Approaches to identify genetic variants that influence the risk for onset of fragile X-associated primary ovarian insufficiency (FXPOI): a preliminary study

X chromosome rearrangement associated with premature ovarian insufficiency as diagnosed by molecular cytogenetic methods: a case report and review of the literature

BACKGROUND

Premature ovarian insufficiency (POI) is a clinical condition characterized by ovarian dysfunction in women under 40. The etiology of most POI cases remains unidentified and is believed to be multifactorial, including factors such as autoimmunity, metabolism, infection, and genetics. POI exhibits significant genetic heterogeneity, and it can result from chromosomal abnormalities and monogenic defects.

CASE PRESENTATION

The study participant, a 33-year-old woman, presented with a history of irregular menstruation that commenced two years ago, progressing to prolonged menstrual episodes and eventual cessation. The participant exhibits a rearrangement of the X chromosome, characterized by heterozygosity duplication on the long arm and heterozygosity deletion on the short arm by whole exome sequencing(WES) combined with cell chromosome detection.

CONCLUSIONS

This study expands the spectrum of mutations associated with POI resulting from X chromosomal abnormalities. WES-Copy number variation analysis, in conjunction with chromosome karyotype analysis and other detection techniques, can provide a more comprehensive understanding of the genetic landscape underlying complex single or multi-system diseases.

My 28 Days - a global digital women's health initiative for evaluation and management of secondary amenorrhea: case report and literature review

There is a need to close the gap between knowledge and action in health care. Effective care requires a convenient and reliable distribution process. As global internet and mobile communication increase capacity, innovative approaches to digital health education platforms and care delivery are feasible. We report the case of a young African woman who developed acute secondary amenorrhea at age 18. Subsequently, she experienced a 10-year delay in the diagnosis of the underlying cause. A global digital medical hub focused on women's health and secondary amenorrhea could reduce the chance of such mismanagement. Such a hub would establish more efficient information integration and exchange processes to better serve patients, family caregivers, health care providers, and investigators. Here, we show proof of concept for a global digital medical hub for women's health. First, we describe the physiological control systems that govern the normal menstrual cycle, and review the pathophysiology and management of secondary amenorrhea. The symptom may lead to broad and profound health implications for the patient and extended family members. In specific situations, there may be significant morbidity related to estradiol deficiency: (1) reduced bone mineral density, 2) cardiovascular disease, and 3) cognitive decline. Using primary ovarian insufficiency (POI) as the paradigm condition, the Mary Elizabeth Conover Foundation has been able to address the specific global educational needs of these women. The Foundation did this by creating a professionally managed Facebook group specifically for these women. POI most commonly presents with secondary amenorrhea. Here we demonstrate the feasibility of conducting a natural history study on secondary amenorrhea with international reach to be coordinated by a global digital medical hub. Such an approach takes full advantage of internet and mobile device communication systems. We refer to this global digital women's health initiative as My 28 Days®.

Premature ovarian insufficiency in adolescence: a chance for early diagnosis?

Premature ovarian insufficiency (POI) is typically diagnosed when amenorrhea is combined with high gonadotrophins and hypoestrogenemia in a woman under 40 years of age, although, more rarely, POI can develop in adolescence and present with delayed puberty or amenorrhea, depending on the timing of follicular depletion or insult to the ovary. In a proportion of girls, the diagnosis may be made at an early stage of POI, presenting with abnormal uterine bleeding, when some follicular function is still retained. The natural history of POI in this group of patients is not clear; however, they could represent a subgroup with a unique opportunity for early intervention and thus the provision of fertility preservation options. While the etiology of POI in a large number of girls remains unknown, a growing number will be identified as carriers of genetic mutations, offering clinicians a yet greater opportunity to provide genetic counseling to other female family members. The aim of this review is to provide information regarding the etiology, diagnosis, and treatment of POI in adolescents while detailing the new options for fertility preservation when POI is diagnosed at an early stage.

Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human

Background

Lack of comprehensive functional annotations across a wide range of tissues and cell types severely hinders the biological interpretations of phenotypic variation, adaptive evolution, and domestication in livestock. Here we used a combination of comparative epigenomics, genome-wide association study (GWAS), and selection signature analysis, to shed light on potential adaptive evolution in cattle.

Results

We cross-mapped 8 histone marks of 1300 samples from human to cattle, covering 178 unique tissues/cell types. By uniformly analyzing 723 RNA-seq and 40 whole genome bisulfite sequencing (WGBS) datasets in cattle, we validated that cross-mapped histone marks captured tissue-specific expression and methylation, reflecting tissue-relevant biology. Through integrating cross-mapped tissue-specific histone marks with large-scale GWAS and selection signature results, we for the first time detected relevant tissues and cell types for 45 economically important traits and artificial selection in cattle. For instance, immune tissues are significantly associated with health and reproduction traits, multiple tissues for milk production and body conformation traits (reflecting their highly polygenic architecture), and thyroid for the different selection between beef and dairy cattle. Similarly, we detected relevant tissues for 58 complex traits and diseases in humans and observed that immune and fertility traits in humans significantly correlated with those in cattle in terms of relevant tissues, which facilitated the identification of causal genes for such traits. For instance, PIK3CG, a gene highly specifically expressed in mononuclear cells, was significantly associated with both age-at-menopause in human and daughter-still-birth in cattle. ICAM, a T cell-specific gene, was significantly associated with both allergic diseases in human and metritis in cattle.

Conclusion

Collectively, our results highlighted that comparative epigenomics in conjunction with GWAS and selection signature analyses could provide biological insights into the phenotypic variation and adaptive evolution. Cattle may serve as a model for human complex traits, by providing additional information beyond laboratory model organisms, particularly when more novel phenotypes become available in the near future.

Premature ovarian insufficiency: clinical orientations for genetic testing and genetic counseling

Premature ovarian insufficiency (POI) is a heterogeneous disorder diagnosed in women before 40 years old and describes a wide range of impaired ovarian function, from diminished ovarian reserve to premature ovarian failure. Genetic etiology accounts for 20% to 25% of patients. The evidence that POI can be isolated (nonsyndromic) or part of a pleiotropic genetic syndrome highlights its high heterogeneous etiology. Chromosomal abnormalities as a cause of POI have a prevalence of 10% to 13%, being 45,X complement the most common cytogenetic cause of primary amenorrhea and mosaicism with a 45,X cell line more frequently associated with secondary amenorrhea. Other X chromosome aberrations include deletions, duplications, balanced, and unbalanced X-autosome rearrangements involving the critical region for the POI phenotype (Xq13-Xq21 to Xq23-Xq27).

The identification of 2 or more pathogenic variants in distinct genes argues in favor of a polygenic origin for POI. Hundreds of pathogenic variants (including mitochondrial) have been involved in POI etiology mainly with key roles in biological processes in the ovary, such as meiosis and DNA damage repair mechanism, homologous recombination, follicular development, granulosa cell differentiation and proliferation, and ovulation.

The most common single gene cause for POI is the premutation for FMR1 gene (associated with fragile X syndrome) with alleles ranging from about 55 to about 200 CGG trinucleotide repeats. POI occurs in 20% of women with this premutation. As females with premutation or full mutation alleles are also at risk of having affected children, their genetic counseling should include the indication for prenatal diagnosis or preimplantation genetic testing after intracytoplasmic sperm injection and trophectoderm biopsy.

In conclusion, in clinical practice high-resolution karyotype and FMR1 gene molecular study should be performed as first-tier tests in the assessment of POI. In addition, array Comparative Genomic Hybridization or specific next generation sequencing panels should be considered to identify chromosomal deletions/duplications under karyotype resolution or other pathogenic variants in specific genes associated with POI. This is particularly important in patients with first- or second-degree relatives also affected with POI, improving their reproductive and genetic counseling.

