Genome Sequencing for Diagnosing Rare Diseases.

BACKGROUND: Genetic variants that cause rare disorders may remain elusive even after expansive testing, such as exome sequencing. The diagnostic yield of genome sequencing, particularly after a negative evaluation, remains poorly defined. METHODS: We sequenced and analyzed the genomes of families with diverse phenotypes who were suspected to have a rare monogenic disease and for whom genetic testing had not revealed a diagnosis, as well as the genomes of a replication cohort at an independent clinical center. RESULTS: We sequenced the genomes of 822 families (744 in the initial cohort and 78 in the replication cohort) and made a molecular diagnosis in 218 of 744 families (29.3%). Of the 218 families, 61 (28.0%) - 8.2% of families in the initial cohort - had variants that required genome sequencing for identification, including coding variants, intronic variants, small structural variants, copy-neutral inversions, complex rearrangements, and tandem repeat expansions. Most families in which a molecular diagnosis was made after previous nondiagnostic exome sequencing (63.5%) had variants that could be detected by reanalysis of the exome-sequence data (53.4%) or by additional analytic methods, such as copy-number variant calling, to exome-sequence data (10.8%). We obtained similar results in the replication cohort: in 33% of the families in which a molecular diagnosis was made, or 8% of the cohort, genome sequencing was required, which showed the applicability of these findings to both research and clinical environments. CONCLUSIONS: The diagnostic yield of genome sequencing in a large, diverse research cohort and in a small clinical cohort of persons who had previously undergone genetic testing was approximately 8% and included several types of pathogenic variation that had not previously been detected by means of exome sequencing or other techniques. (Funded by the National Human Genome Research Institute and others.).

Improved Diagnosis of Rare Disease Patients through Systematic Detection of Runs of Homozygosity.

Autozygosity is associated with an increased risk of genetic rare disease, thus being a relevant factor for clinical genetic studies. More than 2400 exome sequencing data sets were analyzed and screened for autozygosity on the basis of detection of >1 Mbp runs of homozygosity (ROHs). A model was built to predict if an individual is likely to be a consanguineous offspring (accuracy, 98%), and probability of consanguinity ranges were established according to the total ROH size. Application of the model resulted in the reclassification of the consanguinity status of 12% of the patients. The analysis of a subset of 79 consanguineous cases with the Rare Disease (RD)-Connect Genome-Phenome Analysis Platform, combining variant filtering and homozygosity mapping, enabled a 50% reduction in the number of candidate variants and the identification of homozygous pathogenic variants in 41 patients, with an overall diagnostic yield of 52%. The newly defined consanguinity ranges provide, for the first time, specific ROH thresholds to estimate inbreeding within a pedigree on disparate exome sequencing data, enabling confirmation or (re)classification of consanguineous status, hence increasing the efficiency of molecular diagnosis and reporting on secondary consanguinity findings, as recommended by American College of Medical Genetics and Genomics guidelines.

Simulating the Impact of Elevated Levels of Interleukin-6 on the Pharmacokinetics of Various CYP450 Substrates in Patients with Neuromyelitis Optica or Neuromyelitis Optica Spectrum Disorders in Different Ethnic Populations.

A physiologically based pharmacokinetic (PBPK) model was used to simulate the impact of elevated levels of interleukin (IL)-6 on the exposure of several orally administered cytochrome P450 (CYP) probe substrates (caffeine, S-warfarin, omeprazole, dextromethorphan, midazolam, and simvastatin). The changes in exposure of these substrates in subjects with rheumatoid arthritis (and hence elevated IL-6 levels) compared with healthy subjects were predicted with a reasonable degree of accuracy. The PBPK model was then used to simulate the change in oral exposure of the probe substrates in North European Caucasian, Chinese, and Japanese population of patients with neuromyelitis optica (NMO) or NMO spectrum disorder with elevated plasma IL-6 levels (up to 100 pg/mL). Moderate interactions [mean AUC fold change, ≤ 2.08 (midazolam) or 2.36 (simvastatin)] was predicted for CYP3A4 probe substrates and weak interactions (mean AUC fold change, ≤ 1.29-1.97) were predicted for CYP2C19, CYP2C9, and CYP2D6 substrates. No notable interaction was predicted with CYP1A2. Although ethnic differences led to differences in simulated exposure for some of the probe substrates, there were no marked differences in the predicted magnitude of the change in exposure following IL-6-mediated suppression of CYPs. Decreased levels of serum albumin (as reported in NMO patients) had little impact on the magnitude of the simulated IL-6-mediated drug interactions. This PBPK modeling approach allowed us to leverage knowledge from different disease and ethnic populations to make predictions of cytokine-related DDIs in a rare disease population where actual clinical studies would otherwise be difficult to conduct.

