1
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Yang L, Gao Y, Li M, Park KE, Liu S, Kang X, Liu M, Oswalt A, Fang L, Telugu BP, Sattler CG, Li CJ, Cole JB, Seroussi E, Xu L, Yang L, Zhou Y, Li L, Zhang H, Rosen BD, Van Tassell CP, Ma L, Liu GE. Genome-wide recombination map construction from single sperm sequencing in cattle. BMC Genomics 2022; 23:181. [PMID: 35247961 PMCID: PMC8898482 DOI: 10.1186/s12864-022-08415-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/24/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Meiotic recombination is one of the important phenomena contributing to gamete genome diversity. However, except for human and a few model organisms, it is not well studied in livestock, including cattle. RESULTS To investigate their distributions in the cattle sperm genome, we sequenced 143 single sperms from two Holstein bulls. We mapped meiotic recombination events at high resolution based on phased heterozygous single nucleotide polymorphism (SNP). In the absence of evolutionary selection pressure in fertilization and survival, recombination events in sperm are enriched near distal chromosomal ends, revealing that such a pattern is intrinsic to the molecular mechanism of meiosis. Furthermore, we further validated these findings in single sperms with results derived from sequencing its family trio of diploid genomes and our previous studies of recombination in cattle. CONCLUSIONS To our knowledge, this is the first large-scale single sperm whole-genome sequencing effort in livestock, which provided useful information for future studies of recombination, genome instability, and male infertility.
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Affiliation(s)
- Liu Yang
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - Mingxun Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 China
| | - Ki-Eun Park
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Xiaolong Kang
- College of Agriculture, Ningxia University, Yinchuan, 750021 China
| | - Mei Liu
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128 China
| | - Adam Oswalt
- Select Sires Inc, 11740 U.S. 42 North, Plain City, OH 43064 USA
| | - Lingzhao Fang
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG UK
| | - Bhanu P. Telugu
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
- Division of Animal Sciences, University of Missouri, Columbia, MO 65201 USA
| | | | - Cong-jun Li
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - John B. Cole
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Eyal Seroussi
- Agricultural Research Organization (ARO), Volcani Center, Institute of Animal Science, P.O.B 15159, HaMaccabim Road, 7528809 Rishon LeTsiyon, Israel
| | - Lingyang Xu
- Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Lv Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Li Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Hongping Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Curtis P. Van Tassell
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
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2
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Zhou Y, Browning BL, Browning SR. Population-Specific Recombination Maps from Segments of Identity by Descent. Am J Hum Genet 2020; 107:137-148. [PMID: 32533945 PMCID: PMC7332656 DOI: 10.1016/j.ajhg.2020.05.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/20/2020] [Indexed: 12/26/2022] Open
Abstract
Recombination rates vary significantly across the genome, and estimates of recombination rates are needed for downstream analyses such as haplotype phasing and genotype imputation. Existing methods for recombination rate estimation are limited by insufficient amounts of informative genetic data or by high computational cost. We present a method and software, called IBDrecomb, for using segments of identity by descent to infer recombination rates. IBDrecomb can be applied to sequenced population cohorts to obtain high-resolution, population-specific recombination maps. In simulated admixed data, IBDrecomb obtains higher accuracy than admixture-based estimation of recombination rates. When applied to 2,500 simulated individuals, IBDrecomb obtains similar accuracy to a linkage-disequilibrium (LD)-based method applied to 96 individuals (the largest number for which computation is tractable). Compared to LD-based maps, our IBD-based maps have the advantage of estimating recombination rates in the recent past rather than the distant past. We used IBDrecomb to generate new recombination maps for European Americans and for African Americans from TOPMed sequence data from the Framingham Heart Study (1,626 unrelated individuals) and the Jackson Heart Study (2,046 unrelated individuals), and we compare them to LD-based, admixture-based, and family-based maps.
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Affiliation(s)
- Ying Zhou
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.
| | - Brian L Browning
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.
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3
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From molecules to populations: appreciating and estimating recombination rate variation. Nat Rev Genet 2020; 21:476-492. [DOI: 10.1038/s41576-020-0240-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2020] [Indexed: 02/07/2023]
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4
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Fast Estimation of Recombination Rates Using Topological Data Analysis. Genetics 2019; 211:1191-1204. [PMID: 30787042 DOI: 10.1534/genetics.118.301565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 02/13/2019] [Indexed: 01/26/2023] Open
Abstract
Accurate estimation of recombination rates is critical for studying the origins and maintenance of genetic diversity. Because the inference of recombination rates under a full evolutionary model is computationally expensive, we developed an alternative approach using topological data analysis (TDA) on genome sequences. We find that this method can analyze datasets larger than what can be handled by any existing recombination inference software, and has accuracy comparable to commonly used model-based methods with significantly less processing time. Previous TDA methods used information contained solely in the first Betti number ([Formula: see text]) of a set of genomes, which aims to capture the number of loops that can be detected within a genealogy. These explorations have proven difficult to connect to the theory of the underlying biological process of recombination, and, consequently, have unpredictable behavior under perturbations of the data. We introduce a new topological feature, which we call ψ, with a natural connection to coalescent models, and present novel arguments relating [Formula: see text] to population genetic models. Using simulations, we show that ψ and [Formula: see text] are differentially affected by missing data, and package our approach as TREE (Topological Recombination Estimator). TREE's efficiency and accuracy make it well suited as a first-pass estimator of recombination rate heterogeneity or hotspots throughout the genome. Our work empirically and theoretically justifies the use of topological statistics as summaries of genome sequences and describes a new, unintuitive relationship between topological features of the distribution of sequence data and the footprint of recombination on genomes.
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5
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Zhou Y, Shen B, Jiang J, Padhi A, Park KE, Oswalt A, Sattler CG, Telugu BP, Chen H, Cole JB, Liu GE, Ma L. Construction of PRDM9 allele-specific recombination maps in cattle using large-scale pedigree analysis and genome-wide single sperm genomics. DNA Res 2018; 25:183-194. [PMID: 29186399 PMCID: PMC5909443 DOI: 10.1093/dnares/dsx048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/09/2017] [Indexed: 11/23/2022] Open
Abstract
PRDM9 contributes to hybrid sterility and species evolution. However, its role is to be confirmed in cattle, a major domesticated livestock species. We previously found an association near PRDM9 with cattle recombination features, but the causative variants are still unknown. Using millions of genotyped cattle with pedigree information, we characterized five PRDM9 alleles and generated allele-specific recombination maps. By examining allele-specific recombination patterns, we observed the impact of PRDM9 on global distribution of recombination, especially in the two ends of chromosomes. We also showed strong associations between recombination hotspot regions and functional mutations within PRDM9 zinc finger domain. More importantly, we found one allele of PRDM9 to be very different from others in both protein composition and recombination landscape, indicating the causative role of this allele on the association between PRDM9 and cattle recombination. When comparing recombination maps from sperm and pedigree data, we observed similar genome-wide recombination patterns, validating the quality of pedigree-based results. Collectively, these evidence supported PRDM9 alleles as causal variants for the reported association with cattle recombination. Our study comprehensively surveyed the bovine PRDM9 alleles, generated allele-specific recombination maps, and expanded our understanding of the role of PRDM9 on genome distribution of recombination.
