genetic drift, and population isolation. The review highlights key findings, including the heightened risk of recessive genetic disorders, the implications for immune system diversity, and the influence on complex traits and diseases. It underscores the critical role of genetic counseling in addressing these consequences, considering the ethical implications, and respecting cultural practices. The delicate balance between genetic diversity and cultural norms is emphasized, calling for increased awareness and community engagement. Looking ahead, the review suggests emerging technologies, longitudinal studies, and interdisciplinary research as crucial avenues for further exploration, with the ultimate goal of informing effective public health policies and interventions that safeguard genetic diversity and cultural traditions for future generations.
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Affiliation(s)
- Pranjal Prem
- Community Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Komal N Muneshwar
- Community Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Suyash Agrawal
- Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Arpita Jaiswal
- Obstetrics and Gynaecology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
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4
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Pacheco HA, Rossoni A, Cecchinato A, Peñagaricano F. Identification of runs of homozygosity associated with male fertility in Italian Brown Swiss cattle. Front Genet 2023; 14:1227310. [PMID: 37485336 PMCID: PMC10356982 DOI: 10.3389/fgene.2023.1227310] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023] Open
Abstract
Intensive selection for improved productivity has been accompanied by an increase in inbreeding rates and a reduction in genetic diversity. The increase in inbreeding tends to impact performance, especially fitness-related traits such as male fertility. Inbreeding can be monitored using runs of homozygosity (ROH), defined as contiguous lengths of homozygous genotypes observed in an individual's chromosome. The goal of this study was to evaluate the presence of ROH in Italian Brown Swiss cattle and assess its association with bull fertility. First, we evaluated the association between ROH and male fertility using 1,102 Italian Brown Swiss bulls with sire conception rate records and 572 K SNPs spanning the entire genome. Second, we split the entire population into 100 high-fertility and 100 low-fertility bulls to investigate the potential enrichment of ROH segments in the low-fertility group. Finally, we mapped the significant ROH regions to the bovine genome to identify candidate genes associated with sperm biology and male fertility. Notably, there was a negative association between bull fertility and the amount of homozygosity. Four different ROH regions located in chromosomes 6, 10, 11, and 24 were significantly overrepresented in low-fertility bulls (Fisher's exact test, p-value <0.01). Remarkably, these four genomic regions harbor many genes such as WDR19, RPL9, LIAS, UBE2K, DPF3, 5S-rRNA, 7SK, U6, and WDR7 that are related to sperm biology and male fertility. Overall, our findings suggest that inbreeding and increased homozygosity have a negative impact on male fertility in Italian Brown Swiss cattle. The quantification of ROH can contribute to minimizing the inbreeding rate and avoid its negative effect on fitness-related traits, such as male fertility.
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Affiliation(s)
- Hendyel A. Pacheco
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Alessio Cecchinato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padua, Italy
| | - Francisco Peñagaricano
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
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5
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Chaban R, McGrath G, Habibabady Z, Rosales I, Burdorf L, Ayares DL, Rybak E, Zhang T, Harris DG, Dahi S, Ali F, Parsell DM, Braileanu G, Cheng X, Sievert E, Phelps C, Azimzadeh AM, Pierson RN. Increased human complement pathway regulatory protein gene dose is associated with increased endothelial expression and prolonged survival during ex-vivo perfusion of GTKO pig lungs with human blood. Xenotransplantation 2023; 30:e12812. [PMID: 37504492 DOI: 10.1111/xen.12812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/29/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023]
Abstract
INTRODUCTION Expression of human complement pathway regulatory proteins (hCPRP's) such as CD46 or CD55 has been associated with improved survival of pig organ xenografts in multiple different models. Here we evaluate the hypothesis that an increased human CD46 gene dose, through homozygosity or additional expression of a second hCPRP, is associated with increased protein expression and with improved protection from injury when GTKO lung xenografts are perfused with human blood. METHODS Twenty three GTKO lungs heterozygous for human CD46 (GTKO.heteroCD46), 10 lungs homozygous for hCD46 (GTKO.homoCD46), and six GTKO.homoCD46 lungs also heterozygous for hCD55 (GTKO.homoCD46.hCD55) were perfused with human blood for up to 4 h in an ex vivo circuit. RESULTS Relative to GTKO.heteroCD46 (152 min, range 5-240; 6/23 surviving at 4 h), survival was significantly improved for GTKO.homoCD46 (>240 min, range 45-240, p = .034; 7/10 surviving at 4 h) or GTKO.homoCD46.hCD55 lungs (>240 min, p = .001; 6/6 surviving at 4 h). Homozygosity was associated with increased capillary expression of hCD46 (p < .0001). Increased hCD46 expression was associated with significantly prolonged lung survival (p = .048),) but surprisingly not with reduction in measured complement factor C3a. Hematocrit, monocyte count, and pulmonary vascular resistance were not significantly altered in association with increased hCD46 gene dose or protein expression. CONCLUSION Genetic engineering approaches designed to augment hCPRP activity - increasing the expression of hCD46 through homozygosity or co-expressing hCD55 with hCD46 - were associated with prolonged GTKO lung xenograft survival. Increased expression of hCD46 was associated with reduced coagulation cascade activation, but did not further reduce complement activation relative to lungs with relatively low CD46 expression. We conclude that coagulation pathway dysregulation contributes to injury in GTKO pig lung xenografts perfused with human blood, and that the survival advantage for lungs with increased hCPRP expression is likely attributable to improved endothelial thromboregulation.
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Affiliation(s)
- Ryan Chaban
- Center for Transplantation Sciences and Department of Surgery, Massachusetts General Hospital and Harvard School of Medicine, Boston, Massachusetts, USA
- Department of Cardiac and Vascular Surgery, University Hospital of Johannes Gutenberg University Mainz, Mainz, Germany
| | - Gannon McGrath
- Center for Transplantation Sciences and Department of Surgery, Massachusetts General Hospital and Harvard School of Medicine, Boston, Massachusetts, USA
| | - Zahra Habibabady
- Center for Transplantation Sciences and Department of Surgery, Massachusetts General Hospital and Harvard School of Medicine, Boston, Massachusetts, USA
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ivy Rosales
- Center for Transplantation Sciences and Department of Surgery, Massachusetts General Hospital and Harvard School of Medicine, Boston, Massachusetts, USA
| | - Lars Burdorf
- Center for Transplantation Sciences and Department of Surgery, Massachusetts General Hospital and Harvard School of Medicine, Boston, Massachusetts, USA
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Revivicor, Inc., Blacksburg, Virginia, USA
| | | | - Elana Rybak
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Tianshu Zhang
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Donald G Harris
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Siamak Dahi
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Franchesca Ali
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Dawn M Parsell
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Gheorghe Braileanu
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Xiangfei Cheng
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Evelyn Sievert
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | - Agnes M Azimzadeh
- Center for Transplantation Sciences and Department of Surgery, Massachusetts General Hospital and Harvard School of Medicine, Boston, Massachusetts, USA
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Richard N Pierson
- Center for Transplantation Sciences and Department of Surgery, Massachusetts General Hospital and Harvard School of Medicine, Boston, Massachusetts, USA
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
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6
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Peter VG, Kaminska K, Santos C, Quinodoz M, Cancellieri F, Cisarova K, Pescini Gobert R, Rodrigues R, Custódio S, Paris LP, Sousa AB, Coutinho Santos L, Rivolta C. The first genetic landscape of inherited retinal dystrophies in Portuguese patients identifies recurrent homozygous mutations as a frequent cause of pathogenesis. PNAS Nexus 2023; 2:pgad043. [PMID: 36909829 PMCID: PMC10003751 DOI: 10.1093/pnasnexus/pgad043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/15/2023]
Abstract
Inherited retinal diseases (IRDs) are a group of ocular conditions characterized by an elevated genetic and clinical heterogeneity. They are transmitted almost invariantly as monogenic traits. However, with more than 280 disease genes identified so far, association of clinical phenotypes with genotypes can be very challenging, and molecular diagnosis is essential for genetic counseling and correct management of the disease. In addition, the prevalence and the assortment of IRD mutations are often population-specific. In this work, we examined 230 families from Portugal, with individuals suffering from a variety of IRD diagnostic classes (270 subjects in total). Overall, we identified 157 unique mutations (34 previously unreported) in 57 distinct genes, with a diagnostic rate of 76%. The IRD mutational landscape was, to some extent, different from those reported in other European populations, including Spanish cohorts. For instance, the EYS gene appeared to be the most frequently mutated, with a prevalence of 10% among all IRD cases. This was, in part, due to the presence of a recurrent and seemingly founder mutation involving the deletion of exons 13 and 14 of this gene. Moreover, our analysis highlighted that as many as 51% of our cases had mutations in a homozygous state. To our knowledge, this is the first study assessing a cross-sectional genotype-phenotype landscape of IRDs in Portugal. Our data reveal a rather unique distribution of mutations, possibly shaped by a small number of rare ancestral events that have now become prevalent alleles in patients.
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Affiliation(s)
- Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland.,Department of Ophthalmology, Inselspital, Bern University Hospital, Bern 3010, Switzerland
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Cristina Santos
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto (IOGP), Lisbon 1169-019, Portugal.,iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisbon 1169-056, Portugal
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Katarina Cisarova
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | | | - Raquel Rodrigues
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon 1649-035, Portugal
| | - Sónia Custódio
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon 1649-035, Portugal
| | - Liliana P Paris
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto (IOGP), Lisbon 1169-019, Portugal
| | - Ana Berta Sousa
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon 1649-035, Portugal.,Laboratory of Basic Immunology, Faculty of Medicine, University of Lisbon, Lisbon 1649-028, Portugal
| | - Luisa Coutinho Santos
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto (IOGP), Lisbon 1169-019, Portugal
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
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7
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Ziegler TE, Molina A, Ramón M, Sanchez M, Muñoz-Mejías E, Antonini A, Demyda-Peyrás S. Analysis of the genomic landscape of inbreeding in two divergent groups of Spanish Florida goats. J Anim Breed Genet 2023; 140:316-329. [PMID: 36751887 DOI: 10.1111/jbg.12759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 01/14/2023] [Indexed: 02/09/2023]
Abstract
The analysis of the genomic landscape of inbreeding using runs of homozygosity (ROH) patterns is becoming an interesting tool to partially understand phenotypic differences among individuals. In this study, we analysed genome-wide ROH patterns in two groups of Florida goats. We first determined the inbreeding levels of each individual by calculating ROH-based inbreeding coefficients (FROH ). Then, the individuals were divided into two groups based on FROH : high inbreeding (HI, FROH >0.1) and low inbreeding (LI, FROH <0.03). Finally, we performed an extensive in-depth analysis of ROH distribution in each group separately. We found a higher abundance of short ROH in LI, whereas long ROH was more frequent in HI. Furthermore, ROH abundance was not evenly distributed among chromosomes within groups, with some chromosomes showing larger numbers of ROH, like CHI6, CHI7 and CHI27. A different landscape was observed in recent inbreeding (ROH >8 Mb), with significant increases in CHI6, CHI11 and CHI28. Determination of genomic regions with significantly increased ROH (ROH islands-ROHi) showed 13 ROHi related to whole inbreeding and five ROHi associated with recent inbreeding analysis. Within these genomic regions, 123 and 101 genes were identified in HI and LI, respectively, including 10 and seven candidate genes previously related to production, fertility and heat resistance in goats and livestock species.
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Affiliation(s)
- Tatiana E Ziegler
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando N. Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - Antonio Molina
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - Manuel Ramón
- IRIAF-CERSYRA - Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal, Centro Regional de Selección y Reproducción Animal, Ciudad Real, Spain
| | - Manuel Sanchez
- Departamento de Producción Animal, Universidad de Córdoba, Córdoba, Spain
| | - Eva Muñoz-Mejías
- Departamento de Patología Animal, Producción Animal, Bromatología y Tecnología de los Alimentos, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Alicia Antonini
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - Sebastián Demyda-Peyrás
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET LA PLATA), La Plata, Argentina
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8
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Runge J, König B, Lindholm AK, Bendesky A. Parent-offspring inference in inbred populations. Mol Ecol Resour 2022; 22:2981-2993. [PMID: 35770342 PMCID: PMC9796703 DOI: 10.1111/1755-0998.13680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 06/03/2022] [Accepted: 06/16/2022] [Indexed: 01/07/2023]
Abstract
Genealogical relationships are fundamental components of genetic studies. However, it is often challenging to infer correct and complete pedigrees even when genome-wide information is available. For example, inbreeding can obscure genetic differences between individuals, making it difficult to even distinguish first-degree relatives such as parent-offspring from full siblings. Similarly, genotyping errors can interfere with the detection of genetic similarity between parents and their offspring. Inbreeding is common in natural, domesticated, and experimental populations and genotyping of these populations often has more errors than in human data sets, so efficient methods for building pedigrees under these conditions are necessary. Here, we present a new method for parent-offspring inference in inbred pedigrees called specific parent-offspring relationship estimation (spore). spore is vastly superior to existing pedigree-inference methods at detecting parent-offspring relationships, in particular when inbreeding is high or in the presence of genotyping errors, or both. spore therefore fills an important void in the arsenal of pedigree inference tools.
