Form from Function, Order from Chaos in Male Germline Chromatin

Spermatogenesis requires radical restructuring of germline chromatin at multiple stages, involving co-ordinated waves of DNA methylation and demethylation, histone modification, replacement and removal occurring before, during and after meiosis. This Special Issue has drawn together papers addressing many aspects of chromatin organization and dynamics in the male germ line, in humans and in model organisms. Two major themes emerge from these studies: the first is the functional significance of nuclear organisation in the developing germline; the second is the interplay between sperm chromatin structure and susceptibility to DNA damage and mutation. The consequences of these aspects for fertility, both in humans and other animals, is a major health and social welfare issue and this is reflected in these nine exciting manuscripts

What is Karyomapping and where does it fit in the world of preimplantation genetic diagnosis (PGD)?

The first application of preimplantation genetic diagnosis (PGD) recently celebrated its 25th birthday. Aside from the very early days when chromosomal diagnoses were used (by sexing) for the selective implantation of embryos unaffected by sex linked disorders, the paths of chromosomal and monogenic PGD have diverged. For monogenic disorders, progress has been impeded by the need to tailor each diagnosis to the mutation in question. For chromosomal diagnoses, fluorescent in situ hybridization (FISH) technology was replaced by array comparative genomic hybridization (aCGH), and then next generation sequencing (NGS). Karyomapping is a novel approach that allows the detection of the inheritance of (grand) parental haploblocks through the identification of inherited chromosomal segments. It involves genome-wide single nucleotide polymorphism (SNP) analysis of parental DNA, a reference from a related individual of known disease status (typically an affected child) and amplified DNA form biopsied cells of the (usually lastocyst) embryos in question. Identification of informative loci for each of four parental haplotypes is followed by direct comparison to the reference, ultimately creating a Karyomap. The Karyomapping programme (Illumina) displays homologous chromosomes, points of crossing over and the haplotype of each of the embryos. It also detects meiotic trisomy, monosomy, triploidy and uniparental heterodisomy (some of which NGS and aCGH will not). Inherent in the design is the analysis of “key SNPs” (heterozygous informative calls) thereby avoiding the risk of misdiagnoses caused by the phenomenon of allele drop out (ADO). Karyomapping is currently in use for the detection of monogenic disorders and around 1000 clinics offer it worldwide making use of about 20 diagnostic laboratories. At the time of writing, over two and a half thousand clinical cases have been performed. Because of the limited detection of some post-zygotic errors such as post-zygotic trisomy which can also lead to mosaicism, Karyomapping has not yet been fully applied clinically for aneuploidy screening. The diagnostic potential of the technique will be fully recognised with the application of this technology on clinical cases

Why PGT-A, most likely, improves IVF success

Preimplantation genetic testing for aneuploidies (PGT-A), with its vocal advocates and opponents, is at the epicentre of a perpetual, often heated, debate. The main issues include the following. First, how do we interpret the existing evidence-base? Around 100 retrospective and single-centre studies, two non-selection trials and at least two meta-analyses point to its efficacy in improving live birth rates, although randomized controlled trials are more mixed. Second, what should be done in relation to euploid/aneuploid mosaicism? Recent data suggest that low-level mosaic pregnancies can proceed uneventfully to term, so intelligent interpretation of the diagnostic data is appropriate. Third, what is the stance of the Human Fertilisation and Embryology Authority? The ‘traffic light’ system is much debated and is perhaps best described as well-intentioned, but misguided in places. Fourth, what is the motivation of people who maintain their point of view despite the evidence? Sadly, the presentation of new empirical evidence polarizes, rather than reconciles, opinion. Too many have made a career out of either promoting or denigrating PGT-A for them to back down easily. Finally, how can we find common ground and move forward? All patients should be counselled in a non-directive manner on whether to embark on PGT-A, summarizing for them the whole evidence base so they can make up their own mind