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Affiliation(s)
- Yang Zhou
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD 20705, USA
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Botong Shen
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Jicai Jiang
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Abinash Padhi
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Ki-Eun Park
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Adam Oswalt
- Select Sires Inc. 11740 U.S. 42 North, Plain City, Ohio 43064, USA
| | | | - Bhanu P Telugu
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Hong Chen
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - John B Cole
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD 20705, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD 20705, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
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6
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Dapper AL, Payseur BA. Effects of Demographic History on the Detection of Recombination Hotspots from Linkage Disequilibrium. Mol Biol Evol 2018; 35:335-353. [PMID: 29045724 PMCID: PMC5850621 DOI: 10.1093/molbev/msx272] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In some species, meiotic recombination is concentrated in small genomic regions. These "recombination hotspots" leave signatures in fine-scale patterns of linkage disequilibrium, raising the prospect that the genomic landscape of hotspots can be characterized from sequence variation. This approach has led to the inference that hotspots evolve rapidly in some species, but are conserved in others. Historic demographic events, such as population bottlenecks, are known to affect patterns of linkage disequilibrium across the genome, violating population genetic assumptions of this approach. Although such events are prevalent, demographic history is generally ignored when making inferences about the evolution of recombination hotspots. To determine the effect of demography on the detection of recombination hotspots, we use the coalescent to simulate haplotypes with a known recombination landscape. We measure the ability of popular linkage disequilibrium-based programs to detect hotspots across a range of demographic histories, including population bottlenecks, hidden population structure, population expansions, and population contractions. We find that demographic events have the potential to greatly reduce the power and increase the false positive rate of hotspot discovery. Neither the power nor the false positive rate of hotspot detection can be predicted without also knowing the demographic history of the sample. Our results suggest that ignoring demographic history likely overestimates the power to detect hotspots and therefore underestimates the degree of hotspot sharing between species. We suggest strategies for incorporating demographic history into population genetic inferences about recombination hotspots.
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Affiliation(s)
- Amy L Dapper
- Laboratory of Genetics, University of Wisconsin, Madison, WI
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin, Madison, WI
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7
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8
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Recombination hotspots: Models and tools for detection. DNA Repair (Amst) 2016; 40:47-56. [PMID: 26991854 DOI: 10.1016/j.dnarep.2016.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 02/09/2016] [Indexed: 11/22/2022]
Abstract
Recombination hotspots are the regions within the genome where the rate, and the frequency of recombination are optimum with a size varying from 1 to 2kb. The recombination event is mediated by the double-stranded break formation, guided by the combined enzymatic action of DNA topoisomerase and Spo 11 endonuclease. These regions are distributed non-uniformly throughout the human genome and cause distortions in the genetic map. Numerous lines of evidence suggest that the number of hotspots known in humans has increased manifold in recent years. A few facts about the hotspot evolutions were also put forward, indicating the differences in the hotspot position between chimpanzees and humans. In mice, recombination hot spots were found to be clustered within the major histocompatibility complex (MHC) region. Several models, that help explain meiotic recombination has been proposed. Moreover, scientists also developed some computational tools to locate the hotspot position and estimate their recombination rate in humans is of great interest to population and medical geneticists. Here we reviewed the molecular mechanisms, models and in silico prediction techniques of hot spot residues.
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9
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Chen H, Yang P, Guo J, Kwoh CK, Przytycka TM, Zheng J. ARG-walker: inference of individual specific strengths of meiotic recombination hotspots by population genomics analysis. BMC Genomics 2015; 16 Suppl 12:S1. [PMID: 26679564 PMCID: PMC4682399 DOI: 10.1186/1471-2164-16-s12-s1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Meiotic recombination hotspots play important roles in various aspects of genomics, but the underlying mechanisms for regulating the locations and strengths of recombination hotspots are not yet fully revealed. Most existing algorithms for estimating recombination rates from sequence polymorphism data can only output average recombination rates of a population, although there is evidence for the heterogeneity in recombination rates among individuals. For genome-wide association studies (GWAS) of recombination hotspots, an efficient algorithm that estimates the individualized strengths of recombination hotspots is highly desirable. RESULTS In this work, we propose a novel graph mining algorithm named ARG-walker, based on random walks on ancestral recombination graphs (ARG), to estimate individual-specific recombination hotspot strengths. Extensive simulations demonstrate that ARG-walker is able to distinguish the hot allele of a recombination hotspot from the cold allele. Integrated with output of ARG-walker, we performed GWAS on the phased haplotype data of the 22 autosome chromosomes of the HapMap Asian population samples of Chinese and Japanese (JPT+CHB). Significant cis-regulatory signals have been detected, which is corroborated by the enrichment of the well-known 13-mer motif CCNCCNTNNCCNC of PRDM9 protein. Moreover, two new DNA motifs have been identified in the flanking regions of the significantly associated SNPs (single nucleotide polymorphisms), which are likely to be new cis-regulatory elements of meiotic recombination hotspots of the human genome. CONCLUSIONS Our results on both simulated and real data suggest that ARG-walker is a promising new method for estimating the individual recombination variations. In the future, it could be used to uncover the mechanisms of recombination regulation and human diseases related with recombination hotspots.
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Affiliation(s)
- Hao Chen
- Biomedical Informatics Graduate Lab, School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Singapore Immunology Network (SIgN), A*STAR, Biopolis, Singapore 138648, Singapore
| | - Peng Yang
- Biomedical Informatics Graduate Lab, School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Institute for Infocomm Research (I2R), A*STAR (Agency for Science, Technology, and Research), 1 Fusionopolis, Singapore 138632, Singapore
| | - Jing Guo
- Biomedical Informatics Graduate Lab, School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Chee Keong Kwoh
- Biomedical Informatics Graduate Lab, School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Teresa M Przytycka
- Computational Biology Branch, National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), 8600 Rockville Pike, Bethesda, Maryland 20894, USA
| | - Jie Zheng
- Biomedical Informatics Graduate Lab, School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Genome Institute of Singapore, A*STAR, Biopolis, Singapore 138672, Singapore
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10
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Alves JM, Chikhi L, Amorim A, Lopes AM. The 8p23 inversion polymorphism determines local recombination heterogeneity across human populations. Genome Biol Evol 2015; 6:921-30. [PMID: 24682157 PMCID: PMC4007553 DOI: 10.1093/gbe/evu064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
For decades, chromosomal inversions have been regarded as fascinating evolutionary elements as they are expected to suppress recombination between chromosomes with opposite orientations, leading to the accumulation of genetic differences between the two configurations over time. Here, making use of publicly available population genotype data for the largest polymorphic inversion in the human genome (8p23-inv), we assessed whether this inhibitory effect of inversion rearrangements led to significant differences in the recombination landscape of two homologous DNA segments, with opposite orientation. Our analysis revealed that the accumulation of genetic differentiation is positively correlated with the variation in recombination profiles. The observed recombination dissimilarity between inversion types is consistent across all populations analyzed and surpasses the effects of geographic structure, suggesting that both structures (orientations) have been evolving independently over an extended period of time, despite being subjected to the very same demographic history. Aside this mainly independent evolution, we also identified a short segment (350 kb, <10% of the whole inversion) in the central region of the inversion where the genetic divergence between the two structural haplotypes is diminished. Although it is difficult to demonstrate it, this could be due to gene flow (possibly via double-crossing over events), which is consistent with the higher recombination rates surrounding this segment. This study demonstrates for the first time that chromosomal inversions influence the recombination landscape at a fine-scale and highlights the role of these rearrangements as drivers of genome evolution.
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Affiliation(s)
- Joao M Alves
- Doctoral Program in Areas of Basic and Applied Biology (GABBA), University of Porto, Portugal
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11
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Blainey PC, Quake SR. Dissecting genomic diversity, one cell at a time. Nat Methods 2014; 11:19-21. [PMID: 24524132 DOI: 10.1038/nmeth.2783] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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12
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Guo J, Jain R, Yang P, Fan R, Kwoh CK, Zheng J. Reliable and Fast Estimation of Recombination Rates by Convergence Diagnosis and Parallel Markov Chain Monte Carlo. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2014; 11:63-72. [PMID: 26355508 DOI: 10.1109/tcbb.2013.133] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Genetic recombination is an essential event during the process of meiosis resulting in an exchange of segments between paired chromosomes. Estimating recombination rate is crucial for understanding the process of recombination. Experimental methods are normally difficult and limited to small scale estimations. Thus statistical methods using population genetics data are important for large-scale analysis. LDhat is an extensively used statistical method using rjMCMC algorithm to predict recombination rates. Due to the complexity of rjMCMC scheme, LDhat may take a long time for large SNP data sets. In addition, rjMCMC parameters should be manually defined in the original program which directly impact results. To address these issues, we designed an improved algorithm based on LDhat implementing MCMC convergence diagnostic algorithms to automatically predict values of parameters and monitor the mixing process. Then parallel computation methods were employed to further accelerate the new program. The new algorithms have been tested on ten samples from HapMap phase 2 data set. The results were compared with previous code and showed nearly identical output. However, our new methods achieved significant acceleration proving that they are more efficient and reliable for the estimation of recombination rates. The stand-alone package is freely available for download http://www.ntu.edu.sg/home/zhengjie/software/CPLDhat.
