The RD-Connect Registry & Biobank Finder: a tool for sharing aggregated data and metadata among rare disease researchers.

Eur J Hum Genet. 2018 05;26(5):631-643

Authors: Gainotti S, Torreri P, Wang CM, Reihs R, Mueller H, Heslop E, Roos M, Badowska DM, de Paulis F, Kodra Y, Carta C, Martìn EL, Miller VR, Filocamo M, Mora M, Thompson M, Rubinstein Y, Posada de la Paz M, Monaco L, Lochmüller H, Taruscio D

Abstract
In rare disease (RD) research, there is a huge need to systematically collect biomaterials, phenotypic, and genomic data in a standardized way and to make them findable, accessible, interoperable and reusable (FAIR). RD-Connect is a 6 years global infrastructure project initiated in November 2012 that links genomic data with patient registries, biobanks, and clinical bioinformatics tools to create a central research resource for RDs. Here, we present RD-Connect Registry & Biobank Finder, a tool that helps RD researchers to find RD biobanks and registries and provide information on the availability and accessibility of content in each database. The finder concentrates information that is currently sparse on different repositories (inventories, websites, scientific journals, technical reports, etc.), including aggregated data and metadata from participating databases. Aggregated data provided by the finder, if appropriately checked, can be used by researchers who are trying to estimate the prevalence of a RD, to organize a clinical trial on a RD, or to estimate the volume of patients seen by different clinical centers. The finder is also a portal to other RD-Connect tools, providing a link to the RD-Connect Sample Catalogue, a large inventory of RD biological samples available in participating biobanks for RD research. There are several kinds of users and potential uses for the RD-Connect Registry & Biobank Finder, including researchers collaborating with academia and the industry, dealing with the questions of basic, translational, and/or clinical research. As of November 2017, the finder is populated with aggregated data for 222 registries and 21 biobanks.

PMID: 29396563 [PubMed - indexed for MEDLINE]

7 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"Rare Diseases"[Mesh] OR "orphan disease"

These pubmed results were generated on 2019/02/14

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

7 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"Rare Diseases"[Mesh] OR "orphan disease"

These pubmed results were generated on 2019/02/14

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Lung and airway shape in neuroendocrine cell hyperplasia of infancy.

Pediatr Radiol. 2018 11;48(12):1745-1754

Authors: Mastej EJ, DeBoer EM, Humphries SM, Cook MC, Hunter KS, Liptzin DR, Weinman JP, Deterding RR

Abstract
BACKGROUND: Neuroendocrine cell hyperplasia of infancy (NEHI) is a rare lung disease associated with significant air trapping. Although chest CT is crucial in establishing a diagnosis, CT and biopsy findings do not reveal airway abnormalities to explain the air trapping.
OBJECTIVE: We compared lung and airway morphology obtained from chest CT scans in children with NEHI and control children. In the children with NEHI, we explored relationships between lung and airway shape and lung function.
MATERIALS AND METHODS: We performed a retrospective review of children with NEHI who underwent clinical chest CT. We identified control children of similar size and age. We created lung masks and airway skeletons using semi-automated software and compared them using statistical shape modeling methods. Then we calculated a logistic regression model using lung and airway shape to differentiate NEHI from controls, and we compared shape model parameters to lung function measurements.
RESULTS: Airway and lung shapes were statistically different between children with NEHI and controls. We noted a broad lung apex in the children with NEHI and a significantly increased apical anterior-posterior lung diameter. A logistic regression model including lung shape was 90% accurate in differentiating children with NEHI from controls. Correlation coefficients were significant between lung function values and lung and airway shape.
CONCLUSION: Lung and airway shapes were different between children with NEHI and control children in this cohort. Children with NEHI had an increased anteroposterior diameter of their lungs that might be useful in the diagnostic criteria.

PMID: 29955904 [PubMed - indexed for MEDLINE]

Peritoneal Carcinomatosis of Rare Ovarian Origin Treated by Cytoreductive Surgery and Hyperthermic Intraperitoneal Chemotherapy: A Multi-Institutional Cohort from PSOGI and BIG-RENAPE.

