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Olatunde AC, Cornwall DH, Roedel M, Lamb TJ. Mouse Models for Unravelling Immunology of Blood Stage Malaria. Vaccines (Basel) 2022; 10:1525. [PMID: 36146602 PMCID: PMC9501382 DOI: 10.3390/vaccines10091525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Malaria comprises a spectrum of disease syndromes and the immune system is a major participant in malarial disease. This is particularly true in relation to the immune responses elicited against blood stages of Plasmodium-parasites that are responsible for the pathogenesis of infection. Mouse models of malaria are commonly used to dissect the immune mechanisms underlying disease. While no single mouse model of Plasmodium infection completely recapitulates all the features of malaria in humans, collectively the existing models are invaluable for defining the events that lead to the immunopathogenesis of malaria. Here we review the different mouse models of Plasmodium infection that are available, and highlight some of the main contributions these models have made with regards to identifying immune mechanisms of parasite control and the immunopathogenesis of malaria.
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Affiliation(s)
| | | | | | - Tracey J. Lamb
- Department of Pathology, University of Utah, Emma Eccles Jones Medical Research Building, 15 N Medical Drive E, Room 1420A, Salt Lake City, UT 84112, USA
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Genomic inbreeding and runs of homozygosity analysis of indigenous cattle populations in southern China. PLoS One 2022; 17:e0271718. [PMID: 36006904 PMCID: PMC9409551 DOI: 10.1371/journal.pone.0271718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
Runs of homozygosity (ROH) are continuous homozygous segments from the common ancestor of parents. Evaluating ROH pattern can help to understand inbreeding level and genetic basis of important traits. In this study, three representative cattle populations including Leiqiong cattle (LQC), Lufeng cattle (LFC) and Hainan cattle (HNC) were genotyped using the Illumina BovineHD SNPs array (770K) to assess ROH pattern at genome wide level. Totally, we identified 26,537 ROH with an average of 153 ROH per individual. The sizes of ROH ranged from 0.5 to 53.26Mb, and the average length was 1.03Mb. The average of FROH ranged from 0.10 (LQC) to 0.15 (HNC). Moreover, we identified 34 ROH islands (with frequency > 0.5) across genome. Based on these regions, we observed several breed-specific candidate genes related to adaptive traits. Several common genes related to immunity (TMEM173, MZB1 and SIL1), and heat stress (DNAJC18) were identified in all three populations. Three genes related to immunity (UGP2), development (PURA) and reproduction (VPS54) were detected in both HNC and LQC. Notably, we identified several breed-specific genes related to sperm development (BRDT and SPAG6) and heat stress (TAF7) in HNC, and immunity (CDC23 and NME5) and development (WNT87) in LFC. Our findings provided valuable insights into understanding the genomic homozygosity pattern and promoting the conservation of genetic resources of Chinese indigenous cattle.
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Gonzales PR, Andersen EF, Brown TR, Horner VL, Horwitz J, Rehder CW, Rudy NL, Robin NH, Thorland EC, On Behalf Of The Acmg Laboratory Quality Assurance Committee. Interpretation and reporting of large regions of homozygosity and suspected consanguinity/uniparental disomy, 2021 revision: A technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2022; 24:255-261. [PMID: 34906464 DOI: 10.1016/j.gim.2021.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/18/2022] Open
Abstract
Genomic testing, including single-nucleotide variation (formerly single-nucleotide polymorphism)-based chromosomal microarray and exome and genome sequencing, can detect long regions of homozygosity (ROH) within the genome. Genomic testing can also detect possible uniparental disomy (UPD). Platforms that can detect ROH and possible UPD have matured since the initial American College of Medical Genetics and Genomics (ACMG) standard was published in 2013, and the detection of ROH and UPD by these platforms has shown utility in diagnosis of patients with genetic/genomic disorders. The presence of these segments, when distributed across multiple chromosomes, may indicate a familial relationship between the proband's parents. This technical standard describes the detection of possible consanguinity and UPD by genomic testing, as well as the factors confounding the inference of a specific parental relationship or UPD. Current bioethical and legal issues regarding detection and reporting of consanguinity are also discussed.
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Affiliation(s)
| | - Erica F Andersen
- ARUP Laboratories, Salt Lake City, UT; The University of Utah, Salt Lake City, UT
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Agarwal V, Thirthalli J, Kumar CN, Christopher R, U Arunachal G, Reddy KS, Rawat VS, Gangadhar BN, Wood J, Nimgaonkar V. Parental consanguinity among patients with schizophrenia in a rural community of South India: A clinical and genetic investigation. Asian J Psychiatr 2021; 64:102814. [PMID: 34425412 DOI: 10.1016/j.ajp.2021.102814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/12/2021] [Accepted: 08/10/2021] [Indexed: 01/04/2023]
Abstract
BACKGROUND Studies from certain regions of the world indicate that consanguineous marriages are a risk factor for the development of schizophrenia in offspring. However the evidence is inconsistent partly due to methodological limitation of which hospital based recruitment contributing to significant bias. The studies from the Indian subcontinent, is scarce, where rates of consanguinity is high. METHODS The schizophrenia patients living in a geographically defined rural south Indian community and randomly selected controls dwelling in the same community sharing sociocultural, economic and lifestyle factors were recruited. They were assessed for parental consanguinity using the clinical interviews as well as DNA-based estimates. The latter was conducted by calculating the coefficient of inbreeding 'f'. A participant was considered to have consanguineous parentage if his/her parents shared a common ancestor no more remote than a great-great-grandparent, corresponding to DNA-based estimates of 'f' ≥ 0.0156. RESULTS The rates of parental consanguinity assessed by clinical interview were comparable in both groups (Cases: 10.71 %, Controls: 7.25 %; χ2 = 0.493, p = 0.4825). However, DNA-based rates of parental consanguinity showed that 'f' was significantly higher among cases than controls (Mann-Whitney U = 11315.5; p = 0.022). Seventy-five cases (62.5 %) and 108 control participants (48.6 %) had 'f' ≥ 0.0156 (χ2 = 6.008; p = 0.014). The results were consistent across different quality control measures. CONCLUSION Schizophrenia is associated with higher parental consanguinity, suggesting a role for multiple recessive risk alleles in its etiology. Replication in future studies in diverse settings would add further strength to this.
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Affiliation(s)
- Vikas Agarwal
- Department of Psychiatry, National Institute of Mental Health And Neuro Sciences, Bengaluru, India
| | - Jagadisha Thirthalli
- Department of Psychiatry, National Institute of Mental Health And Neuro Sciences, Bengaluru, India.
| | | | - Rita Christopher
- Department of Neurochemistry, National Institute of Mental Health And Neuro Sciences, Bengaluru, India
| | - Gautham U Arunachal
- Department of Human Genetics, National Institute of Mental Health And Neuro Sciences, Bengaluru, India
| | - K Shanivaram Reddy
- Department of Psychiatric Social Work, National Institute of Mental Health And Neuro Sciences, Bengaluru, India
| | - Vikram Singh Rawat
- Department of Psychiatry, All India Institute of Mediacal Sciences, Rishikesh, India
| | - Bangalore N Gangadhar
- Department of Psychiatry, National Institute of Mental Health And Neuro Sciences, Bengaluru, India
| | - Joel Wood
- Department of Psychiatry, University of Pittsburgh School of Medicine, Western Psychiatric Hospital, Pittsburgh, USA
| | - Vishwajit Nimgaonkar
- Department of Psychiatry, University of Pittsburgh School of Medicine, Western Psychiatric Hospital, Pittsburgh, USA; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA
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Hajihosseinlo A, Nejati-Javaremi A, Miraei-Ashtiani SR. Genetic structure analysis in several populations of cattle using SNP genotypes. Anim Biotechnol 2021; 34:288-300. [PMID: 34591729 DOI: 10.1080/10495398.2021.1960360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Parameters such as effective population size (Ne), runs of homozygosity (ROH), and inbreeding based on ROH (FROH) can give new insight into the level of genetic diversity for the population under selection. This research aimed to measure the extent of linkage disequilibrium (LD), effective population size (Ne), Haplotype Block Structure, and runs of homozygosity (ROHs) in several populations of cattle using SNP genotypes. In this study, that the average r2 decreased with the increasing distance of SNP pairs. A general decrease in Ne can be seen for all four populations, indicating a loss of genetic diversity. The Iranian Holstein had the lowest level of genomic inbreeding at an ROH of 1, 5, 10 Mb, while the French Holstein had the highest. The maximum number of ROH is seen at a distance of less than 1 Mb, and the lowest number of ROH is seen at a distance of 10 Mb. The number of ROH decreases with increasing distance due to the increased recombination rate. This is a concern as an increase in inbreeding leads to a reduction in the effective population size, which was also evident in the study populations.