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Affiliation(s)
- Jan‐Niklas Runge
- Department of Ecology, Evolution and Environmental Biology, Zuckerman Mind Brain Behavior InstituteColumbia UniversityNew YorkNYUSA,Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZürichSwitzerland
| | - Barbara König
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZürichSwitzerland
| | - Anna K. Lindholm
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZürichSwitzerland
| | - Andres Bendesky
- Department of Ecology, Evolution and Environmental Biology, Zuckerman Mind Brain Behavior InstituteColumbia UniversityNew YorkNYUSA
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9
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Rafiullah R, Albalawi AM, Alaradi SR, Alluqmani M, Mushtaq M, Wali A, Basit S. An expansion of phenotype: novel homozygous variant in the MED17 identified in patients with progressive microcephaly and global developmental delay. J Neurogenet 2022; 36:108-114. [PMID: 36508181 DOI: 10.1080/01677063.2022.2149748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Global developmental delay (GDD) is a lifelong disability that affects 1-3% of the population around the globe. It is phenotypically variable and highly heterogeneous in terms of the underlying genetics. Patients with GDD are intellectually disabled (ID) manifesting cognitive impairment and deficient adaptive behavior. Here, we investigated a two-looped consanguineous family segregating severe ID, seizure, and progressive microcephaly. Magnetic resonance imaging (MRI) of the brain showed mild brain atrophy and myelination defect. Whole exome sequencing (WES) was performed on the DNA samples of two patients and a novel homozygous missense variant (Chr11:g0.93528085; NM_004268.5_c.871T > C; p. Trp291Gly) was identified in the MED17 gene. Sanger sequencing revealed that the identified variant is heterozygous in both parents and healthy siblings. This variant is conserved among different species, causes a non-conserved amino acid change, and is predicted deleterious by various in silico tools. The variant is not reported in population variant databases. MED17 (OMIM: 613668) encodes for the mediator of RNA polymerase II transcription complex subunit 17. Structure modeling of MED17 protein revealed that Trp291 is involved in different inter-helical interactions, providing structural stability. Replacement of Trp291Gly, a less hydrophobic amino acid loses the inter-helical interaction leading to a perturb variant of MED17 protein.
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Affiliation(s)
- Rafiullah Rafiullah
- Department of Biotechnology, Faculty of Life Sciences & Informatics, BUITEMS, Quetta, Pakistan
| | - Alia M Albalawi
- Center for Genetics and Inherited Diseases, Taibah University, Madinah, Saudi Arabia
| | - Sultan R Alaradi
- Department of Laboratory and Blood Bank, Alwajh General Hospital, Ministry of Health, Alwajh, Saudi Arabia
| | - Majed Alluqmani
- College of Medicine, Taibah University, Madinah, Saudi Arabia
| | - Muhammad Mushtaq
- Department of Biotechnology, Faculty of Life Sciences & Informatics, BUITEMS, Quetta, Pakistan
| | - Abdul Wali
- Department of Biotechnology, Faculty of Life Sciences & Informatics, BUITEMS, Quetta, Pakistan
| | - Sulman Basit
- Center for Genetics and Inherited Diseases, Taibah University, Madinah, Saudi Arabia.,Department of Biochemistry and Molecular Medicine, College of Medicine, Taibah University, Madinah, Saudi Arabia
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10
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Hantgan A, Babiker H, List JM. First steps towards the detection of contact layers in Bangime: a multi-disciplinary, computer-assisted approach. Open Res Eur 2022; 2:10. [PMID: 37645276 PMCID: PMC10445931 DOI: 10.12688/openreseurope.14339.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/12/2022] [Indexed: 08/31/2023]
Abstract
Bangime is a language isolate, which has not been proven to be genealogically related to any other language family, spoken in Central-Eastern Mali. Its speakers, the Bangande, claim affiliation with the Dogon languages and speakers that surround them throughout a cliff range known as the Bandiagara Escarpment. However, recent genetic research has shown that the Bangande are genetically distant from the Dogon and other groups. Furthermore, the Bangande people represent a genetic isolate. Despite the geographic isolation of the Bangande people, evidence of language contact is apparent in the Bangime language. We find a plethora of shared vocabulary with neighboring Atlantic, Dogon, Mande, and Songhai language groups. To address the problem of when and whence this vocabulary emerged in the language, we use a computer-assisted, multidisciplinary approach to investigate layers of contact and inheritance in Bangime. We start from an automated comparison of lexical data from languages belonging to different language families in order to obtain a first account on potential loanword candidates in our sample. In a second step, we use specific interfaces to refine and correct the computational findings. The revised sample is then investigated quantitatively and qualitatively by focusing on vocabularies shared exclusively between specific languages. We couch our results within archeological and historical research from Central-Eastern Mali more generally and propose a scenario in which the Bangande formed part of the expansive Mali Empire that encompassed most of West Africa from the 13th to the 16th centuries. We consider our methods to represent a novel approach to the investigation of a language and population isolate from multiple perspectives using innovative computer-assisted technologies.
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Affiliation(s)
- Abbie Hantgan
- Langage, Langues et Cultures d'Afrique (LLACAN, UMR 8135), Centre national de la recherche scientifique (CNRS) and l’Institut National des Langues et Civilisations Orientales (INALCO), Paris, France
| | - Hiba Babiker
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Johann-Mattis List
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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11
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Hantgan A, Babiker H, List JM. First steps towards the detection of contact layers in Bangime: a multi-disciplinary, computer-assisted approach. Open Res Eur 2022; 2:10. [PMID: 37645276 PMCID: PMC10445931 DOI: 10.12688/openreseurope.14339.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/12/2022] [Indexed: 08/31/2023]
Abstract
Bangime is a language isolate, which has not been proven to be genealogically related to any other language family, spoken in Central-Eastern Mali. Its speakers, the Bangande, claim affiliation with the Dogon languages and speakers that surround them throughout a cliff range known as the Bandiagara Escarpment. However, recent genetic research has shown that the Bangande are genetically distant from the Dogon and other groups. Furthermore, the Bangande people represent a genetic isolate. Despite the geographic isolation of the Bangande people, evidence of language contact is apparent in the Bangime language. We find a plethora of shared vocabulary with neighboring Atlantic, Dogon, Mande, and Songhai language groups. To address the problem of when and whence this vocabulary emerged in the language, we use a computer-assisted, multidisciplinary approach to investigate layers of contact and inheritance in Bangime. We start from an automated comparison of lexical data from languages belonging to different language families in order to obtain a first account on potential loanword candidates in our sample. In a second step, we use specific interfaces to refine and correct the computational findings. The revised sample is then investigated quantitatively and qualitatively by focusing on vocabularies shared exclusively between specific languages. We couch our results within archeological and historical research from Central-Eastern Mali more generally and propose a scenario in which the Bangande formed part of the expansive Mali Empire that encompassed most of West Africa from the 13th to the 16th centuries. We consider our methods to represent a novel approach to the investigation of a language and population isolate from multiple perspectives using innovative computer-assisted technologies.
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Affiliation(s)
- Abbie Hantgan
- Langage, Langues et Cultures d'Afrique (LLACAN, UMR 8135), Centre national de la recherche scientifique (CNRS) and l’Institut National des Langues et Civilisations Orientales (INALCO), Paris, France
| | - Hiba Babiker
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Johann-Mattis List
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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12
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Kannabiran C, Parameswarappa D, Jalali S. Genetics of Inherited Retinal Diseases in Understudied Populations. Front Genet 2022; 13:858556. [PMID: 35295952 PMCID: PMC8919366 DOI: 10.3389/fgene.2022.858556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/03/2022] [Indexed: 11/17/2022] Open
Abstract
Retinitis pigmentosa is one of the major forms of inherited retinal dystrophy transmitted in all Mendelian and non-Mendelian forms of inheritance. It involves the loss of retinal photoreceptor cells with severe loss of vision or blindness within the first 2 decades of life. RP occurs at a relatively high prevalence in India and is often associated with consanguinity in certain South Asian communities where this practice is customary. This review describes the studies that have been published with regard to genetics of retinitis pigmentosa in India and neighboring South Asian countries. These populations have been understudied in these aspects although to a variable degree from one country to another. Genetic studies on RP in India have been carried out with a range of methods aimed at detecting specific mutations, to screening of candidate genes or selected genomic regions, homozygosity mapping to whole genome sequencing. These efforts have led to a molecular genetic characterization of RP in Indian families. Similar studies on large extended families from Pakistan have provided insight into several novel genes underlying the pathogenesis of these diseases. The extreme degree of clinical and genetic heterogeneity of RP renders it challenging to identify the associated genes in these populations, and to translate the research output towards better management of the disease, as there are no unifying genetic features that are characteristic of any population so far.
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Affiliation(s)
- Chitra Kannabiran
- Kallam Anji Reddy Molecular Genetics Laboratory, Prof Brien Holden Eye Research Centre, Hyderabad, India.,L. V. Prasad Eye Institute, Hyderabad, India
| | - Deepika Parameswarappa
- L. V. Prasad Eye Institute, Hyderabad, India.,Smt Kannuri Santhamma Centre for Retina Vitreous Services, Hyderabad, India
| | - Subhadra Jalali
- L. V. Prasad Eye Institute, Hyderabad, India.,Smt Kannuri Santhamma Centre for Retina Vitreous Services, Hyderabad, India
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13
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Bain BJ, Littlewood T, Rees DC. What does the term 'sickle cell disease' mean? Br J Haematol 2021; 197:381-382. [PMID: 34961949 DOI: 10.1111/bjh.18024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Barbara J Bain
- Centre for Haematology, St Mary's Hospital Campus of Imperial College London, St Mary's Hospital, London, UK
| | - Tim Littlewood
- Retired Consultant Haematologist, Oxford University Hospital, Oxford, UK
| | - David C Rees
- Department of Haematological Medicine, King's College London, King's College Hospital, London, UK
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14
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Seitz S, Lange V, Norman PJ, Sauter J, Schmidt AH. Estimating HLA haplotype frequencies from homozygous individuals - A Technical Report. Int J Immunogenet 2021; 48:490-495. [PMID: 34570965 PMCID: PMC9131737 DOI: 10.1111/iji.12553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/28/2021] [Accepted: 07/08/2021] [Indexed: 01/31/2023]
Abstract
We estimated HLA haplotype frequencies based on individuals homozygous for 4, 5 or 6 loci. Validation of our approach using a sample of over 3.4 million German individuals was successful. Compared to an expectation‐maximization algorithm, the errors were larger. However, our approach allows the unequivocal detection of rare haplotypes.
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Affiliation(s)
| | | | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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15
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Dickel L, Arcese P, Nietlisbach P, Keller LF, Jensen H, Reid JM. Are immigrants outbred and unrelated? Testing standard assumptions in a wild metapopulation. Mol Ecol 2021; 30:5674-5686. [PMID: 34516687 DOI: 10.1111/mec.16173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 11/30/2022]
Abstract
Immigration into small recipient populations is expected to alleviate inbreeding and increase genetic variation, and hence facilitate population persistence through genetic and/or evolutionary rescue. Such expectations depend on three standard assumptions: that immigrants are outbred, unrelated to existing natives at arrival, and unrelated to each other. These assumptions are rarely explicitly verified, including in key field systems in evolutionary ecology. Yet, they could be violated due to non-random or repeated immigration from adjacent small populations. We combined molecular genetic marker data for 150-160 microsatellite loci with comprehensive pedigree data to test the three assumptions for a song sparrow (Melospiza melodia) population that is a model system for quantifying effects of inbreeding and immigration in the wild. Immigrants were less homozygous than existing natives on average, with mean homozygosity that closely resembled outbred natives. Immigrants can therefore be considered outbred on the focal population scale. Comparisons of homozygosity of real or hypothetical offspring of immigrant-native, native-native and immigrant-immigrant pairings implied that immigrants were typically unrelated to existing natives and to each other. Indeed, immigrants' offspring would be even less homozygous than outbred individuals on the focal population scale. The three standard assumptions of population genetic and evolutionary theory were consequently largely validated. Yet, our analyses revealed some deviations that should be accounted for in future analyses of heterosis and inbreeding depression, implying that the three assumptions should be verified in other systems to probe patterns of non-random or repeated dispersal and facilitate precise and unbiased estimation of key evolutionary parameters.
