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The carriers : what the fragile X gene reveals about family, heredity, and scientific discovery
\"Fragile X syndrome is a genetic condition that causes a range of neurodevelopmental problems including learning disabilities and cognitive impairment. Boys with the condition are more likely to be born fully affected by it, while women who are seemingly unaffected carriers have an increased risk of giving birth to an affected child. Recent research indicates that Fragile X syndrome is highly unusual in the world of genetic disorders, in that carriers, who were previously thought to show no symptoms at all, are in fact affected in their own ways: into adulthood, they can develop personality and emotional changes, tremors, and difficulty walking. The title characters in The Carriers, then, are the previous generations--mothers and grandparents--of fully affected Fragile X patients. This book aims to tell the stories of how families are affected by this genetic disorder over generations, as well as the initial science that discovered it and the current science that's teaching us how Fragile X is affecting silent carriers in ways that weren't previously recognized. Understanding psychiatric symptoms in premutation carriers is complicated by the fact that many are caring for children with Fragile X syndrome and fathers with the tremor/ataxia symptom (difficulty walking). This story particularly highlights women, who are often the carriers in question and also the genetic researchers achieving scientific breakthroughs\"-- Provided by publisher.
Book
AMPA receptor GluA2 subunit defects are a cause of neurodevelopmental disorders
AMPA receptors (AMPARs) are tetrameric ligand-gated channels made up of combinations of GluA1-4 subunits encoded by
GRIA1-4
genes. GluA2 has an especially important role because, following post-transcriptional editing at the Q607 site, it renders heteromultimeric AMPARs Ca
2+
-impermeable, with a linear relationship between current and trans-membrane voltage. Here, we report heterozygous
de novo GRIA2
mutations in 28 unrelated patients with intellectual disability (ID) and neurodevelopmental abnormalities including autism spectrum disorder (ASD), Rett syndrome-like features, and seizures or developmental epileptic encephalopathy (DEE). In functional expression studies, mutations lead to a decrease in agonist-evoked current mediated by mutant subunits compared to wild-type channels. When GluA2 subunits are co-expressed with GluA1, most
GRIA2
mutations cause a decreased current amplitude and some also affect voltage rectification. Our results show that
de-novo
variants in
GRIA2
can cause neurodevelopmental disorders, complementing evidence that other genetic causes of ID, ASD and DEE also disrupt glutamatergic synaptic transmission.
Genetic variants in ionotropic glutamate receptors have been implicated in neurodevelopmental disorders. Here, the authors report heterozygous
de novo
mutations in the
GRIA2
gene in 28 individuals with intellectual disability and neurodevelopmental abnormalities associated with reduced Ca
2+
transport and AMPAR currents.”
Journal Article
Inactivating Variants in ANGPTL4 and Risk of Coronary Artery Disease
This study showed an association of loss-of-function mutations in
ANGPTL4
with low triglyceride levels and protection against coronary artery disease. Inhibition of Angptl4 in mice and monkeys with a monoclonal antibody reduced triglyceride levels.
The level of serum triglycerides is, in part, heritable, and elevated levels are associated with a risk of ischemic cardiovascular disease.
1
–
3
Mendelian randomization studies of genetically determined triglyceride levels have suggested that this association is causal.
4
Two lines of genetic evidence have further established a causal role for serum triglycerides in the risk of cardiovascular disease. First, inactivating mutations in the gene encoding apolipoprotein C3 (
APOC3
), a component of remnant particles, were reported to be associated with decreased serum triglyceride levels, a decreased burden of subclinical atherosclerosis, and a reduced risk of ischemic cardiovascular disease, which suggests . . .
Journal Article
Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment dependent
Hybrid incompatibilities occur when interactions between opposite ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are “intrinsic,” meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F 2 hybrid crosses between divergent populations of threespine stickleback fish ( Gasterosteus aculeatus L.) that were born and raised in either the field (seminatural experimental ponds) or the laboratory (aquaria). Because selection against incompatibilities results in elevated ancestry heterozygosity, we tested the prediction that ancestry heterozygosity will be higher in pond-raised fish compared to those raised in aquaria. We found that ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Additional analyses support a phenotypic basis for incompatibility and suggest that environment-specific single-locus heterozygote advantage is not the cause of selection on ancestry heterozygosity. Our study provides evidence that, in stickleback, a coarse—albeit indirect—signal of environment-dependent hybrid incompatibility is reliably detectable and suggests that extrinsic incompatibilities can evolve before intrinsic incompatibilities.