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Affiliation(s)
- Abbas Hajihosseinlo
- Department of Animal Science, University of Tehran Aras International Campus, Jolfa, Iran
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Nosrati M, Asadollahpour Nanaei H, Javanmard A, Esmailizadeh A. The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations. Genomics 2021; 113:1407-1415. [PMID: 33705888 DOI: 10.1016/j.ygeno.2021.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 02/21/2021] [Accepted: 03/04/2021] [Indexed: 11/28/2022]
Abstract
Genome-wide pattern of runs of homozygosity (ROH) across ovine genome can provide a useful resource for studying diversity and demography history in sheep. We analyzed 50 k SNPs chip data of 2536 animals to identify pattern, distribution and level of ROHs in 68 global sheep populations. A total of 60,301 ROHs were detected in all breeds. The majority of the detected ROHs were <16 Mb and the average total number of ROHs per individual was 23.8 ± 13.8. The ROHs greater than 1 Mb covered on average 8.2% of the sheep autosomes, 1% of which was related to the ROHs with 1-4 Mb of length. The mean sum of ROH length in two-thirds of the populations was less than 250 Mb ranging from 21.7 to near 570 Mb. The level of genomic inbreeding was relatively low. The average of the inbreeding coefficients based on ROH (FROH) was 0.09 ± 0.05. It was rising in a stepwise manner with distance from Southwest Asia and maximum values were detected in North European breeds. A total of 465 ROH hotspots were detected in 25 different autosomes which partially surrounding 257 Refseq genes across the genome. Most of the detected genes were related to growth, body weight, meat production and quality, wool production and pigmentation. In conclusion, our analysis showed that the sheep genome, compared with other livestock species such as cattle and pig, displays low levels of homozygosity and appropriate genetic diversity for selection response and genetic merit gain.
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Affiliation(s)
- Maryam Nosrati
- Department of Agriculture, Payame Noor University, PO BOX 19395-3697, Tehran, Iran.
| | - Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Arash Javanmard
- Departement of Animal Sceince, Faculty of Agriculture, University of Tabriz, PB 5166616471,Tabriz, Iran
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran.
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Li W, Zhang M, Wang K, Lu Y, Tang H, Wu K. A double-labeling marker-based method for estimating inbreeding and parental genomic components in a population under conservation. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 33:12-23. [PMID: 31480193 PMCID: PMC6946976 DOI: 10.5713/ajas.19.0035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 06/11/2019] [Indexed: 01/13/2023]
Abstract
Objective The objective of a conservation program is to maintain maximum genetic diversity and preserve the viability of a breed. However, the efficiency of a program is influenced by the ability to accurately measure and predict genetic diversity. Methods To examine this question, we conducted a simulation in which common measures (i.e. heterozygosity) and novel measures (identity-by-descent probabilities and parental genomic components) were used to estimate genetic diversity within a conserved population using double-labeled single nucleotide polymorphism markers. Results The results showed that the accuracy and sensitivity of identity-by-state probabilities and heterozygosity were close to identity by descent (IBD) probabilities, which reflect the true genetic diversity. Expected heterozygosity most closely aligned with IBD. All common measures suggested that practices used in the current Chinese pig conservation program result in a ~5% loss in genetic diversity every 10 generations. Parental genomic components were also analyzed to monitor real-time changes in genomic components for each male and female ancestor. The analysis showed that ~7.5% of male families and ~30% of female families were lost every 5 generations. After 50 generations of simulated conservation, 4 male families lost ~50% of their initial genomic components, and the genomic components for 24.8% of the female families were lost entirely. Conclusion In summary, compared with the true genetic diversity value obtained using double-labeled markers, expected heterozygosity appears to be the optimal indicator. Parental genomic components analysis provides a more detailed picture of genetic diversity and can be used to guide conservation management practices.
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Affiliation(s)
- Wenting Li
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.,College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - Mengmeng Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Kejun Wang
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yunfeng Lu
- School of Life Science and Technology, Nanyang Normal University, Nanyang Henan, 473061, China
| | - Hui Tang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Keliang Wu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
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Rehberg J, Stipčić A, Ćorić T, Kolčić I, Polašek O. Mortality patterns in Southern Adriatic islands of Croatia: a registry-based study. Croat Med J 2018; 59:118-123. [PMID: 29972734 PMCID: PMC6045898 DOI: 10.3325/cmj.2018.59.118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Aim To investigate the mortality patterns on the Southern Adriatic islands of Croatia and compare them with those in two, mainly coastal, mainland counties. Methods In this registry-based study we used the official mortality register data to analyze the mortality patterns on seven Croatian islands (Brač, Hvar, Korčula, Lastovo, Mljet, Šolta, and Vis) and Pelješac peninsula in the 1998-2013 period and calculated the average lifespan, life expectancy, and standardized mortality ratios (SMR). We compared the leading causes of death with those in the mainland population of two southernmost Croatian counties. Results The average lifespan of the island population was 3-10 years longer for men and 2-7 years longer for women than that on the mainland. All-cause SMRs were significantly lower for both men and women on Korčula, Brač, Mljet, and Pelješac but significantly higher for women on Šolta (1.22; 95% confidence intervals 1.07-1.38). The leading causes of death on the islands were cardiovascular diseases, with higher percentages in men and lower in women in comparison with those on the mainland. There were no substantial differences in the life expectancy at birth. Conclusions Despite longer lifespan, lack of differences in life expectancy at birth suggests that the recent generations of islanders no longer show beneficial mortality patterns, possibly due to diminishing adherence to the Mediterranean diet and lifestyle. Restoring the traditional lifestyles is a public health priority, with the ultimate aim of reducing inequalities and improving the health of island inhabitants.
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Affiliation(s)
| | | | | | | | - Ozren Polašek
- Ozren Polašek, University of Split School of Medicine, Šoltanska 2, 21220 Split, Croatia,
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Lemes RB, Nunes K, Carnavalli JEP, Kimura L, Mingroni-Netto RC, Meyer D, Otto PA. Inbreeding estimates in human populations: Applying new approaches to an admixed Brazilian isolate. PLoS One 2018; 13:e0196360. [PMID: 29689090 PMCID: PMC5916862 DOI: 10.1371/journal.pone.0196360] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/11/2018] [Indexed: 02/06/2023] Open
Abstract
The analysis of genomic data (~400,000 autosomal SNPs) enabled the reliable estimation of inbreeding levels in a sample of 541 individuals sampled from a highly admixed Brazilian population isolate (an African-derived quilombo in the State of São Paulo). To achieve this, different methods were applied to the joint information of two sets of markers (one complete and another excluding loci in patent linkage disequilibrium). This strategy allowed the detection and exclusion of markers that biased the estimation of the average population inbreeding coefficient (Wright's fixation index FIS), which value was eventually estimated as around 1% using any of the methods we applied. Quilombo demographic inferences were made by analyzing the structure of runs of homozygosity (ROH), which were adapted to cope with a highly admixed population with a complex foundation history. Our results suggest that the amount of ROH <2Mb of admixed populations should be somehow proportional to the genetic contribution from each parental population.
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Affiliation(s)
- Renan B. Lemes
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Kelly Nunes
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Juliana E. P. Carnavalli
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Lilian Kimura
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Regina C. Mingroni-Netto
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Paulo A. Otto
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
- * E-mail:
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Peripolli E, Stafuzza NB, Munari DP, Lima ALF, Irgang R, Machado MA, Panetto JCDC, Ventura RV, Baldi F, da Silva MVGB. Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle. BMC Genomics 2018; 19:34. [PMID: 29316879 PMCID: PMC5759835 DOI: 10.1186/s12864-017-4365-3] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 12/04/2017] [Indexed: 11/10/2022] Open
Abstract
Background Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dairy cattle genome; (ii) identify ROH islands for gene content and enrichment in segments shared by more than 50% of the samples, and (iii) compare estimates of molecular inbreeding calculated from ROH (FROH), genomic relationship matrix approach (FGRM) and based on the observed versus expected number of homozygous genotypes (FHOM), and from pedigree-based coefficient (FPED). Results ROH were identified in all animals, with an average number of 55.12 ± 10.37 segments and a mean length of 3.17 Mb. Short segments (ROH1–2 Mb) were abundant through the genomes, which accounted for 60% of all segments identified, even though the proportion of the genome covered by them was relatively small. The findings obtained in this study suggest that on average 7.01% (175.28 Mb) of the genome of this population is autozygous. Overlapping ROH were evident across the genomes and 14 regions were identified with ROH frequencies exceeding 50% of the whole population. Genes associated with lactation (TRAPPC9), milk yield and composition (IRS2 and ANG), and heat adaptation (HSF1, HSPB1, and HSPE1), were identified. Inbreeding coefficients were estimated through the application of FROH, FGRM, FHOM, and FPED approaches. FPED estimates ranged from 0.00 to 0.327 and FROH from 0.001 to 0.201. Low to moderate correlations were observed between FPED-FROH and FGRM-FROH, with values ranging from −0.11 to 0.51. Low to high correlations were observed between FROH-FHOM and moderate between FPED-FHOM and FGRM-FHOM. Correlations between FROH from different lengths and FPED gradually increased with ROH length. Conclusions Genes inside ROH islands suggest a strong selection for dairy traits and enrichment for Gyr cattle environmental adaptation. Furthermore, low FPED-FROH correlations for small segments indicate that FPED estimates are not the most suitable method to capture ancient inbreeding. The existence of a moderate correlation between larger ROH indicates that FROH can be used as an alternative to inbreeding estimates in the absence of pedigree records. Electronic supplementary material The online version of this article (10.1186/s12864-017-4365-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisa Peripolli
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Nedenia Bonvino Stafuzza
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Ciências Exatas, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Danísio Prado Munari
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Ciências Exatas, 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
| | - André Luís Ferreira Lima
- Centro de Ciências Agrárias, Departamento de Zootecnia e Desenvolvimento Rural, Universidade Federal de Santa Catarina, Florianópolis, 88034-000, Brazil
| | - Renato Irgang
- Centro de Ciências Agrárias, Departamento de Zootecnia e Desenvolvimento Rural, Universidade Federal de Santa Catarina, Florianópolis, 88034-000, Brazil
| | - Marco Antonio Machado
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil.,Embrapa Gado de Leite, Juiz de Fora, 36038-330, Brazil
| | | | - Ricardo Vieira Ventura
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, 13635-900, Brazil.,Beef Improvement Opportunities, Elora, ON, N0B 1S0, Canada.,University of Guelph, Centre for Genetic Improvement of Livestock, ABScBG, Guelph, N1G 2W1, Canada
| | - Fernando Baldi
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, 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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Relationship of runs of homozygosity with adaptive and production traits in a paternal broiler line. Animal 2017; 12:1126-1134. [PMID: 29065939 DOI: 10.1017/s1751731117002671] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Genomic regions under high selective pressure present specific runs of homozygosity (ROH), which provide valuable information on the genetic mechanisms underlying the adaptation to environment imposed challenges. In broiler chickens, the adaptation to conventional production systems in tropical environments lead the animals with favorable genotypes to be naturally selected, increasing the frequency of these alleles in the next generations. In this study, ~1400 chickens from a paternal broiler line were genotyped with the 600 K Affymetrix® Axiom® high-density (HD) genotyping array for estimation of linkage disequilibrium (LD), effective population size (N e ), inbreeding and ROH. The average LD between adjacent single nucleotide polymorphisms (SNPs) in all autosomes was 0.37, and the LD decay was higher in microchromosomes followed by intermediate and macrochromosomes. The N e of the ancestral population was high and declined over time maintaining a sufficient number of animals to keep the inbreeding coefficient of this population at low levels. The ROH analysis revealed genomic regions that harbor genes associated with homeostasis maintenance and immune system mechanisms, which may have been selected in response to heat stress. Our results give a comprehensive insight into the relationship between shared ROH regions and putative regions related to survival and production traits in a paternal broiler line selected for over 20 years. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the chicken genome.