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Affiliation(s)
- Lisa Dickel
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Peter Arcese
- Department of Forest & Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pirmin Nietlisbach
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Lukas F Keller
- Department of Evolutionary Biology & Environmental Studies, University of Zurich, Zurich, Switzerland.,Zoological Museum, University of Zurich, Zurich, Switzerland
| | - Henrik Jensen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jane M Reid
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway.,School of Biological Sciences, University of Aberdeen, Aberdeen, UK
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16
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Doekes HP, Bijma P, Windig JJ. How Depressing Is Inbreeding? A Meta-Analysis of 30 Years of Research on the Effects of Inbreeding in Livestock. Genes (Basel) 2021; 12:926. [PMID: 34207101 DOI: 10.3390/genes12060926] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022] Open
Abstract
Inbreeding depression has been widely documented for livestock and other animal and plant populations. Inbreeding is generally expected to have a stronger unfavorable effect on fitness traits than on other traits. Traditionally, the degree of inbreeding depression in livestock has been estimated as the slope of the linear regression of phenotypic values on pedigree-based inbreeding coefficients. With the increasing availability of SNP-data, pedigree inbreeding can now be replaced by SNP-based measures. We performed a meta-analysis of 154 studies, published from 1990 to 2020 on seven livestock species, and compared the degree of inbreeding depression (1) across different trait groups, and (2) across different pedigree-based and SNP-based measures of inbreeding. Across all studies and traits, a 1% increase in pedigree inbreeding was associated with a median decrease in phenotypic value of 0.13% of a trait’s mean, or 0.59% of a trait’s standard deviation. Inbreeding had an unfavorable effect on all sorts of traits and there was no evidence for a stronger effect on primary fitness traits (e.g., reproduction/survival traits) than on other traits (e.g., production traits or morphological traits). p-values of inbreeding depression estimates were smaller for SNP-based inbreeding measures than for pedigree inbreeding, suggesting more power for SNP-based measures. There were no consistent differences in p-values for percentage of homozygous SNPs, inbreeding based on runs of homozygosity (ROH) or inbreeding based on a genomic relationship matrix. The number of studies that directly compares these different measures, however, is limited and comparisons are furthermore complicated by differences in scale and arbitrary definitions of particularly ROH-based inbreeding. To facilitate comparisons across studies in future, we provide the dataset with inbreeding depression estimates of 154 studies and stress the importance of always reporting detailed information (on traits, inbreeding coefficients, and models used) along with inbreeding depression estimates.
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17
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Moore A, Machiela MJ, Machado M, Wang SS, Kane E, Slager SL, Zhou W, Carrington M, Lan Q, Milne RL, Birmann BM, Adami HO, Albanes D, Arslan AA, Becker N, Benavente Y, Bisanzi S, Boffetta P, Bracci PM, Brennan P, Brooks-Wilson AR, Canzian F, Caporaso N, Clavel J, Cocco P, Conde L, Cox DG, Cozen W, Curtin K, De Vivo I, de Sanjose S, Foretova L, Gapstur SM, Ghesquières H, Giles GG, Glenn M, Glimelius B, Gao C, Habermann TM, Hjalgrim H, Jackson RD, Liebow M, Link BK, Maynadie M, McKay J, Melbye M, Miligi L, Molina TJ, Monnereau A, Nieters A, North KE, Offit K, Patel AV, Piro S, Ravichandran V, Riboli E, Salles G, Severson RK, Skibola CF, Smedby KE, Southey MC, Spinelli JJ, Staines A, Stewart C, Teras LR, Tinker LF, Travis RC, Vajdic CM, Vermeulen RCH, Vijai J, Weiderpass E, Weinstein S, Doo NW, Zhang Y, Zheng T, Chanock SJ, Rothman N, Cerhan JR, Dean M, Camp NJ, Yeager M, Berndt SI. Genome-wide homozygosity and risk of four non-Hodgkin lymphoma subtypes. J Transl Genet Genom 2021; 5:200-217. [PMID: 34622145 PMCID: PMC8494431 DOI: 10.20517/jtgg.2021.08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
AIM Recessive genetic variation is thought to play a role in non-Hodgkin lymphoma (NHL) etiology. Runs of homozygosity (ROH), defined based on long, continuous segments of homozygous SNPs, can be used to estimate both measured and unmeasured recessive genetic variation. We sought to examine genome-wide homozygosity and NHL risk. METHODS We used data from eight genome-wide association studies of four common NHL subtypes: 3061 chronic lymphocytic leukemia (CLL), 3814 diffuse large B-cell lymphoma (DLBCL), 2784 follicular lymphoma (FL), and 808 marginal zone lymphoma (MZL) cases, as well as 9374 controls. We examined the effect of homozygous variation on risk by: (1) estimating the fraction of the autosome containing runs of homozygosity (FROH); (2) calculating an inbreeding coefficient derived from the correlation among uniting gametes (F3); and (3) examining specific autosomal regions containing ROH. For each, we calculated beta coefficients and standard errors using logistic regression and combined estimates across studies using random-effects meta-analysis. RESULTS We discovered positive associations between FROH and CLL (β = 21.1, SE = 4.41, P = 1.6 × 10-6) and FL (β = 11.4, SE = 5.82, P = 0.02) but not DLBCL (P = 1.0) or MZL (P = 0.91). For F3, we observed an association with CLL (β = 27.5, SE = 6.51, P = 2.4 × 10-5). We did not find evidence of associations with specific ROH, suggesting that the associations observed with FROH and F3 for CLL and FL risk were not driven by a single region of homozygosity. CONCLUSION Our findings support the role of recessive genetic variation in the etiology of CLL and FL; additional research is needed to identify the specific loci associated with NHL risk.
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Affiliation(s)
- Amy Moore
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Moara Machado
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Sophia S Wang
- Division of Health Analytics, City of Hope Beckman Research Institute, Duarte, CA 91010, USA
| | - Eleanor Kane
- Department of Health Sciences, University of York, York YO10 5DD, UK
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD 20877, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD 20892, USA
- Ragon Institute of MGH, Cambridge, MA 02139, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria 3800, Australia
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hans-Olov Adami
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17176, Sweden
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Institute of Health and Society, Clinical Effectiveness Research Group, University of Oslo, Oslo 0315, Norway
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alan A Arslan
- Department of Obstetrics and Gynecology, New York University School of Medicine, New York, NY 10016, USA
- Department of Population Health, New York University School of Medicine, New York, NY 10016, USA
- Perlmutter Comprehensive Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Nikolaus Becker
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg 69120, Germany
| | - Yolanda Benavente
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Barcelona 08036, Spain
| | - Simonetta Bisanzi
- Regional Cancer Prevention Laboratory, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence 50139, Italy
| | - Paolo Boffetta
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Medical and Surgical Sciences, University of Bologna, Bologna 41026, Italy
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94118, USA
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon 69372, France
| | - Angela R Brooks-Wilson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z1L3, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jacqueline Clavel
- Center of Research in Epidemiology and Statistics Sorbonne Paris Cité (CRESS), UMR1153, INSERM, Villejuif 75004, France
| | - Pierluigi Cocco
- Department of Public Health, Clinical and Molecular Medicine, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Lucia Conde
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - David G Cox
- INSERM U1052, Cancer Research Center of Lyon, Centre Léon Bérard, Lyon 69008, France
| | - Wendy Cozen
- Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Karen Curtin
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Immaculata De Vivo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Silvia de Sanjose
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Barcelona 08036, Spain
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno 656 53, Czech Republic
| | - Susan M Gapstur
- Department of Population Science, American Cancer Society, Atlanta, GA 30303, USA
| | - Hervè Ghesquières
- Department of Hematology, Centre Léon Bérard, Lyon 69008, France
- INSERM U1052, Cancer Research Center of Lyon, Lyon-1 University, Pierre-Bénite Cedex 69008, France
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria 3800, Australia
| | - Martha Glenn
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75105, Sweden
| | - Chi Gao
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Henrik Hjalgrim
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, Copenhagen 2300, Denmark
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, OH 43210, USA
| | - Mark Liebow
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Brian K Link
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Marc Maynadie
- U1231, Registre des Hémopathies Malignes de Côte d'Or, University of Burgundy and Dijon University Hospital, Dijon 21070, France
| | - James McKay
- International Agency for Research on Cancer (IARC), Lyon 69372, France
| | - Mads Melbye
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, Copenhagen 2300, Denmark
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lucia Miligi
- Environmental and Occupational Epidemiology Branch-Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence 50139, Italy
| | - Thierry J Molina
- Department of Pathology, AP-HP, Necker Enfants Malades, Université Paris Descartes, EA 7324, Sorbonne Paris Cité 75015, France
| | - Alain Monnereau
- Center of Research in Epidemiology and Statistics Sorbonne Paris Cité (CRESS), UMR1153, INSERM, Villejuif 75004, France
- Registre des Hémopathies Malignes de la Gironde, Institut Bergonié, Bordeaux Cedex 33076, France
| | - Alexandra Nieters
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Baden-Württemberg 79108, Germany
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alpa V Patel
- Department of Population Science, American Cancer Society, Atlanta, GA 30303, USA
| | - Sara Piro
- Environmental and Occupational Epidemiology Branch-Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence 50139, Italy
| | - Vignesh Ravichandran
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elio Riboli
- School of Public Health, Imperial College London, London W2 1PG, UK
| | - Gilles Salles
- INSERM U1052, Cancer Research Center of Lyon, Lyon-1 University, Pierre-Bénite Cedex 69008, France
- Department of Hematology, Hospices Civils de Lyon, Pierre Benite Cedex 69495, France
- Department of Hematology, Université Lyon-1, Pierre Benite Cedex 69495, France
| | - Richard K Severson
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Christine F Skibola
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Karin E Smedby
- Department of Medicine, Solna, Karolinska Institutet, Stockholm 17176, Sweden
- Hematology Center, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - John J Spinelli
- Cancer Control Research, BC Cancer Agency, Vancouver, British Columbia V5Z1L3, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia V6T1Z3, Canada
| | - Anthony Staines
- School of Nursing, Psychotherapy and Community Health, Dublin City University, Dublin 9, Ireland
| | - Carolyn Stewart
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lauren R Teras
- Department of Population Science, American Cancer Society, Atlanta, GA 30303, USA
| | - Lesley F Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98117, USA
| | - Ruth C Travis
- Cancer Epidemiology Unit, University of Oxford, Oxford OX3 7LF, UK
| | - Claire M Vajdic
- Centre for Big Data Research in Health, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Roel C H Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CG, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Nicole Wong Doo
- Concord Clinical School, University of Sydney, Concord, New South Wales 2139, Australia
| | - Yawei Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT 06520, USA
| | - Tongzhang Zheng
- Department of Epidemiology, Brown University, Providence, RI 02903, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Nicola J Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD 20877, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
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Cornetti L, Fields PD, Ebert D. Genomic characterization of selfing in the cyclic parthenogen Daphnia magna. J Evol Biol 2021; 34:792-802. [PMID: 33704857 DOI: 10.1111/jeb.13780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/23/2021] [Accepted: 03/06/2021] [Indexed: 11/29/2022]
Abstract
Inbreeding refers to the fusion of related individuals' gametes, with self-fertilization (selfing) being an extreme form of inbreeding-involving gametes produced by the same individual. Selfing is expected to reduce heterozygosity by an average of 50% in one generation; however, little is known about the empirical variation on a genome level surrounding this figure and the factors that affect variation. We selfed genotypes of the cyclic parthenogen Daphnia magna and analysed whole genomes of mothers and selfed offspring, observing the predicted 50% heterozygosity reduction on average. We also saw substantial variation around this value and significant differences among mother-offspring pairs. Crossover analysis confirmed the known trend of recombination occurring more often towards the telomeres. This effect was shown, through simulations, to increase the variance of heterozygosity reduction compared to when a uniform distribution of crossovers was used. Similarly, we simulated inbred line production after several generations of selfing and we observed higher variance in achieved homozygosity when we consider a higher recombination rate towards the telomeres. Our empirical and simulation study highlights that the expected mean values of heterozygosity reduction show remarkable variation, which can help understand, for example, differences among inbred individuals.
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Affiliation(s)
- Luca Cornetti
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
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19
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Liang R, Wang Z, Kong X, Xiao X, Chen T, Yang H, Li Y, Zhao X. Differentiation of Human Parthenogenetic Embryonic Stem Cells into Functional Hepatocyte-like Cells. Organogenesis 2020; 16:137-148. [PMID: 33236954 DOI: 10.1080/15476278.2020.1848237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Stem cell and tissue engineering-based therapies for acute liver failure (ALF) have been limited by the lack of an optimal cell source. We aimed to determine the suitability of human parthenogenetic embryonic stem cells (hPESCs) for the development of strategies to treat ALF. We studied the ability of human parthenogenetic embryonic stem cells (hPESCs) with high whole-genome SNP homozygosity, which were obtained by natural activation during in vitro fertilization (IVF), to differentiate into functional hepatocyte-like cells in vitro by monolayer plane orientation. hPESCs were induced on a single-layer flat plate for 21 d in complete medium with the inducers activin A, FGF-4, BMP-2, HGF, OSM, DEX, and B27. Polygonal cell morphology and binuclear cells were observed after 21 d of induction by using an inverted microscope. RT-qPCR results showed that the levels of hepatocyte-specific genes such as AFP, ALB, HNF4a, CYP3A4, SLCO1B3, and ABCC2 significantly increased after induction. Immunocytochemical assay showed CK18 and Hepa expression in the induced cells. Indocyanine green (ICG) staining showed that the cells had the ability to absorb and metabolize dyes. Detection of marker proteins and urea in cell culture supernatants showed that the cells obtained after 21 d of induction had synthetic and secretory functions. The typical ultrastructure of liver cells was observed using TEM after 21 d of induction. The results indicate that naturally activated hPESCs can be induced to differentiate into hepatocellular cells by monolayer planar induction.