Fragile X Premutation Associated Conditions (FXPAC)

The European Fragile X Network (EFXN) proposes that Fragile X Premutation Associated Conditions (FXPAC) be adopted as a universal term covering any condition linked to the Fragile X premutation. To date, there has not been an umbrella term assigned to issues associated with the FMR1 premutation, though several defined conditions which affect some premutation carriers, namely Fragile X-associated Primary Ovarian Insufficiency (FXPOI) and Fragile X-associated Tremor/Ataxia Syndrome (FXTAS), are now commonly accepted. An overarching term covering all FX premutation conditions will help doctors in determining how the premutation might be affecting their patient; and encourage researchers to explore the interrelationships of the various conditions affecting premutation carriers. Further, there are ongoing discoveries about physical and psychological issues faced by premutation carriers, and a new term helps encompass all of these burgeoning developments.

Women who carry a fragile X premutation are biologically older than noncarriers as measured by telomere length

Women who carry a fragile X premutation, defined as having 55-200 unmethylated CGG repeats in the 5' UTR of the X-linked FMR1 gene, have a 20-fold increased risk for primary ovarian insufficiency (FXPOI). We tested the hypothesis that women with a premutation + FXPOI have shorter telomeres than those without FXPOI because they are "biologically older." Using linear regression, we found that women carrying a premutation (n = 172) have shorter telomeres and hence, are "biologically older" than women carrying the normal size allele (n = 81). Strikingly, despite having shorter telomeres, age was not statistically associated with their telomere length, in contrast to non-carrier controls. Further, telomere length within premutation carriers was not associated with repeat length but was associated with a diagnosis of FXPOI, although the latter finding may depend on FXPOI age of onset.

Extreme Trait Whole-Genome Sequencing Identifies PTPRO as a Novel Candidate Gene in Emphysema with Severe Airflow Obstruction

RATIONALE

Genetic association studies in chronic obstructive pulmonary disease have primarily tested for association with common variants, the results of which explain only a portion of disease heritability. Because rare variation is also likely to contribute to susceptibility, we used whole-genome sequencing of subjects with clinically extreme phenotypes to identify genomic regions enriched for rare variation contributing to chronic obstructive pulmonary disease susceptibility.

OBJECTIVES

To identify regions of rare genetic variation contributing to emphysema with severe airflow obstruction.

METHODS

We identified heavy smokers that were resistant (n = 65) or susceptible (n = 64) to emphysema with severe airflow obstruction in the Pittsburgh Specialized Center of Clinically Oriented Research cohort. We filtered whole-genome sequencing results to include only rare variants and conducted single variant tests, region-based tests across the genome, gene-based tests, and exome-wide tests.

MEASUREMENTS AND MAIN RESULTS

We identified several suggestive associations with emphysema with severe airflow obstruction, including a suggestive association of all rare variation in a region within the gene ZNF816 (19q13.41; P = 4.5 × 10^-6), and a suggestive association of nonsynonymous coding rare variation in the gene PTPRO (P = 4.0 × 10^-5). Association of rs61754411, a rare nonsynonymous variant in PTPRO, with emphysema and obstruction was demonstrated in all non-Hispanic white individuals in the Pittsburgh Specialized Center of Clinically Oriented Research cohort. We found that cells containing this variant have decreased signaling in cellular pathways necessary for survival and proliferation.

CONCLUSIONS

PTPRO is a novel candidate gene in emphysema with severe airflow obstruction, and rs61754411 is a previously unreported rare variant contributing to emphysema susceptibility. Other suggestive candidate genes, such as ZNF816, are of interest for future studies.

Genetic variants of age at menopause are not related to timing of ovarian failure in breast cancer survivors

OBJECTIVE

To determine if interindividual genetic variation in single-nucleotide polymorphisms (SNPs) related to age at natural menopause is associated with risk of ovarian failure in breast cancer survivors.

