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1.
BMC Bioinformatics ; 20(1): 496, 2019 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-31615419

RESUMO

BACKGROUND: When applying genomic medicine to a rare disease patient, the primary goal is to identify one or more genomic variants that may explain the patient's phenotypes. Typically, this is done through annotation, filtering, and then prioritization of variants for manual curation. However, prioritization of variants in rare disease patients remains a challenging task due to the high degree of variability in phenotype presentation and molecular source of disease. Thus, methods that can identify and/or prioritize variants to be clinically reported in the presence of such variability are of critical importance. METHODS: We tested the application of classification algorithms that ingest variant annotations along with phenotype information for predicting whether a variant will ultimately be clinically reported and returned to a patient. To test the classifiers, we performed a retrospective study on variants that were clinically reported to 237 patients in the Undiagnosed Diseases Network. RESULTS: We treated the classifiers as variant prioritization systems and compared them to four variant prioritization algorithms and two single-measure controls. We showed that the trained classifiers outperformed all other tested methods with the best classifiers ranking 72% of all reported variants and 94% of reported pathogenic variants in the top 20. CONCLUSIONS: We demonstrated how freely available binary classification algorithms can be used to prioritize variants even in the presence of real-world variability. Furthermore, these classifiers outperformed all other tested methods, suggesting that they may be well suited for working with real rare disease patient datasets.


Assuntos
Algoritmos , Doenças Genéticas Inatas/diagnóstico , Genômica/métodos , Mutação , Doenças Raras/diagnóstico , Doenças Genéticas Inatas/genética , Predisposição Genética para Doença , Genoma Humano , Humanos , Fenótipo , Polimorfismo Genético , Medicina de Precisão/métodos , Doenças Raras/genética , Estudos Retrospectivos , Análise de Sequência de DNA/métodos , Software
3.
Medicine (Baltimore) ; 98(35): e16909, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31464924

RESUMO

RATIONALE: Congenital hepatic fibrosis (CHF) is an autosomal recessive disease characterized by periportal fibrosis, portal hypertension, and renal cystic disease. Essentially, CHF is a variant of fibrocystic disorder in which liver and kidney are commonly affected. Other frequently associated conditions include Caroli syndrome and polycystic kidney disease. CHF is also a known accompaniment in an array of inherited disorders with multiorgan involvement. PATIENT CONCERNS: The 20-year-old male patient with declining vision (14 years duration), intermittent gingival bleeding (7 years duration), and abdominal distension (5 years duration), presented with exacerbation of these symptoms during the prior 2 months. The patient had been previously diagnosed with retinal macular degeneration, idiopathic thrombocytopenic purpura, and hepatosplenomegaly. DIAGNOSES: Liver biopsy showed disordered hepatic acini and fibrous parenchymal banding, indicative of CHF. INTERVENTIONS: After the treatment of diuresis and liver protectants, the clinical symptoms of the patients were improved. We subsequently recommend chromosomal analysis, although the family refused. OUTCOMES: Three months after discharge, the patient was followed up by telephone. The patient had obvious abdominal distension and we advised that he should be admitted again. But the family refused. LESSONS: CHF is an AR disease resulting in portal hypertension and often associated with renal malformations. CHF is also linked to a number of other disorders, many of which are ciliopathies. Because the clinical manifestations of CHF are nonspecific or lacking, its diagnosis is problematic, relying largely on liver biopsy. Once CHF is identified, physicians are obligated to investigate other organ systems, particularly a search for neuromuscular, retina or renal involvement. This case underscores the value of radiologic imaging, pathologic examination, and genetic testing in successfully diagnosing a rare disease.