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Affiliation(s)
- Rui Liang
- Department of Pathology, The Second Hospital of Tianjin Medical University , Tianjin, China
| | - Zhiqiang Wang
- Department of General Surgery, The Second Hospital of Tianjin Medical University , Tianjin, China
| | - Xiangyang Kong
- School of Medicine, Kunming University of Science and Technology , Kunming, China
| | - Xiaoxiao Xiao
- Faculty of Chinese medicine, Macau University of Science and Technology , Macao, China
| | - Tianxing Chen
- Department of Pathology, The First People's Hospital of Yunnan Province , Kunming, China
| | - Hui Yang
- Department of Pathology, The First People's Hospital of Yunnan Province , Kunming, China
| | - Ying Li
- Department of Pathology, The First People's Hospital of Yunnan Province , Kunming, China
| | - Xingqi Zhao
- College of Life Sciences, Nanjing Normal University , Nanjing, China
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20
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van Lieshout N, van der Burgt A, de Vries ME, Ter Maat M, Eickholt D, Esselink D, van Kaauwen MPW, Kodde LP, Visser RGF, Lindhout P, Finkers R. Solyntus, the New Highly Contiguous Reference Genome for Potato ( Solanum tuberosum). G3 (Bethesda) 2020; 10:3489-95. [PMID: 32759330 DOI: 10.1534/g3.120.401550] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
With the rapid expansion of the application of genomics and sequencing in plant breeding, there is a constant drive for better reference genomes. In potato (Solanum tuberosum), the third largest food crop in the world, the related species S. phureja, designated “DM”, has been used as the most popular reference genome for the last 10 years. Here, we introduce the de novo sequenced genome of Solyntus as the next standard reference in potato genome studies. A true Solanum tuberosum made up of 116 contigs that is also highly homozygous, diploid, vigorous and self-compatible, Solyntus provides a more direct and contiguous reference then ever before available. It was constructed by sequencing with state-of-the-art long and short read technology and assembled with Canu. The 116 contigs were assembled into scaffolds to form each pseudochromosome, with three contigs to 17 contigs per chromosome. This assembly contains 93.7% of the single-copy gene orthologs from the Solanaceae set and has an N50 of 63.7 Mbp. The genome and related files can be found at https://www.plantbreeding.wur.nl/Solyntus/. With the release of this research line and its draft genome we anticipate many exciting developments in (diploid) potato research.
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Vaes L, Tiller GE, Pérez B, Boyer SW, Berry SA, Sarafoglou K, Morava E. PMM2-CDG caused by uniparental disomy: Case report and literature review. JIMD Rep 2020; 54:16-21. [PMID: 32685345 PMCID: PMC7358672 DOI: 10.1002/jmd2.12122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 04/01/2020] [Accepted: 04/06/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Phosphomannomutase 2 deficiency (PMM2-CDG) affects glycosylation pathways such as the N-glycosylation pathway, resulting in loss of function of multiple proteins. This disorder causes multisystem involvement with a high variability among patients. PMM2-CDG is an autosomal recessive disorder, which can be caused by inheriting two pathogenic variants, de novo mutations or uniparental disomy. CASE PRESENTATION Our patient presented with multisystem symptoms at an early age including developmental delay, ataxia, and seizures. No diagnosis was obtained till the age of 31 years, when genetic testing was reinitiated. The patient was diagnosed with a complete maternal mixed hetero/isodisomy of chromosome 16, with a homozygous pathogenic PMM2 variant (p.Phe119Leu) causing PMM2-CDG.A literature review revealed eight cases of uniparental disomy as an underlying cause of CDG, four of which are PMM2-CDG. CONCLUSION Since the incidence of homozygosity for PMM2 variants is rare, we suggest further investigations for every homozygous PMM2-CDG patient where the segregation does not fit. These investigations include testing for UPD or a deletion in one of the two alleles, as this will have an impact on recurrence risk in genetic counseling.
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Affiliation(s)
| | | | - Belén Pérez
- Center of Molecular Biology‐Severo OchoaUniversity Autonomous of Madrid, La Paz Institute for Health Research, Center for Biomedical Research on Rare DiseasesMadridSpain
| | | | - Susan A. Berry
- Division of Genetics and Metabolism, Department of PediatricsUniversity of Minnesota Medical SchoolMinneapolisMinnesotaUSA
| | - Kyriakie Sarafoglou
- Department of PediatricsUniversity of Minnesota Masonic Children's HospitalMinneapolisMinnesotaUSA
| | - Eva Morava
- Department of Clinical Genomics, and Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
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22
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Hübner CT, Meyer R, Kenawy A, Ambrozaityte L, Matuleviciene A, Kraft F, Begemann M, Elbracht M, Eggermann T. HMGA2 Variants in Silver-Russell Syndrome: Homozygous and Heterozygous Occurrence. J Clin Endocrinol Metab 2020; 105:5839772. [PMID: 32421827 DOI: 10.1210/clinem/dgaa273] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 05/13/2020] [Indexed: 02/06/2023]
Abstract
CONTEXT Silver-Russell syndrome (SRS) is a clinical and molecular heterogeneous disorder associated with short stature, typical facial gestalt, and body asymmetry. Though molecular causes of SRS can be identified in a significant number of patients, about one-half of patients currently remain without a molecular diagnosis. However, determination of the molecular cause is required for a targeted treatment and genetic counselling. OBJECTIVE The aim of this study was to corroborate the role of HMGA2 as an SRS-causing gene and reevaluate its mode of inheritance. DESIGN, SETTING, PATIENTS Patients were part of an ongoing study aiming on SRS-causing genes. They were classified according to the Netchine-Harbison clinical scoring system, and DNA samples were investigated by whole exome sequencing. Common molecular causes of SRS were excluded before. RESULTS Three novel pathogenic HMGA2 variants were identified in 5 patients from 3 SRS families, and fulfilling diagnostic criteria of SRS. For the first time, homozygosity for a variant in HMGA2 could be identified in a severely affected sibpair, whereas parents carrying heterozygous variants had a mild phenotype. Treatment with recombinant growth hormone led to a catch-up growth in 1 patient, whereas all others did not receive growth hormone and stayed small. One patient developed type 2 diabetes at age 30 years. CONCLUSIONS Identification of novel pathogenic variants confirms HMGA2 as an SRS-causing gene; thus, HMGA2 testing should be implemented in molecular SRS diagnostic workup. Furthermore, inheritance of HMGA2 is variable depending on the severity of the variant and its consequence for protein function.
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Affiliation(s)
| | - Robert Meyer
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Asmaa Kenawy
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Laima Ambrozaityte
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Ausra Matuleviciene
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Florian Kraft
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Matthias Begemann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Thomas Eggermann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
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23
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Oliveira HR, McEwan JC, Jakobsen J, Blichfeldt T, Meuwissen T, Pickering N, Clarke SM, Brito LF. Genetic Connectedness Between Norwegian White Sheep and New Zealand Composite Sheep Populations With Similar Development History. Front Genet 2020; 11:371. [PMID: 32391056 PMCID: PMC7194024 DOI: 10.3389/fgene.2020.00371] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/26/2020] [Indexed: 11/25/2022] Open
Abstract
The Norwegian White sheep (NWS) and New Zealand Terminal Sire Composite (NZC) sheep breeds have been developed based on crossing of multiple breeds, mainly of Northern European origin. A close genetic relationship between these populations could enable across-country genomic evaluations. The main objectives of this study were to assess the genetic connectedness between Norwegian and New Zealand sheep populations and estimate numerous genetic diversity metrics for these two populations. A total of 792 NWS and 16,912 NZC animals were genotyped using a high-density Illumina SNP chip panel (∼606K SNPs). The NZC animals were grouped based on their breed composition as: Finn, Lamb Supreme, Primera, Texel, “Other Dual Purpose”, and “Other Terminal Sire”. The average level of linkage disequilibrium ranged from 0.156 (for Primera) to 0.231 (for Finn). The lowest consistency of gametic phase was estimated between NWS and Finn (0.397), and between NWS and Texel (0.443), respectively. Similar consistency of gametic phase was estimated between NWS and the other NZC populations (∼ 0.52). For all composite sheep populations analyzed in this study, the majority of runs of homozygosity (ROH) segments identified had short length (<2,500 kb), indicating ancient (instead of recent) inbreeding. The variation in the number of ROH segments observed in the NWS was similar to the variation observed in Primera and Lamb Supreme. There was no clear discrimination between NWS and NZC based on the first few principal components. In addition, based on admixture analyses, there seems to be a significant overlap of the ancestral populations that contributed to the development of both NWS and NZC. There were no evident signatures of selection in these populations, which might be due to recent crossbreeding. In conclusion, the NWS composite breed was shown to be moderately related to NZC populations, especially Primera and Lamb Supreme. The findings reported here indicate a promising opportunity for collaborative genomic analyses involving NWS and NZC sheep populations.
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Affiliation(s)
- Hinayah Rojas Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States.,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - John Colin McEwan
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Jette Jakobsen
- The Norwegian Association of Sheep and Goat Breeders, Ås, Norway
| | - Thor Blichfeldt
- The Norwegian Association of Sheep and Goat Breeders, Ås, Norway
| | - Theodorus Meuwissen
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | | | | | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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Moh'd Al-Rawashdeh B, Sada Alhanjori A, Ali E, Zihlif M. Association of IL-4 Polymorphisms with Allergic Rhinitis in Jordanian Population. ACTA ACUST UNITED AC 2020; 56:E179. [PMID: 32295284 DOI: 10.3390/medicina56040179] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/05/2020] [Accepted: 04/10/2020] [Indexed: 12/13/2022]
Abstract
Background and objectives: Allergic rhinitis has complex patterns of inheritance, and single nucleotide polymorphisms, a common genetic variation in a population, exert a significant role in allergic rhinitis pathology. The current study aimed to investigate the association of Interleukin-4 (IL-4) polymorphisms with allergic rhinitis. Materials and Methods: Our study included 158 patients with allergic rhinitis and 140 healthy controls from Jordan that were genotyped for IL-4 single nucleotide polymorphisms (SNPs) C-589T (rs2243250) and T-2979G (rs2227284) using restriction fragment length polymorphism-polymerase chain reaction. Statistical analysis was conducted using IBM SPSS Statistics version 24 software. Results: The results showed that the allelic frequency of the minor alleles was 0.19 and 0.67 for C-589T (rs2243250) and T-2979G (rs2227284) in the allergic rhinitis patients, respectively, while it was 0.18 for C-589T (rs2243250) and 0.64 T-2979G (rs2227284) in the control group. The homozygous (TT) genotype of C-589T (rs2243250) was significantly associated with allergic rhinitis (p < 0.05), while there was no association of any of T-2979G (rs2227284) genotypes with allergic rhinitis. Conclusions: The results of this study indicate that genetic inter-population variation precipitates the differences in the percentages of many diseases among populations, including allergic rhinitis.
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25
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Zsolnai A, Maróti-Agóts Á, Kovács A, Bâlteanu AV, Kaltenecker E, Anton I. Genetic position of Hungarian Grey among European cattle and identification of breed-specific markers. Animal 2020; 14:1786-92. [PMID: 32248869 DOI: 10.1017/S1751731120000634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Hungarian Grey is an indigenous cattle breed that is one of the national symbols of Hungary. However, genetic description of the Hungarian Grey cattle has not yet been conducted based on whole-genome screening. Using the GeneSeek high-density Bovine SNP (single nucleotide polymorphism) 150 K BeadChip, we sampled the genome of 36 Hungarian Grey, 12 Maremmana, 13 Hungarian Fleckvieh and 5 Holstein-Friesian cattle for population studies and used data of 139 other cattle from an additional dataset created on European cattle breeds (Upadhyay et al.2017. Heredity 118, 169-176). The performance of a multidimensional scaling plot showed that Hungarian Grey clustered independently from other European cattle. The number and total length of runs of homozygosity (ROH) is similar or slightly below the value of other European cattle; FROH coefficients (proportion of the autosomal genome covered by ROH) are similar to Maremmana and Maronesa. The frequency of ROH does not show increased values as it can be noticed in Heck and Maltese. These results indicate that the Hungarian Grey cattle have been successfully maintained avoiding negative genetic effects, and reflect the uniqueness among European cattle. The identification of breed-specific loci has been aimed at differentiating Hungarian Grey (n = 136 in this case) from other cattle breeds (n = 169). Ten loci (-log10P > 5) were identified as markers capable for differentiation of Hungarian Grey. These markers are located on chromosomes 6, 14, 15, 16, 20 and 24.