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13
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Mougel F, Poursat MA, Beaume N, Vautrin D, Solignac M. High-resolution linkage map for two honeybee chromosomes: the hotspot quest. Mol Genet Genomics 2013; 289:11-24. [PMID: 24162559 DOI: 10.1007/s00438-013-0784-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 10/07/2013] [Indexed: 10/26/2022]
Abstract
Meiotic recombination is a fundamental process ensuring proper disjunction of homologous chromosomes and allele shuffling in successive generations. In many species, this cellular mechanism occurs heterogeneously along chromosomes and mostly concentrates in tiny fragments called recombination hotspots. Specific DNA motifs have been shown to initiate recombination in these hotspots in mammals, fission yeast and drosophila. The aim of this study was to check whether recombination also occurs in a heterogeneous fashion in the highly recombinogenic honeybee genome and whether this heterogeneity can be connected with specific DNA motifs. We completed a previous picture drawn from a routine genetic map built with an average resolution of 93 kb. We focused on the two smallest honeybee chromosomes to increase the resolution and even zoomed at very high resolution (3.6 kb) on a fragment of 300 kb. Recombination rates measured in these fragments were placed in relation with occurrence of 30 previously described motifs through a Poisson regression model. A selection procedure suitable for correlated variables was applied to keep significant motifs. These fine and ultra-fine mappings show that recombination rate is significantly heterogeneous although poorly contrasted between high and low recombination rate, contrarily to most model species. We show that recombination rate is probably associated with the DNA methylation state. Moreover, three motifs (CGCA, GCCGC and CCAAT) are good candidates of signals promoting recombination. Their influence is however moderate, doubling at most the recombination rate. This discovery extends the way to recombination dissection in insects.
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Affiliation(s)
- Florence Mougel
- Laboratoire Evolution Génomes Spéciation, CNRS, avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France,
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14
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Illingworth CJR, Parts L, Bergström A, Liti G, Mustonen V. Inferring genome-wide recombination landscapes from advanced intercross lines: application to yeast crosses. PLoS One 2013; 8:e62266. [PMID: 23658715 PMCID: PMC3642125 DOI: 10.1371/journal.pone.0062266] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 03/19/2013] [Indexed: 01/23/2023] Open
Abstract
Accurate estimates of recombination rates are of great importance for understanding evolution. In an experimental genetic cross, recombination breaks apart and rejoins genetic material, such that the genomes of the resulting isolates are comprised of distinct blocks of differing parental origin. We here describe a method exploiting this fact to infer genome-wide recombination profiles from sequenced isolates from an advanced intercross line (AIL). We verified the accuracy of the method against simulated data. Next, we sequenced 192 isolates from a twelve-generation cross between West African and North American yeast Saccharomyces cerevisiae strains and inferred the underlying recombination landscape at a fine genomic resolution (mean segregating site distance 0.22 kb). Comparison was made with landscapes inferred for a similar cross between four yeast strains, and with a previous single-generation, intra-strain cross (Mancera et al., Nature 2008). Moderate congruence was identified between landscapes (correlation 0.58-0.77 at 5 kb resolution), albeit with variance between mean genome-wide recombination rates. The multiple generations of mating undergone in the AILs gave more precise inference of recombination rates than could be achieved from a single-generation cross, in particular in identifying recombination cold-spots. The recombination landscapes we describe have particular utility; both AILs are part of a resource to study complex yeast traits (see e.g. Parts et al., Genome Res 2011). Our results will enable future applications of this resource to take better account of local linkage structure heterogeneities. Our method has general applicability to other crossing experiments, including a variety of experimental designs.
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Affiliation(s)
| | - Leopold Parts
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Anders Bergström
- Institute of Research on Cancer and Ageing of Nice, Université de Nice Sophia Antipolis, Nice, France
| | - Gianni Liti
- Institute of Research on Cancer and Ageing of Nice, Université de Nice Sophia Antipolis, Nice, France
| | - Ville Mustonen
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
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15
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Kirkness EF, Grindberg RV, Yee-Greenbaum J, Marshall CR, Scherer SW, Lasken RS, Venter JC. Sequencing of isolated sperm cells for direct haplotyping of a human genome. Genome Res 2013; 23:826-32. [PMID: 23282328 PMCID: PMC3638138 DOI: 10.1101/gr.144600.112] [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: 12/16/2022]
Abstract
There is increasing evidence that the phenotypic effects of genomic sequence variants are best understood in terms of variant haplotypes rather than as isolated polymorphisms. Haplotype analysis is also critically important for uncovering population histories and for the study of evolutionary genetics. Although the sequencing of individual human genomes to reveal personal collections of sequence variants is now well established, there has been slower progress in the phasing of these variants into pairs of haplotypes along each pair of chromosomes. Here, we have developed a distinct approach to haplotyping that can yield chromosome-length haplotypes, including the vast majority of heterozygous single-nucleotide polymorphisms (SNPs) in an individual human genome. This approach exploits the haploid nature of sperm cells and employs a combination of genotyping and low-coverage sequencing on a short-read platform. In addition to generating chromosome-length haplotypes, the approach can directly identify recombination events (averaging 1.1 per chromosome) with a median resolution of <100 kb.
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16
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Abstract
During meiosis, homologous chromosomes (homologs) undergo recombinational interactions, resulting in the formation of crossovers (COs) or noncrossovers (NCOs). Both COs and NCOs are initiated by the same event: programmed double-strand DNA breaks (DSBs), which occur preferentially at hotspots throughout the genome. COs contribute to the genetic diversity of gametes and are needed to promote proper meiotic chromosome segregation. Accordingly, their formation is tightly controlled. In the mouse, the sites of preferred CO formation differ between male and female chromosomes, both on a regional level and on the level of individual hotspots. Sperm typing using (half-sided) allele-specific PCR has proven a powerful technique to characterize COs and all detectable NCOs at hotspots on male human and mouse chromosomes. In contrast, very little is known about the properties of hotspots in female meiosis. This chapter describes an adaptation of sperm typing to analyze recombinants in a hotspot, using DNA isolated from an ovary cell suspension enriched for oocytes.
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Affiliation(s)
- Esther de Boer
- Institut de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
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17
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Abstract
Homologous recombination during meiosis is critical for the formation of gametes. Recombination is initiated by programmed DNA double-strand breaks which preferentially occur at hotspots dispersed throughout the genome. These double-strand breaks are repaired from the homolog, resulting in either a crossover or noncrossover product. Multiple noncrossover events are required for homolog pairing, and at least one crossover is critical for proper chromosome segregation at the first meiotic division. Consequently, homologous recombination in meiosis occurs at high frequencies. This chapter describes how to characterize crossovers and noncrossovers at a hotspot in mice using allele-specific PCR. Amplification of recombinant products directly from sperm DNA is a powerful approach to determine recombination frequencies and map recombination breakpoints, providing insight into homologous recombination mechanisms.
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Affiliation(s)
- Francesca Cole
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
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18
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Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome. Genome Biol 2010; 11:R103. [PMID: 20961408 PMCID: PMC3218659 DOI: 10.1186/gb-2010-11-10-r103] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 09/25/2010] [Accepted: 10/20/2010] [Indexed: 12/02/2022] Open
Abstract
Background Meiotic recombination events tend to cluster into narrow spans of a few kilobases long, called recombination hotspots. Such hotspots are not conserved between human and chimpanzee and vary between different human ethnic groups. At the same time, recombination hotspots are heritable. Previous studies showed instances where differences in recombination rate could be associated with sequence polymorphisms. Results In this work we developed a novel computational approach, LDsplit, to perform a large-scale association study of recombination hotspots with genetic polymorphisms. LDsplit was able to correctly predict the association between the FG11 SNP and the DNA2 hotspot observed by sperm typing. Extensive simulation demonstrated the accuracy of LDsplit under various conditions. Applying LDsplit to human chromosome 6, we found that for a significant fraction of hotspots, there is an association between variations in intensity of historical recombination and sequence polymorphisms. From flanking regions of the SNPs output by LDsplit we identified a conserved 11-mer motif GGNGGNAGGGG, whose complement partially matches 13-mer CCNCCNTNNCCNC, a critical motif for the regulation of recombination hotspots. Conclusions Our result suggests that computational approaches based on historical recombination events are likely to be more powerful than previously anticipated. The putative associations we identified may be a promising step toward uncovering the mechanisms of recombination hotspots.