Assuntos
Doenças Genéticas Inatas/diagnóstico , Cirrose Hepática/diagnóstico , Fígado/patologia , Biópsia , Doenças Genéticas Inatas/complicações , Doenças Genéticas Inatas/patologia , Hemorragia Gengival/etiologia , Humanos , Cirrose Hepática/complicações , Cirrose Hepática/patologia , Degeneração Macular , Masculino , Recusa do Paciente ao Tratamento , Adulto Jovem
6.
Hum Genet ; 138(10): 1117-1122, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31243543

RESUMO

The Israeli population mainly includes Jews, Muslim and Christian Arabs, and Druze. Data on genetic diseases present in the population have been systematically collected and are available online in the Israeli national genetic database. Among the Israeli Arabs in December 31 2018, the database included molecular data on six diseases relatively frequent in the whole population: thalassemia, familial Mediterranean fever (FMF), cystic fibrosis, deafness, phenylketonuria or congenital adrenal hyperplasia as well as data on 632 autosomal recessive diseases among Muslim Israeli Arabs, 52 among the Christian Arabs and 79 among Druze. A single variant was characterized in 590 out of the 771 genes causing disorders in which the molecular basis was known. Many of the variants reported among Arabs in Israel are novels, most being found in one community only. Some variants are ancient and for instance, consistent with the migration history, several variants are found in the Bedouins from the Negev as well as from the Arab peninsula. In the 181 other disorders more than one variant was characterized either in the same gene or in more than one gene. While it is probable that most of these cases represent random events in some cases the reason may be a selective advantage to the heterozygotes.


Assuntos
Árabes/genética , Genes Recessivos , Doenças Genéticas Inatas/epidemiologia , Doenças Genéticas Inatas/genética , Predisposição Genética para Doença , Doenças Genéticas Inatas/diagnóstico , Variação Genética , Heterozigoto , Humanos , Israel/epidemiologia , Programas de Rastreamento , Vigilância da População
9.
Medicine (Baltimore) ; 98(20): e15600, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31096464

RESUMO

INTRODUCTION: Congenital hepatic fibrosis (CHF) is a rare autosomal recessive disease derived from biliary dysgenesis secondary to ductal plate malformation and is often accompanied by renal cysts or increased renal echogenicity. PATIENT CONCERNS: A 25-year-old woman was admitted to our hospital with splenomegaly and hepatic cirrhosis of a 3-month duration and fever accompanied by abdominal pain for 3 days. The second patient was a 25-year-old male referred to our hospital with hepatomegaly and splenomegaly of 6-year duration who had experienced fever for 3 months and abdominal distension for 1 week. Both 25-year-old patients were found to have CHF with polycystic kidney disease. DIAGNOSIS: Radiological imaging, including computed tomography (CT), magnetic resonance imaging (MRI), and sonography, revealed hepatic fibrosis, portal hypertension, splenomegaly, ascites, bile duct malformation, polycystic kidneys, and CHF. For the first patient, a liver biopsy confirmed the pathological features of CHF, and genetic testing revealed three heterozygous missense mutations, which were classified as "undetermined" in the public Wilson's disease/ATP7B and ADPKD/PKD1 databases. INTERVENTIONS: The first patient had undergone a splenectomy for anemia 2 months previously. Because there is no radical cure for CHF, and due to economic reasons, neither patient received liver transplantation. Therefore, we administered only anti-fibrotic supportive treatment for symptoms. OUTCOMES: Both patients were discharged after their symptoms improved, and both survived for 2 years of follow-up. CONCLUSION: These cases highlight the value of radiological imaging, pathological examination, and genetic evaluation for the diagnosis of CHF. When an individual with unexplained cirrhosis presents with bile duct dilation and malformation as well as polycystic kidneys, the possibility of CHF should be considered. For individuals found to have polycystic kidneys at a young age, the results of liver function tests and imaging examinations including Fibroscan imaging should be continuously and dynamically monitored to enable early diagnosis of CHF.


Assuntos
Doenças Genéticas Inatas/diagnóstico , Cirrose Hepática/diagnóstico , Adulto , Doenças dos Ductos Biliares/etiologia , Feminino , Doenças Genéticas Inatas/complicações , Doenças Genéticas Inatas/diagnóstico por imagem , Doenças Genéticas Inatas/patologia , Humanos , Hipertensão Portal/etiologia , Cirrose Hepática/complicações , Cirrose Hepática/diagnóstico por imagem , Cirrose Hepática/patologia , Masculino , Doenças Renais Policísticas/etiologia , Esplenomegalia/etiologia
10.
J Med Case Rep ; 13(1): 113, 2019 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-31036085