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12
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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] [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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13
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Howrigan DP, Simonson MA, Davies G, Harris SE, Tenesa A, Starr JM, Liewald DC, Deary IJ, McRae A, Wright MJ, Montgomery GW, Hansell N, Martin NG, Payton A, Horan M, Ollier WE, Abdellaoui A, Boomsma DI, DeRosse P, Knowles EEM, Glahn DC, Djurovic S, Melle I, Andreassen OA, Christoforou A, Steen VM, Hellard SL, Sundet K, Reinvang I, Espeseth T, Lundervold AJ, Giegling I, Konte B, Hartmann AM, Rujescu D, Roussos P, Giakoumaki S, Burdick KE, Bitsios P, Donohoe G, Corley RP, Visscher PM, Pendleton N, Malhotra AK, Neale BM, Lencz T, Keller MC. Genome-wide autozygosity is associated with lower general cognitive ability. Mol Psychiatry 2016; 21:837-43. [PMID: 26390830 PMCID: PMC4803638 DOI: 10.1038/mp.2015.120] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/23/2015] [Accepted: 07/13/2015] [Indexed: 01/12/2023]
Abstract
Inbreeding depression refers to lower fitness among offspring of genetic relatives. This reduced fitness is caused by the inheritance of two identical chromosomal segments (autozygosity) across the genome, which may expose the effects of (partially) recessive deleterious mutations. Even among outbred populations, autozygosity can occur to varying degrees due to cryptic relatedness between parents. Using dense genome-wide single-nucleotide polymorphism (SNP) data, we examined the degree to which autozygosity associated with measured cognitive ability in an unselected sample of 4854 participants of European ancestry. We used runs of homozygosity-multiple homozygous SNPs in a row-to estimate autozygous tracts across the genome. We found that increased levels of autozygosity predicted lower general cognitive ability, and estimate a drop of 0.6 s.d. among the offspring of first cousins (P=0.003-0.02 depending on the model). This effect came predominantly from long and rare autozygous tracts, which theory predicts as more likely to be deleterious than short and common tracts. Association mapping of autozygous tracts did not reveal any specific regions that were predictive beyond chance after correcting for multiple testing genome wide. The observed effect size is consistent with studies of cognitive decline among offspring of known consanguineous relationships. These findings suggest a role for multiple recessive or partially recessive alleles in general cognitive ability, and that alleles decreasing general cognitive ability have been selected against over evolutionary time.
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Affiliation(s)
- D P Howrigan
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge Center, Cambridge, MA, USA
| | - M A Simonson
- Division of Data Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - G Davies
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - S E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Medical Genetics Section, University of Edinburgh Centre for Genomic and Experimental Medicine and MRC Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - A Tenesa
- Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit, Western General Hospital, University of Edinburgh, Edinburgh, UK
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, UK
| | - J M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - D C Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - I J Deary
- Department of Psychology, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - A McRae
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - M J Wright
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
| | - G W Montgomery
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
| | - N Hansell
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
| | - N G Martin
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
| | - A Payton
- Centre for Integrated Genomic Medical Research, Institute of Population Health, University of Manchester, Manchester, UK
| | - M Horan
- Centre for Clinical and Cognitive Neurosciences, Institute of Brain Behaviour and Mental Health, University of Manchester, Salford Royal NHS Foundation Trust, Salford, UK
| | - W E Ollier
- Centre for Integrated Genomic Medical Research, Institute of Population Health, University of Manchester, Manchester, UK
| | - A Abdellaoui
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
- Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
| | - D I Boomsma
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
- Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
- EMGO+ Institute for Health and Care Research, Amsterdam, The Netherlands
| | - P DeRosse
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY, USA
- Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY, USA
- Hofstra North Shore - LIJ School of Medicine, Departments of Psychiatry and Molecular Medicine, Hempstead, NY, USA
| | - E E M Knowles
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - D C Glahn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - S Djurovic
- NORMENT, KG Jebsen Centre, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
| | - I Melle
- NORMENT, KG Jebsen Centre, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
- University of Oslo, Oslo, Norway
| | - O A Andreassen
- NORMENT, KG Jebsen Centre, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
- University of Oslo, Oslo, Norway
| | - A Christoforou
- K.G. Jebsen Centre for Psychosis Research, Dr. Einar Martens Research Group for Biological Psychiatry, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - V M Steen
- K.G. Jebsen Centre for Psychosis Research, Dr. Einar Martens Research Group for Biological Psychiatry, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - S L Hellard
- K.G. Jebsen Centre for Psychosis Research, Dr. Einar Martens Research Group for Biological Psychiatry, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - K Sundet
- NORMENT, KG Jebsen Centre, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
| | - I Reinvang
- Department of Psychology, University of Oslo, Oslo, Norway
| | - T Espeseth
- Department of Psychology, University of Oslo, Oslo, Norway
- Norwegian Center for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Oslo University Hospital, Oslo, Norway
| | - A J Lundervold
- K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
- Department of Biological and Medical Psychology, University of Bergen, Bergen, Norway
- Kavli Research Centre for Aging and Dementia, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - I Giegling
- Department of Psychiatry, University of Halle, Halle, Germany
| | - B Konte
- Department of Psychiatry, University of Halle, Halle, Germany
| | - A M Hartmann
- Department of Psychiatry, University of Halle, Halle, Germany
| | - D Rujescu
- Department of Psychiatry, University of Halle, Halle, Germany
| | - P Roussos
- Department of Psychiatry, Friedman Brain Institute, Department of Genetics and Genomic Sciences, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Mental Illness Research Education and Clinical Center (MIRECC), Bronx, NY, USA
| | - S Giakoumaki
- Department of Psychology, University of Crete, Rethymno, Crete, Greece
| | - K E Burdick
- Department of Psychiatry, Friedman Brain Institute, Department of Genetics and Genomic Sciences, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - P Bitsios
- Department of Psychiatry, Faculty of Medicine, University of Crete, Heraklion, Crete, Greece
- Computational Medicine Laboratory, Institute of Computer Science at FORTH, Heraklion, Greece
| | - G Donohoe
- School of Psychology, National University of Ireland Galway, Galway, Ireland
| | - R P Corley
- Institute for Behavioral Genetics, University of Colorado at Boulder, Boulder, CO, USA
| | - P M Visscher
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- University of Queensland Diamantina Institute, The University of Queensland, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - N Pendleton
- Centre for Integrated Genomic Medical Research, Institute of Population Health, University of Manchester, Manchester, UK
| | - A K Malhotra
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY, USA
- Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY, USA
- Hofstra North Shore - LIJ School of Medicine, Departments of Psychiatry and Molecular Medicine, Hempstead, NY, USA
| | - B M Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge Center, Cambridge, MA, USA
| | - T Lencz
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY, USA
- Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY, USA
- Hofstra North Shore - LIJ School of Medicine, Departments of Psychiatry and Molecular Medicine, Hempstead, NY, USA
| | - M C Keller
- Institute for Behavioral Genetics, University of Colorado at Boulder, Boulder, CO, USA
- Department of Psychology, University of Colorado at Boulder, Boulder, CO, USA
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14
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Szmatoła T, Gurgul A, Ropka-Molik K, Jasielczuk I, Ząbek T, Bugno-Poniewierska M. Characteristics of runs of homozygosity in selected cattle breeds maintained in Poland. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.04.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Vieira FG, Albrechtsen A, Nielsen R. Estimating IBD tracts from low coverage NGS data. Bioinformatics 2016; 32:2096-102. [DOI: 10.1093/bioinformatics/btw212] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 04/12/2016] [Indexed: 11/13/2022] Open
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16
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Gurgul A, Szmatoła T, Topolski P, Jasielczuk I, Żukowski K, Bugno-Poniewierska M. The use of runs of homozygosity for estimation of recent inbreeding in Holstein cattle. J Appl Genet 2016; 57:527-530. [DOI: 10.1007/s13353-016-0337-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 09/24/2015] [Accepted: 01/08/2016] [Indexed: 01/06/2023]
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17
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Ben Halim N, Nagara M, Regnault B, Hsouna S, Lasram K, Kefi R, Azaiez H, Khemira L, Saidane R, Ammar SB, Besbes G, Weil D, Petit C, Abdelhak S, Romdhane L. Estimation of Recent and Ancient Inbreeding in a Small Endogamous Tunisian Community Through Genomic Runs of Homozygosity. Ann Hum Genet 2015; 79:402-17. [PMID: 26420437 DOI: 10.1111/ahg.12131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 07/08/2015] [Indexed: 01/21/2023]
Abstract
Runs of homozygosity (ROHs) are extended genomic regions of homozygous genotypes that record populations' mating patterns in the past. We performed microarray genotyping on 15 individuals from a small isolated Tunisian community. We estimated the individual and population genome-wide level of homozygosity from data on ROH above 0.5 Mb in length. We found a high average number of ROH per individual (48.2). The smallest ROH category (0.5-1.49 Mb) represents 0.93% of the whole genome, while medium-size (1.5-4.99 Mb) and long-size ROH (≥5 Mb) cover 1.18% and 0.95%, respectively. We found that genealogical individual inbreeding coefficients (Fped ) based on three- to four-generation pedigrees are not reliable indicators of the current proportion of genome-wide homozygosity inferred from ROH (FROH ) either for 0.5 or 1.5 Mb ROH length thresholds, while identity-by-descent sharing is a function of shared coancestry. This study emphasizes the effect of reproductive isolation and a prolonged practice of consanguinity that limits the genetic heterogeneity. It also provides evidence of both recent and ancient parental relatedness contribution to the current level of genome-wide homozygosity in the studied population. These findings may be useful for evaluation of long-term effects of inbreeding on human health and for future applications of ROHs in identifying recessive susceptibility genes.