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19
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Clark AG, Wang X, Matise T. Contrasting methods of quantifying fine structure of human recombination. Annu Rev Genomics Hum Genet 2010; 11:45-64. [PMID: 20690817 DOI: 10.1146/annurev-genom-082908-150031] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There has been considerable excitement over the ability to construct linkage maps based only on genome-wide genotype data for single nucleotide polymorphic sites (SNPs) in a population sample. These maps, which are derived from estimates of linkage disequilibrium (LD), rely on population genetics theory to relate the decay of LD to the local rate of recombination, but other population processes also come into play. Here we contrast these LD maps to the classically derived, pedigree-based human recombination maps. The LD maps have a level of resolution greatly exceeding that of the pedigree maps, and at this fine scale, sperm typing allows a means of validation. While at a gross level both the pedigree maps and the sperm typing methods generally agree with LD maps, there are significant local differences between them, and the fact that these maps measure different genetic features should be remembered when using them for other genetic inferences.
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Affiliation(s)
- Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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20
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Khil PP, Camerini-Otero RD. Genetic crossovers are predicted accurately by the computed human recombination map. PLoS Genet 2010; 6:e1000831. [PMID: 20126534 PMCID: PMC2813264 DOI: 10.1371/journal.pgen.1000831] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Accepted: 12/28/2009] [Indexed: 11/26/2022] Open
Abstract
Hotspots of meiotic recombination can change rapidly over time. This instability and the reported high level of inter-individual variation in meiotic recombination puts in question the accuracy of the calculated hotspot map, which is based on the summation of past genetic crossovers. To estimate the accuracy of the computed recombination rate map, we have mapped genetic crossovers to a median resolution of 70 Kb in 10 CEPH pedigrees. We then compared the positions of crossovers with the hotspots computed from HapMap data and performed extensive computer simulations to compare the observed distributions of crossovers with the distributions expected from the calculated recombination rate maps. Here we show that a population-averaged hotspot map computed from linkage disequilibrium data predicts well present-day genetic crossovers. We find that computed hotspot maps accurately estimate both the strength and the position of meiotic hotspots. An in-depth examination of not-predicted crossovers shows that they are preferentially located in regions where hotspots are found in other populations. In summary, we find that by combining several computed population-specific maps we can capture the variation in individual hotspots to generate a hotspot map that can predict almost all present-day genetic crossovers. In eukaryotes genetic crossovers are responsible for generating genetic diversity and ensuring the proper segregation of chromosomes. Genetic crossovers are tightly clustered in hotspots. Although the existence of hotspots in humans is clearly proven, mechanisms of their formation and the regulation of meiotic recombination in general remain poorly understood. An additional complication in studies of meiotic recombination is the fact that the direct experimental mapping of human hotspots on a genome-wide scale is not feasible with current methods. The best available indirect methods compute the position of hotspots from patterns of historic associations between genetic markers in population samples. In this study we determined the positions of genetic crossovers in ten pedigrees of European origin and then compared the positions of crossovers with the hotspots computed from HapMap data. Importantly, we find that the population-averaged computed map is in close agreement with the observed distribution of genetic crossovers. We also find that cryptic hotspots that are not easily detected in the computed European map can be more effectively identified if other populations are included in the analysis. Our analysis shows that high-resolution recombination profiles are highly similar between distantly related populations and that by including computed hotspots from several populations we can predict nearly all crossovers.
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Affiliation(s)
- Pavel P. Khil
- Genetics and Biochemistry Branch, The National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - R. Daniel Camerini-Otero
- Genetics and Biochemistry Branch, The National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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21
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Tiemann-Boege I, Curtis C, Shinde DN, Goodman DB, Tavaré S, Arnheim N. Product length, dye choice, and detection chemistry in the bead-emulsion amplification of millions of single DNA molecules in parallel. Anal Chem 2009; 81:5770-6. [PMID: 19601653 DOI: 10.1021/ac900633y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The amplification of millions of single molecules in parallel can be performed on microscopic magnetic beads that are contained in aqueous compartments of an oil-buffer emulsion. These bead-emulsion amplification (BEA) reactions result in beads that are covered by almost-identical copies derived from a single template. The post-amplification analysis is performed using different fluorophore-labeled probes. We have identified BEA reaction conditions that efficiently produce longer amplicons of up to 450 base pairs. These conditions include the use of a Titanium Taq amplification system. Second, we explored alternate fluorophores coupled to probes for post-PCR DNA analysis. We demonstrate that four different Alexa fluorophores can be used simultaneously with extremely low crosstalk. Finally, we developed an allele-specific extension chemistry that is based on Alexa dyes to query individual nucleotides of the amplified material that is both highly efficient and specific.
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22
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Fraction of informative recombinations: a heuristic approach to analyze recombination rates. Genetics 2008; 178:2069-79. [PMID: 18430934 DOI: 10.1534/genetics.107.082255] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this article we present a new heuristic approach (informative recombinations, InfRec) to analyze recombination density at the sequence level. InfRec is intuitive and easy and combines previously developed methods that (i) resolve genotypes into haplotypes, (ii) estimate the minimum number of recombinations, and (iii) evaluate the fraction of informative recombinations. We tested this approach in its sliding-window version on 117 genes from the SeattleSNPs program, resequenced in 24 African-Americans (AAs) and 23 European-Americans (EAs). We obtained population recombination rate estimates (rho(obs)) of 0.85 and 0.37 kb(-1) in AAs and EAs, respectively. Coalescence simulations indicated that these values account for both the recombinations and the gene conversions in the history of the sample. The intensity of rho(obs) varied considerably along the sequence, revealing the presence of recombination hotspots. Overall, we observed approximately 80% of recombinations in one-third and approximately 50% in only 10% of the sequence. InfRec performance, tested on published simulated and additional experimental data sets, was similar to that of other hotspot detection methods. Fast, intuitive, and visual, InfRec is not constrained by sample size limitations. It facilitates understanding data and provides a simple and flexible tool to analyze recombination intensity along the sequence.
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Abstract
Our understanding of the details of mammalian meiotic recombination has recently advanced significantly. Sperm typing technologies, linkage studies, and computational inferences from population genetic data have together provided information in unprecedented detail about the location and activity of the sites of crossing-over in mice and humans. The results show that the vast majority of meiotic recombination events are localized to narrow DNA regions (hot spots) that constitute only a small fraction of the genome. The data also suggest that the molecular basis of hot spot activity is unlikely to be strictly determined by specific DNA sequence motifs in cis. Further molecular studies are needed to understand how hot spots originate, function and evolve.
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Affiliation(s)
- Norman Arnheim
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089-2910, USA.
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24
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Buard J, de Massy B. Playing hide and seek with mammalian meiotic crossover hotspots. Trends Genet 2007; 23:301-9. [PMID: 17434233 DOI: 10.1016/j.tig.2007.03.014] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2006] [Revised: 03/14/2007] [Accepted: 03/29/2007] [Indexed: 11/30/2022]
Abstract
Crossovers (COs) are essential for meiosis and contribute to genome diversity by promoting the reassociation of alleles, and thus improve the efficiency of selection. COs are not randomly distributed but are found at specific regions, or CO hotspots. Recent results have revealed the historical recombination rates and the distribution of hotspots across the human genome. Surprisingly, CO hotspots are highly dynamic, as shown by differences in activity between individuals, populations and closely related species. We propose a role for DNA methylation in preventing the formation of COs, a regulation that might explain, in part, the correlation between recombination rates and GC content in mammals.