RESUMO

BACKGROUND: Isolated adrenocorticotropic hormone deficiency is one kind of hypopituitarism and is triggered by various diseases including autoimmune disorder and/or autoimmune hypophysitis. Adrenocorticotropic hormone deficiency brings out various serious symptoms such as severe hypoglycemia, hypotensive shock, and disturbance of consciousness. CASE PRESENTATION: Here we report a case of 65-year-old Japanese man who developed idiopathic and isolated adrenocorticotropic hormone deficiency. He had continued epigastric comfort without any symptom of hypoglycemia or any autoimmune abnormality. Since he continued to complain of mild epigastric discomfort and general malaise, he was misdiagnosed as having functional dyspepsia and a depression state and took medicine for them for several months. Infection markers and several antibodies which we examined were all negative. An abdominal computed tomography scan showed no mass in adrenal tissue; contrast magnetic resonance imaging of his brain showed that pituitary size was within normal range, and pituitary gland deep dyeing delay and/or deeply stained deficit were not observed. However, in a corticotropin-releasing hormone load test, response of adrenocorticotropic hormone and cortisol was poor after corticotropin-releasing hormone loading, and in growth hormone-releasing peptide 2 load test, adrenocorticotropic hormone response was poor, suggesting the presence of adrenocorticotropic hormone deficiency. Therefore, we started treatment with hydrocortisone, and his various symptoms were soon mitigated. CONCLUSIONS: We should bear in mind the possibility of adrenocorticotropic hormone deficiency even when patients complain of epigastric discomfort or general malaise alone.


Assuntos
Dor Abdominal/diagnóstico , Hormônio Adrenocorticotrópico/deficiência , Anti-Inflamatórios/uso terapêutico , Doenças do Sistema Endócrino/diagnóstico , Doenças Genéticas Inatas/diagnóstico , Hidrocortisona/uso terapêutico , Hipoglicemia/diagnóstico , Dor Abdominal/etiologia , Idoso , Diagnóstico Tardio , Doenças do Sistema Endócrino/complicações , Doenças Genéticas Inatas/complicações , Humanos , Hipoglicemia/complicações , Masculino , Testes de Função Hipofisária , Resultado do Tratamento
11.
Hum Genet ; 138(6): 673-679, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31069506

RESUMO

The study of Mendelian diseases and the identification of their causative genes are of great significance in the field of genetics. The evaluation of the pathogenicity of genes and the total number of Mendelian disease genes are both important questions worth studying. However, very few studies have addressed these issues to date, so we attempt to answer them in this study. We calculated the gene pathogenicity prediction (GPP) score by a machine learning approach (random forest algorithm) to evaluate the pathogenicity of genes. When we applied the GPP score to the testing gene set, we obtained an accuracy of 80%, recall of 93% and area under the curve of 0.87. Our results estimated that a total of 10,384 protein-coding genes were Mendelian disease genes. Furthermore, we found the GPP score was positively correlated with the severity of disease. Our results indicate that GPP score may provide a robust and reliable guideline to predict the pathogenicity of protein-coding genes. To our knowledge, this is the first trial to estimate the total number of Mendelian disease genes.


Assuntos
Algoritmos , Doenças Genéticas Inatas/genética , Predisposição Genética para Doença/genética , Aprendizado de Máquina , Genes Dominantes/genética , Genes Recessivos/genética , Doenças Genéticas Inatas/diagnóstico , Humanos , Curva ROC
12.
Int J Lab Hematol ; 41 Suppl 1: 131-141, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31069978

