Novel PHEX gene locus-specific database: Comprehensive characterization of vast number of variants associated with X-linked hypophosphatemia (XLH)

X‐linked hypophosphatemia (XLH), the most common form of hereditary hypophosphatemia, is caused by disrupting variants in the PHEX gene, located on the X chromosome. XLH is inherited in an X‐linked pattern with complete penetrance observed for both males and females. Patients experience lifelong symptoms resulting from chronic hypophosphatemia, including impaired bone mineralization, skeletal deformities, growth retardation, and diminished quality of life. This chronic condition requires life‐long management with disease‐specific therapies, which can improve patient outcomes especially when initiated early in life. To centralize and disseminate PHEX variant information, we have established a new PHEX gene locus‐specific database, PHEX LSDB. As of April 30, 2021, 870 unique PHEX variants, compiled from an older database of PHEX variants, a comprehensive literature search, a sponsored genetic testing program, and XLH clinical trials, are represented in the PHEX LSDB. This resource is publicly available on an interactive, searchable website (https://www.rarediseasegenes.com/), which includes a table of variants and associated data, graphical/tabular outputs of genotype‐phenotype analyses, and an online submission form for reporting new PHEX variants. The database will be updated regularly with new variants submitted on the website, identified in the published literature, or shared from genetic testing programs.

Cost effectiveness of romosozumab versus teriparatide for severe postmenopausal osteoporosis in Japan

This study assessed the cost effectiveness of romosozumab versus teriparatide, both sequenced to alendronate, for the treatment of severe postmenopausal osteoporosis in Japan, using bone mineral density (BMD) efficacy data. Results show that romosozumab/alendronate produces greater health benefits at a lower cost than teriparatide/alendronate.

INTRODUCTION

This study aims to assess the cost effectiveness of romosozumab versus teriparatide, both sequenced to alendronate, for the treatment of severe postmenopausal osteoporosis in Japanese women previously treated with bisphosphonates.

METHODS

A Markov model was used to assess the relative cost effectiveness of 1 year of romosozumab versus 2 years of teriparatide, both sequenced to alendronate for a total treatment duration of 5 years. Outcomes for a cohort of women with a mean age of 78 years, a T-score ≤-2.5 and a previous fragility fracture were simulated over a lifetime horizon. The analysis was conducted from the perspective of the Japanese healthcare system and used a discount rate of 2% per annum. To inform relative fracture incidence, the bone mineral density (BMD) advantage of romosozumab over teriparatide was translated into relative risks of fracture, using relationships provided by a meta-regression of osteoporosis therapy trials. Outcomes were assessed in terms of lifetime costs (2020 US dollars) and quality-adjusted life years (QALYs).

RESULTS

Base case results showed that, compared with teriparatide/alendronate, romosozumab/alendronate reduced costs by $5134 per patient and yielded 0.045 additional QALYs. Scenario analyses and probabilistic sensitivity analysis confirmed that results are robust to uncertainty in model assumptions and inputs.

CONCLUSION

Results show that romosozumab/alendronate produces greater health benefits at a lower total cost than teriparatide/alendronate.

Hypophosphatemia Gene Panel Sponsored Program: A High Yield of Molecular Diagnoses from Clinically Confirmed XLH and Suspected Genetic Hypophosphatemia