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Affiliation(s)
- Jérôme Buard
- Institute of Human Genetics, UPR1142-CNRS, 141 rue de la Cardonille, 34396 Montpellier cedex 5, France
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25
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Clark VJ, Ptak SE, Tiemann I, Qian Y, Coop G, Stone AC, Przeworski M, Arnheim N, Di Rienzo A. Combining sperm typing and linkage disequilibrium analyses reveals differences in selective pressures or recombination rates across human populations. Genetics 2006; 175:795-804. [PMID: 17151245 PMCID: PMC1800598 DOI: 10.1534/genetics.106.064964] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A previous polymorphism survey of the type 2 diabetes gene CAPN10 identified a segment showing an excess of polymorphism levels in all population samples, coinciding with localized breakdown of linkage disequilibrium (LD) in a sample of Hausa from Cameroon, but not in non-African samples. This raised the possibility that a recombination hotspot is present in all populations and we had insufficient power to detect it in the non-African data. To test this possibility, we estimated the crossover rate by sperm typing in five non-African men; these estimates were consistent with the LD decay in the non-African, but not in the Hausa data. Moreover, resequencing the orthologous region in a sample of Western chimpanzees did not show either an excess of polymorphism level or rapid LD decay, suggesting that the processes underlying the patterns observed in humans operated only on the human lineage. These results suggest that a hotspot of recombination has recently arisen in humans and has reached higher frequency in the Hausa than in non-Africans, or that there is no elevation in crossover rate in any human population, and the observed variation results from long-standing balancing selection.
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Affiliation(s)
- Vanessa J Clark
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
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26
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Abstract
Meiotic recombination occurs preferentially at certain regions called hot spots and is important for generating genetic diversity and proper segregation of chromosomes during meiosis. Hot spots have been characterized most extensively in yeast, mice and humans. The development of methods based on sperm typing and population genetics has facilitated rapid and high-resolution mapping of hot spots in mice and humans in recent years. With increasing information becoming available on meiotic recombination in different species, it is now possible to compare several molecular features associated with hot-spot loci. Further, there have been advances in our knowledge of the factors influencing hot-spot activity and the role that they play in structuring the genome into haplotype blocks. We review the molecular features associated with hot spots in terms of their properties and mechanisms underlying their function and distribution. A large number of these features seem to be shared among hot spots from different species suggesting common mechanisms for their formation and function.
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Affiliation(s)
- K T Nishant
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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27
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Reed FA, Tishkoff SA. Positive selection can create false hotspots of recombination. Genetics 2006; 172:2011-4. [PMID: 16387873 PMCID: PMC1456281 DOI: 10.1534/genetics.105.052183] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2005] [Accepted: 12/23/2005] [Indexed: 11/18/2022] Open
Abstract
Simulations of positive directional selection, under parameter values appropriate for approximating human genetic diversity and rates of recombination, reveal that the effects of strong selective sweeps on patterns of linkage disequilibrium (LD) mimic the pattern expected with recombinant hotspots.
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Affiliation(s)
- Floyd A Reed
- Department of Biology, University of Maryland, College Park, Maryland 20742, USA.
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28
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Jasper MJ, Hu DG, Liebelt J, Sherrin D, Watson R, Tremellen KP, Hussey ND. Singleton births after routine preimplantation genetic diagnosis using exclusion testing (D4S43 and D4S126) for Huntington’s disease. Fertil Steril 2006; 85:597-602. [PMID: 16500325 DOI: 10.1016/j.fertnstert.2005.08.050] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2005] [Revised: 08/25/2005] [Accepted: 08/25/2005] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To develop exclusion testing protocols for Huntington's disease (HD) linkage markers suitable for use in a clinical preimplantation genetic diagnosis (PGD) setting for couples in whom a partner was at 50% risk of inheriting HD, but who choose not to undergo presymptomatic mutation testing. DESIGN Preimplantation genetic diagnosis using exclusion testing. SETTING In vitro fertilization clinic. PATIENT(S) Three couples with family histories of HD, two couples opposed to direct mutation testing. INTERVENTION(S) Development of single-cell polymerase chain reaction tests for PGD for the HD mutation and two HD gene-flanking markers (D4S43 and D4S126), allowing the identification of an individual embryo as being at either low or high risk for developing HD without being diagnostic of the presence of the mutation. MAIN OUTCOME MEASURE(S) D4S43, D4S126, and HD mutation. RESULT(S) After PGD for HD, couple 1 gave birth to a healthy girl after a frozen embryo transfer, and genetic status was confirmed by prenatal diagnosis to be very low risk for developing HD. Couple 2 gave birth to a healthy boy after their second cycle of PGD, and couple 3, after a third cycle, gave birth to a boy with congenital heart defects, which were successfully corrected with surgery at age 5 days. Both couples 2 and 3 declined prenatal testing, and therefore relinquished the opportunity to confirm the PGD. CONCLUSION(S) Preimplantation genetic diagnosis for HD using exclusion testing resulted in three live singleton births after six oocyte recovery procedures. The diagnostic protocol provided couples the opportunity to minimize the likelihood of disease transmission to their children, without the requirement for predictive testing.
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Affiliation(s)
- Melinda J Jasper
- Department of Obstetrics and Gynaecology, University of Adelaide, The Queen Elizabeth Hospital, Adelaide, South Australia, Australia.
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29
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Abstract
Meiotic recombination occurs preferentially at certain regions in the genome referred to as hot spots. The number of hot spots known in humans has increased manifold in recent years. The identification of these hot spots in humans is of great interest to population and medical geneticists since they influence the structure of Linkage Disequilibrium and Haplotype blocks in human populations, whose patterns have applications in mapping disease genes. HUMHOT is a web-based database of Human Meiotic Recombination Hot Spots. The database comprises DNA sequences corresponding to the hot spot regions from the literature that have been mapped to a high resolution (<4 kb) in humans. It also provides flanking sequence information for the hot spot region along with references describing the hot spot. The database can be queried based on hot spot identity, chromosome position or by homology to user-defined sequences. It is also updated with new hot spot sequences as they are discovered and provides hyperlinks to commonly used tools for estimating recombination rates, performing genetic analysis and new advances in our understanding of meiotic hot spots. Public access to the HUMHOT database is available at .
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Affiliation(s)
- K T Nishant
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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30
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Holloway K, Lawson VE, Jeffreys AJ. Allelic recombination and de novo deletions in sperm in the human beta-globin gene region. Hum Mol Genet 2006; 15:1099-111. [PMID: 16501000 DOI: 10.1093/hmg/ddl025] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Meiotic recombination is of fundamental importance in creating haplotype diversity in the human genome and has the potential to cause genomic rearrangements by ectopic recombination between repeat sequences and through other changes triggered by recombination-initiating events. However, the relationship between allelic recombination and genome instability in the human germline remains unclear. We have therefore analysed recombination and DNA instability in the delta-, beta-globin gene region and its associated recombination hotspot. Sperm typing has for the first time accurately defined the hotspot and shown it to be the most active autosomal crossover hotspot yet described, although unusually inactive in non-exchange gene conversion. The hotspot just extends into a homology block shared by the delta- and beta-globin genes, within which ectopic exchanges can generate Hb Lepore deletions. We developed a physical selection method for recovering and validating extremely rare de novo deletions in human DNA and used it to characterize the dynamics of these Hb Lepore deletions in sperm as well as other deletions not arising from ectopic exchanges between homologous DNA sequences. Surprisingly, both classes of deletion showed breakpoints that avoided the beta-globin hotspot, establishing that it possesses remarkable fidelity and does not play a significant role in triggering these DNA rearrangements. This study also provides the first direct analysis of de novo deletion in the human germline and points to a possible deletion-controlling element in the beta-globin gene separate from the crossover hotspot.