RESUMO

Advances in molecular genetic sequencing techniques have contributed to the elucidation of previously unknown germline mutations responsible for inherited thrombocytopenia (IT). Regardless of age of presentation and severity of symptoms related to thrombocytopenia and/or platelet dysfunction, a subset of patients with IT are at increased risk of developing myeloid neoplasms during their life time, particularly those with germline autosomal dominant mutations in RUNX1, ANKRD26, and ETV6. Patients may present with isolated thrombocytopenia and megakaryocytic dysmorphia or atypia on baseline bone marrow evaluation, without constituting myelodysplasia (MDS). Bone marrow features may overlap with idiopathic thrombocytopenic purpura (ITP) or sporadic MDS leading to misdiagnosis. Progression to myelodysplastic syndrome/ acute myeloid leukemia (MDS/AML) may be accompanied by progressive bi- or pancytopenia, multilineage dysplasia, increased blasts, cytogenetic abnormalities, acquisition of bi-allelic mutations in the underlying gene with germline mutation, or additional somatic mutations in genes associated with myeloid malignancy. A subset of patients may present with MDS/AML at a young age, underscoring the growing concern for evaluating young patients with MDS/AML for germline mutations predisposing to myeloid neoplasm. Early recognition of germline mutation and predisposition to myeloid malignancy permits appropriate treatment, adequate monitoring for disease progression, proper donor selection for hematopoietic stem cell transplantation, as well as genetic counseling of the affected patients and their family members. Herein, we describe the clinical and diagnostic features of IT with germline mutations predisposing to myeloid neoplasms focusing on mutations involving RUNX1, ANKRD26, and ETV6.


Assuntos
Doenças Genéticas Inatas , Predisposição Genética para Doença , Mutação em Linhagem Germinativa , Leucemia Mieloide Aguda , Síndromes Mielodisplásicas , Proteínas de Neoplasias , Trombocitopenia , Aloenxertos , Genes Dominantes , Aconselhamento Genético , Doenças Genéticas Inatas/sangue , Doenças Genéticas Inatas/diagnóstico , Doenças Genéticas Inatas/genética , Doenças Genéticas Inatas/terapia , Neoplasias Hematológicas/sangue , Neoplasias Hematológicas/diagnóstico , Neoplasias Hematológicas/genética , Neoplasias Hematológicas/terapia , Transplante de Células-Tronco Hematopoéticas , Leucemia Mieloide Aguda/sangue , Leucemia Mieloide Aguda/diagnóstico , Leucemia Mieloide Aguda/genética , Leucemia Mieloide Aguda/terapia , Mutação , Síndromes Mielodisplásicas/sangue , Síndromes Mielodisplásicas/diagnóstico , Síndromes Mielodisplásicas/genética , Síndromes Mielodisplásicas/terapia , Trombocitopenia/sangue , Trombocitopenia/diagnóstico , Trombocitopenia/genética , Trombocitopenia/terapia
13.
Fertil Steril ; 111(6): 1151-1158, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31005312

RESUMO

OBJECTIVE: To evaluate the growth, health, and motor development of children born after preimplantation genetic diagnosis (PGD). DESIGN: Observational cohort study and comparison of 5-year-old children born after PGD to similar aged children born after IVF/intracytoplasmic sperm injection (ICSI) and children from families with a genetic disorder born after natural conception (NC). SETTING: University hospital. PATIENT(S): One hundred three children were included in the PGD group. The two control groups consisted of 90 children born after IVF/ICSI and 58 children born after NC. INTERVENTION(S): PGD. MAIN OUTCOME MEASURE(S): We measured height, weight, body circumferences, body mass index, and blood pressure and performed a dysmorphological and neurological examination. We also collected data about the children's medical history, health care consultations, and motor milestones. RESULT(S): The mean height, weight, and body mass index were comparable for all groups. Six (5.8%) PGD, four (4.4%) IVF/ICSI, and five (8.6%) NC children had a major congenital abnormality. The incidence of acute and chronic illnesses was similar in all groups. Motor milestones were achieved on time, but the IVF/ICSI group had a slightly younger mean sitting age. None of the children had severe neurological problems. CONCLUSION(S): Five-year-old children born after PGD show normal growth, health, and motor development when compared with children born after IVF/ICSI and NC children from families with a genetic disorder. TRIAL REGISTRATION NUMBER: NCT02149485.