Ann Surg Oncol. 2018 Jun;25(6):1668-1675

Authors: Mercier F, Bakrin N, Bartlett DL, Goere D, Quenet F, Dumont F, Heyd B, Abboud K, Marolho C, Villeneuve L, Glehen O, PSOGI Working Group, BIG-RENAPE Working Group

Abstract
PURPOSE: Ovarian cancer is the most common deadly cancer of gynecologic origin. Patients often are diagnosed at advanced stage with peritoneal metastasis. There are many rare histologies of ovarian cancer; some have outcomes worse than serous ovarian cancer. Cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) can be considered for patients with recurrence. This study was designed to assess the impact of CRS and HIPEC on survival of patient with peritoneal metastasis from rare ovarian malignancy.
METHODS: A prospective, multicentric, international database was retrospectively searched to identify all patients with rare ovarian tumor (mucinous, clear cells, endometrioid, small cell hypercalcemic, and other) and peritoneal metastasis who underwent CRS and HIPEC through the Peritoneal Surface Oncology Group International (PSOGI) and BIG-RENAPE working group. The postoperative complications, long-term results, and principal prognostic factors were analyzed.
RESULTS: The analysis included 210 patients with a median follow-up of 43.5 months. Median overall survival (OS) was 69.3 months, and the 5-year OS was 57.7%. For mucinous tumors, median OS and DFS were not reached at 5 years. For granulosa tumors, median overall survival was not reached at 5 years, and median DFS was 34.6 months. Teratoma or germinal tumor showed median overall survival and DFS that were not reached at 5 years. Differences in OS were not statistically significant between histologies (p = 0.383), whereas differences in DFS were (p < 0.001).
CONCLUSIONS: CRS and HIPEC may increases long-term survival in selected patients with peritoneal metastasis from rare ovarian tumors especially in mucinous, granulosa, or teratoma histological subtypes.

PMID: 29637438 [PubMed - indexed for MEDLINE]

Meeting Patients' Right to the Correct Diagnosis: Ongoing International Initiatives on Undiagnosed Rare Diseases and Ethical and Social Issues.

Int J Environ Res Public Health. 2018 09 21;15(10):

Authors: Gainotti S, Mascalzoni D, Bros-Facer V, Petrini C, Floridia G, Roos M, Salvatore M, Taruscio D

Abstract
The time required to reach a correct diagnosis is a key concern for rare disease (RD) patients. Diagnostic delay can be intolerably long, often described as an "odyssey" and, for some, a diagnosis may remain frustratingly elusive. The International Rare Disease Research Consortium proposed, as ultimate goal for 2017⁻2027, to enable all people with a suspected RD to be diagnosed within one year of presentation, if the disorder is known. Subsequently, unsolved cases would enter a globally coordinated diagnostic and research pipeline. In-depth analysis of the genotype through next generation sequencing, together with a standardized in-depth phenotype description and sophisticated high-throughput approaches, have been applied as diagnostic tools to increase the chance of a timely and accurate diagnosis. The success of this approach is evident in the Orphanet database. From 2010 to March 2017 over 600 new RDs and roughly 3600 linked genes have been described and identified. However, combination of -omics and phenotype data, as well as international sharing of this information, has raised ethical concerns. Values to be assessed include not only patient autonomy but also family implications, beneficence, non-maleficence, justice, solidarity and reciprocity, which must be respected and promoted and, at the same time, balanced among each other. In this work we suggest that, to maximize patients' involvement in the search for a diagnosis and identification of new causative genes, undiagnosed patients should have the possibility to: (1) actively participate in the description of their phenotype; (2) choose the level of visibility of their profile in matchmaking databases; (3) express their preferences regarding return of new findings, in particular which level of Variant of Unknown Significance (VUS) significance should be considered relevant to them. The quality of the relationship between individual patients and physicians, and between the patient community and the scientific community, is critically important for optimizing the use of available data and enabling international collaboration in order to provide a diagnosis, and the attached support, to unsolved cases. The contribution of patients to collecting and coding data comprehensively is critical for efficient use of data downstream of data collection.

PMID: 30248891 [PubMed - indexed for MEDLINE]

[Enforcement of a new data protection law in Europe: A threat and an opportunity for registries and cohorts in the field of rare diseases].