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Affiliation(s)
- Kim Holloway
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
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31
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Jiang Z, Zhang X, Deka R, Jin L. Genome amplification of single sperm using multiple displacement amplification. Nucleic Acids Res 2005; 33:e91. [PMID: 15942023 PMCID: PMC1143700 DOI: 10.1093/nar/gni089] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Sperm typing is an effective way to study recombination rate on a fine scale in regions of interest. There are two strategies for the amplification of single meiotic recombinants: repulsion-phase allele-specific PCR and whole genome amplification (WGA). The former can selectively amplify single recombinant molecules from a batch of sperm but is not scalable for high-throughput operation. Currently, primer extension pre-amplification is the only method used in WGA of single sperm, whereas it has limited capacity to produce high-coverage products enough for the analysis of local recombination rate in multiple large regions. Here, we applied for the first time a recently developed WGA method, multiple displacement amplification (MDA), to amplify single sperm DNA, and demonstrated its great potential for producing high-yield and high-coverage products. In a 50 mul reaction, 76 or 93% of loci can be amplified at least 2500- or 250-fold, respectively, from single sperm DNA, and second-round MDA can further offer >200-fold amplification. The MDA products are usable for a variety of genetic applications, including sequencing and microsatellite marker and single nucleotide polymorphism (SNP) analysis. The use of MDA in single sperm amplification may open a new era for studies on local recombination rates.
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Affiliation(s)
- Zhengwen Jiang
- Department of Environmental Health, Center for Genome Information, University of Cincinnati College of Medicine3223 Eden Ave, Cincinnati, OH 45267, USA
| | - Xingqi Zhang
- Department of Obstetrics and Gynecology, Northwestern University Medical SchoolChicago, IL, USA
| | - Ranjan Deka
- Department of Environmental Health, Center for Genome Information, University of Cincinnati College of Medicine3223 Eden Ave, Cincinnati, OH 45267, USA
| | - Li Jin
- Department of Environmental Health, Center for Genome Information, University of Cincinnati College of Medicine3223 Eden Ave, Cincinnati, OH 45267, USA
- State Key Laboratory of Genetic Engineering and Center for Anthropological Studies, School of Life Sciences and Morgan-Tan International Center for Life Sciences, Fudan UniversityShanghai, China
- To whom correspondence should be addressed at Liren Biology Building, Room 220, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China. Tel: +86 21 65642800; Fax: +86 21 55664388;
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32
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Bannai M, Higuchi K, Akesaka T, Furukawa M, Yamaoka M, Sato K, Tokunaga K. Single-nucleotide-polymorphism genotyping for whole-genome-amplified samples using automated fluorescence correlation spectroscopy. Anal Biochem 2004; 327:215-21. [PMID: 15051538 DOI: 10.1016/j.ab.2004.01.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2003] [Indexed: 11/26/2022]
Abstract
Whole-genome amplification (WGA) methods were adopted for single-nucleotide-polymorphism (SNP) typing to minimize the amount of genomic DNA that has to be used in typing for thousands of different SNPs in large-scale studies; 5-10 ng of genomic DNA was amplified by a WGA method (improved primer-extension-preamplification-polymerase chain reaction (I-PEP-PCR), degenerated oligonucleotide primer-PCR (DOP-PCR), or multiple displacement amplification (MDA)). Using 1/100 to 1/500 amounts of the whole-genome-amplified products as templates, subsequent analyses were successfully performed. SNPs were genotyped by the sequence-specific primer (SSP)-PCR method followed by fluorescence correlation spectroscopy (FCS). The typing results were evaluated for four different SNPs on tumor necrosis factor receptor 1 and 2 genes (TNFR1 and TNFR2). The genotypes determined by the SSP-FCS method using the WGA products were 100% in concordance with those determined by nucleotide sequencing using genomic DNAs. We have already carried out typing of more than 300 different SNPs and are currently performing 7,500-10,000 typings per day using WGA samples from patients with several common diseases. WGA coupled with FCS allows specific and high-throughput genotyping of thousands of samples for thousands of different SNPs.
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Affiliation(s)
- Makoto Bannai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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33
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Kauppi L, Jeffreys AJ, Keeney S. Where the crossovers are: recombination distributions in mammals. Nat Rev Genet 2004; 5:413-24. [PMID: 15153994 DOI: 10.1038/nrg1346] [Citation(s) in RCA: 238] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Liisa Kauppi
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK.
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34
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Ptak SE, Roeder AD, Stephens M, Gilad Y, Pääbo S, Przeworski M. Absence of the TAP2 human recombination hotspot in chimpanzees. PLoS Biol 2004; 2:e155. [PMID: 15208713 PMCID: PMC423135 DOI: 10.1371/journal.pbio.0020155] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2003] [Accepted: 03/21/2004] [Indexed: 11/30/2022] Open
Abstract
Recent experiments using sperm typing have demonstrated that, in several regions of the human genome, recombination does not occur uniformly but instead is concentrated in “hotspots” of 1–2 kb. Moreover, the crossover asymmetry observed in a subset of these has led to the suggestion that hotspots may be short-lived on an evolutionary time scale. To test this possibility, we focused on a region known to contain a recombination hotspot in humans, TAP2, and asked whether chimpanzees, the closest living evolutionary relatives of humans, harbor a hotspot in a similar location. Specifically, we used a new statistical approach to estimate recombination rate variation from patterns of linkage disequilibrium in a sample of 24 western chimpanzees (Pan troglodytes verus). This method has been shown to produce reliable results on simulated data and on human data from the TAP2 region. Strikingly, however, it finds very little support for recombination rate variation at TAP2 in the western chimpanzee data. Moreover, simulations suggest that there should be stronger support if there were a hotspot similar to the one characterized in humans. Thus, it appears that the human TAP2 recombination hotspot is not shared by western chimpanzees. These findings demonstrate that fine-scale recombination rates can change between very closely related species and raise the possibility that rates differ among human populations, with important implications for linkage-disequilibrium based association studies. The human TAP2 recombination hotspot is absent from the homologous region in western chimpanzees, with important implications for association studies, the HapMap project and understanding fine-scale variation in recombination rates
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Affiliation(s)
- Susan E Ptak
- 1Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Amy D Roeder
- 1Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Matthew Stephens
- 2Department of Statistics, University of WashingtonSeattle, WashingtonUnited States of America
| | - Yoav Gilad
- 1Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Svante Pääbo
- 1Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Molly Przeworski
- 1Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
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35
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Pedersen C, Giese H, Linde-Laursen I. Towards an Integration of the Physical and the Genetic Chromosome Maps of Barley by in Situ Hybridization. Hereditas 2004. [DOI: 10.1111/j.1601-5223.1995.00077.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Carrington M, Cullen M. Justified chauvinism: advances in defining meiotic recombination through sperm typing. Trends Genet 2004; 20:196-205. [PMID: 15041174 DOI: 10.1016/j.tig.2004.02.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Sperm typing offers an efficient means of studying the quantitative and qualitative aspects of meiotic recombination that are virtually unapproachable by pedigree analysis. Since the initial development of the technique >10 years ago, several salient findings based on empirically derived recombination data have been described. The precise rates and distributions of recombination have been reported for specific regions of the genome, serving as the prototype for high-resolution genome-wide recombination patterns. Identification and characterization of molecular genetic events, such as unequal crossing over, gene conversion and crossover asymmetry, are under close inspection for the first time as a result of this technology. The influence of these phenomena on the evolution of the genome is of primary interest from a scientific and medical perspective. In this article, we review the novel discoveries in mammalian meiotic recombination that have been revealed through sperm typing.
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Affiliation(s)
- Mary Carrington
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick, National Institutes of Health, SAIC-Frederick, MD 21702, USA.
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37
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Affiliation(s)
- Stephen F Schaffner
- Whitehead/MIT Center for Genome Research, Cambridge, Massachusetts 02139, USA.
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38
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Wall JD, Frisse LA, Hudson RR, Di Rienzo A. Comparative linkage-disequilibrium analysis of the beta-globin hotspot in primates. Am J Hum Genet 2003; 73:1330-40. [PMID: 14628290 PMCID: PMC1180398 DOI: 10.1086/380311] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2003] [Accepted: 09/24/2003] [Indexed: 11/03/2022] Open
Abstract
Recombination rates vary both across the genome and between different species, but little information is available about the temporal and physical scales over which such rates change. To shed light on these questions, we performed a high-resolution analysis of a genomic region within the beta-globin gene cluster that is known to experience elevated recombination rates in humans. For this purpose, we developed new linkage disequilibrium-based methods that thoroughly search for subsets of the data with unusually high or unusually low estimated values of the population-recombination parameter (4Nr, where N is the effective population size and r is the crossover rate between adjacent base pairs). By resequencing a 15-kb segment in a human population sample, we were able to narrow the recombinational hotspot to a segment <2 kb in length that coincides with the beta-globin replication origin. In addition, we analyzed the orthologous region in samples of rhesus macaques and common chimpanzees. Whereas the analysis of the chimpanzee data is complicated by the sample structure, the macaque data imply that this region may not be a hotspot in that species. These results suggest a time scale for the evolution of hotspots in primates. Furthermore, they allow us to propose diverged sequence elements that may contribute to the differences in the recombinational landscape in the two species.
