Rare genetic disease in China: a call to improve clinical services

Joint, multifaceted genomic analysis enables diagnosis of diverse, ultra-rare monogenic presentations

Genomics for rare disease diagnosis has advanced at a rapid pace due to our ability to perform "N-of-1" analyses on individual patients with ultra-rare diseases. The increasing sizes of ultra-rare disease cohorts internationally newly enables cohort-wide analyses for new discoveries, but well-calibrated statistical genetics approaches for jointly analyzing these patients are still under development.1,2 The Undiagnosed Diseases Network (UDN) brings multiple clinical, research and experimental centers under the same umbrella across the United States to facilitate and scale N-of-1 analyses. Here, we present the first joint analysis of whole genome sequencing data of UDN patients across the network. We introduce new, well-calibrated statistical methods for prioritizing disease genes with de novo recurrence and compound heterozygosity. We also detect pathways enriched with candidate and known diagnostic genes. Our computational analysis, coupled with a systematic clinical review, recapitulated known diagnoses and revealed new disease associations. We further release a software package, RaMeDiES, enabling automated cross-analysis of deidentified sequenced cohorts for new diagnostic and research discoveries. Gene-level findings and variant-level information across the cohort are available in a public-facing browser (https://dbmi-bgm.github.io/udn-browser/). These results show that N-of-1 efforts should be supplemented by a joint genomic analysis across cohorts.

Simulation of undiagnosed patients with novel genetic conditions

Rare Mendelian disorders pose a major diagnostic challenge and collectively affect 300-400 million patients worldwide. Many automated tools aim to uncover causal genes in patients with suspected genetic disorders, but evaluation of these tools is limited due to the lack of comprehensive benchmark datasets that include previously unpublished conditions. Here, we present a computational pipeline that simulates realistic clinical datasets to address this deficit. Our framework jointly simulates complex phenotypes and challenging candidate genes and produces patients with novel genetic conditions. We demonstrate the similarity of our simulated patients to real patients from the Undiagnosed Diseases Network and evaluate common gene prioritization methods on the simulated cohort. These prioritization methods recover known gene-disease associations but perform poorly on diagnosing patients with novel genetic disorders. Our publicly-available dataset and codebase can be utilized by medical genetics researchers to evaluate, compare, and improve tools that aid in the diagnostic process.

Development of preimplantation genetic testing for monogenic diseases in China

Preimplantation genetic testing for monogenic diseases (PGT-M) can effectively interrupt the transmission of genetic diseases from parents to the offspring before pregnancy. In China, there are over ten million individuals afflicted with monogenic disorders. This literature review summarizes the development of PGT-M in China for the past 24 years, covering the general steps such as the indications and contraindications, genetic and reproductive counselling, biopsy methods, detecting techniques and strategies during PGT-M application in China. The ethical considerations of PGT-M are also be emphasized, including sexual selection, transferring for mosaic embryos, the three-parent baby, and the different opinions for serious adult-onset conditions. Some key policies of the Chinese government for the application of PGT-M are also considered. Methods for regulation of this technique, as well as specific management to increase the accuracy and reliability of PGT-M, are regarded as priority issues in China. The third-generation sequencing and variants testing from RNA level, and non-invasive preimplantation genetic testing using blastocoel fluid and free DNA particles within spent blastocyst medium might be potential techniques and strategies for PGT-M in future.

Genetics Evaluation of Targeted Exome Sequencing in 223 Chinese Probands With Genetic Skeletal Dysplasias

Genetic skeletal dysplasias (GSDs) are a type of disease with complex phenotype and high heterogeneity, characterized by cartilage and bone growth abnormalities. The variable phenotypes of GSD make clinical diagnosis difficult. To explore the clinical utility of targeted exome sequencing (TES) in the diagnosis of GSD, 223 probands with suspected GSD were enrolled for TES with a panel of 322 known disease-causing genes. After bioinformatics analysis, all candidate variants were prioritized by pathogenicity. Sanger sequencing was used to verify candidate variants in the probands and parents and to trace the source of variants in family members. We identified the molecular diagnoses for 110/223 probands from 24 skeletal disorder groups and confirmed 129 pathogenic/likely pathogenic variants in 48 genes. The overall diagnostic rate was 49%. The molecular diagnostic results modified the diagnosis in 25% of the probands, among which mucopolysaccharidosis and spondylo-epi-metaphyseal dysplasias were more likely to be misdiagnosed. The clinical management of 33% of the probands also improved; 21 families received genetic counseling; 4 families accepted prenatal genetic diagnosis, 1 of which was detected to carry pathogenic variants. The results showed that TES achieved a high diagnostic rate for GSD, helping clinicians confirm patients’ molecular diagnoses, formulate treatment directions, and carry out genetic counseling. TES could be an economical diagnostic method for patients with GSD.