Assuntos
Desenvolvimento Infantil , Saúde da Criança , Fertilização In Vitro/efeitos adversos , Doenças Genéticas Inatas/genética , Testes Genéticos , Infertilidade/terapia , Destreza Motora , Diagnóstico Pré-Implantação/métodos , Fatores Etários , Pressão Sanguínea , Estatura , Índice de Massa Corporal , Pré-Escolar , Feminino , Doenças Genéticas Inatas/diagnóstico , Doenças Genéticas Inatas/fisiopatologia , Nível de Saúde , Humanos , Infertilidade/diagnóstico , Infertilidade/fisiopatologia , Masculino , Medição de Risco , Fatores de Risco , Injeções de Esperma Intracitoplásmicas/efeitos adversos , Resultado do Tratamento , Ganho de Peso
16.
Mol Genet Genomic Med ; 7(2): e00606, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30816028

RESUMO

Attention has been focused on the field of genetics and genomics in Iran in recent years and some efforts have been enforced and implemented. However, they are totally not adequate, considering the advances in medical genetics and genomics in the past two decades around the world. Overall, considering the lack of medical genetics residency programs in the Iranian health education system, big demand due to high consanguinity and intraethnic marriages, there is a lag in genetic services and necessity to an immediate response to fill this big gap in Iran. As clarified in the National constitution fundamental law and re-emphasized in the 6th National Development Plan, the Iranian government authority is in charge of providing the standard level of health including genetic services to all Iranian individuals who are in need.


Assuntos
Utilização de Instalações e Serviços , Doenças Genéticas Inatas/diagnóstico , Testes Genéticos/estatística & dados numéricos , Genética Médica/estatística & dados numéricos , Diagnóstico Pré-Natal/estatística & dados numéricos , Análise de Sequência de DNA/estatística & dados numéricos , Bases de Dados Genéticas , Doenças Genéticas Inatas/epidemiologia , Doenças Genéticas Inatas/genética , Testes Genéticos/economia , Testes Genéticos/legislação & jurisprudência , Genética Médica/economia , Genética Médica/legislação & jurisprudência , Genética Médica/organização & administração , Humanos , Irã (Geográfico) , Diagnóstico Pré-Natal/economia , Análise de Sequência de DNA/economia
17.
Hum Genet ; 138(4): 389-409, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30887117

RESUMO

Incidence rates of Mendelian diseases vary among ethnic groups, and frequencies of variant types of causative genes also vary among human populations. In this study, we examined to what extent we can predict population frequencies of recessive disorders from genomic data, and explored better strategies for variant interpretation and classification. We used a whole-genome reference panel from 3552 general Japanese individuals constructed by the Tohoku Medical Megabank Organization (ToMMo). Focusing on 32 genes for 17 congenital metabolic disorders included in newborn screening (NBS) in Japan, we identified reported and predicted pathogenic variants through variant annotation, interpretation, and multiple ways of classifications. The estimated carrier frequencies were compared with those from the Japanese NBS data based on 1,949,987 newborns from a previous study. The estimated carrier frequency based on genomic data with a recent guideline of variant interpretation for the PAH gene, in which defects cause hyperphenylalaninemia (HPA) and phenylketonuria (PKU), provided a closer estimate to that by the observed incidence than the other methods. In contrast, the estimated carrier frequencies for SLC25A13, which causes citrin deficiency, were much higher compared with the incidence rate. The results varied greatly among the 11 NBS diseases with single responsible genes; the possible reasons for departures from the carrier frequencies by reported incidence rates were discussed. Of note, (1) the number of pathogenic variants increases by including additional lines of evidence, (2) common variants with mild effects also contribute to the actual frequency of patients, and (3) penetrance of each variant remains unclear.


Assuntos
Doenças Genéticas Inatas/diagnóstico , Doenças Genéticas Inatas/genética , Doenças do Recém-Nascido/diagnóstico , Doenças do Recém-Nascido/genética , Triagem Neonatal/métodos , Grupo com Ancestrais do Continente Asiático/genética , Grupo com Ancestrais do Continente Asiático/estatística & dados numéricos , Estudos de Coortes , Feminino , Frequência do Gene , Doenças Genéticas Inatas/epidemiologia , Estudo de Associação Genômica Ampla/normas , Heterozigoto , Humanos , Incidência , Recém-Nascido , Doenças do Recém-Nascido/epidemiologia , Japão/epidemiologia , Masculino , Padrões de Referência
18.
Pediatr Clin North Am ; 66(2): 281-293, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30819336