An Atypical Case of Idiopathic Pulmonary Fibrosis in a Patient from Africa.

A 39 years old African man presented with fatigue, loss of weight and night sweats; radiology showed a possible usual interstitial pneumonia pattern. The patient missed follow-up visits, and presented again after 3 years with productive cough and general illness. Pulmonary function tests showed a decline of FVC compared to a previous investigation. The CT scans showed progression of the interstitial lung disease, and a multidisciplinary conference recommended to proceed with a surgical lung biopsy. Histopathology showed an atypical pattern, with bronchiolar metaplasia. A new multidisciplinary conference made a diagnosis of IPF, and the patient was treated with antifibrotic drugs with a good effect, reaching stability of lung function. This case report highlights the need to improve knowledge and to better characterize rare pulmonary diseases, and especially IPF, among African patients.

Inclusion and exclusion in the globalisation of genomics; the case of rare genetic disease in Brazil.

Within the context of a globalising agenda for genetic research where 'global health' is increasingly seen as necessarily informed by and having to account for genomics, the focus on rare genetic diseases is becoming prominent. Drawing from ethnographic research carried out separately by both authors in Brazil, this paper examines how an emerging focus on two different arenas of rare genetic disease, cancer genetics and a class of degenerative neurological diseases known as Ataxias, is subject to and a product of the dynamics of inclusion and exclusion as this concerns participation in research and access to health care. It examines how in these different cases 'rarenesss' has been diversely situated and differently politicised and how clinicians, patients and their families grapple with the slippery boundaries between research, rights to health and the limits of care, therapy or prevention. It illustrates how attention to rare genetic disease in Brazil emerges at the intersection of a particular history of genetic research and public health infrastructure, densely complicated feedback loops between clinical care and research, patient mobilisation around the 'judicialisation' of health and recent state legislation regarding rare disease in Brazil. It highlights the relevance of local configurations in the way rare genetic disease is being made relevant for and by different communities.

Head and neck squamous cell cancers in the United States are rare and the risk now is higher among white individuals compared with black individuals.

BACKGROUND: The increasing incidence of oropharyngeal squamous cell cancer (OPSCC) is well established. However, up-to-date incidence estimates and trends for head and neck squamous cell cancers (HNSCCs) overall, including major anatomic sites, and nonoropharyngeal (non-OP) HNSCCs by sex, race, and age in the United States are not well described. METHODS: A retrospective analysis of incident HNSCCs during 1992 through 2014 using the Surveillance, Epidemiology, and End Results database was performed to evaluate the incidence of HNSCCs overall, OPSCC, and non-OP HNSCC (those of the larynx, oral cavity, hypopharynx, nasopharynx, and nasal cavity). Incidence rates were calculated overall and by subgroups of interest, and incidence rate ratios were used to compare rates between groups. The incidence rates presented were per 100,000 population and were age adjusted to the 2000 US standard population (19 age groups; Census P25-1130). The annual percent change (APC) was modeled with and without joinpoints. RESULTS: The incidence of HNSCC overall declined (average APC [aAPC], -0.8; P<.001) despite significant increases in the incidence of OPSCCs, most notably between 2000 and 2014 (APC, 2.1; P<.001). Significant declines in incidence were observed for all non-OP HNSCC sites for both women and men (P<.001 each). Among women, the risk of OPSCC also significantly decreased (aAPC, -0.8; P = .002), whereas the risk among men was stable during 1992 through 2001 (APC, 0.4; P = .42) and then significantly increased from 2001 to 2014 (APC, 2.7; P<.001). Decreases in the risk of non-OP HNSCC were especially large for black women (aAPC, -2.6; P<.001) and men (aAPC, -3.0; P<.001). Although the incidence of HNSCC previously was highest among black individuals, since 2009 its incidence has been higher among white compared with black individuals. CONCLUSIONS: The incidence of HNSCC is declining, especially for non-OP HNSCC and among black individuals. Cancer 2018;124:2125-33. © 2018 American Cancer Society.