Economic burden and health related quality of life of ultra-rare Gaucher disease in China

Background

The diagnosis and health care of patients with rare diseases present a tremendous challenge worldwide. This study described the health care service utilization through participants’ perspective and estimated the cost of illness (COI), and patients with Gaucher disease (GD)’s/caregivers’ health-related quality of life in China.

Method

An online retrospective survey of patients with GD and their caregivers was conducted during May–June 2018. Socio-demographic, health service utilization, disease-related expenses, social support, sleep quality (Pittsburgh Sleep Quality Index [PSQI]), and the Short Form Health Survey (SF-36) were investigated. Using self-reported information, we estimated the annual COI, including direct healthcare, direct non-healthcare, and indirect costs.

Results

Forty patients and their 49 caregivers were surveyed. The patients’ onset age of GD was 9.3 ± 10.9; their disease course was 3.5 ± 3.1 years. 21 (42.9%) patients had ≥ 2 caregivers, but 35 (71.4%) caregivers reported have no experience as a caregiver. 79.6% caregivers have stopped working, and 87.8% changed weekly working schedule. Before final diagnosis, patients visited 3.9 ± 3.1 (max = 20) hospitals and took 1.2 ± 1.7 (max = 6.6) years for confirmed diagnosis. On average, 5.0 ± 9.6 misdiagnoses occurred, and the per-patient diagnoses cost was USD ($) 7576. After GD confirmation, 8 (16.3%) patients received no treatment, 40 (81.6%) received pharmacotherapy, 10 (20.4%) received surgery, 38 (77.6%) received outpatient service (8.8 ± 9.1 times/annually), and 37 (77.5%) received inpatient service (4.0 ± 3.5 times/annually). Annual per-patient COI was USD ($) 49,925 (95% confidence interval: 29,178, 70,672). Average direct healthcare cost was $41,816, including pharmaceutical ($29,908), inpatient ($7,451), and outpatient ($1,838). Productivity loss per-caregiver was $1,980, and their Zarit Burden Inventory score was moderate-severe (48.6 ± 19.6). Both patients/caregivers reported lower social support (32.4 ± 7.4, 34.9 ± 7.6), two times higher PSQI (7.9 ± 2.9, 8.7 ± 3.6), and half lower SF-36 (41.3 ± 18.6, 46.5 ± 19.3) than those reported for healthy Chinese individuals.

Conclusions

The high misdiagnosis rate, together with delayed diagnosis, substantial costs, and deteriorated health-related quality of life of GD patients as well as their heavy care burden, calls for extreme attention from policymakers in China. Further efforts of government and society are urgently demanded, including pharmaceutical reimbursement, screening newborns, developing precise diagnostic tools, and training doctors.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13023-021-01963-6.

How Far Have We Come? Challenges to Orphan Drug Access in China, 2011-2017

Rare diseases are an important global public health issue. One significant challenge is to ensure the access to orphan drugs for patients with rare disease. This study aims to evaluate the accessibility of orphan drugs in China. Information pertaining to the availability and costs of each orphan drug in each hospital was obtained from the Chinese Medicine Economic Information database during 2011-2017. We measured the accessibility of orphan drugs from 3 aspects: availability, daily costs, and affordability to patients.The market availability rate of orphan drugs in China was 28.8% by June 30, 2017. The median availability rate at the hospital level was less than 15% but was increasing over time. The cost of a defined daily dose of orphan drugs varied significantly with a decreasing trend in all areas. Less than half of all surveyed orphan drugs had a cost of a defined daily dose no more than residents' average daily income.This study reveals the challenges of access to orphan drugs in China. The availability of marketed orphan drugs in China was relatively low and most orphan drugs placed a heavy financial burden on patients with rare disease. It is necessary to develop legislation for orphan drugs and encourage domestic generics.

Next generation sequencing: Coping with rare genetic diseases in China

With a population of 1.4 billion, China shares the largest burden of rare genetic diseases worldwide. Current estimates suggest that there are over ten million individuals afflicted with chromosome disease syndromes and well over one million individuals with monogenic disease. Care of patients with rare genetic diseases remains a largely unmet need due to the paucity of available and affordable treatments. Over recent years, there is increasing recognition of the need for affirmative action by government, health providers, clinicians and patients. The advent of new next generation sequencing (NGS) technologies such as whole genome/exome sequencing, offers an unprecedented opportunity to provide large-scale population screening of the Chinese population to identify the molecular causes of rare genetic diseases. As a surrogate for lack of effective treatments, recent development and implementation of noninvasive prenatal testing (NIPT) in China has the greatest potential, as a single technology, for reducing the number of children born with rare genetic diseases.