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Affiliation(s)
- Nizar Ben Halim
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | - Majdi Nagara
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | | | - Sana Hsouna
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | - Khaled Lasram
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | - Hela Azaiez
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | - Laroussi Khemira
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | - Rachid Saidane
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | - Slim Ben Ammar
- Clinical Biochemistry Laboratory, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | - Ghazi Besbes
- ENT Department, la Rabta Hospital, Tunis, Tunisia
| | - Dominique Weil
- Inserm UMRS587, Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris Cedex 15, France
| | - Christine Petit
- Inserm UMRS587, Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris Cedex 15, France
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
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18
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Pedigrees or markers: Which are better in estimating relatedness and inbreeding coefficient? Theor Popul Biol 2015; 107:4-13. [PMID: 26344786 DOI: 10.1016/j.tpb.2015.08.006] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 07/15/2015] [Accepted: 08/28/2015] [Indexed: 11/21/2022]
Abstract
Individual inbreeding coefficient (F) and pairwise relatedness (r) are fundamental parameters in population genetics and have important applications in diverse fields such as human medicine, forensics, plant and animal breeding, conservation and evolutionary biology. Traditionally, both parameters are calculated from pedigrees, but are now increasingly estimated from genetic marker data. Conceptually, a pedigree gives the expected F and r values, FP and rP, with the expectations being taken (hypothetically) over an infinite number of individuals with the same pedigree. In contrast, markers give the realised (actual) F and r values at the particular marker loci of the particular individuals, FM and rM. Both pedigree (FP, rP) and marker (FM, rM) estimates can be used as inferences of genomic inbreeding coefficients FG and genomic relatedness rG, which are the underlying quantities relevant to most applications (such as estimating inbreeding depression and heritability) of F and r. In the pre-genomic era, it was widely accepted that pedigrees are much better than markers in delineating FG and rG, and markers should better be used to validate, amend and construct pedigrees rather than to replace them. Is this still true in the genomic era when genome-wide dense SNPs are available? In this simulation study, I showed that genomic markers can yield much better estimates of FG and rG than pedigrees when they are numerous (say, 10(4) SNPs) under realistic situations (e.g. genome and population sizes). Pedigree estimates are especially poor for species with a small genome, where FG and rG are determined to a large extent by Mendelian segregations and may thus deviate substantially from their expectations (FP and rP). Simulations also confirmed that FM, when estimated from many SNPs, can be much more powerful than FP for detecting inbreeding depression in viability. However, I argue that pedigrees cannot be replaced completely by genomic SNPs, because the former allows for the calculation of more complicated IBD coefficients (involving more than 2 individuals, more than one locus, and more than 2 genes at a locus) for which the latter may have reduced capacity or limited power, and because the former has social and other significance for remote relationships which have little genetic significance and cannot be inferred reliably from markers.
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19
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Polašek O. Global mobility and the break-up of human population isolates - neglected mechanisms in health, demographics, and anthropology. Croat Med J 2015; 56:324-5. [PMID: 26321024 PMCID: PMC4576745 DOI: 10.3325/cmj.2015.56.324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Ozren Polašek
- Ozren Polašek, Medical School, University of Split, Split, Croatia,
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20
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Bjelland DW, Weigel KA, Coburn AD, Wilson RD. Using a family-based structure to detect the effects of genomic inbreeding on embryo viability in Holstein cattle. J Dairy Sci 2015; 98:4934-44. [PMID: 25958282 DOI: 10.3168/jds.2014-9014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 03/25/2015] [Indexed: 11/19/2022]
Abstract
Recent evidence has suggested that some of the decline in reproductive ability in dairy cattle has been caused by embryonic death. The current study compared expected genomic inbreeding from sire-dam mating pairs to genomic inbreeding from live progeny in an attempt to determine how embryonic inbreeding may affect fertility. A total of 11,484 Holstein cattle with 43,485 SNP markers and pedigree information were available for analysis. A total of 412 sire-dam-progeny trios in which all animals had reliable genotypes were discovered. After removal of trios because of parentage errors, 374 remained for analysis. Additionally, a total of 3,031 animals comprising 3,906 genotyped full-sibling pairs were available for comparison. Expected genomic inbreeding measures were calculated by predicting homozygosity independently per SNP (FPHE) in sire-dam mating pairs and by simulating progeny using phased haplotype information (FROHE and FPHE). Actual genomic inbreeding measures were calculated using the percent homozygosity of all SNP (FPH) and using runs of homozygosity (FROH). Average FPHE values (62.8±0.78%) were slightly lower than FPH (63.1±1.12%), when considering each SNP independently. After phasing haplotypes, FPHE (62.5±0.83%) was again slightly lower than FPH (62.7±1.16%), and FROHE (3.46±1.54%) was slightly lower than FROH (3.53±2.17%). Results suggest increases in expected genomic inbreeding do not explain a large effect on embryo viability at average levels of expected inbreeding. Higher variation in FROH values was present with sire-dam mating pairs exhibiting high FROHE, which may suggest high levels of genomic inbreeding are required for a noticeable effect on overall embryo viability. Genomic inbreeding between full siblings was also compared with moderate correlations (0.47-0.52) present. Overall, expected genomic inbreeding measures were calculated, but results did not suggest a large effect of expected inbreeding on embryo viability.
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Affiliation(s)
- D W Bjelland
- Department of Dairy Science, University of Wisconsin, Madison 53706.
| | - K A Weigel
- Department of Dairy Science, University of Wisconsin, Madison 53706
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21
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Marras G, Gaspa G, Sorbolini S, Dimauro C, Ajmone-Marsan P, Valentini A, Williams JL, Macciotta NPP. Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy. Anim Genet 2014; 46:110-21. [DOI: 10.1111/age.12259] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Gabriele Marras
- Dipartimento di Agraria-Sezione Scienze Zootecniche; Università di Sassari; Sassari 07100 Italy
- Parco Tecnologico Padano; Lodi 26900 Italy
| | - Giustino Gaspa
- Dipartimento di Agraria-Sezione Scienze Zootecniche; Università di Sassari; Sassari 07100 Italy
| | - Silvia Sorbolini
- Dipartimento di Agraria-Sezione Scienze Zootecniche; Università di Sassari; Sassari 07100 Italy
| | - Corrado Dimauro
- Dipartimento di Agraria-Sezione Scienze Zootecniche; Università di Sassari; Sassari 07100 Italy
| | - Paolo Ajmone-Marsan
- Istituto di Zootecnica; Università Cattolica del Sacro Cuore; Piacenza 29100 Italy
| | - Alessio Valentini
- Dipartimento per l'innovazione dei sistemi biologici agroalimentari e forestali DIBAF; Università della Tuscia; Viterbo 01000 Italy
| | | | - Nicolò P. P. Macciotta
- Dipartimento di Agraria-Sezione Scienze Zootecniche; Università di Sassari; Sassari 07100 Italy
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22
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Álvarez G, Ceballos FC, Berra TM. Darwin was right: inbreeding depression on male fertility in the Darwin family. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12433] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Gonzalo Álvarez
- Department of Genetics; Faculty of Biology; University of Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Francisco C. Ceballos
- Department of Genetics; Faculty of Biology; University of Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Tim M. Berra
- Department of Evolution; Ecology and Organismal Biology; The Ohio State University; 1760 University Dr.; Mansfield OH 44906 USA
- Research Institute for the Environment and Livelihoods; Charles Darwin University; Darwin NT Australia
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23
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24
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Pemberton TJ, Rosenberg NA. Population-genetic influences on genomic estimates of the inbreeding coefficient: a global perspective. Hum Hered 2014; 77:37-48. [PMID: 25060268 DOI: 10.1159/000362878] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND/AIMS Culturally driven marital practices provide a key instance of an interaction between social and genetic processes in shaping patterns of human genetic variation, producing, for example, increased identity by descent through consanguineous marriage. A commonly used measure to quantify identity by descent in an individual is the inbreeding coefficient, a quantity that reflects not only consanguinity, but also other aspects of kinship in the population to which the individual belongs. Here, in populations worldwide, we examine the relationship between genomic estimates of the inbreeding coefficient and population patterns in genetic variation. METHODS Using genotypes at 645 microsatellites, we compare inbreeding coefficients from 5,043 individuals representing 237 populations worldwide to demographic consanguinity frequency estimates available for 26 populations as well as to other quantities that can illuminate population-genetic influences on inbreeding coefficients. RESULTS We observe higher inbreeding coefficient estimates in populations and geographic regions with known high levels of consanguinity or genetic isolation and in populations with an increased effect of genetic drift and decreased genetic diversity with increasing distance from Africa. For the small number of populations with specific consanguinity estimates, we find a correlation between inbreeding coefficients and consanguinity frequency (r = 0.349, p = 0.040). CONCLUSIONS The results emphasize the importance of both consanguinity and population-genetic factors in influencing variation in inbreeding coefficients, and they provide insight into factors useful for assessing the effect of consanguinity on genomic patterns in different populations.
