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      “Genome-wide recombination and chromosome segregation in human oocytes and embryos reveal selection for maternal recombination rates”

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          Abstract

          Crossover recombination reshuffles genes and prevents errors in segregation that lead to extra or missing chromosomes (aneuploidy) in human eggs, a major cause of pregnancy failure and congenital disorders. Here, we generate genome-wide maps of crossovers and chromosome segregation patterns by recovering all three products of single female meioses. Genotyping > 4 million informative single-nucleotide polymorphisms (SNPs) from 23 complete meioses allowed us to map 2,032 maternal and 1,342 paternal crossovers and to infer the segregation patterns of 529 chromosome pairs. We uncover a novel reverse chromosome segregation pattern in which both homologs separate their sister chromatids at meiosis I; detect selection for higher recombination rates in the female germline by the elimination of aneuploid embryos; and report chromosomal drive against non-recombinant chromatids at meiosis II. Collectively, our findings reveal that recombination not only affects homolog segregation at meiosis I but also the fate of sister chromatids at meiosis II.

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          Most cited references48

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          A high-resolution recombination map of the human genome.

          Determination of recombination rates across the human genome has been constrained by the limited resolution and accuracy of existing genetic maps and the draft genome sequence. We have genotyped 5,136 microsatellite markers for 146 families, with a total of 1,257 meiotic events, to build a high-resolution genetic map meant to: (i) improve the genetic order of polymorphic markers; (ii) improve the precision of estimates of genetic distances; (iii) correct portions of the sequence assembly and SNP map of the human genome; and (iv) build a map of recombination rates. Recombination rates are significantly correlated with both cytogenetic structures (staining intensity of G bands) and sequence (GC content, CpG motifs and poly(A)/poly(T) stretches). Maternal and paternal chromosomes show many differences in locations of recombination maxima. We detected systematic differences in recombination rates between mothers and between gametes from the same mother, suggesting that there is some underlying component determined by both genetic and environmental factors that affects maternal recombination rates.
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            Fine-scale recombination rate differences between sexes, populations and individuals.

            Meiotic recombinations contribute to genetic diversity by yielding new combinations of alleles. Recently, high-resolution recombination maps were inferred from high-density single-nucleotide polymorphism (SNP) data using linkage disequilibrium (LD) patterns that capture historical recombination events. The use of these maps has been demonstrated by the identification of recombination hotspots and associated motifs, and the discovery that the PRDM9 gene affects the proportion of recombinations occurring at hotspots. However, these maps provide no information about individual or sex differences. Moreover, locus-specific demographic factors like natural selection can bias LD-based estimates of recombination rate. Existing genetic maps based on family data avoid these shortcomings, but their resolution is limited by relatively few meioses and a low density of markers. Here we used genome-wide SNP data from 15,257 parent-offspring pairs to construct the first recombination maps based on directly observed recombinations with a resolution that is effective down to 10 kilobases (kb). Comparing male and female maps reveals that about 15% of hotspots in one sex are specific to that sex. Although male recombinations result in more shuffling of exons within genes, female recombinations generate more new combinations of nearby genes. We discover novel associations between recombination characteristics of individuals and variants in the PRDM9 gene and we identify new recombination hotspots. Comparisons of our maps with two LD-based maps inferred from data of HapMap populations of Utah residents with ancestry from northern and western Europe (CEU) and Yoruba in Ibadan, Nigeria (YRI) reveal population differences previously masked by noise and map differences at regions previously described as targets of natural selection.
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              The nature of aneuploidy with increasing age of the female partner: a review of 15,169 consecutive trophectoderm biopsies evaluated with comprehensive chromosomal screening.

              To determine the relationship between the age of the female partner and the prevalence and nature of human embryonic aneuploidy. Retrospective. Academic. Trophectoderm biopsies. Comprehensive chromosomal screening performed on patients with blastocysts available for biopsy. Evaluation of the impact of maternal age on the prevalence of aneuploidy, the probability of having no euploid embryos within a cohort, the complexity of aneuploidy as gauged by the number of aneuploid chromosomes, and the trisomy/monosomy ratio. Aneuploidy increased predictably after 26 years of age. A slightly increased prevalence was noted at younger ages, with >40% aneuploidy in women 23 years and under. The no euploid embryo rate was lowest (2% to 6%) in women aged 26 to 37, was 33% at age 42, and was 53% at age 44. Among the biopsies with aneuploidy, 64% involved a single chromosome, 20% two chromosomes, and 16% three chromosomes, with the proportion of more complex aneuploidy increasing with age. Finally, the trisomy/monosomy ratio approximated 1 and increased minimally with age. The lowest risk for embryonic aneuploidy was between ages 26 and 30. Both younger and older age groups had higher rates of aneuploidy and an increased risk for more complex aneuploidies. The overall risk did not measurably change after age 43. Trisomies and monosomies are equally prevalent. Copyright © 2014 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.
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                Author and article information

                Journal
                9216904
                2419
                Nat Genet
                Nat. Genet.
                Nature genetics
                1061-4036
                1546-1718
                6 August 2015
                18 May 2015
                July 2015
                29 February 2016
                : 47
                : 7
                : 727-735
                Affiliations
                [1 ]The Bridge Centre, London, UK.
                [2 ]School of Biosciences, University of Kent, Canterbury, UK.
                [3 ]Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
                [4 ]G.E.N.E.R.A., Centers for Reproductive Medicine, Rome, Italy.
                [5 ]Illumina, Capital Park CPC4, Fulbourn, Cambridge, UK.
                [6 ]Department of Mathematics and Statistics, University of Indiana, Bloomington, Indiana, US.
                [7 ]Institute of Integrative and Comparative Biology, University of Leeds, Leeds, UK.
                Author notes
                Correspondence and request for data should be sent to ERH ( eh58@ 123456sussex.ac.uk ) or AH ( ahandyside@ 123456illumina.com )

                AUTHOR CONTRIBUTIONS.

                AC, CO, DC, LR, FU, KS, MS, and AT were responsible for donor consenting, oocyte collection and oocyte activation. LR, FU, AH, KS oversaw ethical and legal regulation in Italy and the UK. AC, CO, SN, HJ, DC carried out amplification, SNP array and array CGH experiments. AH, LJN, CO, ERH analysed the encoded data. ERH and ADH carried out data analysis and simulations; ERH and EH carried out statistical analyses; ERH, AH and LJN generated the figures; ERH, AH, LJN, CO wrote the manuscript; AH, CO, AC, LJN and ERH, edited the manuscript. All authors proof-read and accepted the manuscript.

                Article
                EMS63148
                10.1038/ng.3306
                4770575
                25985139
                5a750695-3aa4-4426-b64a-24fddaa0aef2

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                Genetics

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