Rev Med Interne. 2018 10;39(10):769-771

Authors: Aymé S

PMID: 29625715 [PubMed - indexed for MEDLINE]

SPEG-deficient skeletal muscles exhibit abnormal triad and defective calcium handling.

Hum Mol Genet. 2018 05 01;27(9):1608-1617

Authors: Huntoon V, Widrick JJ, Sanchez C, Rosen SM, Kutchukian C, Cao S, Pierson CR, Liu X, Perrella MA, Beggs AH, Jacquemond V, Agrawal PB

Abstract
Centronuclear myopathies (CNM) are a subtype of congenital myopathies (CM) characterized by skeletal muscle weakness and an increase in the number of central myonuclei. We have previously identified three CNM probands, two with associated dilated cardiomyopathy, carrying striated preferentially expressed gene (SPEG) mutations. Currently, the role of SPEG in skeletal muscle function is unclear as constitutive SPEG-deficient mice developed severe dilated cardiomyopathy and died in utero. We have generated a conditional Speg-KO mouse model and excised Speg by crosses with striated muscle-specific cre-expressing mice (MCK-Cre). The resulting litters had a delay in Speg excision consistent with cre expression starting in early postnatal life and, therefore, an extended lifespan up to a few months. KO mice were significantly smaller and weaker than their littermate-matched controls. Histopathological skeletal muscle analysis revealed smaller myofibers, marked fiber-size variability, and poor integrity and low number of triads. Further, SPEG-deficient muscle fibers were weaker by physiological and in vitro studies and exhibited abnormal Ca2+ handling and excitation-contraction (E-C) coupling. Overall, SPEG deficiency in skeletal muscle is associated with fewer and abnormal triads, and defective calcium handling and excitation-contraction coupling, suggesting that therapies targeting calcium signaling may be beneficial in such patients.

PMID: 29474540 [PubMed - indexed for MEDLINE]

[Point-of-care ultrasound for diagnosis and treatment of rare diseases: an unusual case of a peculiar thrombus in transit].

Emergencias. 2017 10;29(5):361-362

Authors: Lazzari R, Moline Pareja A, Turbau Valls M

PMID: 29077302 [PubMed - indexed for MEDLINE]

Erythematous Nodule on the Face of a Child: Challenge.

Am J Dermatopathol. 2018 Sep;40(9):e119-e120

Authors: Biederman L, Bhatti T, Taylor JA, Rubin AI

PMID: 30124487 [PubMed - indexed for MEDLINE]

Erythematous Nodule on the Face of a Child: Answer.

Am J Dermatopathol. 2018 Sep;40(9):699-700

Authors: Biederman L, Bhatti T, Taylor JA, Rubin AI

PMID: 30119103 [PubMed - indexed for MEDLINE]

ROHHAD Syndrome, a Rare Cause of Hypothalamic Obesity: Report of Two Cases

J Clin Res Pediatr Endocrinol. 2018 11 29;10(4):382-386

Authors: Şiraz ÜG, Ökdemir D, Direk G, Akın L, Hatipoğlu N, Kendirci M, Kurtoğlu S

Abstract
Rapid-onset obesity with hypoventilation, hypothalamic dysfunction and autonomic dysregulation (ROHHAD) syndrome is a rare disease that is difficult to diagnosis and distinguish from genetic obesity syndromes. The underlying causes of the disease have not been fully explained. Hypothalamic dysfunction causes endocrine problems, respiratory dysfunction and autonomic alterations. Currently there are around 80 reported patients although this is likely due to underdiagnosis due to lack of recognition. We present two female patients suspected of ROHHAD due to weight gain starting in early childhood. Clinical and biochemical findings such as respiratory and circulatory dysfunction, hypothalamic hypernatremia, central hypothyrodism, hyperprolactinemia and central early puberty in these patients matched the criteria for ROHHAD syndrome. ROHHAD syndrome should be considered in the differential diagnosis of monogenic obesity.

PMID: 29553042 [PubMed - indexed for MEDLINE]

Liquid Chromatography-High Resolution Mass Spectrometry Analysis of Platelet Frataxin as a Protein Biomarker for the Rare Disease Friedreich's Ataxia.