Dietary patterns, cost and compliance with low-protein diet of phenylketonuria and other inherited metabolic diseases.

BACKGROUND/OBJECTIVES: Phenylketonuria (PKU) and several other inherited metabolic diseases (IMD) require a lifelong low-protein diet (LPD), otherwise they lead to many health complications. LPDs, however, carry a significant economic burden for patients and their families. The objective of this study was to explore the costs of low-protein foods (LPFs) necessary for LPD as well as dietary patterns and compliance towards an LPD. SUBJECTS/METHODS: A detailed questionnaire was created in cooperation with National Association of PKU and other IMD (NSPKU), and consequently sent to all NSPKU members treated with an LPD (n=303). A total of 184 respondents from the Czech Republic were included in the study (174 had PKU, 10 had other IMD). RESULTS: The average daily consumption of LPF was equal to 411.7 g (PKU) and 345.6 g (other IMD), which corresponds to energy value of 5558 kJ and 4438 kJ, respectively, per patient per day. Patients mostly consumed low-protein flour (≈30% of energy intake), pasta (≈18%), basic pastry (≈15%) and sweets (≈10%). The average monthly costs of LPDs were equal to [euro ]130 (PKU) and [euro ]129 (other IMD) per patient per month. The compliance with LPD was decreasing with increasing age (P<0.0001). CONCLUSIONS: This is the largest study examining costs and dietary patterns of LPDs in patients with PKU and the first study of this kind in other IMD patients requiring an LPD. The study clearly showed that an LPD carries a very high economic burden for families, which may lead to less LPD compliance and potential severe health consequences.

Indigenous Genetics and Rare Diseases: Harmony, Diversity and Equity.

Advances in our understanding of genetic and rare diseases are changing the face of healthcare. Crucially, the global community must implement these advances equitably to reduce health disparities, including between Indigenous and non-Indigenous peoples. We take an Australian perspective to illustrate some key areas that are fundamental to the equitable translation of new knowledge for the improved diagnosis of genetic and rare diseases for Indigenous people. Specifically, we focus on inequalities in access to clinical genetics services and the lack of genetic and phenomic reference data to inform diagnoses. We provide examples of ways in which these inequities are being addressed through Australian partnerships to support a harmonious and inclusive approach to ensure that benefits from traditional wisdom, community knowledge and shared experiences are interwoven to support and inform implementation of new knowledge from genomics and precision public health. This will serve to deliver benefits to all of our diverse citizens, including Indigenous populations.

The burden of rare cancers in the United States.

There are limited published data on the burden of rare cancers in the United States. By using data from the North American Association of Central Cancer Registries and the Surveillance, Epidemiology, and End Results program, the authors provide information on incidence rates, stage at diagnosis, and survival for more than 100 rare cancers (defined as an incidence of fewer than 6 cases per 100,000 individuals per year) in the United States. Overall, approximately 20% of patients with cancer in the United States are diagnosed with a rare cancer. Rare cancers make up a larger proportion of cancers diagnosed in Hispanic (24%) and Asian/Pacific Islander (22%) patients compared with non-Hispanic blacks (20%) and non-Hispanic whites (19%). More than two-thirds (71%) of cancers occurring in children and adolescents are rare cancers compared with less than 20% of cancers diagnosed in patients aged 65 years and older. Among solid tumors, 59% of rare cancers are diagnosed at regional or distant stages compared with 45% of common cancers. In part because of this stage distribution, 5-year relative survival is poorer for patients with a rare cancer compared with those diagnosed with a common cancer among both males (55% vs 75%) and females (60% vs 74%). However, 5-year relative survival is substantially higher for children and adolescents diagnosed with a rare cancer (82%) than for adults (46% for ages 65-79 years). Continued efforts are needed to develop interventions for prevention, early detection, and treatment to reduce the burden of rare cancers. Such discoveries can often advance knowledge for all cancers. CA Cancer J Clin 2017. © 2017 American Cancer Society. CA Cancer J Clin 2017;67:261-272. © 2017 American Cancer Society.