A new Approach for Accurate Detection of Chromosome Rearrangements That Affect Fertility in Cattle

Globally, cattle production has more than doubled since the 1960s, with widespread use of artificial insemination (AI) and an emphasis on a small pool of high genetic merit animals. Selecting AI bulls with optimal fertility is, therefore, vital, as impaired fertility reduces genetic gains and production, resulting in heavy financial and environmental losses. Chromosome translocations, particularly the 1;29 Robertsonian translocation, are a common cause of reduced fertility; however, reciprocal translocations are significantly underreported due to the difculties inherent in analysing cattle chromosomes. Based on our porcine work, we have developed an approach for the unambiguous detection of Robertsonian and reciprocal translocations, using a multiple-hybridization probe detection strategy. We applied this method on the chromosomes of 39 bulls, detecting heterozygous and homozygous 1;29 translocations and a 12;23 reciprocal translocation in a total of seven animals. Previously, karyotype analysis was the only method of diagnosing chromosomal rearrangements in cattle, and was time-consuming and error-prone. With calving rates of only 50–60%, it is vital to reduce further fertility loss in order to maximise productivity. The approach developed here identifies abnormalities that DNA sequencing will not, and has the potential to lead to long-term gains, delivering meat and milk products in a more cost-effective and environmentally-responsible manner to a growing population

PGT-SR: A Comprehensive Overview and a Requiem for the Interchromosomal Effect

Preimplantation genetic testing for structural rearrangements (PGT-SR) was one of the first applications of PGT, with initial cases being worked up in the Delhanty lab. It is the least well-known of the various forms of PGT but nonetheless provides effective treatment for many carrier couples. Structural chromosomal rearrangements (SRs) lead to infertility, repeated implantation failure, pregnancy loss, and congenitally affected children, despite the balanced parent carrier having no obvious phenotype. A high risk of generating chromosomally unbalanced gametes and embryos is the rationale for PGT-SR, aiming to select for those that are chromosomally normal, or at least balanced like the carrier parent. PGT-SR largely uses the same technology as PGT-A, i.e., initially FISH, superseded by array CGH, SNP arrays, Karyomapping, and, most recently, next-generation sequencing (NGS). Trophectoderm biopsy is now the most widely used sampling approach of all PGT variants, though there are prospects for non-invasive methods. In PGT-SR, the most significant limiting factor is the availability of normal or balanced embryo(s) for transfer. Factors directly affecting this are rearrangement type, chromosomes involved, and sex of the carrier parent. De novo aneuploidy, especially for older mothers, is a common limiting factor. PGT-SR studies provide a wealth of information, much of which can be useful to genetic counselors and the patients they treat. It is applicable in the fundamental study of basic chromosomal biology, in particular the purported existence of an interchromosomal effect (ICE). An ICE means essentially that the existence of one chromosomal defect (e.g., brought about by malsegregation of translocation chromosomes) can perpetuate the existence of others (e.g., de novo aneuploidy). Recent large cohort studies of PGT-SR patients seem, however, to have laid this notion to rest, at least for human embryonic development. Unless new evidence comes to light, this comprehensive review should serve as a requiem

Karyomapping and how is it improving preimplantation genetics?

Introduction: Preimplantation genetic diagnosis and screening (PGD/PGS) has been applied clinically for >25 years however inherent drawbacks include the necessity to tailor each case to the trait in question, and that technology to detect monogenic and chromosomal disorders respectively is fundamentally different. Areas Covered: The area of preimplantation genetics has evolved over the last 25 years, adapting to changes in technology and the need for more efficient, streamlined diagnoses. Karyomapping allows the determination of inheritance from the (grand)parental haplobocks through assembly of inherited chromosomal segments. The output displays homologous chromosomes, crossovers and the genetic status of the embryos by linkage comparison, as well as chromosomal disorders. It also allows for determination of heterozygous SNP calls, avoiding the risks of allele dropout, a common problem with other PGD techniques. Manuscripts documenting the evolution of preimplantation genetics, especially those investigating technologies that would simultaneously detect monogenic and chromosomal disorders, were selected for review. Expert Commentary: Karyomapping is currently available for detection of single gene disorders; ~1000 clinics worldwide offer it (via ~20 diagnostic laboratories) and ~2500 cases have been performed. Due an inability to detect post-zygotic trisomy reliably however and confounding problems of embryo mosaicism, karyomapping has yet to be applied clinically for detection of chromosome disorders