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Affiliation(s)
- Trevor J Pemberton
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Man., Canada
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25
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The application of genome-wide SNP genotyping methods in studies on livestock genomes. J Appl Genet 2014; 55:197-208. [PMID: 24566962 DOI: 10.1007/s13353-014-0202-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/14/2014] [Accepted: 02/04/2014] [Indexed: 01/07/2023]
Abstract
Animal genomics is currently undergoing dynamic development, which is driven by the flourishing of high-throughput genome analysis methods. Recently, a large number of animals has been genotyped with the use of whole-genome genotyping assays in the course of genomic selection programmes. The results of such genotyping can also be used for studies on different aspects of livestock genome functioning and diversity. In this article, we review the recent literature concentrating on various aspects of animal genomics, including studies on linkage disequilibrium, runs of homozygosity, selection signatures, copy number variation and genetic differentiation of animal populations. Our work is aimed at providing insight into certain achievements of animal genomics and to arouse interest in basic research on the complexity and structure of the genomes of livestock.
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Marker-based estimates of relatedness and inbreeding coefficients: an assessment of current methods. J Evol Biol 2014; 27:518-30. [DOI: 10.1111/jeb.12315] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 12/03/2013] [Accepted: 12/05/2013] [Indexed: 12/17/2022]
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Vieira FG, Fumagalli M, Albrechtsen A, Nielsen R. Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation. Genome Res 2013; 23:1852-61. [PMID: 23950147 PMCID: PMC3814885 DOI: 10.1101/gr.157388.113] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Most methods for next-generation sequencing (NGS) data analyses incorporate information regarding allele frequencies using the assumption of Hardy–Weinberg equilibrium (HWE) as a prior. However, many organisms including those that are domesticated, partially selfing, or with asexual life cycles show strong deviations from HWE. For such species, and specially for low-coverage data, it is necessary to obtain estimates of inbreeding coefficients (F) for each individual before calling genotypes. Here, we present two methods for estimating inbreeding coefficients from NGS data based on an expectation-maximization (EM) algorithm. We assess the impact of taking inbreeding into account when calling genotypes or estimating the site frequency spectrum (SFS), and demonstrate a marked increase in accuracy on low-coverage highly inbred samples. We demonstrate the applicability and efficacy of these methods in both simulated and real data sets.
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Affiliation(s)
- Filipe G Vieira
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720, USA
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Bjelland DW, Weigel KA, Vukasinovic N, Nkrumah JD. Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding. J Dairy Sci 2013; 96:4697-706. [PMID: 23684028 DOI: 10.3168/jds.2012-6435] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 04/02/2013] [Indexed: 11/19/2022]
Abstract
The effects of increased pedigree inbreeding in dairy cattle populations have been well documented and result in a negative impact on profitability. Recent advances in genotyping technology have allowed researchers to move beyond pedigree analysis and study inbreeding at a molecular level. In this study, 5,853 animals were genotyped for 54,001 single nucleotide polymorphisms (SNP); 2,913 cows had phenotypic records including a single lactation for milk yield (from either lactation 1, 2, 3, or 4), reproductive performance, and linear type conformation. After removing SNP with poor call rates, low minor allele frequencies, and departure from Hardy-Weinberg equilibrium, 33,025 SNP remained for analyses. Three measures of genomic inbreeding were evaluated: percent homozygosity (FPH), inbreeding calculated from runs of homozygosity (FROH), and inbreeding derived from a genomic relationship matrix (FGRM). Average FPH was 60.5±1.1%, average FROH was 3.8±2.1%, and average FGRM was 20.8±2.3%, where animals with larger values for each of the genomic inbreeding indices were considered more inbred. Decreases in total milk yield to 205d postpartum of 53, 20, and 47kg per 1% increase in FPH, FROH, and FGRM, respectively, were observed. Increases in days open per 1% increase in FPH (1.76 d), FROH (1.72 d), and FGRM (1.06 d) were also noted, as well as increases in maternal calving difficulty (0.09, 0.03, and 0.04 on a 5-point scale for FPH, FROH, and FGRM, respectively). Several linear type traits, such as strength (-0.40, -0.11, and -0.19), rear legs rear view (-0.35, -0.16, and -0.14), front teat placement (0.35, 0.25, 0.18), and teat length (-0.24, -0.14, and -0.13) were also affected by increases in FPH, FROH, and FGRM, respectively. Overall, increases in each measure of genomic inbreeding in this study were associated with negative effects on production and reproductive ability in dairy cows.
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Affiliation(s)
- D W Bjelland
- Department of Dairy Science, University of Wisconsin, Madison, WI 53706, USA.
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Rehder CW, David KL, Hirsch B, Toriello HV, Wilson CM, Kearney HM. American College of Medical Genetics and Genomics: standards and guidelines for documenting suspected consanguinity as an incidental finding of genomic testing. Genet Med 2013; 15:150-2. [DOI: 10.1038/gim.2012.169] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Ben Halim N, Ben Alaya Bouafif N, Romdhane L, Kefi Ben Atig R, Chouchane I, Bouyacoub Y, Arfa I, Cherif W, Nouira S, Talmoudi F, Lasram K, Hsouna S, Ghazouani W, Azaiez H, El Matri L, Abid A, Tebib N, Ben Dridi MF, Kachboura S, Amouri A, Mokni M, Ben Arab S, Dellagi K, Abdelhak S. Consanguinity, endogamy, and genetic disorders in Tunisia. J Community Genet 2012. [PMID: 23208456 DOI: 10.1007/s12687-012-0128-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Nizar Ben Halim
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, BP 74, 13 Place Pasteur, Tunis, Le Belvédère, 1002, Tunisia,
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Ferenčaković M, Hamzić E, Gredler B, Solberg TR, Klemetsdal G, Curik I, Sölkner J. Estimates of autozygosity derived from runs of homozygosity: empirical evidence from selected cattle populations. J Anim Breed Genet 2012; 130:286-93. [PMID: 23855630 DOI: 10.1111/jbg.12012] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 09/14/2012] [Indexed: 11/27/2022]
Abstract
Using genome-wide SNP data, we calculated genomic inbreeding coefficients (FROH > 1 Mb , FROH > 2 Mb , FROH > 8 Mb and FROH > 16 Mb ) derived from runs of homozygosity (ROH) of different lengths (>1, >2, >8 and > 16 Mb) as well as from levels of homozygosity (FHOM ). We compared these values of inbreeding coefficients with those calculated from pedigrees (FPED ) of 1422 bulls comprising Brown Swiss (304), Fleckvieh (502), Norwegian Red (499) and Tyrol Grey (117) cattle breeds. For all four breeds, population inbreeding levels estimated by the genomic inbreeding coefficients FROH > 8 Mb and FROH > 16 Mb were similar to the levels estimated from pedigrees. The lowest values were obtained for Fleckvieh (FPED = 0.014, FROH > 8 Mb = 0.019 and FROH > 16 Mb = 0.008); the highest, for Brown Swiss (FPED = 0.048, FROH > 8 Mb = 0.074 and FROH > 16 Mb = 0.037). In contrast, inbreeding estimates based on the genomic coefficients FROH > 1 Mb and FROH > 2 Mb were considerably higher than pedigree-derived estimates. Standard deviations of genomic inbreeding coefficients were, on average, 1.3-1.7-fold higher than those obtained from pedigrees. Pearson correlations between genomic and pedigree inbreeding coefficients ranged from 0.50 to 0.62 in Norwegian Red (lowest correlations) and from 0.64 to 0.72 in Tyrol Grey (highest correlations). We conclude that the proportion of the genome present in ROH provides a good indication of inbreeding levels and that analysis based on ROH length can indicate the relative amounts of autozygosity due to recent and remote ancestors.
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Affiliation(s)
- M Ferenčaković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
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Maximum likelihood estimation of individual inbreeding coefficients and null allele frequencies. Genet Res (Camb) 2012; 94:151-61. [PMID: 22805896 DOI: 10.1017/s0016672312000341] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
In this paper, we developed and compared several expectation-maximization (EM) algorithms to find maximum likelihood estimates of individual inbreeding coefficients using molecular marker information. The first method estimates the inbreeding coefficient for a single individual and assumes that allele frequencies are known without error. The second method jointly estimates inbreeding coefficients and allele frequencies for a set of individuals that have been genotyped at several loci. The third method generalizes the second method to include the case in which null alleles may be present. In particular, it is able to jointly estimate individual inbreeding coefficients and allele frequencies, including the frequencies of null alleles, and accounts for missing data. We compared our methods with several other estimation procedures using simulated data and found that our methods perform well. The maximum likelihood estimators consistently gave among the lowest root-mean-square-error (RMSE) of all the estimators that were compared. Our estimator that accounts for null alleles performed particularly well and was able to tease apart the effects of null alleles, randomly missing genotypes and differing degrees of inbreeding among members of the datasets we analysed. To illustrate the performance of our estimators, we analysed previously published datasets on mice (Mus musculus) and white-tailed deer (Odocoileus virginianus).