METHODS

A prospective cohort of 169 premenopausal breast cancer survivors recruited at diagnosis with stages 0 to III disease were followed longitudinally for menstrual pattern via self-reported daily menstrual diaries. Participants were genotyped for 13 SNPs previously found to be associated with age at natural menopause: EXO1, TLK1, HELQ, UIMC1, PRIM1, POLG, TMEM224, BRSK1, and MCM8. A risk variable summed the total number of risk alleles in each participant. The association between individual genotypes, and also the risk variable, and time to ovarian failure (>12 months of amenorrhea) was tested using time-to-event methods.

RESULTS

Median age at enrollment was 40.5 years (range 20.6-46.1). The majority of participants were white (69%) and underwent chemotherapy (76%). Thirty-eight participants (22%) experienced ovarian failure. None of the candidate SNPs or the summary risk variable was significantly associated with time to ovarian failure. Sensitivity analysis restricted to whites or only to participants receiving chemotherapy yielded similar findings. Older age, chemotherapy exposure, and lower body mass index were related to shorter time to ovarian failure.

CONCLUSIONS

Thirteen previously identified genetic variants associated with time to natural menopause were not related to timing of ovarian failure in breast cancer survivors.

Study of the Genetic Etiology of Primary Ovarian Insufficiency: FMR1 Gene

Menopause is a period of women’s life characterized by the cessation of menses in a definitive way. The mean age for menopause is approximately 51 years. Primary ovarian insufficiency (POI) refers to ovarian dysfunction defined as irregular menses and elevated gonadotrophin levels before or at the age of 40 years. The etiology of POI is unknown but several genes have been reported as being of significance. The fragile X mental retardation 1 gene (FMR1) is one of the most important genes associated with POI. The FMR1 gene contains a highly polymorphic CGG repeat in the 5′ untranslated region of exon 1. Four allelic forms have been defined with respect to CGG repeat length and instability during transmission. Normal (5–44 CGG) alleles are usually transmitted from parent to offspring in a stable manner. The full mutation form consists of over 200 repeats, which induces hypermethylation of the FMR1 gene promoter and the subsequent silencing of the gene, associated with Fragile X Syndrome (FXS). Finally, FMR1 intermediate (45–54 CGG) and premutation (55–200 CGG) alleles have been principally associated with two phenotypes, fragile X tremor ataxia syndrome (FXTAS) and fragile X primary ovarian insufficiency (FXPOI).

Associated Clinical Disorders Diagnosed by Medical Specialists in 188 FMR1 Premutation Carriers Found in the Last 25 Years in the Spanish Basque Country: A Retrospective Study

Fragile X-associated tremor/ataxia syndrome (FXTAS) and fragile X-associated primary ovarian insufficiency (FXPOI) are definitely related to the fragile X mental retardation 1 (FMR1) premutation (PM). Additional medical problems have also been associated with the PM, such as fibromyalgia, endocrine, and psychiatric disorders. To improve our understanding in the field, we reviewed all PM carriers and their reasons for any medical referrals from 104 fragile X families molecularly diagnosed in our laboratory and living in the Spanish Basque Country. After signing the written informed consent, we studied their electronic medical records in order to identify the disorders associated with the PM and their frequencies. We obtained clinical data in 188 PM carriers (147 women and 41 men). In women, the frequency of FXPOI (22.61%) was similar to that previously reported in PM carriers. In men, the frequency of definite FXTAS (28.57%) was lower than reported elsewhere. Furthermore, thyroid pathology was associated with the PM, the frequency of hypothyroidism being much higher in the studied region than in the general population (8.84% vs. 0.93%). Finally, we found no association with fibromyalgia or psychiatric problems. These findings represent another population contribution in this field and may be useful for the clinical management of PM carriers.

Length of FMR1 repeat alleles within the normal range does not substantially affect the risk of early menopause

STUDY QUESTION

Is the length of FMR1 repeat alleles within the normal range associated with the risk of early menopause?