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Affiliation(s)
- Jeffrey D Wall
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
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39
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Mucha M, Król J, Goc A, Filipski J. Mapping candidate hotspots of meiotic recombination in segments of human DNA cloned in the yeast Saccharomyces cerevisiae. Mol Genet Genomics 2003; 270:165-72. [PMID: 12942369 DOI: 10.1007/s00438-003-0915-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2003] [Accepted: 08/01/2003] [Indexed: 11/24/2022]
Abstract
The hotspots of meiotic recombination in the human genome can be localized by genetic techniques. The resolution of these techniques is in the range of kilobases and depends on the density of the physical markers identifying allelic variants of the chromosomal loci. We thought it would be interesting to localize these sites with higher resolution. Assuming that some human chromosomal sites conserve their propensity for recombination when cloned in yeast, we localized the hotspots of recombination in several yeast artificial chromosomes (YACs) carrying human DNA. A number of potential recombination hotspots could be identified in the clones studied. Among them there are two classes of sites that are particularly recombination prone also in human meiotic cells: sites associated with CpG islands and sites located in the vicinity of long minisatellite sequences.
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Affiliation(s)
- M Mucha
- Laboratoire de Biochimie de la Chromatine, Institut J. Monod, Université Paris VI et Paris VII, 2, Place Jussieu Tour 43, 75251, Paris, France
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Abstract
There is great interest in the patterns and extent of linkage disequilibrium (LD) in humans and other species. Characterizing LD is of central importance for gene-mapping studies and can provide insights into the biology of recombination and human demographic history. Here, we review recent developments in this field, including the recently proposed 'haplotype-block' model of LD. We describe some of the recent data in detail and compare the observed patterns to those seen in simulations.
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Affiliation(s)
- Jeffrey D Wall
- Department of Human Genetics, The University of Chicago, 920 East 58th Street, CLSC 507, Chicago, Illinois 60637, USA.
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41
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Arnheim N, Calabrese P, Nordborg M. Hot and cold spots of recombination in the human genome: the reason we should find them and how this can be achieved. Am J Hum Genet 2003; 73:5-16. [PMID: 12772086 PMCID: PMC1180590 DOI: 10.1086/376419] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2003] [Accepted: 04/10/2003] [Indexed: 11/03/2022] Open
Affiliation(s)
- Norman Arnheim
- Molecular and Computational Biology Program, University of Southern California, 835 West 37th Street, SHS 172, Los Angeles, CA 90089-1340, USA.
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42
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Cruciani F, Bernardini L, Santolamazza P, Modiano D, Torroni A, Scozzari R. Linkage disequilibrium analysis of the human adenosine deaminase (ada) gene provides evidence for a lack of correlation between hot spots of equal and unequal homologous recombination. Genomics 2003; 82:20-33. [PMID: 12809673 DOI: 10.1016/s0888-7543(03)00096-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The linkage disequilibrium (LD) pattern within the adenosine deaminase (ADA) gene was analyzed by studying 13 polymorphic loci in 137 families from two European and three African populations. Evidence for the presence of a 12-kb meiotic crossover hot spot, spanning part of the first and the second intron and flanked by regions of reduced recombination activity, was obtained. Moreover, segregation analysis of 113 informative meioses revealed two recombination events that are internal or overlap the 12-kb region, thus suggesting a recombination rate for the hot-spot region about 50-fold higher than the mean rate across the human genome. Within the hot spot, a 144-bp palindromic sequence was also identified and its possible involvement in the recombination process is discussed. The 12-kb region characterized by the low degree of LD does not include the 3.2-kb region that is deleted, as a result of recurrent unequal homologous recombination between two Alu elements, in patients affected by autosomal severe combined immunodeficiency. This observation provides the first evidence for an absence of correlation between hot spots of equal and unequal homologous recombination.
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Affiliation(s)
- Fulvio Cruciani
- Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza, P.le Aldo Moro 5, 00185 Rome, Italy.
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Berloff N, Perola M, Lange K. Spline methods for the comparison of physical and genetic maps. J Comput Biol 2003; 9:465-75. [PMID: 12162886 DOI: 10.1089/106652702760138565] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The first genetic maps were constructed by linkage analysis. Physical mapping techniques, such as radiation hybrids and complete sequencing, produce a different picture. For the purposes of population genetics, clinical genetics, and genetic epidemiology, it is important to harmonize and amalgamate existing genetic and physical maps. Among other things, comparisons of the two kinds of maps promotes better understanding of the wide variation in local recombination rates per unit physical length of DNA. The current paper presents methods for estimating recombination intensity as a function of physical distance along a chromosome. Genetic map distance is the integral of intensity. We derive fast reliable estimation algorithms based on a Poisson process model, penalized likelihoods, and cubic spline interpolation. Our methods provide a rigorous and statistically sound foundation for comparing physical and genetic maps. To illustrate the possibilities, we apply the methods to published recombination data on CEPH families and the complete sequences of chromosomes 21 and 22. Our results are in good agreement with previous studies and the biological data.
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Affiliation(s)
- Natalia Berloff
- Department of Mathematics, University of California, Los Angeles, CA 90095, USA
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Cullen M, Perfetto SP, Klitz W, Nelson G, Carrington M. High-resolution patterns of meiotic recombination across the human major histocompatibility complex. Am J Hum Genet 2002; 71:759-76. [PMID: 12297984 PMCID: PMC378534 DOI: 10.1086/342973] [Citation(s) in RCA: 171] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2002] [Accepted: 06/27/2002] [Indexed: 11/03/2022] Open
Abstract
Definitive characteristics of meiotic recombination events over large (i.e., >1 Mb) segments of the human genome remain obscure, yet they are essential for establishing the haplotypic structure of the genome and for efficient mapping of complex traits. We present a high-resolution map of recombination at the kilobase level across a 3.3-Mb interval encompassing the major histocompatibility complex (MHC). Genotyping of 20,031 single sperm from 12 individuals resulted in the identification and fine mapping of 325 recombinant chromosomes within genomic intervals as small as 7 kb. Several principal characteristics of recombination in this region were observed: (1) rates of recombination can differ significantly between individuals; (2) intense hot spots of recombination occur at least every 0.8 Mb but are not necessarily evenly spaced; (3) distribution in the location of recombination events can differ significantly among individuals; (4) between hot spots, low levels of recombination occur fairly evenly across 100-kb segments, suggesting the presence of warm spots of recombination; and (5) specific sequence motifs associate significantly with recombination distribution. These data provide a plausible model for recombination patterns of the human genome overall.