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Engelsma KA, Veerkamp RF, Calus MPL, Bijma P, Windig JJ. Pedigree- and marker-based methods in the estimation of genetic diversity in small groups of Holstein cattle. J Anim Breed Genet 2012; 129:195-205. [PMID: 22583324 DOI: 10.1111/j.1439-0388.2012.00987.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genetic diversity is often evaluated using pedigree information. Currently, diversity can be evaluated in more detail over the genome based on large numbers of SNP markers. Pedigree- and SNP-based diversity were compared for two small related groups of Holstein animals genotyped with the 50 k SNP chip, genome-wide, per chromosome and for part of the genome examined. Diversity was estimated with coefficient of kinship (pedigree) and expected heterozygosity (SNP). SNP-based diversity at chromosome regions was determined using 5-Mb sliding windows, and significance of difference between groups was determined by bootstrapping. Both pedigree- and SNP-based diversity indicated more diversity in one of the groups; 26 of the 30 chromosomes showed significantly more diversity for the same group, as did 25.9% of the chromosome regions. Even in small populations that are genetically close, differences in diversity can be detected. Pedigree- and SNP-based diversity give comparable differences, but SNP-based diversity shows on which chromosome regions these differences are based. For maintaining diversity in a gene bank, SNP-based diversity gives a more detailed picture than pedigree-based diversity.
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Affiliation(s)
- K A Engelsma
- Wageningen UR Livestock Research, Animal Breeding and Genomics Centre, Lelystad, The Netherlands.
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Khorshidi A, Russell L, Bamforth S, Drummond G, Johnson R, Lehmann OJ. Homozygosity mapping in an anophthalmic pedigree provides evidence of additional genetic heterogeneity. Ophthalmic Genet 2012; 33:208-20. [DOI: 10.3109/13816810.2011.648364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Gialluisi A, Pippucci T, Anikster Y, Ozbek U, Medlej-Hashim M, Mégarbané A, Romeo G. Estimating the allele frequency of autosomal recessive disorders through mutational records and consanguinity: the Homozygosity Index (HI). Ann Hum Genet 2011; 76:159-67. [PMID: 22188137 DOI: 10.1111/j.1469-1809.2011.00693.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In principle mutational records make it possible to estimate frequencies of disease alleles (q) for autosomal recessive disorders using a novel approach based on the calculation of the Homozygosity Index (HI), i.e., the proportion of homozygous patients, which is complementary to the proportion of compound heterozygous patients P(CH). In other words, the rarer the disorder, the higher will be the HI and the lower will be the P(CH). To test this hypothesis we used mutational records of individuals affected with Familial Mediterranean Fever (FMF) and Phenylketonuria (PKU), born to either consanguineous or apparently unrelated parents from six population samples of the Mediterranean region. Despite the unavailability of precise values of the inbreeding coefficient for the general population, which are needed in the case of apparently unrelated parents, our estimates of q are very similar to those of previous descriptive epidemiological studies. Finally, we inferred from simulation studies that the minimum sample size needed to use this approach is 25 patients either with unrelated or first cousin parents. These results show that the HI can be used to produce a ranking order of allele frequencies of autosomal recessive disorders, especially in populations with high rates of consanguineous marriages.
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Affiliation(s)
- Alessandro Gialluisi
- Unità Operativa di Genetica Medica, Dipartimento di Scienze Ginecologiche, Ostetriche e Pediatriche, Policlinico Sant'Orsola Malpighi, Università di Bologna, Bologna, Italy
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Wang J. A new likelihood estimator and its comparison with moment estimators of individual genome-wide diversity. Heredity (Edinb) 2011; 107:433-43. [PMID: 21522168 PMCID: PMC3199925 DOI: 10.1038/hdy.2011.30] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 03/09/2011] [Accepted: 03/21/2011] [Indexed: 11/08/2022] Open
Abstract
The inbreeding coefficient of an individual, F, is one of the central parameters in population genetics theory. It has found important applications in evolutionary biology, conservation and ecology, such as the study of inbreeding depression. In the absence of detailed and reliable pedigree records, researchers have developed quite a few estimators to estimate F or the genome-wide homozygosity from genetic marker data. The statistical properties and comparative performances of these metrics are rarely known, however, which impedes an informed choice of the most appropriate one in practical applications. In this investigation, I propose a new likelihood F estimator that makes efficient use of marker information and takes into account of allelic dropouts, null alleles and prior knowledge of inbreeding. I compare the likelihood estimator with three moment estimators of F and three metrics of genomic homozygosity (or heterozygosity) by analysing both simulated and empirical datasets. It is shown that the likelihood estimator invariably outperforms the other estimators and metrics across all datasets analysed. For a typical dataset in heterozygosity-fitness correlation studies involving 10-20 microsatellites and 50 individuals, the correlation between the likelihood estimator and F (the simulated true inbreeding coefficient) is about 8 ∼ 35% higher than that between the moment estimators and F. A frequently applied metric, multilocus heterozygosity (MLH), and an F estimator based on the consideration of the proportion of alleles in homozygous conditions, [F R'), are shown to have particularly poor performances. The low correlation between MLH and fitness traits, which is widely observed in numerous empirical studies, might be partially caused by the adoption of this inefficient estimator of genomic inbreeding.
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Affiliation(s)
- J Wang
- Institute of Zoology, Zoological Society of London, London, UK.
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Quantification of inbreeding due to distant ancestors and its detection using dense single nucleotide polymorphism data. Genetics 2011; 189:237-49. [PMID: 21705750 PMCID: PMC3176119 DOI: 10.1534/genetics.111.130922] [Citation(s) in RCA: 289] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Inbreeding depression, which refers to reduced fitness among offspring of related parents, has traditionally been studied using pedigrees. In practice, pedigree information is difficult to obtain, potentially unreliable, and rarely assessed for inbreeding arising from common ancestors who lived more than a few generations ago. Recently, there has been excitement about using SNP data to estimate inbreeding (F) arising from distant common ancestors in apparently “outbred” populations. Statistical power to detect inbreeding depression using SNP data depends on the actual variation in inbreeding in a population, the accuracy of detecting that with marker data, the effect size, and the sample size. No one has yet investigated what variation in F is expected in SNP data as a function of population size, and it is unclear which estimate of F is optimal for detecting inbreeding depression. In the present study, we use theory, simulated genetic data, and real genetic data to find the optimal estimate of F, to quantify the likely variation in F in populations of various sizes, and to estimate the power to detect inbreeding depression. We find that F estimated from runs of homozygosity (Froh), which reflects shared ancestry of genetic haplotypes, retains variation in even large populations (e.g., SD = 0.5% when Ne = 10,000) and is likely to be the most powerful method of detecting inbreeding effects from among several alternative estimates of F. However, large samples (e.g., 12,000–65,000) will be required to detect inbreeding depression for likely effect sizes, and so studies using Froh to date have probably been underpowered.
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Consanguinity around the world: what do the genomic data of the HGDP-CEPH diversity panel tell us? Eur J Hum Genet 2011; 19:583-7. [PMID: 21364699 DOI: 10.1038/ejhg.2010.205] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Inbreeding coefficients and consanguineous mating types are usually inferred from population surveys or pedigree studies. Here, we present a method to estimate them from dense genome-wide single-nucleotide polymorphism genotypes and apply it to 940 unrelated individuals from the Human Genome Diversity Panel (HGDP-CEPH). Inbreeding is observed in almost all populations of the panel, and the highest inbreeding levels and frequencies of inbred individuals are found in populations of the Middle East, Central South Asia and the Americas. In these regions, first cousin (1C) marriages are the most frequent, but we also observed marriages between double first cousins (2 × 1C) and between avuncular (AV) pairs. Interestingly, if 2 × 1C marriages are preferred to AV marriages in Central South Asia and the Middle East, the contrary is found in the Americas. There are thus some regional trends but there are also some important differences between populations within a region. Individual results can be found on the CEPH website at ftp://ftp.cephb.fr/hgdp_hbd/.
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Powell JE, Visscher PM, Goddard ME. Reconciling the analysis of IBD and IBS in complex trait studies. Nat Rev Genet 2010; 11:800-5. [PMID: 20877324 DOI: 10.1038/nrg2865] [Citation(s) in RCA: 225] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Identity by descent (IBD) is a fundamental concept in genetics and refers to alleles that are descended from a common ancestor in a base population. Identity by state (IBS) simply refers to alleles that are the same, irrespective of whether they are inherited from a recent ancestor. In modern applications, IBD relationships are estimated from genetic markers in individuals without any known relationship. This can lead to erroneous inference because a consistent base population is not used. We argue that the purpose of most IBD calculations is to predict IBS at unobserved loci. Recognizing this aim leads to better methods to estimating IBD with benefits in mapping genes, estimating genetic variance and predicting inbreeding depression.
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Affiliation(s)
- Joseph E Powell
- Queensland Statistical Genetics Laboratory, Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia.