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Bâlteanu VA, Cardoso TF, Amills M, Egerszegi I, Anton I, Beja-Pereira A, Zsolnai A. The footprint of recent and strong demographic decline in the genomes of Mangalitza pigs. Animal 2019; 13:2440-2446. [PMID: 30947762 DOI: 10.1017/s1751731119000582] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The Mangalitza pig breed has suffered strong population reductions due to competition with more productive cosmopolitan breeds. In the current work, we aimed to investigate the effects of this sustained demographic recession on the genomic diversity of Mangalitza pigs. By using the Porcine Single Nucleotid Polymorphism BeadChip, we have characterized the genome-wide diversity of 350 individuals including 45 Red Mangalitza (number of samples; n=20 from Hungary and n=25 from Romania), 37 Blond Mangalitza, 26 Swallow-belly Mangalitza, 48 Blond Mangalitza × Duroc crossbreds, 5 Bazna swine, 143 pigs from the Hampshire, Duroc, Landrace, Large White and Pietrain breeds and 46 wild boars from Romania (n=18) and Hungary (n=28). Performance of a multidimensional scaling plot showed that Landrace, Large White and Pietrain pigs clustered independently from Mangalitza pigs and Romanian and Hungarian wild boars. The number and total length of ROH (runs of homozygosity), as well as FROH coefficients (proportion of the autosomal genome covered ROH) did not show major differences between Mangalitza pigs and other wild and domestic pig populations. However, Romanian and Hungarian Red Mangalitza pigs displayed an increased frequency of very long ROH (>30 Mb) when compared with other porcine breeds. These results indicate that Red Mangalitza pigs underwent recent and strong inbreeding probably as a consequence of severe reductions in census size.
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Affiliation(s)
- V A Bâlteanu
- Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine, Calea Mănăştur 3-5, 400372 Cluj-Napoca, Romania
| | - T F Cardoso
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- CAPES Foundation, Ministry of Education of Brazil, 7004020 Brasilia D. F., Brazil
| | - M Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - I Egerszegi
- Szent István University, Páter Károly u. 1., 2100 Gödöllő, Hungary
| | - I Anton
- NAIK-Research Institute for Animal Breeding, Nutrition and Food Science, Gesztenyes u. 1., 2053 Herceghalom, Hungary
| | - A Beja-Pereira
- Centro de Investigacao em Biodiversidade e Recursos Geneticos, Universidade do Porto (CIBIO-UP), Rua Padre Armando Quintas 7, 4485-661 Vairao, Portugal
| | - A Zsolnai
- NAIK-Research Institute for Animal Breeding, Nutrition and Food Science, Gesztenyes u. 1., 2053 Herceghalom, Hungary
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Szpiech ZA, Mak ACY, White MJ, Hu D, Eng C, Burchard EG, Hernandez RD. Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity. Am J Hum Genet 2019; 105:747-762. [PMID: 31543216 PMCID: PMC6817522 DOI: 10.1016/j.ajhg.2019.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/27/2019] [Indexed: 12/20/2022] Open
Abstract
Runs of homozygosity (ROH) are important genomic features that manifest when an individual inherits two haplotypes that are identical by descent. Their length distributions are informative about population history, and their genomic locations are useful for mapping recessive loci contributing to both Mendelian and complex disease risk. We have previously shown that ROH, and especially long ROH that are likely the result of recent parental relatedness, are enriched for homozygous deleterious coding variation in a worldwide sample of outbred individuals. However, the distribution of ROH in admixed populations and their relationship to deleterious homozygous genotypes is understudied. Here we analyze whole-genome sequencing data from 1,441 unrelated individuals from self-identified African American, Puerto Rican, and Mexican American populations. These populations are three-way admixed between European, African, and Native American ancestries and provide an opportunity to study the distribution of deleterious alleles partitioned by local ancestry and ROH. We re-capitulate previous findings that long ROH are enriched for deleterious variation genome-wide. We then partition by local ancestry and show that deleterious homozygotes arise at a higher rate when ROH overlap African ancestry segments than when they overlap European or Native American ancestry segments of the genome. These results suggest that, while ROH on any haplotype background are associated with an inflation of deleterious homozygous variation, African haplotype backgrounds may play a particularly important role in the genetic architecture of complex diseases for admixed individuals, highlighting the need for further study of these populations.
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Affiliation(s)
- Zachary A Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Department of Biological Sciences, Auburn University, Auburn, AL 36842, USA.
| | - Angel C Y Mak
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Marquitta J White
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada; Genome Quebec Innovation Center, McGill University, Montreal, QC H3A 0G1, Canada.
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28
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Bouyacoub Y, Falfoul Y, Ouederni M, Sayeb M, Chedli A, Chargui M, Sassi H, Chakroun Chenguel I, Munier FL, El Matri L, Abdelhak S, Cheour M. Granular type I corneal dystrophy in a large consanguineous Tunisian family with homozygous p.R124S mutation in the TGFBI gene. Ophthalmic Genet 2019; 40:329-337. [PMID: 31322463 DOI: 10.1080/13816810.2019.1639202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Purpose: We report the clinical features and the mutational analysis in a large Tunisian family with granular corneal dystrophy type I (GCD1). Patients and Methods: Thirty-three members of the Tunisian family underwent a complete ophthalmologic examination. DNA extraction and direct Sanger sequencing of the exons 4 and 12 of transforming growth factor β Induced (TGFBI) gene was performed for 42 members. For the molecular modeling of TGFBI protein, we used pGenTHREADER method to identify templates, 3D-EXPRESSO program to align sequences, MODELLER to get a homology model for the FAS1 (fasciclin-like) domains and finally NOMAD-ref web server for the energy minimization. Results: The diagnosis of GCD1 was clinically and genetically confirmed. Sequencing of exon 4 of TGFBI gene revealed the p.[R124S] mutation at heterozygous and homozygous states in patients with different clinical severities. Visual acuity was severely affected in the homozygous patients leading to a first penetrating keratoplasty. Recurrence occurred rapidly, began in the seat of the corneal stitches and remained superficial up to 40 years after the graft. For heterozygous cases, visual acuity ranged from 6/10 to 10/10. Corneal opacities were deeper and predominating in the stromal center. According to bioinformatic analysis, this mutation likely perturbs the protein physicochemical properties and reduces its solubility without structural modification. Conclusions: Our study describes for the first time phenotype-genotype correlation in a large Tunisian family with GCDI and illustrates for the first time clinical and histopathological presentation of homozygous p.[R124S] mutation. These results help to understand pathophysiology of the disease.
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Affiliation(s)
- Yosra Bouyacoub
- Laboratory of Biomedical Genetics and Oncogenetics, Université Tunis El Manar, Institut Pasteur de Tunis, LR16IPT05 , Tunis , Tunisia.,Institut Supérieur de Biotechnologie, Université de Monastir , Monastir , Tunisia
| | - Yousra Falfoul
- B Department, Hedi Raies Institute of Ophthalmology , Tunis , Tunisia.,Oculogenetic Laboratory, LR14SP01, Hedi Raies Institute of Ophthalmology , Tunis , Tunisia
| | - Mariem Ouederni
- Department of Ophthalmology, Habib Thameur Hospital , Tunis , Tunisia
| | - Marwa Sayeb
- Laboratory of Biomedical Genetics and Oncogenetics, Université Tunis El Manar, Institut Pasteur de Tunis, LR16IPT05 , Tunis , Tunisia
| | - Aschraf Chedli
- Department of Anatomopathology, Habib Thameur Hospital , Tunis , Tunisia
| | - Mariem Chargui
- Laboratory of Biomedical Genetics and Oncogenetics, Université Tunis El Manar, Institut Pasteur de Tunis, LR16IPT05 , Tunis , Tunisia
| | - Hela Sassi
- Department of Ophthalmology, Habib Thameur Hospital , Tunis , Tunisia
| | | | - Francis L Munier
- Jules-Gonin Eye Hospital, University of Lausanne , Lausanne , Switzerland
| | - Leila El Matri
- B Department, Hedi Raies Institute of Ophthalmology , Tunis , Tunisia.,Oculogenetic Laboratory, LR14SP01, Hedi Raies Institute of Ophthalmology , Tunis , Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genetics and Oncogenetics, Université Tunis El Manar, Institut Pasteur de Tunis, LR16IPT05 , Tunis , Tunisia
| | - Monia Cheour
- Department of Ophthalmology, Habib Thameur Hospital , Tunis , Tunisia
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Wang L, Mu Y, Xu L, Li K, Han J, Wu T, Liu L, Gao Q, Xia Y, Hou G, Yang S, He X, Liu GE, Feng S. Genomic Analysis Reveals Specific Patterns of Homozygosity and Heterozygosity in Inbred Pigs. Animals (Basel) 2019; 9:E314. [PMID: 31159442 PMCID: PMC6617223 DOI: 10.3390/ani9060314] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 11/29/2022] Open
Abstract
The inbred strain of miniature pig is an ideal model for biomedical research due to its high level of homozygosity. In this study, we investigated genetic diversity, relatedness, homozygosity, and heterozygosity using the Porcine SNP60K BeadChip in both inbred and non-inbred Wuzhishan pigs (WZSPs). Our results from multidimensional scaling, admixture, and phylogenetic analyses indicated that the inbred WZSP, with its unique genetic properties, can be utilized as a novel genetic resource for pig genome studies. Inbreeding depression and run of homozygosity (ROH) analyses revealed an average of 61 and 12 ROH regions in the inbred and non-inbred genomes of WZSPs, respectively. By investigating ROH number, length, and distribution across generations, we further briefly studied the impacts of recombination and demography on ROH in these WZSPs. Finally, we explored the SNPs with higher heterozygosity across generations and their potential functional implications in the inbred WZSP. We detected 56 SNPs showing constant heterozygosity with He = 1 across six generations in inbred pigs, while only one was found in the non-inbred population. Among these SNPs, we observed nine SNPs located in swine RefSeq genes, which were found to be involved in signaling and immune processes. Together, our findings indicate that the inbred-specific pattern of homozygosity and heterozygosity in inbred pigs can offer valuable insights for elucidating the mechanisms of inbreeding in farm animals.
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Affiliation(s)
- Ligang Wang
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Yulian Mu
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Linyang Xu
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Kui Li
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Jianlin Han
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Tianwen Wu
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Lan Liu
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Qian Gao
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Ying Xia
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Guanyu Hou
- Institute of Tropical Crop Variety Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.
| | - Shulin Yang
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Xiaohong He
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, U.S. Department of Agriculture-Agricultural Research Services, Beltsville, MD 20705, USA.
| | - Shutang Feng
- Key Laboratory of Farm Animal Genetic Resources and Utilization of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
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30
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Bhinder MA, Sadia H, Mahmood N, Qasim M, Hussain Z, Rashid MM, Zahoor MY, Bhatti R, Shehzad W, Waryah AM, Jahan S. Consanguinity: A blessing or menace at population level? Ann Hum Genet 2019; 83:214-219. [PMID: 30891741 DOI: 10.1111/ahg.12308] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 02/15/2019] [Accepted: 03/01/2019] [Indexed: 12/18/2022]
Abstract
Consanguinity has highly complex and multifaceted aspects with sociocultural as well as biological debates on its pros and cons. The biological upshot of consanguinity includes the increased homozygosity, which results in manifold increased risk of genetic disorders at family and population levels. On the other hand, in addition to social, cultural, political, and economic benefits, consanguineous marriages have biological advantages at the population level. The consequence of consanguineous marriages is an upsurge in the number of homozygous diseased individuals with fewer chances of mating and reduced chances of survival, therefore evolutionarily confining the transmission of disease alleles to future generations and encouraging its elimination from a population. Protective effects of consanguinity have also been observed in a few diseases in different populations. Although attractive for many reasons, nonconsanguineous marriages will cause risk alleles to spread throughout the population, making most individuals carriers, and ultimately will resume the production of recessive diseases in subsequent generations. Although consanguinity, from an evolutionary point of view, is beneficial at the population level, it increases the risk of diseases in the very next generation. Presently, there is no treatment for most of the genetic disorders; we cannot opt for consanguinity for long-term benefits. Nonconsanguineous marriages are a better strategy by which we may delay disease manifestation for some generations until science offers a viable solution.