RESUMO

All patients should be offered prenatal screening and diagnosis. Testing options depend on many factors, including patient age, family history, and patient preference. Options are rapidly changing with emerging technology. Aneuploidy screening options include ultrasound, maternal analytes, and cell-free DNA. Prenatal chromosomal microarray is the recommended diagnostic test for patients with anomalies visualized on prenatal ultrasound. Prenatal whole exome sequencing is clinically available but is limited by challenges with counseling, interpretation, and turn-around time. Future technologies are emerging and may soon allow for translation of prenatal diagnosis to in utero therapy.


Assuntos
Doenças Genéticas Inatas/diagnóstico , Testes Genéticos/métodos , Diagnóstico Pré-Natal/métodos , Feminino , Feto , Humanos , Gravidez
19.
Pediatr. aten. prim ; 21(81): e1-e5, ene.-mar. 2019. tab
Artigo em Espanhol | IBECS | ID: ibc-184528

RESUMO

Solo puede asegurarse que la función tiroidea es normal cuando los niveles de hormona estimulante del tiroides y hormonas tiroideas tiroxina y triyodotironina libres son normales. Un patrón hormonal con tiroxina y triyodotironina libres elevadas y hormona estimulante del tiroides no suprimida es muy poco habitual, su principal causa es el síndrome de resistencia a hormonas tiroideas, entidad poco frecuente de causa genética que puede asociar síntomas de hipo e hipertiroidismo y cuyo diagnóstico requiere un alto índice de sospecha. En niños la única o principal manifestación puede ser un trastorno por déficit de atención con hiperactividad. Presentamos una familia caracterizada a partir del diagnóstico inicial de dos hermanas gemelas a los 20 meses de edad


It can only be ensured that thyroid function is normal when thyroid-stimulating hormone and free thyroid hormones thyroxine and triiodothyronine levels are normal. A hormonal pattern with elevated free thyroxine and triiodothyronine and unsuppressed thyroid-stimulating hormone is very rare, and its main cause is thyroid hormone resistance syndro¬me, a rare genetic entity that can associate symptoms of hypo and hyperthyroidism and whose diagnosis requires a high rate of suspicion. In children, the sole or main manifestation may be an attention deficit hyperactivity disorder. We present a family characterized by the initial diagnosis of twin sisters at 20 months of age


Assuntos
Humanos , Feminino , Lactente , Síndrome da Resistência aos Hormônios Tireóideos/diagnóstico , Hormônios Tireóideos/sangue , Transtornos do Crescimento/etiologia , Testes de Função Tireóidea/estatística & dados numéricos , Doenças Genéticas Inatas/diagnóstico
20.
Rev. lab. clín ; 12(1): 27-37, ene.-mar. 2019. ilus, graf
Artigo em Espanhol | IBECS | ID: ibc-176972

RESUMO

El término diagnóstico prenatal comprende todas las modalidades de diagnóstico dirigidas a detectar durante la gestación una anomalía congénita que incluya trastornos estructurales o funcionales. Un porcentaje de las mismas se debe a factores genéticos. El presente documento pretende detallar las indicaciones actuales de las pruebas invasivas y de las no invasivas, describir las pruebas de laboratorio que se utilizan en el diagnóstico prenatal de alteraciones genéticas y proponer esquemas de trabajo para el estudio de estas alteraciones genéticas


The term prenatal diagnosis includes all diagnostic modalities aimed at detecting a congenital anomaly during pregnancy that includes structural or functional disorders. A percentage of them are due to genetic factors. This document intends to detail the current indications of invasive and non-invasive tests, describe the laboratory tests used in the prenatal diagnosis of genetic alterations, and propose work schemes for the study of these genetic alterations


Assuntos
Humanos , Testes Genéticos/métodos , Diagnóstico Pré-Natal/métodos , Doenças Genéticas Inatas/diagnóstico , Transtornos Cromossômicos/diagnóstico , Marcadores Genéticos/genética , Aneuploidia , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Fatores de Risco , Padrões de Prática Médica
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