Journal Article
On the importance of balancing selection in plants
Balancing selection refers to a variety of selective regimes that maintain advantageous genetic diversity within populations. We review the history of the ideas regarding the types of selection that maintain such polymorphism in flowering plants, notably heterozygote advantage, negative frequency-dependent selection, and spatial heterogeneity. One shared feature of these mechanisms is that whether an allele is beneficial or detrimental is conditional on its frequency in the population. We highlight examples of balancing selection on a variety of discrete traits. These include the well-referenced case of self-incompatibility and recent evidence from species with nuclear-cytoplasmic gynodioecy, both of which exhibit trans-specific polymorphism, a hallmark of balancing selection. We also discuss and give examples of how spatial heterogeneity in particular, which is often thought unlikely to allow protected polymorphism, can maintain genetic variation in plants (which are rooted in place) as a result of microhabitat selection. Lastly, we discuss limitations of the protected polymorphism concept for quantitative traits, where selection can inflate the genetic variance without maintaining specific alleles indefinitely. We conclude that while discrete-morph variation provides the most unambiguous cases of protected polymorphism, they represent only a fraction of the balancing selection at work in plants.
Journal Article
Phenotypes of carriers of two mutated alleles in major cancer susceptibility genes
Purpose
While cancer phenotypes in carriers of a single mutant allele in most major cancer susceptibility genes are well-established, there is a paucity of data on the phenotype of carriers of two pathogenic variants—double heterozygotes (DH) or homozygous carriers. Here, we describe the phenotype of carriers of homozygous and DH pathogenic sequence variants (PSVs) in major cancer susceptibility genes.
Methods
Individuals referred for multigene panel testing at Blueprint Genetics laboratory were included. Ethically approved comparison of cancer type and age at diagnosis between DH, homozygous, and single PSV carriers was performed per gene.
Results
Of 6,685 eligible participants, 928 (13.9%) were single heterozygous PSV carriers, 6 (0.09%) were homozygous PSV carriers, and 17 (0.25%) were DH PSV carriers. Mean age at diagnosis of any cancer among single PSV age was 46.8 ± 14.9 years and among DH PSV carriers 37.6 ± 13.0 years (
P
< 0.0001). Notably, age at diagnosis for breast cancer among single
BRCA1
PSV carriers (
n
= 59) was 43.8 ± 8.7 years (
p
= 0.7606), among single
BRCA2
PSV carriers (
n
= 52)—47.9 ± 13.0 years (
p
= 0.2274) compared with 42.3 ± 13.0 years among DH PSV carriers (
n
= 10- 9 of whom were carriers of either
BRCA1
or
BRCA2
).
Conclusion
DH for PSV in two cancer susceptibility genes is a rare event, and the mean age at cancer diagnosis is younger in DH PSV carriers compared with single PSV carriers.
Journal Article
Complex evolutionary processes maintain an ancient chromosomal inversion
Genome re-arrangements such as chromosomal inversions are often involved in adaptation. As such, they experience natural selection, which can erode genetic variation. Thus, whether and how inversions can remain polymorphic for extended periods of time remains debated. Here we combine genomics, experiments, and evolutionary modeling to elucidate the processes maintaining an inversion polymorphism associated with the use of a challenging host plant (Redwood trees) in Timema stick insects. We show that the inversion is maintained by a combination of processes, finding roles for life-history trade-offs, heterozygote advantage, local adaptation to different hosts, and gene flow. We use models to show how such multi-layered regimes of balancing selection and gene flow provide resilience to help buffer populations against the loss of genetic variation, maintaining the potential for future evolution. We further show that the inversion polymorphism has persisted for millions of years and is not a result of recent introgression. We thus find that rather than being a nuisance, the complex interplay of evolutionary processes provides a mechanism for the long-term maintenance of genetic variation.