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Affiliation(s)
- Munir Ahmad Bhinder
- Department of Human Genetics & Molecular Biology, University of Health Sciences, Lahore, 54600, Pakistan
| | - Haleema Sadia
- Balochistan University of Information Technology, Engineering and Management Sciences, Takatu Campus, Quetta, Pakistan
| | - Nasir Mahmood
- University of Health Sciences, Lahore, 54600, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | - Zawar Hussain
- Department of Zoology, University of Education, Lahore, Pakistan
| | - Muhammad Mudassar Rashid
- Department of Human Genetics & Molecular Biology, University of Health Sciences, Lahore, 54600, Pakistan
| | - Muhammad Yasir Zahoor
- Institute of Biochemistry & Biotechnology, University of Veterinary & Animal Sciences, Lahore, Pakistan
| | - Rashid Bhatti
- National Centre of Excellence in Molecular Biology, Lahore, Pakistan
| | - Wasim Shehzad
- Institute of Biochemistry & Biotechnology, University of Veterinary & Animal Sciences, Lahore, Pakistan
| | - Ali Muhammad Waryah
- Molecular Biology & Genetics Department, Medical Research Center, Liaquat University of Medical & Health Sciences, Jamshoro, Pakistan
| | - Shah Jahan
- University of Health Sciences, Lahore, 54600, Pakistan
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31
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Onzima RB, Upadhyay MR, Doekes HP, Brito LF, Bosse M, Kanis E, Groenen MAM, Crooijmans RPMA. Genome-Wide Characterization of Selection Signatures and Runs of Homozygosity in Ugandan Goat Breeds. Front Genet 2018; 9:318. [PMID: 30154830 PMCID: PMC6102322 DOI: 10.3389/fgene.2018.00318] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/25/2018] [Indexed: 01/06/2023] Open
Abstract
Both natural and artificial selection are among the main driving forces shaping genetic variation across the genome of livestock species. Selection typically leaves signatures in the genome, which are often characterized by high genetic differentiation across breeds and/or a strong reduction in genetic diversity in regions associated with traits under intense selection pressure. In this study, we evaluated selection signatures and genomic inbreeding coefficients, FROH, based on runs of homozygosity (ROH), in six Ugandan goat breeds: Boer (n = 13), and the indigenous breeds Karamojong (n = 15), Kigezi (n = 29), Mubende (n = 29), Small East African (n = 29), and Sebei (n = 29). After genotyping quality control, 45,294 autosomal single nucleotide polymorphisms (SNPs) remained for further analyses. A total of 394 and 6 breed-specific putative selection signatures were identified across all breeds, based on marker-specific fixation index (FST-values) and haplotype differentiation (hapFLK), respectively. These regions were enriched with genes involved in signaling pathways associated directly or indirectly with environmental adaptation, such as immune response (e.g., IL10RB and IL23A), growth and fatty acid composition (e.g., FGF9 and IGF1), and thermo-tolerance (e.g., MTOR and MAPK3). The study revealed little overlap between breeds in genomic regions under selection and generally did not display the typical classic selection signatures as expected due to the complex nature of the traits. In the Boer breed, candidate genes associated with production traits, such as body size and growth (e.g., GJB2 and GJA3) were also identified. Furthermore, analysis of ROH in indigenous goat breeds showed very low levels of genomic inbreeding (with the mean FROH per breed ranging from 0.8% to 2.4%), as compared to higher inbreeding in Boer (mean FROH = 13.8%). Short ROH were more frequent than long ROH, except in Karamojong, providing insight in the developmental history of these goat breeds. This study provides insights into the effects of long-term selection in Boer and indigenous Ugandan goat breeds, which are relevant for implementation of breeding programs and conservation of genetic resources, as well as their sustainable use and management.
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Affiliation(s)
- Robert B. Onzima
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
- National Agricultural Research Organization (NARO), Entebbe, Uganda
| | - Maulik R. Upadhyay
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Harmen P. Doekes
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
| | - Luiz. F. Brito
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock (CGIL), University of Guelph, Guelph, ON, Canada
| | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
| | - Egbert Kanis
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
| | - Martien A. M. Groenen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
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32
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Pemberton TJ, Szpiech ZA. Relationship between Deleterious Variation, Genomic Autozygosity, and Disease Risk: Insights from The 1000 Genomes Project. Am J Hum Genet 2018; 102:658-75. [PMID: 29551419 DOI: 10.1016/j.ajhg.2018.02.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/19/2018] [Indexed: 12/11/2022] Open
Abstract
Genomic regions of autozygosity (ROAs) represent segments of individual genomes that are homozygous for haplotypes inherited identical-by-descent (IBD) from a common ancestor. ROAs are nonuniformly distributed across the genome, and increased ROA levels are a reported risk factor for numerous complex diseases. Previously, we hypothesized that long ROAs are enriched for deleterious homozygotes as a result of young haplotypes with recent deleterious mutations-relatively untouched by purifying selection-being paired IBD as a consequence of recent parental relatedness, a pattern supported by ROA and whole-exome sequence data on 27 individuals. Here, we significantly bolster support for our hypothesis and expand upon our original analyses using ROA and whole-genome sequence data on 2,436 individuals from The 1000 Genomes Project. Considering CADD deleteriousness scores, we reaffirm our previous observation that long ROAs are enriched for damaging homozygotes worldwide. We show that strongly damaging homozygotes experience greater enrichment than weaker damaging homozygotes, while overall enrichment varies appreciably among populations. Mendelian disease genes and those encoding FDA-approved drug targets have significantly increased rates of gain in damaging homozygotes with increasing ROA coverage relative to all other genes. In genes implicated in eight complex phenotypes for which ROA levels have been identified as a risk factor, rates of gain in damaging homozygotes vary across phenotypes and populations but frequently differ significantly from non-disease genes. These findings highlight the potential confounding effects of population background in the assessment of associations between ROA levels and complex disease risk, which might underlie reported inconsistencies in ROA-phenotype associations.
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33
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Peer-Zada AA, Al-Asmari AM. Excessive homozygosity identified by chromosomal microarray at a known GCDH mutation locus correlates with brain MRI abnormalities in an infant with glutaric aciduria. Clin Case Rep 2017; 5:1303-1308. [PMID: 28781846 PMCID: PMC5538054 DOI: 10.1002/ccr3.1054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/06/2017] [Indexed: 11/12/2022] Open
Abstract
Herein, we report a conceptually novel clinical case highlighting the diagnostic implications of excessive homozygosity and its correlation with brain MRI abnormalities in an infant with GA1. The case also points a need for an extra amount of caution to be exercised when evaluating patients with “negative exomes.”
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Affiliation(s)
- Abdul Ali Peer-Zada
- Molecular Pathology (Genetics) Section Pathology and Clinical Laboratory Medicine Administration King Fahad Medical City Riyadh Saudi Arabia
| | - Ali M Al-Asmari
- Department of Pediatrics Medical Genetics Section King Fahad Medical City Riyadh Saudi Arabia
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34
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Yengo L, Zhu Z, Wray NR, Weir BS, Yang J, Robinson MR, Visscher PM. Detection and quantification of inbreeding depression for complex traits from SNP data. Proc Natl Acad Sci U S A 2017; 114:8602-7. [PMID: 28747529 DOI: 10.1073/pnas.1621096114] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Quantifying the effects of inbreeding is critical to characterizing the genetic architecture of complex traits. This study highlights through theory and simulations the strengths and shortcomings of three SNP-based inbreeding measures commonly used to estimate inbreeding depression (ID). We demonstrate that heterogeneity in linkage disequilibrium (LD) between causal variants and SNPs biases ID estimates, and we develop an approach to correct this bias using LD and minor allele frequency stratified inference (LDMS). We quantified ID in 25 traits measured in [Formula: see text] participants of the UK Biobank, using LDMS, and confirmed previously published ID for 4 traits. We find unique evidence of ID for handgrip strength, waist/hip ratio, and visual and auditory acuity (ID between -2.3 and -5.2 phenotypic SDs for complete inbreeding; [Formula: see text]). Our results illustrate that a careful choice of the measure of inbreeding combined with LDMS stratification improves both detection and quantification of ID using SNP data.
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35
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Peripolli E, Munari DP, Silva MVGB, Lima ALF, Irgang R, Baldi F. Runs of homozygosity: current knowledge and applications in livestock. Anim Genet 2016; 48:255-271. [PMID: 27910110 DOI: 10.1111/age.12526] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2016] [Indexed: 12/17/2022]
Abstract
This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome. The frequency, size and distribution of ROH in the genome are influenced by factors such as natural and artificial selection, recombination, linkage disequilibrium, population structure, mutation rate and inbreeding level. Calculating the inbreeding coefficient from molecular information from ROH (FROH ) is more accurate for estimating autozygosity and for detecting both past and more recent inbreeding effects than are estimates from pedigree data (FPED ). The better results of FROH suggest that FROH can be used to infer information about the history and inbreeding levels of a population in the absence of genealogical information. The selection of superior animals has produced large phenotypic changes and has reshaped the ROH patterns in various regions of the genome. Additionally, selection increases homozygosity around the target locus, and deleterious variants are seen to occur more frequently in ROH regions. Studies involving ROH are increasingly common and provide valuable information about how the genome's architecture can disclose a population's genetic background. By revealing the molecular changes in populations over time, genome-wide information is crucial to understanding antecedent genome architecture and, therefore, to maintaining diversity and fitness in endangered livestock breeds.
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Affiliation(s)
- E Peripolli
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - D P Munari
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil
| | - M V G B Silva
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil.,Embrapa Gado de Leite, Juiz de Fora, 36038-330, Brazil
| | - A L F Lima
- Departamento de Zootecnia e Desenvolvimento Rural, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Florianópolis, 88034-000, Brazil
| | - R Irgang
- Departamento de Zootecnia e Desenvolvimento Rural, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Florianópolis, 88034-000, Brazil
| | - F Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil
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Abstract
Hb Constant Spring (Hb CS, HBA2: c.427T > C) is a common nondeletional α-thalassemia (α-thal) that results from a nucleotide substitution at the termination codon of the α2-globin gene. Homozygosity for Hb CS (α(CS)α/α(CS)α) is relatively rare, and generally characterized with mild hemolytic anemia, jaundice, and splenomegaly. In this report we present a fetus with cardiomegaly, pericardial effusion, enlarged placenta and increased middle cerebral artery-peak systolic velocity (MCA-PSV) at 24 weeks' gestation. Fetal blood sampling revealed the severe anemia [hemoglobin (Hb) level being 4.8 g/dL] and Hb H (β4) disease-like hematological findings with Hb Bart's (γ4) level of 17.9%. DNA sequencing of the α-globin genes found that both partners were Hb CS carriers and the fetus was an Hb CS homozygote. Therefore, this was a rare case of homozygous Hb CS which demonstrated an unusual and serious anemia and hydrops fetalis in utero.
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Affiliation(s)
- Yi He
- a Prenatal Diagnostic Center, Dongguan Maternal & Children Health Hospital , Dongguan, Guangdong , People's Republic of China and
| | - Ying Zhao
- a Prenatal Diagnostic Center, Dongguan Maternal & Children Health Hospital , Dongguan, Guangdong , People's Republic of China and
| | - Ji-Wu Lou
- a Prenatal Diagnostic Center, Dongguan Maternal & Children Health Hospital , Dongguan, Guangdong , People's Republic of China and
| | - Yan-Hui Liu
- a Prenatal Diagnostic Center, Dongguan Maternal & Children Health Hospital , Dongguan, Guangdong , People's Republic of China and
| | - Dong-Zhi Li
- b Prenatal Diagnostic Center, Guangzhou Women & Children Medical Center affiliated to Guangzhou Medical University , Guangzhou, Guangdong , People's Republic of China
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37
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Grumach AS, Stieber C, Veronez CL, Cagini N, Constantino-Silva RN, Cordeiro E, Nöthen MM, Pesquero JB, Cichon S. Homozygosity for a factor XII mutation in one female and one male patient with hereditary angio-oedema. Allergy 2016; 71:119-23. [PMID: 26392288 DOI: 10.1111/all.12769] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2015] [Indexed: 11/27/2022]
Abstract
Hereditary angio-oedema (HAE) with normal C1 inhibitor is associated with heterozygous mutations in the factor XII gene (FXII-HAE). We report two Brazilian FXII-HAE families segregating the mutation c.983 C>A (p.Thr328Lys). In each family, one patient with a homozygous mutation was found. The homozygous female patient in family 1 displayed a severe phenotype. However, this falls within the clinical phenotype spectrum reported for heterozygous female mutation carriers. The homozygous male patient in family 2 also showed a severe phenotype. This finding is intriguing, as to our knowledge, it is the first such report for a male FXII-HAE mutation carrier. In the rare instances in which male mutation carriers are affected, a mild phenotype is typical. The present findings therefore suggest that homozygous FXII-HAE mutation status leads to a severe phenotype in females and males, and to an increased risk of manifest symptoms in the latter.