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Santos LL, da Fonseca CG, Vaintraub MT, Vaintraub P, Januário JN, de Aguiar MJ, Raquel Santos Carvalho M. Inbreeding and PKU allele frequency: Estimating by microsatellite approaches. Am J Hum Biol 2010; 22:716-9. [DOI: 10.1002/ajhb.21072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Teeuw ME, Henneman L, Bochdanovits Z, Heutink P, Kuik DJ, Cornel MC, Ten Kate LP. Do consanguineous parents of a child affected by an autosomal recessive disease have more DNA identical-by-descent than similarly-related parents with healthy offspring? Design of a case-control study. BMC MEDICAL GENETICS 2010; 11:113. [PMID: 20637082 PMCID: PMC3161348 DOI: 10.1186/1471-2350-11-113] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Accepted: 07/16/2010] [Indexed: 11/26/2022]
Abstract
Background The offspring of consanguineous relations have an increased risk of congenital/genetic disorders and early mortality. Consanguineous couples and their offspring account for approximately 10% of the global population. The increased risk for congenital/genetic disorders is most marked for autosomal recessive disorders and depends on the degree of relatedness of the parents. For children of first cousins the increased risk is 2-4%. For individual couples, however, the extra risk can vary from zero to 25% or higher, with only a minority of these couples having an increased risk of at least 25%. It is currently not possible to differentiate between high-and low-risk couples. The quantity of DNA identical-by-descent between couples with the same degree of relatedness shows a remarkable variation. Here we hypothesize that consanguineous partners with children affected by an autosomal recessive disease have more DNA identical-by-descent than similarly-related partners who have only healthy children. The aim of the study is thus to establish whether the amount of DNA identical-by-descent in consanguineous parents of children with an autosomal recessive disease is indeed different from its proportion in consanguineous parents who have healthy children only. Methods/Design This project is designed as a case-control study. Cases are defined as consanguineous couples with one or more children with an autosomal recessive disorder and controls as consanguineous couples with at least three healthy children and no affected child. We aim to include 100 case couples and 100 control couples. Control couples are matched by restricting the search to the same family, clan or ethnic origin as the case couple. Genome-wide SNP arrays will be used to test our hypothesis. Discussion This study contains a new approach to risk assessment in consanguineous couples. There is no previous study on the amount of DNA identical-by-descent in consanguineous parents of affected children compared to the consanguineous parents of healthy children. If our hypothesis proves to be correct, further studies are needed to obtain different risk figure estimates for the different proportions of DNA identical-by-descent. With more precise information about their risk status, empowerment of couples can be improved when making reproductive decisions.
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Affiliation(s)
- Marieke E Teeuw
- Department of Clinical Genetics, Section Community Genetics, EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands
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Littink KW, Koenekoop RK, van den Born LI, Collin RWJ, Moruz L, Veltman JA, Roosing S, Zonneveld MN, Omar A, Darvish M, Lopez I, Kroes HY, van Genderen MM, Hoyng CB, Rohrschneider K, van Schooneveld MJ, Cremers FPM, den Hollander AI. Homozygosity mapping in patients with cone-rod dystrophy: novel mutations and clinical characterizations. Invest Ophthalmol Vis Sci 2010; 51:5943-51. [PMID: 20554613 DOI: 10.1167/iovs.10-5797] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To determine the genetic defect and to describe the clinical characteristics in a cohort of mainly nonconsanguineous cone-rod dystrophy (CRD) patients. METHODS One hundred thirty-nine patients with diagnosed CRD were recruited. Ninety of them were screened for known mutations in ABCA4, and those carrying one or two mutations were excluded from further research. Genome-wide homozygosity mapping was performed in the remaining 108. Known genes associated with autosomal recessive retinal dystrophies located within a homozygous region were screened for mutations. Patients in whom a mutation was detected underwent further ophthalmic examination. RESULTS Homozygous sequence variants were identified in eight CRD families, six of which were nonconsanguineous. The variants were detected in the following six genes: ABCA4, CABP4, CERKL, EYS, KCNV2, and PROM1. Patients carrying mutations in ABCA4, CERKL, and PROM1 had typical CRD symptoms, but a variety of retinal appearances on funduscopy, optical coherence tomography, and autofluorescence imaging. CONCLUSIONS Homozygosity mapping led to the identification of new mutations in consanguineous and nonconsanguineous patients with retinal dystrophy. Detailed clinical characterization revealed a variety of retinal appearances, ranging from nearly normal to extensive retinal remodeling, retinal thinning, and debris accumulation. Although CRD was initially diagnosed in all patients, the molecular findings led to a reappraisal of the diagnosis in patients carrying mutations in EYS, CABP4, and KCNV2.
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Gunjaca G, Boban M, Pehlić M, Zemunik T, Budimir D, Kolcić I, Lauc G, Rudan I, Polasek O. Predictive value of 8 genetic loci for serum uric acid concentration. Croat Med J 2010; 51:23-31. [PMID: 20162742 DOI: 10.3325/cmj.2010.51.23] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
AIM To investigate the value of genomic information in prediction of individual serum uric acid concentrations. METHODS Three population samples were investigated: from isolated Adriatic island communities of Vis (n=980) and Korcula (n=944), and from general population of the city of Split (n=507). Serum uric acid concentration was correlated with the genetic risk score based on 8 previously described genes: PDZK1, GCKR, SLC2A9, ABCG2, LRRC16A, SLC17A1, SLC16A9, and SLC22A12, represented by a total of 16 single-nucleotide polymorphisms (SNP). The data were analyzed using classification and regression tree (CART) and general linear modeling. RESULTS The most important variables for uric acid prediction with CART were genetic risk score in men and age in women. The percent of variance for any single SNP in predicting serum uric acid concentration varied from 0.0%-2.0%. The use of genetic risk score explained 0.1%-2.5% of uric acid variance in men and 3.9%-4.9% in women. The highest percent of variance was obtained when age, sex, and genetic risk score were used as predictors, with a total of 30.9% of variance in pooled analysis. CONCLUSION Despite overall low percent of explained variance, uric acid seems to be among the most predictive human quantitative traits based on the currently available SNP information. The use of genetic risk scores is a valuable approach in genetic epidemiology and increases the predictability of human quantitative traits based on genomic information compared with single SNP approach.
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Affiliation(s)
- Grgo Gunjaca
- University of Split School of Medicine, Split, Croatia
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Polasek O, Jeroncić I, Mulić R, Klismanic Z, Pehlić M, Zemunik T, Kolcić I. Common variants in SLC17A3 gene affect intra-personal variation in serum uric acid levels in longitudinal time series. Croat Med J 2010; 51:32-9. [PMID: 20162743 DOI: 10.3325/cmj.2010.51.32] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
AIM To investigate whether intra-personal variation in serum uric acid concentration is influenced by genes that were described to be associated with serum uric acid levels in cross-sectional studies. METHODS The study included 92 participants from the isolated community of the Croatian island of Vis. For each participant, two uric acid concentration measurements were available, one from 2002 and one from 2003. Changes in uric acid concentration were correlated with a set of 8 genes known to affect it: PDZK1, GCKR, SLC2A9, ABCG2, LRRC16A, SLC17A3, SLC16A9, and SLC22A12. RESULTS Thirteen participants (14%) had uric acid concentration change greater than 130 micromol/L. Greater variability of uric acid concentration was recorded in women (coefficient of variation 49% vs 12% in men). Two SNPs belonging to SLC17A3 gene (rs9393672 and rs942379) yielded significant association with serum uric acid concentration changes in women. These two single-nucleotide polymorphisms (SNP) explained 0.2%-1.3% of variance for 2002 or 2003 uric acid measurement and 1.1%-1.8% of variance for the average value of these two measurements. CONCLUSIONS Repeated measurements offer a possibility to enrich the percent of explained variance and contribute to the understanding of the "missing heritability" concept. Although a number of genes have been shown to affect serum uric acid concentration, SLC17A3 seems to have a major role in determination of serum uric acid repeated measurements variation.
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Affiliation(s)
- Ozren Polasek
- Andrija Stampar School of Public Health, Medical School, University of Zagreb, Rockefellerova 4, 10000 Zagreb, Croatia.
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Polasek O, Gunjaca G, Kolcić I, Zgaga L, Dzijan S, Smolić R, Smolić M, Milas-Ahić J, Serić V, Galić J, Tucak-Zorić S, Tucak A, Rudan I, Lauc G. Association of nephrolithiasis and gene for glucose transporter type 9 (SLC2A9): study of 145 patients. Croat Med J 2010; 51:48-53. [PMID: 20162745 DOI: 10.3325/cmj.2010.51.48] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
AIM To investigate the association of nephrolithiasis and solute carrier family 2, facilitated glucose transporter, member 9 (SLC2A9), also known as glucose transporter type 9, Glut9. METHODS A total of 145 participants were recruited in the period April-October 2008 from the Department of Mineral Research of the Medical School Osijek, Osijek, Croatia; 58 (40%) had confirmed nephrolithiasis and 87 (60%) were asymptomatic. Four single nucleotide polymorphisms (SNP) from the SLC2A9 gene were genotyped in both groups (rs733175, rs6449213, rs1014290, and rs737267). RESULTS There was a weak but significant association of all 4 SNPs and nephrolithiasis (P=0.029 for rs733175; P=0.006 for rs6449213; P=0.020 for rs1014290, and P=0.011 for rs737267). Logistic regression in an age- and sex-adjusted model suggested that genotype C/T for rs6449213 had odds ratio for nephrolithiasis of 2.89 (95% confidence interval 1.13-7.40). This SNP explained a total of 4.4% of nephrolithiasis variance. CONCLUSION Development of nephrolithiasis may be associated with SLC2A9 gene. Further studies are needed to clarify the role of SLC2A9 gene as a link between uric acid and nephrolithiasis.