Journal Article
GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes
An important assessment prior to genome assembly and related analyses is genome profiling, where the k-mer frequencies within raw sequencing reads are analyzed to estimate major genome characteristics such as size, heterozygosity, and repetitiveness. Here we introduce GenomeScope 2.0 (
https://github.com/tbenavi1/genomescope2.0
), which applies combinatorial theory to establish a detailed mathematical model of how k-mer frequencies are distributed in heterozygous and polyploid genomes. We describe and evaluate a practical implementation of the polyploid-aware mixture model that quickly and accurately infers genome properties across thousands of simulated and several real datasets spanning a broad range of complexity. We also present a method called Smudgeplot (
https://github.com/KamilSJaron/smudgeplot
) to visualize and estimate the ploidy and genome structure of a genome by analyzing heterozygous k-mer pairs. We successfully apply the approach to systems of known variable ploidy levels in the
Meloidogyne
genus and the extreme case of octoploid
Fragaria
×
ananassa
.
Prior to genome assembly, the raw sequencing reads must be analyzed for assessment of major genome characteristics such as genome size, heterozygosity, and repetitiveness. For this purpose, the authors introduce GenomeScope 2.0, an extension of GenomeScope for polyploid genomes, and Smudgeplot, which can estimate a genome’s ploidy.
Journal Article
Common conditions associated with hereditary haemochromatosis genetic variants: cohort study in UK Biobank
AbstractObjectiveTo compare prevalent and incident morbidity and mortality between those with the HFE p.C282Y genetic variant (responsible for most hereditary haemochromatosis type 1) and those with no p.C282Y mutations, in a large UK community sample of European descent.DesignCohort study.Setting22 centres across England, Scotland, and Wales in UK Biobank (2006-10).Participants451 243 volunteers of European descent aged 40 to 70 years, with a mean follow-up of seven years (maximum 9.4 years) through hospital inpatient diagnoses and death certification.Main outcome measureOdds ratios and Cox hazard ratios of disease rates between participants with and without the haemochromatosis mutations, adjusted for age, genotyping array type, and genetic principal components. The sexes were analysed separately as morbidity due to iron excess occurs later in women.ResultsOf 2890 participants homozygous for p.C282Y (0.6%, or 1 in 156), haemochromatosis was diagnosed in 21.7% (95% confidence interval 19.5% to 24.1%, 281/1294) of men and 9.8% (8.4% to 11.2%, 156/1596) of women by end of follow-up. p.C282Y homozygous men aged 40 to 70 had a higher prevalence of diagnosed haemochromatosis (odds ratio 411.1, 95% confidence interval 299.0 to 565.3, P<0.001), liver disease (4.30, 2.97 to 6.18, P<0.001), rheumatoid arthritis (2.23, 1.51 to 3.31, P<0.001), osteoarthritis (2.01, 1.71 to 2.36, P<0.001), and diabetes mellitus (1.53, 1.16 to 1.98, P=0.002), versus no p.C282Y mutations (n=175 539). During the seven year follow-up, 15.7% of homozygous men developed at least one incident associated condition versus 5.0% (P<0.001) with no p.C282Y mutations (women 10.1% v 3.4%, P<0.001). Haemochromatosis diagnoses were more common in p.C282Y/p.H63D heterozygotes, but excess morbidity was modest.ConclusionsIn a large community sample, HFE p.C282Y homozygosity was associated with substantial prevalent and incident clinically diagnosed morbidity in both men and women. As p.C282Y associated iron overload is preventable and treatable if intervention starts early, these findings justify re-examination of options for expanded early case ascertainment and screening.
Journal Article
Tezacaftor–Ivacaftor in Residual-Function Heterozygotes with Cystic Fibrosis
Approximately 5% of patients with cystic fibrosis express one allele with some retained CFTR function. In a prospective trial, tezacaftor–ivacaftor had a greater effect on increasing FEV
1
than ivacaftor alone, and both ivacaftor alone and the combination were more effective than placebo.
Journal Article