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Affiliation(s)
- A. S. Grumach
- Outpatient Group of Recurrent Infections and Laboratory of Clinical Immunology; Faculty of Medicine ABC; Santo André Brazil
| | - C. Stieber
- Department of Genomics, Life & Brain Center; Institute of Human Genetics; University of Bonn; Bonn Germany
- Center for Rare Diseases Bonn; University Hospital of Bonn; Bonn Germany
| | - C. L. Veronez
- Department of Biophysics; Universidade Federal de Sao Paulo; São Paulo Brazil
| | - N. Cagini
- Department of Biophysics; Universidade Federal de Sao Paulo; São Paulo Brazil
| | - R. N. Constantino-Silva
- Outpatient Group of Recurrent Infections and Laboratory of Clinical Immunology; Faculty of Medicine ABC; Santo André Brazil
| | - E. Cordeiro
- Outpatient Group of Recurrent Infections and Laboratory of Clinical Immunology; Faculty of Medicine ABC; Santo André Brazil
| | - M. M. Nöthen
- Department of Genomics, Life & Brain Center; Institute of Human Genetics; University of Bonn; Bonn Germany
- Center for Rare Diseases Bonn; University Hospital of Bonn; Bonn Germany
| | - J. B. Pesquero
- Department of Biophysics; Universidade Federal de Sao Paulo; São Paulo Brazil
| | - S. Cichon
- Department of Genomics, Life & Brain Center; Institute of Human Genetics; University of Bonn; Bonn Germany
- Center for Rare Diseases Bonn; University Hospital of Bonn; Bonn Germany
- Division of Medical Genetics; Department of Biomedicine; University Hospital Basel; Basel Switzerland
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38
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Wiedmer M, Oevermann A, Borer-Germann SE, Gorgas D, Shelton GD, Drögemüller M, Jagannathan V, Henke D, Leeb T. A RAB3GAP1 SINE Insertion in Alaskan Huskies with Polyneuropathy, Ocular Abnormalities, and Neuronal Vacuolation (POANV) Resembling Human Warburg Micro Syndrome 1 (WARBM1). G3 (Bethesda) 2015; 6:255-62. [PMID: 26596647 DOI: 10.1534/g3.115.022707] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We observed a hereditary phenotype in Alaskan Huskies that was characterized by polyneuropathy with ocular abnormalities and neuronal vacuolation (POANV). The affected dogs developed a progressive severe ataxia, which led to euthanasia between 8 and 16 months of age. The pedigrees were consistent with a monogenic autosomal recessive inheritance. We localized the causative genetic defect to a 4 Mb interval on chromosome 19 by a combined linkage and homozygosity mapping approach. Whole genome sequencing of one affected dog, an obligate carrier, and an unrelated control revealed a 218-bp SINE insertion into exon 7 of the RAB3GAP1 gene. The SINE insertion was perfectly associated with the disease phenotype in a cohort of 43 Alaskan Huskies, and it was absent from 541 control dogs of diverse other breeds. The SINE insertion induced aberrant splicing and led to a transcript with a greatly altered exon 7. RAB3GAP1 loss-of-function variants in humans cause Warburg Micro Syndrome 1 (WARBM1), which is characterized by additional developmental defects compared to canine POANV, whereas Rab3gap1-deficient mice have a much milder phenotype than either humans or dogs. Thus, the RAB3GAP1 mutant Alaskan Huskies provide an interesting intermediate phenotype that may help to better understand the function of RAB3GAP1 in development. Furthermore, the identification of the presumed causative genetic variant will enable genetic testing to avoid the nonintentional breeding of affected dogs.
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Nickerson SL, Marquis-Nicholson R, Claxton K, Ashton F, Leong IU, Prosser DO, Love JM, George AM, Taylor G, Wilson C, Gardner RJ, Love DR. SNP Analysis and Whole Exome Sequencing: Their Application in the Analysis of a Consanguineous Pedigree Segregating Ataxia. Microarrays (Basel) 2015; 4:490-502. [PMID: 27600236 DOI: 10.3390/microarrays4040490] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/12/2015] [Accepted: 10/15/2015] [Indexed: 11/23/2022]
Abstract
Autosomal recessive cerebellar ataxia encompasses a large and heterogeneous group of neurodegenerative disorders. We employed single nucleotide polymorphism (SNP) analysis and whole exome sequencing to investigate a consanguineous Maori pedigree segregating ataxia. We identified a novel mutation in exon 10 of the SACS gene: c.7962T>G p.(Tyr2654*), establishing the diagnosis of autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS). Our findings expand both the genetic and phenotypic spectrum of this rare disorder, and highlight the value of high-density SNP analysis and whole exome sequencing as powerful and cost-effective tools in the diagnosis of genetically heterogeneous disorders such as the hereditary ataxias.
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Chiancone B, Karasawa MMG, Gianguzzi V, Abdelgalel AM, Bárány I, Testillano PS, Marinoni DT, Botta R, Germanà MA. Early embryo achievement through isolated microspore culture in Citrus clementina Hort. ex Tan., cvs. 'Monreal Rosso' and 'Nules'. Front Plant Sci 2015; 6:413. [PMID: 26124764 PMCID: PMC4463929 DOI: 10.3389/fpls.2015.00413] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/22/2015] [Indexed: 05/06/2023]
Abstract
Microspore embryogenesis is a method of achieving complete homozygosity from plants. It is particularly useful for woody species, like Citrus, characterized by long juvenility, a high degree of heterozygosity and often self-incompatibility. Anther culture is currently the method of choice for microspore embryogenesis in many crops. However, isolated microspore culture is a better way to investigate the processes at the cellular, physiological, biochemical, and molecular levels as it avoids the influence of somatic anther tissue. To exploit the potential of this technique, it is important to separate the key factors affecting the process and, among them, culture medium composition and particularly the plant growth regulators and their concentration, as they can greatly enhance regeneration efficiency. To our knowledge, the ability of meta-Topolin, a naturally occurring aromatic cytokinin, to induce gametic embryogenesis in isolated microspores of Citrus has never been investigated. In this study, the effect of two concentrations of meta-Topolin instead of benzyladenine or zeatin in the culture medium was investigated in isolated microspore culture of two genotypes of Citrus. After 11 months of isolated microspore culture, for both genotypes and for all the four tested media, the microspore reprogramming and their sporophytic development was observed by the presence of multinucleated calli and microspore-derived embryos at different stages. Microsatellite analysis of parental and embryo samples was performed to determine the embryo alleles constitution of early embryos produced in all tested media, confirming their origin from microspores. To our knowledge, this is the first successful report of Citrus microspore embryogenesis with isolated microspore culture in Citrus, and in particular in Citrus clementina Hort. ex Tan, cvs. 'Monreal Rosso' and 'Nules.'
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Affiliation(s)
- Benedetta Chiancone
- Dipartimento di Scienze degli Alimenti, Università degli Studi di Parma, ParmaItaly
| | | | - Valeria Gianguzzi
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi di Palermo, PalermoItaly
| | - Ahmed M. Abdelgalel
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi di Palermo, PalermoItaly
| | - Ivett Bárány
- Centro de Investigaciones Biològicas – Consejo Superior de Investigaciones Científicas, MadridSpain
| | - Pilar S. Testillano
- Centro de Investigaciones Biològicas – Consejo Superior de Investigaciones Científicas, MadridSpain
| | - Daniela Torello Marinoni
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di TorinoGrugliasco, Italy
| | - Roberto Botta
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di TorinoGrugliasco, Italy
| | - Maria Antonietta Germanà
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi di Palermo, PalermoItaly
- *Correspondence: Maria Antonietta Germanà, Dipartimento di Scienze Agrarie e Forestali, Università degli Studi di Palermo, Viale Delle Scienze 11, 90128 Palermo, Italy
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Melhem NM, Lu C, Dresbold C, Middleton FA, Klei L, Wood S, Faraone SV, Vinogradov S, Tiobech J, Yano V, Roeder K, Byerley W, Myles-Worsley M, Devlin B. Characterizing runs of homozygosity and their impact on risk for psychosis in a population isolate. Am J Med Genet B Neuropsychiatr Genet 2014; 165B:521-30. [PMID: 24980794 PMCID: PMC5058445 DOI: 10.1002/ajmg.b.32255] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 06/04/2014] [Indexed: 11/12/2022]
Abstract
An increased abundance of runs of homozygosity (ROH) has been associated with risk for various diseases, including schizophrenia. Here we investigate the characteristics of ROH in Palau, an Oceanic population, evaluating whether these characteristics are related to risk for psychotic disorders and the nature of this association. To accomplish these aims we evaluate a sample of 203 cases with schizophrenia and related psychotic disorders-representing almost complete ascertainment of affected individuals in the population-and contrast their ROH to that of 125 subjects chosen to function as controls. While Palauan diagnosed with psychotic disorders tend to have slightly more ROH regions than controls, the distinguishing features are that they have longer ROH regions, greater total length of ROH, and their ROH tends to co-occur more often at the same locus. The nature of the sample allows us to investigate whether rare, highly penetrant recessive variants generate such case-control differences in ROH. Neither rare, highly penetrant recessive variants nor individual common variants of large effect account for a substantial proportion of risk for psychosis in Palau. These results suggest a more nuanced model for risk is required to explain patterns of ROH for this population.
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Affiliation(s)
- Nadine M. Melhem
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Cong Lu
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA
| | - Cara Dresbold
- Department of Human Genetics, University of Pittsburgh
| | | | | | - Shawn Wood
- University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Stephen V Faraone
- Department of Psychiatry, SUNY Upstate Medical University; Syracuse NY
| | | | | | - Victor Yano
- Palauan Ministry of Health, Republic of Palau
| | - Kathryn Roeder
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA
| | - William Byerley
- Department of Psychiatry, University of California San Francisco
| | | | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA
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Abstract
Many organisms have been reported to choose their mates in order to increase the heterozygosity of their offspring by avoiding mating with relatives or homozygous individuals. Most previous studies using Drosophila melanogaster have used artificial chromosomes or extreme inbreeding treatments, situations unlikely to be matched in nature. Additionally, few studies have examined the interaction between female inbreeding status and her choice of mate. Using females and males from populations that had experienced either random mating or one generation of sib-sib inbreeding, we measured the preferences of females for males. Our results indicate that outbred males were chosen more often than inbred males and that this preference may be more pronounced in outbred females than in inbred ones.
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Affiliation(s)
- Amberle A McKee
- Department of Biological Sciences, California State University Long Beach, Hall of Science 104 1250 Bellflower Blvd, Long Beach, CA 90840, USA
| | - Shanna M Newton
- Department of Biological Sciences, California State University Long Beach, Hall of Science 104 1250 Bellflower Blvd, Long Beach, CA 90840, USA
| | - Ashley J R Carter
- Department of Biological Sciences, California State University Long Beach, Hall of Science 104 1250 Bellflower Blvd, Long Beach, CA 90840, USA
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Tang G, Lu X, Wang SA, Roney EK, Zhang L, Hu S, Lu G, Medeiros LJ, Patel A. Homozygous inv(11)(q21q23) and MLL gene rearrangement in two patients with myeloid neoplasms. Int J Clin Exp Pathol 2014; 7:3196-3201. [PMID: 25031740 PMCID: PMC4097224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 05/25/2014] [Indexed: 06/03/2023]
Abstract
Rearrangements of the MLL gene located at chromosome 11q23 are common chromosomal abnormalities associated with acute leukemias. In vast majority of cases with MLL gene rearrangements, only one chromosome 11 or a single MLL allele got involved. We report two very unusual cases of myeloid neoplasms with homozygous inv(11)(q21q23) and biallelic MLL rearrangement. Both patients, a 12-year old boy and a 29-year old woman, presented initially with T lymphoblastic leukemia/lymphoma (T-ALL), achieved complete remission with intensive chemotherapy, then recurred as acute myeloid leukemia in one patient and therapy-related myelodysplastic syndromes in the other patient, 24 and 15 months after initial T-ALL diagnosis, respectively. In both cases, biallelic MLL gene rearrangements were confirmed by fluorescence in situ hybridization. Mastermind like 2 gene was identified as MLL partner gene in one case. To our knowledge, homozygous inv(11)(q21q23) with two MLL genes rearrangement are extremely rare; it is likely a result of acquired uniparental disomy.