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Affiliation(s)
- Ozren Polasek
- Department of Medical Statistics, Epidemiology, and Medical Informatics, Andrija Stampar School of Public Health, Medical School, University of Zagreb, Rockefellerova 4, 10000 Zagreb, Croatia.
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Knežević A, Gornik O, Polašek O, Pučić M, Redžić I, Novokmet M, Rudd PM, Wright AF, Campbell H, Rudan I, Lauc G. Effects of aging, body mass index, plasma lipid profiles, and smoking on human plasma N-glycans. Glycobiology 2010; 20:959-69. [DOI: 10.1093/glycob/cwq051] [Citation(s) in RCA: 176] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Polasek O, Hayward C, Bellenguez C, Vitart V, Kolcić I, McQuillan R, Saftić V, Gyllensten U, Wilson JF, Rudan I, Wright AF, Campbell H, Leutenegger AL. Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data. BMC Genomics 2010; 11:139. [PMID: 20184767 PMCID: PMC2848240 DOI: 10.1186/1471-2164-11-139] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 02/25/2010] [Indexed: 11/21/2022] Open
Abstract
Background Genome-wide homozygosity estimation from genomic data is becoming an increasingly interesting research topic. The aim of this study was to compare different methods for estimating individual homozygosity-by-descent based on the information from human genome-wide scans rather than genealogies. We considered the four most commonly used methods and investigated their applicability to single-nucleotide polymorphism (SNP) data in both a simulation study and by using the human genotyped data. A total of 986 inhabitants from the isolated Island of Vis, Croatia (where inbreeding is present, but no pedigree-based inbreeding was observed at the level of F > 0.0625) were included in this study. All individuals were genotyped with the Illumina HumanHap300 array with 317,503 SNP markers. Results Simulation data suggested that multi-point FEstim is the method most strongly correlated to true homozygosity-by-descent. Correlation coefficients between the homozygosity-by-descent estimates were high but only for inbred individuals, with nearly absolute correlation between single-point measures. Conclusions Deciding who is really inbred is a methodological challenge where multi-point approaches can be very helpful once the set of SNP markers is filtered to remove linkage disequilibrium. The use of several different methodological approaches and hence different homozygosity measures can help to distinguish between homozygosity-by-state and homozygosity-by-descent in studies investigating the effects of genomic autozygosity on human health.
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Affiliation(s)
- Ozren Polasek
- Public Health Sciences, University of Edinburgh, Edinburgh, UK.
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Polasek O, Marusić A, Rotim K, Hayward C, Vitart V, Huffman J, Campbell S, Janković S, Boban M, Biloglav Z, Kolcić I, Krzelj V, Terzić J, Matec L, Tometić G, Nonković D, Nincević J, Pehlić M, Zedelj J, Velagić V, Juricić D, Kirac I, Belak Kovacević S, Wright AF, Campbell H, Rudan I. Genome-wide association study of anthropometric traits in Korcula Island, Croatia. Croat Med J 2009; 50:7-16. [PMID: 19260139 DOI: 10.3325/cmj.2009.50.7] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
AIM To identify genetic variants underlying six anthropometric traits: body height, body weight, body mass index, brachial circumference, waist circumference, and hip circumference, using a genome-wide association study. METHODS The study was carried out in the isolated population of the island of Korcula, Croatia, with 898 adult examinees who participated in the larger DNA-based genetic epidemiological study in 2007. Anthropometric measurements followed standard internationally accepted procedures. Examinees were genotyped using HumanHap 370CNV chip by Illumina, with a genome-wide scan containing 316730 single nucleotide polymorphisms (SNP). RESULTS A total of 11 SNPs were associated with the investigated traits at the level of P<10(-5), with one SNP (rs7792939 in gene zinc finger protein 498, ZNF498) associated with body weight, hip circumference, and brachial circumference (P=3.59-5.73 x 10(-6)), and another one (rs157350 in gene delta-sarcoglycan, SGCD) with both brachial and hip circumference (P=3.70-6.08 x 10(-6). Variants in CRIM1, a gene regulating delivery of bone morphogenetic proteins to the cell surface, and ITGA1, involved in the regulation of mesenchymal stem cell proliferation and cartilage production, were also associated with brachial circumference (P=7.82 and 9.68 x 10(-6), respectively) and represent interesting functional candidates. Other associations involved those between genes SEZ6L2 and MAX and waist circumference, XTP6 and brachial circumference, and AMPA1/GRIA1 and height. CONCLUSION Although the study was underpowered for the reported associations to reach formal threshold of genome-wide significance under the assumption of independent multiple testing, the consistency of association between the 2 variants and a set of anthropometric traits makes CRIM1 and ITGA1 highly interesting for further replication and functional follow-up. Increased linkage disequilibrium between the used markers in an isolated population makes the formal significance threshold overly stringent, and changed allele frequencies in isolate population may contribute to identifying variants that would not be easily identified in large outbred populations.
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Affiliation(s)
- Ozren Polasek
- Andrija Stampar School of Public Health, School of Medicine, University of Zagreb, Croatia
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Vatavuk Z, Skunca Herman J, Bencić G, Andrijević Derk B, Lacmanović Loncar V, Petric Vicković I, Bucan K, Mandić K, Mandić A, Skegro I, Pavicić Astalos J, Merc I, Martinović M, Kralj P, Knezević T, Barać-Juretić K, Zgaga L. Common variant in myocilin gene is associated with high myopia in isolated population of Korcula Island, Croatia. Croat Med J 2009; 50:17-22. [PMID: 19260140 DOI: 10.3325/cmj.2009.50.17] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
AIM To study the association between genetic variants in myocilin and collagen type I alpha 1 genes and high myopia in an isolated island population. METHODS A total of 944 examinees from the genetic epidemiology study conducted on the island of Korcula, Croatia, were included in the study. We selected 2 short nucleotide polymorphisms (SNP) available in our genome-wide scan set of SNPs that were previously associated with high myopia and used them to replicate previous claims of possible association. RESULTS Nineteen cases of high myopia, defined as the refraction of </=-6.00 diopters, were identified and included in the analysis. We showed that rs2075555 in the COL1A1 gene was not associated with high myopia. In contrast, rs2421853 in the myocilin gene was significantly associated in both bivariate (P=0.006) and age- and sex-adjusted analysis (P=0.049). CONCLUSION Myocilin seems to be a very strong candidate for explaining some of the pathophysiological pathways leading to the development of both glaucoma and high myopia. As our finding was obtained in a relatively under-powered sample, further research and replication of these results is needed.
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Affiliation(s)
- Zoran Vatavuk
- Department of Ophthalmology, Sisters of Mercy University Hospital, Vinogradska 29, Zagreb, Croatia.
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Zemunik T, Boban M, Lauc G, Janković S, Rotim K, Vatavuk Z, Bencić G, Dogas Z, Boraska V, Torlak V, Susac J, Zobić I, Rudan D, Pulanić D, Modun D, Mudnić I, Gunjaca G, Budimir D, Hayward C, Vitart V, Wright AF, Campbell H, Rudan I. Genome-wide association study of biochemical traits in Korcula Island, Croatia. Croat Med J 2009; 50:23-33. [PMID: 19260141 DOI: 10.3325/cmj.2009.50.23] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AIM To identify genetic variants underlying biochemical traits--total cholesterol, low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, triglycerides, uric acid, albumin, and fibrinogen, in a genome-wide association study in an isolated population where rare variants of larger effect may be more easily identified. METHODS The study included 944 adult inhabitants of the island of Korcula, as a part of larger DNA-based genetic epidemiological study in 2007. Biochemical measurements were performed in a single laboratory with stringent internal and external quality control procedures. Examinees were genotyped using Human Hap370CNV chip by Illumina, with a genome-wide scan containing 346027 single nucleotide polymorphisms (SNP). RESULTS A total of 31 SNPs were associated with 7 investigated traits at the level of P<1.00 x 10(-5). Nine of SNPs implicated the role of SLC2A9 in uric acid regulation (P=4.10 x 10(-6)-2.58 x 10(-12)), as previously found in other populations. All 22 remaining associations fell into the P=1.00 x 10(-5)-1.00 x 10(-6) significance range. One of them replicated the association between cholesteryl ester transfer protein (CETP) and HDL, and 7 associations were more than 100 kilobases away from the closest known gene. Nearby SNPs, rs4767631 and rs10444502, in gene kinase suppressor of ras 2 (KSR2) on chromosome 12 were associated with LDL cholesterol levels, and rs10444502 in the same gene with total cholesterol levels. Similarly, rs2839619 in gene PBX/knotted 1 homeobox 1 (PKNOX1) on chromosome 21 was associated with total and LDL cholesterol levels. The remaining 9 findings implied possible associations between phosphatidylethanolamine N-methyltransferase (PEMT) gene and total cholesterol; USP46, RAP1GDS1, and ZCCHC16 genes and triglycerides; BCAT1 and SLC14A2 genes and albumin; and NR3C2, GRIK2, and PCSK2 genes and fibrinogen. CONCLUSION Although this study was underpowered for most of the reported associations to reach formal threshold of genome-wide significance under the assumption of independent multiple testing, replications of previous findings and consistency of association between the identified variants and more than one studied trait make such findings interesting for further functional follow-up studies. Changed allele frequencies in isolate population may contribute to identifying variants that would not be easily identified in much larger samples in outbred populations.
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Affiliation(s)
- Tatijana Zemunik
- University of Split School of Medicine, Soltanska 2, 21000 Split, Croatia
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