[A rare cause of severe panniculitis]. / Eine seltene Ursache einer schweren Pannikulitis.

A 58-year-old patient presented with a severe, episodic panniculitis of the upper legs. Necrosis of the fatty tissue and a suspected superinfection led to amputation of one leg. The panniculitis was caused by a hereditary deficiency of alpha-1 antitrypsin (AAT) due to a ZZ mutation of the AAT gene. Neutrophilic panniculitis is found in 0.1% of patients with the ZZ mutation and therefore is the rarest clinical manifestation of AAT deficiency. With the exception of mild COPD, the patient had no other typical clinical symptoms of AAT deficiency. Treatment with colchicum reduced the frequency and severity of the flares.

Global Carrier Rates of Rare Inherited Disorders Using Population Exome Sequences.

Exome sequencing has revealed the causative mutations behind numerous rare, inherited disorders, but it is challenging to find reliable epidemiological values for rare disorders. Here, I provide a genetic epidemiology method to identify the causative mutations behind rare, inherited disorders using two population exome sequences (1000 Genomes and NHLBI). I created global maps of carrier rate distribution for 18 recessive disorders in 16 diverse ethnic populations. Out of a total of 161 mutations associated with 18 recessive disorders, I detected 24 mutations in either or both exome studies. The genetic mapping revealed strong international spatial heterogeneities in the carrier patterns of the inherited disorders. I next validated this methodology by statistically evaluating the carrier rate of one well-understood disorder, sickle cell anemia (SCA). The population exome-based epidemiology of SCA [African (allele frequency (AF) = 0.0454, N = 2447), Asian (AF = 0, N = 286), European (AF = 0.000214, N = 4677), and Hispanic (AF = 0.0111, N = 362)] was not significantly different from that obtained from a clinical prevalence survey. A pair-wise proportion test revealed no significant differences between the two exome projects in terms of AF (46/48 cases; P > 0.05). I conclude that population exome-based carrier rates can form the foundation for a prospectively maintained database of use to clinical geneticists. Similar modeling methods can be applied to many inherited disorders.

Improving power for robust trans-ethnic meta-analysis of rare and low-frequency variants with a partitioning approach.

While genome-wide association studies have discovered numerous bona fide variants that are associated with common diseases and complex traits; these variants tend to be common in the population and explain only a small proportion of the phenotype variance. The search for the missing heritability has thus switched to rare and low-frequency variants, defined as <5% in the population, but which are expected to have a bigger impact on phenotypic outcomes. The rarer nature of these variants coupled with the curse of testing multiple variants across the genome meant that large sample sizes will still be required despite the assumption of bigger effect sizes. Combining data from multiple studies in a meta-analysis will continue to be the natural approach in boosting sample sizes. However, the population genetics of rare variants suggests that allelic and effect size heterogeneity across populations of different ancestries is likely to pose a greater challenge to trans-ethnic meta-analysis of rare variants than to similar analyses of common variants. Here, we introduce a novel method to perform trans-ethnic meta-analysis of rare and low-frequency variants. The approach is centered on partitioning the studies into distinct clusters using local inference of genomic similarity between population groups, with the aim to minimize both the number of clusters and between-study heterogeneity in each cluster. Through a series of simulations, we show that our approach either performs similarly to or outperforms conventional and recently introduced meta-analysis strategies, particularly in the presence of allelic heterogeneity.

Evaluation of SNP calling using single and multiple-sample calling algorithms by validation against array base genotyping and Mendelian inheritance.