Anal Chem. 2018 02 06;90(3):2216-2223

Authors: Guo L, Wang Q, Weng L, Hauser LA, Strawser CJ, Rocha AG, Dancis A, Mesaros C, Lynch DR, Blair IA

Abstract
Friedreich's ataxia (FA) is an autosomal recessive disease caused by an intronic GAA triplet expansion in the FXN gene, leading to reduced expression of the mitochondrial protein frataxin. FA is estimated to affect 1 in 50 000 with a mean age of death in the fourth decade of life. There are no approved treatments for FA, although experimental approaches, which involve up-regulation or replacement of frataxin protein, are being tested. Frataxin is undetectable in serum or plasma, and whole blood cannot be used because it is present in long-lived erythrocytes. Therefore, an assay was developed for analyzing frataxin in platelets, which have a half-life of 10 days. The assay is based on stable isotope dilution immunopurification two-dimensional nano-ultra high performance liquid chromatography/parallel reaction monitoring/mass spectrometry. The lower limit of quantification was 0.078 pg frataxin/μg protein, and the assay had 100% sensitivity and specificity for discriminating between controls and FA cases. The mean levels of control and FA platelet frataxin were 9.4 ± 2.6 and 2.4 ± 0.6 pg/μg protein, respectively. The assay should make it possible to rigorously monitor the effects of therapeutic interventions on frataxin expression in this devastating disease.

PMID: 29272104 [PubMed - indexed for MEDLINE]

Cryptococcoma mimicking a brain tumor in an immunocompetent patient: case report of an extremely rare presentation.

Sao Paulo Med J. 2018 Sep-Oct;136(5):492-496

Authors: Paiva ALC, Aguiar GB, Lovato RM, Zanetti AVD, Panagopoulos AT, Veiga JCE

Abstract
CONTEXT: Central nervous system (CNS) infectious diseases have high prevalence in developing countries and their proper diagnosis and treatment are very important for public health planning. Cryptococcus neoformans is a fungus that may cause several CNS manifestations, especially in immunocompromised patients. Cryptococcal meningitis is the most common type of involvement. Mass-effect lesions are uncommon: they are described as cryptococcomas and their prevalence is even lower among immunocompetent patients. The aim here was to report an extremely rare case of cryptococcoma causing a mass effect and mimicking a brain tumor in an immunocompetent patient. The literature on CNS cryptococcal infections was reviewed with emphasis on cryptococcomas. Clinical, surgical and radiological data on a female patient with this rare presentation of cryptococcoma mimicking a brain tumor are described.
CASE REPORT: A 54-year-old female patient presented to the emergency department with a rapid-onset progressive history of confusion and completely dependency for basic activities. Neuroimaging showed a left occipital lesion and neurosurgical treatment was proposed. From histopathological evaluation, a diagnosis of cryptococcoma was established. She received clinical support with antifungals, but despite optimal clinical treatment, her condition evolved to death.
CONCLUSIONS: Cryptococcal infections have several forms of presentation and, in immunocompetent patients, their manifestation may be even more different. Cryptococcoma is an extremely rare presentation in which proper surgical and clinical treatment should be instituted as quickly as possible, but even so, there is a high mortality rate.

PMID: 29116307 [PubMed - indexed for MEDLINE]

20 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"Rare Diseases"[Mesh] OR "orphan disease"

These pubmed results were generated on 2019/02/07

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

7 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"Rare Diseases"[Mesh] OR "orphan disease"

These pubmed results were generated on 2019/02/06

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

20 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"Rare Diseases"[Mesh] OR "orphan disease"

These pubmed results were generated on 2019/02/05

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

20 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"Rare Diseases"[Mesh] OR "orphan disease"

These pubmed results were generated on 2019/02/05

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Mammalian Hbs1L deficiency causes congenital anomalies and developmental delay associated with Pelota depletion and 80S monosome accumulation.