X-linked hypophosphatemia (XLH), a dominant disorder caused by a disease-associated variant in the PHEX gene, affects males and females of all ages. Rickets and osteomalacia may be present along with short stature, lower limb deformity, muscle pain and/or weakness/fatigue, bone pain, joint pain/stiffness, hearing difficulty, enthesopathy, osteoarthritis, and dental abscesses. Patients with XLH have below-normal serum phosphate and elevated serum FGF23. XLH is one of multiple etiologies of hypophosphatemia; depending on genetic cause, management may differ. Acquired hypophosphatemia (e.g. tumor induced osteomalacia) is non-hereditary in nature. This program provides a no-charge genetic test to confirm a clinical XLH diagnosis or to aid suspected genetic hypophosphatemia diagnosis. Patients aged >/= 6 months with either a clinical XLH diagnosis or suspicion of genetic hypophosphatemia, as evidenced by 2 or more clinical signs/ symptoms, were eligible for testing. The next generation sequencing panel includes 13 genes: ALPL, CLCN5, CYP2R1, CYP27B1, DMP1, ENPP1, FAH, FAM20C, FGF23, FGFR1, PHEX, SLC34A3 and VDR. Copy number variant detection was performed. 831 unrelated individuals were tested as of June 30, 2020. 569 (68.5%) of these subjects had a PHEX variant: 519 (91.2%) were either pathogenic or likely pathogenic (P/LP) and 50 (8.8%) were variants of uncertain significance (VUS). Of the 312 (37.5%) cases where no PHEX molecular diagnosis was found, 38 (12.2%) had molecular diagnoses associated with other genes/disorders: 4 had a variant (P/LP) in FGF23 (autosomal dominant [AD] hypophosphatemic rickets), 2 had two variants (P/LP) in CYP27B1 (autosomal recessive [AR] vitamin D dependent rickets), 1 had P/LP variants in ENPP1 (AR hypophosphatemic rickets Type 2). There were 27 cases with single P or LP variants in ALPL (AD hypophosphatasia, HPP); 4 cases carried two variants (P/LP) in ALPL (AR form). Of 237 unique P/LP PHEX variants detected: 59 were deletions, duplications or insertions; 37 were copy number variants; 52 were splice-site variants; 89 were single nucleotide variants. Additional family member testing/clinical information resulted in 48 cases having VUS reclassified to P/LP, highlighting the value of cascade family testing/clinical info to resolve VUS. RNA analyses to resolve VUS may further improve molecular diagnostic yield. Program results demonstrate a high diagnostic yield for XLH/ genetic hypophosphatemia and new insight into XLH-associated PHEX variants.

Prioritizing genes for systematic variant effect mapping

MOTIVATION

When rare missense variants are clinically interpreted as to their pathogenicity, most are classified as variants of uncertain significance (VUS). Although functional assays can provide strong evidence for variant classification, such results are generally unavailable. Multiplexed assays of variant effect can generate experimental 'variant effect maps' that score nearly all possible missense variants in selected protein targets for their impact on protein function. However, these efforts have not always prioritized proteins for which variant effect maps would have the greatest impact on clinical variant interpretation.

RESULTS

Here, we mined databases of clinically interpreted variants and applied three strategies, each building on the previous, to prioritize genes for systematic functional testing of missense variation. The strategies ranked genes (i) by the number of unique missense VUS that had been reported to ClinVar; (ii) by movability- and reappearance-weighted impact scores, to give extra weight to reappearing, movable VUS and (iii) by difficulty-adjusted impact scores, to account for the more resource-intensive nature of generating variant effect maps for longer genes. Our results could be used to guide systematic functional testing of missense variation toward greater impact on clinical variant interpretation.

AVAILABILITY AND IMPLEMENTATION

Source code available at: https://github.com/rothlab/mave-gene-prioritization.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

STAT3 gain-of-function mutation in a patient with pulmonary Mycobacterium abscessus infection

Background

Signal transducer and activator of transcription 3 (STAT3) is a transcription factor involved in cellular proliferation, apoptosis, and differentiation. Mutations in the STAT3 gene have been associated with dysregulation of the immune system giving rise to primary immunodeficiency syndromes (PID). Clinically, patients may present with very broad manifestations, and its diagnosis is usually very challenging. Proper treatment remains unclear, and limited options are available.

Methods

We report an adult male patient with long-standing history of immunodeficiency, who was found to have Mycobacterium abscessus infection. Two-hundred and seven immunogenes were sequenced using next-generation sequencing technology (NGS).

Results

A STAT3 heterozygous missense pathologic variant was identified in the patient located in the transactivation domain (TA) of STAT3, associated with a gain of functionality, leading to recurrent bronchopulmonary infections, and involvement of multiple organ systems.

Conclusions

Severe cases of autoimmunity should prompt for evaluation of PIDs in the setting of genetic mutations. Anti-IL-6 therapy may benefit patients with STAT3 GOF mutations. These patients should also be screened for lymphoproliferative disorders.