BACKGROUND: With diminishing costs of next generation sequencing (NGS), whole genome analysis becomes a standard tool for identifying genetic causes of inherited diseases. Commercial NGS service providers in general not only provide raw genomic reads, but further deliver SNP calls to their clients. However, the question for the user arises whether to use the SNP data as is, or process the raw sequencing data further through more sophisticated SNP calling pipelines with more advanced algorithms. RESULTS: Here we report a detailed comparison of SNPs called using the popular GATK multiple-sample calling protocol to SNPs delivered as part of a 40x whole genome sequencing project by Illumina Inc of 171 human genomes of Arab descent (108 unrelated Qatari genomes, 19 trios, and 2 families with rare diseases) and compare them to variants provided by the Illumina CASAVA pipeline. GATK multi-sample calling identifies more variants than the CASAVA pipeline. The additional variants from GATK are robust for Mendelian consistencies but weak in terms of statistical parameters such as TsTv ratio. However, these additional variants do not make a difference in detecting the causative variants in the studied phenotype. CONCLUSION: Both pipelines, GATK multi-sample calling and Illumina CASAVA single sample calling, have highly similar performance in SNP calling at the level of putatively causative variants.

A call for action to improve access to care and treatment for patients with rare diseases in the Asia-Pacific region.

This article is a call for action to the relevant stakeholders to improve access to care and treatment for patients with rare diseases in the Asia-Pacific region by looking into three main areas: (a) developing legislative definitions to confer enforceable protection, (b) creating or strengthening policies by objectively measuring the impact brought about by rare diseases and establishing platforms to reach out to the rare disease community, and (c) fostering collaboration across sectors and countries. It is hoped that these suggested actions can catalyze discussions and progress in the region.

Ethical and economic considerations of rare diseases in ethnic minorities: the case of mucopolysaccharidosis VI in Colombia.

Mucopolysaccharidosis VI is an autosomal recessive lysosomal storage disorder associated with severe disability and premature death. The presence of a mucopolysaccharidosis-like disease in indigenous ethnic groups in Colombia can be inferred from archaeological findings. There are several indigenous patients with mucopolysaccharidosis VI currently receiving enzyme replacement therapy. We discuss the ethical and economic considerations, regarding both direct and indirect costs, of a high-cost orphan disease in a marginalised minority population in a developing country.

Bilateral Wyburn-Mason syndrome presenting as acute subarachnoid haemorrhage - a very rare congenital neurocutaneous [corrected] disorder.

A 30 year old young male was admitted to our department after experiencing clinical symptoms of a subarachnoid haemorrhage. Imaging studies revealed large cerebral AVMs. Fundus examination of the left eye demonstrated a retinal racemose AVM almost completely covering the posterior pole of the eye. Wyburn-Mason syndrome is a very rare congenital neurocutaneous disorder comprising of vascular malformations of the retina, ipsilateral cerebral AVMs and occasionally lesions in the oronasopharyngeal area. Subarachnoid haemorrhage associated with Wyburn-Mason syndrome has been described in only 5 patients in the literature since 1973. The finding of retinal AVMs should warrant cerebral imaging studies including CT- or MR-angiography.

Ethics, policy, and rare genetic disorders: the case of Gaucher disease in Israel.

Gaucher disease is a rare, chronic, ethnic-specific genetic disorder affecting Jews of Eastern European descent. It is extremely expensive to treat and presents difficult dilemmas for officials and patients in Israel where many patients live. First, high-cost, high-benefit, but low volume treatment for Gaucher creates severe allocation dilemmas for policy makers. Allocation policies driven by cost effectiveness, age, opportunity or need make it difficult to justify funding. Process oriented decision making based on terms of fair cooperation or decisions invoking the "rule of rescue" risk discriminating against minorities who may already suffer from inequitable distribution of heath care resources. Apart from cost, Gaucher disease prompts questions about abortion. Unlike severe genetic disorders, Gaucher offers no grounds for abortion and, in many ways, is analogous to gender based abortions that are prohibited regardless of fetal age. Finally, Gaucher raises concerns about the disclosure of genetic information. These affect potential carriers asked to participate in population studies and carriers and patients who must consider disclosure to others. These concerns weigh the right to privacy against communal interests and bilateral commitments.