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Affiliation(s)
- Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Xinyan Lu
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Sa A Wang
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Erin K Roney
- Department of Molecular and Human Genetics, Baylor College of MedicineHouston, TX 77030, USA
| | - Liping Zhang
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Shimin Hu
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Gary Lu
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of MedicineHouston, TX 77030, USA
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van Dijk T, Pagliarani G, Pikunova A, Noordijk Y, Yilmaz-Temel H, Meulenbroek B, Visser RGF, van de Weg E. Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map. BMC Plant Biol 2014; 14:55. [PMID: 24581289 PMCID: PMC3944823 DOI: 10.1186/1471-2229-14-55] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/18/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Breeders in the allo-octoploid strawberry currently make little use of molecular marker tools. As a first step of a QTL discovery project on fruit quality traits and resistance to soil-borne pathogens such as Phytophthora cactorum and Verticillium we built a genome-wide SSR linkage map for the cross Holiday x Korona. We used the previously published MADCE method to obtain full haplotype information for both of the parental cultivars, facilitating in-depth studies on their genomic organisation. RESULTS The linkage map incorporates 508 segregating loci and represents each of the 28 chromosome pairs of octoploid strawberry, spanning an estimated length of 2050 cM. The sub-genomes are denoted according to their sequence divergence from F. vesca as revealed by marker performance. The map revealed high overall synteny between the sub-genomes, but also revealed two large inversions on LG2C and LG2D, of which the latter was confirmed using a separate mapping population. We discovered interesting breeding features within the parental cultivars by in-depth analysis of our haplotype data. The linkage map-derived homozygosity level of Holiday was similar to the pedigree-derived inbreeding level (33% and 29%, respectively). For Korona we found that the observed homozygosity level was over three times higher than expected from the pedigree (13% versus 3.6%). This could indicate selection pressure on genes that have favourable effects in homozygous states. The level of kinship between Holiday and Korona derived from our linkage map was 2.5 times higher than the pedigree-derived value. This large difference could be evidence of selection pressure enacted by strawberry breeders towards specific haplotypes. CONCLUSION The obtained SSR linkage map provides a good base for QTL discovery. It also provides the first biologically relevant basis for the discernment and notation of sub-genomes. For the first time, we revealed genomic rearrangements that were verified in a separate mapping population. We believe that haplotype information will become increasingly important in identifying marker-trait relationships and regions that are under selection pressure within breeding material. Our attempt at providing a biological basis for the discernment of sub-genomes warrants follow-up studies to streamline the naming of the sub-genomes among different octoploid strawberry maps.
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Affiliation(s)
- Thijs van Dijk
- Wageningen-UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
- Graduate School Experimental Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Giulia Pagliarani
- Wageningen-UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
- Department of Agricultural Science, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Anna Pikunova
- Wageningen-UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
- The All-Russian Research Institute of Horticultural Breeding (VNIISPK), p/o Zhilina, Orel, Russia
| | - Yolanda Noordijk
- Wageningen-UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
| | - Hulya Yilmaz-Temel
- Wageningen-UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
- Department of Bioengineering, Ege University, 35100 Izmir, Bornova, Turkey
| | - Bert Meulenbroek
- Fresh Forward Breeding B.V, Wielseweg 38a, Eck en Wiel, The Netherlands
| | - Richard GF Visser
- Wageningen-UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
| | - Eric van de Weg
- Wageningen-UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
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Mok K, Laaksovirta H, Tienari PJ, Peuralinna T, Myllykangas L, Chiò A, Traynor BJ, Nalls MA, Gurunlian N, Shatunov A, Restagno G, Mora G, Nigel Leigh P, Shaw CE, Morrison KE, Shaw PJ, Al-Chalabi A, Hardy J, Orrell RW. Homozygosity analysis in amyotrophic lateral sclerosis. Eur J Hum Genet 2013; 21:1429-35. [PMID: 23612577 PMCID: PMC3829775 DOI: 10.1038/ejhg.2013.59] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 02/21/2013] [Accepted: 02/28/2013] [Indexed: 01/20/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) may appear to be familial or sporadic, with recognised dominant and recessive inheritance in a proportion of cases. Sporadic ALS may be caused by rare homozygous recessive mutations. We studied patients and controls from the UK and a multinational pooled analysis of GWAS data on homozygosity in ALS to determine any potential recessive variant leading to the disease. Six-hundred and twenty ALS and 5169 controls were studied in the UK cohort. A total of 7646 homozygosity segments with length >2 Mb were identified, and 3568 rare segments remained after filtering 'common' segments. The mean total of the autosomal genome with homozygosity segments was longer in ALS than in controls (unfiltered segments, P=0.05). Two-thousand and seventeen ALS and 6918 controls were studied in the pooled analysis. There were more regions of homozygosity segments per case (P=1 × 10(-5)), a greater proportion of cases harboured homozygosity (P=2 × 10(-5)), a longer average length of segment (P=1 × 10(-5)), a longer total genome coverage (P=1 × 10(-5)), and a higher rate of these segments overlapped with RefSeq gene regions (P=1 × 10(-5)), in ALS patients than controls. Positive associations were found in three regions. The most significant was in the chromosome 21 SOD1 region, and also chromosome 1 2.9-4.8 Mb, and chromosome 5 in the 65 Mb region. There are more than twenty potential genes in these regions. These findings point to further possible rare recessive genetic causes of ALS, which are not identified as common variants in GWAS.
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Affiliation(s)
- Kin Mok
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, and Department of Clinical Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - Hannu Laaksovirta
- Helsinki University Central Hospital, Department of Neurology, Molecular Neurology Research Program, Biomedicum, University of Helsinki, Helsinki, Finland
- Molecular Genetics Section and Neuromuscular Diseases Research Group, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD, USA
| | - Pentti J Tienari
- Molecular Genetics Section and Neuromuscular Diseases Research Group, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD, USA
| | - Terhi Peuralinna
- Molecular Genetics Section and Neuromuscular Diseases Research Group, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD, USA
| | - Liisa Myllykangas
- Department of Pathology, Haartman Institute, University of Helsinki and HUSLAB, and Folkhalsan Institute of Genetics, Helsinki, Finland
| | - Adriano Chiò
- Department of Neuroscience, University of Turin and Azienda Ospedaliera Universitaria San Giovanni Battista, Turin, Italy
| | - Bryan J Traynor
- Molecular Genetics Section and Neuromuscular Diseases Research Group, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD, USA
| | - Michael A Nalls
- Molecular Genetics Section and Neuromuscular Diseases Research Group, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD, USA
| | - Nicole Gurunlian
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, and Department of Clinical Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - Aleksey Shatunov
- Medical Research Council Centre for Neurodegeneration Research, King's College London, Institute of Psychiatry, London, UK
| | - Gabriella Restagno
- Molecular Genetics Laboratory, Azienda Ospedaliera OIRM-Sant'Anna, Turin, Italy
| | - Gabriele Mora
- Fondazione Salvatore Mangeri, IRCCS Scientific Institute of Milan, Milan, Italy
| | - P Nigel Leigh
- Brighton and Sussex Medical School, Trafford Centre for Biomedical Research, University of Sussex, Falmer, UK
| | - Chris E Shaw
- Medical Research Council Centre for Neurodegeneration Research, King's College London, Institute of Psychiatry, London, UK
| | - Karen E Morrison
- School of Clinical and Experimental Medicine, University of Birmingham and Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Pamela J Shaw
- Department of Neuroscience, The Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Ammar Al-Chalabi
- Medical Research Council Centre for Neurodegeneration Research, King's College London, Institute of Psychiatry, London, UK
| | - John Hardy
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, and Department of Clinical Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - Richard W Orrell
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, and Department of Clinical Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
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Al-Hamed M, Sayer JA, Al-Hassoun I, Aldahmesh MA, Meyer B. A novel mutation in NPHS2 causing nephrotic syndrome in a Saudi Arabian family. NDT Plus 2010; 3:545-8. [PMID: 25949463 PMCID: PMC4421432 DOI: 10.1093/ndtplus/sfq149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 07/20/2010] [Indexed: 11/21/2022] Open
Abstract
We report a consanguineous family from Saudi Arabia with three affected children presenting with infantile nephrotic syndrome. In order to provide a molecular diagnosis, a genome-wide SNP analysis of the affected patients was performed. We identified a region of homozygosity on chromosome 1, containing the NPHS2 gene. Direct sequencing, by exon PCR, of NPHS2 identified a homozygous nucleotide change 385C > T within exon 3 in the three affected children, leading to a premature stop codon (Q129X). This homozygous truncating mutation in NPHS2 is novel and was associated with a severe clinical phenotype. Additional mutations in related genes NPHS1, PLCE1 and NEPH1 were not identified, excluding tri-allelism within these genes in this family.
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Affiliation(s)
- Mohamed Al-Hamed
- King Faisal Specialist Hospital and Research Centre , Department of Genetics, Riyadh , Saudi Arabia ; Institute of Human Genetics, International Centre of Life, Newcastle University , Central Parkway, Newcastle upon Tyne, NE1 3BZ UK
| | - John A Sayer
- Institute of Human Genetics, International Centre of Life, Newcastle University , Central Parkway, Newcastle upon Tyne, NE1 3BZ UK
| | - Ibrahim Al-Hassoun
- King Faisal Specialist Hospital and Research Centre , Department of Genetics, Riyadh , Saudi Arabia
| | - Mohamed A Aldahmesh
- King Faisal Specialist Hospital and Research Centre , Department of Genetics, Riyadh , Saudi Arabia
| | - Brian Meyer
- King Faisal Specialist Hospital and Research Centre , Department of Genetics, Riyadh , Saudi Arabia
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Watanabe N, Nisitani S, Ikuta K, Suzuki M, Chiba T, Honjo T. Expression levels of B cell surface immunoglobulin regulate efficiency of allelic exclusion and size of autoreactive B-1 cell compartment. J Exp Med 1999; 190:461-69. [PMID: 10449517 PMCID: PMC2195600 DOI: 10.1084/jem.190.4.461] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Surface-expressed immunoglobulin (Ig) has been shown to have a critical role in allelic exclusion of Ig heavy (H) and light (L) chains. Although various degrees of suppression of endogenous Ig expression are observed in Ig transgenic (Tg) mice, it was not clear whether this difference is due to different onsets of Tg expression or to different levels of Tg expression, which are obviously affected by integration sites of the transgene. In this study we generated antierythrocyte antibody Tg mice that carry tandem joined H and L chain transgenes (H+L) and confirmed that homozygosity of the transgene loci enhances the level of transgene expression as compared with heterozygosity. Suppression of endogenous H and L chain gene expression was stronger in homozygous than in heterozygous Tg mice. Similar results were obtained in control Tg mice carrying the H chain only. These results suggest that there is a threshold of the B cell receptor expression level that induces allelic exclusion. In addition, despite the same B cell receptor specificity, the size of Tg autoreactive B-1 cell compartment in the peritoneal cavity is larger in homozygous than in heterozygous mice, although the number of the Tg B-2 cell subset decreased in the spleen and bone marrow of homozygous Tg mice as compared with heterozygous Tg mice. By contrast, homozygosity of the H chain alone Tg line, which does not recognize self-antigens, did not increase the size of the peritoneal B-1 subset. These results suggest that the size of the B-1 cell subset in the Tg mice may depend on strength of signals through B cell receptors triggered by self-antigens.
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Affiliation(s)
- Norihiko Watanabe
- From the Department of Medical Chemistry, Faculty of Medicine, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
- From the Department of Gastroenterology, Faculty of Medicine, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Sazuku Nisitani
- From the Department of Medical Chemistry, Faculty of Medicine, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Koichi Ikuta
- From the Department of Medical Chemistry, Faculty of Medicine, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Misao Suzuki
- Center for Animal Resources and Development, Kumamoto University, Kuhonji, Kumamoto 862-0976, Japan
| | - Tsutomu Chiba
- From the Department of Gastroenterology, Faculty of Medicine, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tasuku Honjo
- From the Department of Medical Chemistry, Faculty of Medicine, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
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48
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De La Concha EG, Fernandez-Arquero M, Martinez A, Vidal F, Vigil P, Conejero L, Garcia-Rodriguez MC, Fontan G. HLA class II homozygosity confers susceptibility to common variable immunodeficiency (CVID). Clin Exp Immunol 1999; 116:516-20. [PMID: 10361244 PMCID: PMC1905305 DOI: 10.1046/j.1365-2249.1999.00926.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Most cases of CVID occur sporadically, but familial cases do also occur and 15% of the patients with the disease have first degree relatives with IgA deficiency (IgAD). Our purpose was to study CVID association with HLA class II alleles and to ascertain whether this disease shares a common genetic background with IgAD in our population. Patients with CVID (n = 42), were typed using gene amplification and sequence-specific oligonucleotide probing for HLA-DRB1, DRB3, DQA1 and DQB1 loci and their typing compared with that of 96 IgAD and 334 healthy controls. We observed a positive association between non-Asp residues at position 57 of the HLA-DQbeta chain and CVID, although much weaker than in IgAD. Further, we found an association between CVID and homozygosity for genes encoding HLA class II molecules, especially HLA-DQ, not seen in IgAD. The data support the hypothesis that a restricted diversity of HLA class II molecules may contribute to susceptibility to CVID.
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Affiliation(s)
- E G De La Concha
- Department of Immunology, San Carlos University Hospital, Madrid, Spain
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