SUMMARY ANSWER

The length of repeat alleles within the normal range does not substantially affect risk of early menopause.

WHAT IS KNOWN ALREADY

There is a strong, well-established relationship between length of premutation FMR1 alleles and age at menopause, suggesting that this relationship could continue into the normal range. Within the normal range, there is conflicting evidence; differences in ovarian reserve have been identified with FMR1 repeat allele length, but a recent population-based study did not find any association with age at menopause as a quantitative trait.

STUDY DESIGN, SIZE, DURATION

We analysed cross-sectional baseline survey data collected at recruitment from 2004 to 2010 from a population-based, prospective epidemiological cohort study of >110 000 women to investigate whether repeat allele length was associated with early menopause.

PARTICIPANTS/MATERIALS, SETTING, METHOD

We included 4333 women from the Breakthrough Generations Study (BGS), of whom 2118 were early menopause cases (menopause under 46 years) and 2215 were controls. We analysed the relationship between length of FMR1 alleles and early menopause using logistic regression with allele length as continuous and categorical variables. We also conducted analyses with the outcome age at menopause as a quantitative trait as well as appropriate sensitivity and exploratory analyses.

MAIN RESULTS AND THE ROLE OF CHANCE

There was no association of the shorter or longer FMR1 allele or their combined genotype with the clinically relevant end point of early menopause in our main analysis. Likewise, there were no associations with age at menopause as a quantitative trait in our secondary analysis.

LIMITATIONS, REASONS FOR CAUTION

Women with homozygous alleles in the normal range may have undetected FMR1 premutation alleles, although there was no evidence to suggest this. We estimate minor dilution of risk of early menopause from the likely inclusion of some women with menopause at over 45 years in the early menopause cases due to age-rounding bias in self-reports.

WIDER IMPLICATIONS OF THE FINDINGS

There is no robust evidence in this large study that variation within the normal range of FMR1 repeat alleles influences timing of menopause in the general population, which contradicts findings from some earlier, mainly smaller studies. The FMR1 CGG repeat polymorphism in the normal range is unlikely to contribute to genetic susceptibility to early menopause.

STUDY FUNDING/COMPETING INTERESTS

We thank Breast Cancer Now and The Institute of Cancer Research for funding the BGS. The Institute of Cancer Research acknowledges NHS funding to the NIHR Biomedical Research Centre. The study was funded by the Wellcome Trust (grant number 085943). There are no competing interests.

TRIAL REGISTRATION NUMBER

Not applicable.

Update on primary ovarian insufficiency in adolescents

PURPOSE OF REVIEW

We provide an overview of new insights into the genetic causes of primary ovarian insufficiency (POI) and address the challenges faced by clinicians who care for adolescents with this condition.

RECENT FINDINGS

In most cases, the cause of POI remains a mystery after appropriate clinical testing has been completed. Large-scale genomic sequencing approaches are uncovering new mechanisms underlying the disorder. Gene variants that affect the normal processes of primordial germ-cell proliferation and migration, oocyte meiosis, and ovarian follicle formation/activation are plausible mechanisms. Whole exome sequencing has been used to associate many of these variants with human POI. POI is a serious chronic condition with no cure. It qualifies as a rare disease and as such presents special challenges to patients, parents, and clinicians. Although the diagnosis of POI is often delayed because of the assumption that irregular menses are common among adolescents, early detection is critical for the maintenance of bone and cardiovascular health. Treatment options have focused on hormonal therapy and fertility preservation. However, many studies prove the increasing need to incorporate mental health support and a family systems approach into the management plan.

SUMMARY

Large-scale genomic sequencing has recently identified new mechanisms of POI. However, at present this testing is not clinically indicated as routine. Practice will change as genomic medicine is integrated into standard care. Adolescents with POI are best served by an integrated personal care approach centered on the patient and provided by a primary care clinician who has support from a multidisciplinary team.