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Affiliation(s)
- Michael Cullen
- Basic Research Program, SAIC–Frederick, National Cancer Institute, Frederick, MD; Graduate Genetics Program, Institute for Biomedical Sciences, The George Washington University, Washington DC; USA Program Vaccine Research Center, National Institutes of Health, Bethesda; Children’s Hospital Oakland Research Institute, Oakland, CA; and School of Public Health, University of California, Berkeley
| | - Stephen P. Perfetto
- Basic Research Program, SAIC–Frederick, National Cancer Institute, Frederick, MD; Graduate Genetics Program, Institute for Biomedical Sciences, The George Washington University, Washington DC; USA Program Vaccine Research Center, National Institutes of Health, Bethesda; Children’s Hospital Oakland Research Institute, Oakland, CA; and School of Public Health, University of California, Berkeley
| | - William Klitz
- Basic Research Program, SAIC–Frederick, National Cancer Institute, Frederick, MD; Graduate Genetics Program, Institute for Biomedical Sciences, The George Washington University, Washington DC; USA Program Vaccine Research Center, National Institutes of Health, Bethesda; Children’s Hospital Oakland Research Institute, Oakland, CA; and School of Public Health, University of California, Berkeley
| | - George Nelson
- Basic Research Program, SAIC–Frederick, National Cancer Institute, Frederick, MD; Graduate Genetics Program, Institute for Biomedical Sciences, The George Washington University, Washington DC; USA Program Vaccine Research Center, National Institutes of Health, Bethesda; Children’s Hospital Oakland Research Institute, Oakland, CA; and School of Public Health, University of California, Berkeley
| | - Mary Carrington
- Basic Research Program, SAIC–Frederick, National Cancer Institute, Frederick, MD; Graduate Genetics Program, Institute for Biomedical Sciences, The George Washington University, Washington DC; USA Program Vaccine Research Center, National Institutes of Health, Bethesda; Children’s Hospital Oakland Research Institute, Oakland, CA; and School of Public Health, University of California, Berkeley
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Lien S, Szyda J, Leeflang EP, Hubert R, Zhang L, Schmitt K, Arnheim N. Single‐Sperm Typing. ACTA ACUST UNITED AC 2002; Chapter 1:Unit 1.6. [DOI: 10.1002/0471142905.hg0106s32] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | | | | | - Rene Hubert
- University of Southern California Los Angeles California
| | - Lin Zhang
- University of Southern California Los Angeles California
| | - Karin Schmitt
- University of Southern California Los Angeles California
| | - Norman Arnheim
- University of Southern California Los Angeles California
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Abstract
Meiotic recombination events are distributed unevenly throughout eukaryotic genomes. This inhomogeneity leads to distortions of genetic maps that can hinder the ability of geneticists to identify genes by map-based techniques. Various lines of evidence, particularly from studies of yeast, indicate that the distribution of recombination events might reflect, at least in part, global features of chromosome structure, such as the distribution of modified nucleosomes.
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Affiliation(s)
- T D Petes
- Department of biology, University of North Carolina, Chapel Hill 27599-3280, USA.
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Middle F, Jones I, McCandless F, Barrett T, Khanim F, Owen MJ, Lendon C, Craddock N. Bipolar disorder and variation at a common polymorphism (A1832G) within exon 8 of the Wolfram gene. AMERICAN JOURNAL OF MEDICAL GENETICS 2000; 96:154-7. [PMID: 10893487 DOI: 10.1002/(sici)1096-8628(20000403)96:2<154::aid-ajmg5>3.0.co;2-f] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A number of linkage studies provide evidence consistent with the existence of a bipolar susceptibility gene on chromosome 4p16. The gene for Wolfram syndrome, a rare recessive neurodegenerative disorder, lies in this region and has recently been cloned. Psychiatric disturbances including psychosis, mood disorder, and suicide have been reported at increased frequency in Wolfram patients and in heterozygous carriers of a Wolfram mutation. In the current investigation we have undertaken a case-control association study using a single nucleotide polymorphism (causing an amino acid change) in exon 8 of the Wolfram gene in a UK Caucasian sample of 312 Diagnostic and Statistical Manual of Mental Disorders (fourth edition; DSM IV) bipolar I probands and 301 comparison individuals. We found no evidence that variation at this polymorphism influences susceptibility to bipolar disorder. It remains possible that variation at other sites within or near the Wolfram gene plays important roles in determining susceptibility to affective illness. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 96:154-157, 2000.
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Affiliation(s)
- F Middle
- Division of Neuroscience, University of Birmingham, Birmingham, United Kingdom
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48
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Lien S, Szyda J, Schechinger B, Rappold G, Arnheim N. Evidence for heterogeneity in recombination in the human pseudoautosomal region: high resolution analysis by sperm typing and radiation-hybrid mapping. Am J Hum Genet 2000; 66:557-66. [PMID: 10677316 PMCID: PMC1288109 DOI: 10.1086/302754] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Accurate genetic and physical maps for the human pseudoautosomal region were constructed by use of sperm typing and high-resolution radiation-hybrid mapping. PCR analysis of 1,912 sperm was done with a manual, single-sperm isolation method. Data on four donors show highly significant linkage heterogeneity among individuals. The most significant difference was observed in a marker interval located in the middle of the Xp/Yp pseudoautosomal region, where one donor showed a particularly high recombination fraction. Longitudinal models were fitted to the data to test whether linkage heterogeneity among donors was significant for multiple intervals across the region. The results indicated that increased recombination in particular individuals and regions is compensated for by reduced recombination in neighboring intervals. To investigate correspondence between physical and genetic distances within the region, we constructed a high-resolution radiation-hybrid map containing 29 markers. The recombination fraction per unit of physical distance varies between regions ranging from 13- to 70-fold greater than the genome-average rate.
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Affiliation(s)
- S Lien
- Department of Animal Science, Agricultural University of Norway, Aas, Norway
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49
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Matsunaga S, Schütze K, Donnison IS, Grant SR, Kuroiwa T, Kawano S. Technical advance: single pollen typing combined with laser-mediated manipulation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1999; 20:371-378. [PMID: 10571898 DOI: 10.1046/j.1365-313x.1999.00612.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We combined single pollen typing with laser-mediated manipulation. After drilling a hole in the wall of a pollen grain from a dioecious plant (Silene latifolia) with a UV-laser microbeam, the single pollen grain was recovered directly in the cap of a PCR tube, using a non-contact method called laser pressure catapulting. The entire genome of the single pollen grain was then amplified with improved primer-extension-preamplification PCR (I-PEP PCR). Nested PCR with sequence tagged site (STS)-specific primers was used to analyze several loci in the haploid genome. The single copy gene MROS1 was detected in most of the single pollen grains analyzed. Bgl10, which is localized on the Y chromosome, was detected in approximately half of the pollen grains. MROS3 is reported to be localized on the X chromosome. Using inverse PCR, we isolated two genomic clones of MROS3: MROS3A and MROS3B. The single pollen analysis using nested PCR showed that MROS3A and MROS3B are derived from different loci that are not located on the X chromosome. Single pollen typing not only reveals sex chromosome-linkage within the haploid genome, but can also discriminate between alleles and different loci. This method should also be useful for measuring recombination frequencies without genetic crossover analysis.
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Affiliation(s)
- S Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Japan.
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Park C, Frank MT, Lewin HA. Fine-mapping of a region of variation in recombination rate on BTA23 to the D23S22-D23S23 interval using sperm typing and meiotic breakpoint analysis. Genomics 1999; 59:143-9. [PMID: 10409425 DOI: 10.1006/geno.1999.5869] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Meiotic recombination rate (theta) within chromosome segments of similar physical size is known to vary widely throughout the genome. This variation has a genetic component, occurring between the sexes and among individuals of the same sex. We reported previously the existence of variation in theta between males in the DYA-PRL interval on bovine chromosome 23 (BTA23). This region contains the bovine major histocompatibility complex and has been shown to contain recombination hotspots in humans and mice. The aim of this study was to map more finely the interval(s) on BTA23 where variation in theta occurs using sperm typing and meiotic breakpoint analysis. By adding a marker (DRB3) between DYA and PRL, the DYA-PRL interval was subdivided into two adjacent intervals, thus permitting evaluation and comparison of theta among five bulls. Significant variation in theta was found for both intervals; theta(DYA-DRB3) ranged from 13.2 to 28.1%, and theta(DRB3-PRL) ranged from 2.4 to 13.0%. The variation in theta was individual- and region-specific. A meiotic breakpoint strategy employing PCR amplification products from recombinant sperm was then used to refine the chromosomal location associated with variation in theta within the DYA-DRB3 interval. The subinterval D23S22-D23S23 exhibited the greatest degree of variation among bulls having high and low theta within the DYA-DRB3 interval. To confirm this result, theta(D23S22-D23S23) was directly evaluated in three additional randomly chosen bulls using sperm typing. The region showing variation in theta was narrowed to the D23S22-D23S23 subinterval, ranging from 4.6 to 9.2%. Identification of the molecular basis for variation in theta may be useful for map-dependent applications, such as marker-assisted selection and positional cloning of genes affecting physiologically important traits.
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Affiliation(s)
- C Park
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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