PLoS Genet. 2019 Feb 01;15(2):e1007917

Authors: O'Connell AE, Gerashchenko MV, O'Donohue MF, Rosen SM, Huntzinger E, Gleeson D, Galli A, Ryder E, Cao S, Murphy Q, Kazerounian S, Morton SU, Schmitz-Abe K, Gladyshev VN, Gleizes PE, Séraphin B, Agrawal PB

Abstract
Hbs1 has been established as a central component of the cell's translational quality control pathways in both yeast and prokaryotic models; however, the functional characteristics of its human ortholog (Hbs1L) have not been well-defined. We recently reported a novel human phenotype resulting from a mutation in the critical coding region of the HBS1L gene characterized by facial dysmorphism, severe growth restriction, axial hypotonia, global developmental delay and retinal pigmentary deposits. Here we further characterize downstream effects of the human HBS1L mutation. HBS1L has three transcripts in humans, and RT-PCR demonstrated reduced mRNA levels corresponding with transcripts V1 and V2 whereas V3 expression was unchanged. Western blot analyses revealed Hbs1L protein was absent in the patient cells. Additionally, polysome profiling revealed an abnormal aggregation of 80S monosomes in patient cells under baseline conditions. RNA and ribosomal sequencing demonstrated an increased translation efficiency of ribosomal RNA in Hbs1L-deficient fibroblasts, suggesting that there may be a compensatory increase in ribosome translation to accommodate the increased 80S monosome levels. This enhanced translation was accompanied by upregulation of mTOR and 4-EBP protein expression, suggesting an mTOR-dependent phenomenon. Furthermore, lack of Hbs1L caused depletion of Pelota protein in both patient cells and mouse tissues, while PELO mRNA levels were unaffected. Inhibition of proteasomal function partially restored Pelota expression in human Hbs1L-deficient cells. We also describe a mouse model harboring a knockdown mutation in the murine Hbs1l gene that shared several of the phenotypic elements observed in the Hbs1L-deficient human including facial dysmorphism, growth restriction and retinal deposits. The Hbs1lKO mice similarly demonstrate diminished Pelota levels that were rescued by proteasome inhibition.

PMID: 30707697 [PubMed - as supplied by publisher]

Diagnosis of Mucopolysaccharidosis Based on History and Clinical Features: Evidence from the Bajio Region of Mexico.

Cureus. 2018 Nov 20;10(11):e3617

Authors: Colmenares-Bonilla D, Colin-Gonzalez C, Gonzalez-Segoviano A, Esquivel Garcia E, Vela-Huerta MM, Lopez-Gomez FG

Abstract
Introduction Mucopolysaccharidosis (MPS) are infrequent deposit diseases; generally, the diagnosis is delayed until symptoms appear. Age or presentation is related to the severity of the disease. A substantial number of patients are misdiagnosed since they describe nonspecific initial symptoms and signs in common. The aim of this study is to describe the common characteristics of patients with mucopolysaccharidosis already diagnosed, treated in hospitals of the Guanajuato Health System, with a special focus on early manifestations in order to review early clinical suspect manifestations. Methods A multicenter, descriptive, observational study was conducted to evaluate the cases of mucopolysaccharidosis treated and diagnosed. The study was carried out in the Pediatric departments of five big important hospitals of Bajio Mexico region in the period from February to August 2016. Results Eighteen patients were identified, 13 men and five women, with an average age of 8.6 years. The most frequent mucopolysaccharidosis was type IV A (Morquio) in seven patients, followed by type I (Hurler) in four patients, three patients for type III (San Filippo), two patients for type II (Hunter), and two patients for type VI (Maroteaux-Lamie). The commonest clinical manifestations at diagnosis were dimorphism, triangular dorsal hump, skeletal alterations (genu valgus, short stature, and flat feet), and a limited range of movement in the major joints. Non-skeletal manifestations, such as an umbilical/inguinal hernia and hepato-splenomegaly, were very frequent. In a majority of patients with mucopolysaccharidosis, the radiological data of the disease were found: they were most severe in type IV and type VI, mild in type I and II, and none in MPS III. A diagnosis was made in all patients by a clinical and radiological evaluation and confirmed by an enzymatic study. Conclusions In all rare diseases, a suspicion diagnosis is based on subtle characteristics that manifest themselves in a few different organs and systems may be mild. Suspicion by the physician and the need to strengthen collaboration patterns between different specialities play an important role in the early diagnosis and treatment of these conditions.

PMID: 30705788 [PubMed]