Preimplantation Testing for Polygenic Disease (PGT-P): Brave New World or Mad Pursuit?

In preimplantation testing for monogenic disease (PGT-M), we are used to specific and directed diagnoses. Preimplantation testing for polygenic disease (PGT-P), however, represents a further level of complexity in that multiple genes are tested for with an associated polygenic risk score (PRS), usually established by a genome-wide association study (GWAS). PGT-P has a series of pros and cons and, like many areas of genetics in reproductive medicine, there are vocal proponents and opponents on both sides. As with all things, the question needs to be asked, how much benefit does PGT-P provide in comparison to the risks involved? For each disease, a case will need to be made for PGT-P, as will a justification that the family involved will actually benefit; the worry is that this might be more work than the cost justifies

Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes

Background Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. The identification of such changes and their time of occurrence can shed light on the biology of each species, clade and their evolutionary history. However, this is impeded by both the fragmented nature of the majority of genome assemblies and the limitations of the available software to work with them. These limitations are particularly apparent in birds, with only 10 chromosome-level assemblies reported thus far. Algorithmic approaches applied to fragmented genome assemblies can nonetheless help define patterns of chromosomal change in defined taxonomic groups. Results Here, we make use of the DESCHRAMBLER algorithm to perform the first large-scale study of ancestral chromosome structure and evolution in birds. This algorithm allows us to reconstruct the overall genome structure of 14 key nodes of avian evolution from the Avian ancestor to the ancestor of the Estrildidae, Thraupidae and Fringillidae families. Conclusions Analysis of these reconstructions provides important insights into the variability of rearrangement rates during avian evolution and allows the detection of patterns related to the chromosome distribution of evolutionary breakpoint regions. Moreover, the inclusion of microchromosomes in our reconstructions allows us to provide novel insights into the evolution of these avian chromosomes, specifically

Integrative comparative analysis of avian chromosome evolution by in-silico mapping of the gene ontology of homologous synteny blocks and evolutionary breakpoint regions

Avian chromosomes undergo more intra- than interchromosomal rearrangements, which either induce or are associated with genome variations among birds. Evolving from a common ancestor with a karyotype not dissimilar from modern chicken, two evolutionary elements characterize evolutionary change: homologous synteny blocks (HSBs) constitute common conserved parts at the sequence level, while evolutionary breakpoint regions (EBRs) occur between HSBs, defining the points where rearrangement occurred. Understanding the link between the structural organization and functionality of HSBs and EBRs provides insight into the mechanistic basis of chromosomal change. Previously, we identified gene ontology (GO) terms associated with both; however, here we revisit our analyses in light of newly developed bioinformatic algorithms and the chicken genome assembly galGal6. We aligned genomes available for six birds and one lizard species, identifying 630 HSBs and 19 EBRs. We demonstrate that HSBs hold vast functionality expressed by GO terms that have been largely conserved through evolution. Particularly, we found that genes within microchromosomal HSBs had specific functionalities relevant to neurons, RNA, cellular transport and embryonic development, and other associations. Our findings suggest that microchromosomes may have conserved throughout evolution due to the specificity of GO terms within their HSBs. The detected EBRs included those found in the genome of the anole lizard, meaning they were shared by all saurian descendants, with others being unique to avian lineages. Our estimate of gene richness in HSBs supported the fact that microchromosomes contain twice as many genes as macrochromosomes