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1.
Orphanet J Rare Dis ; 18(1): 59, 2023 03 19.
Artículo en Inglés | MEDLINE | ID: mdl-36935482

RESUMEN

BACKGROUND: Terminal 6q deletions are rare, and the number of well-defined published cases is limited. Since parents of children with these aberrations often search the internet and unite via international social media platforms, these dedicated platforms may hold valuable knowledge about additional cases. The Chromosome 6 Project is a collaboration between researchers and clinicians at the University Medical Center Groningen and members of a Chromosome 6 support group on Facebook. The aim of the project is to improve the surveillance of patients with chromosome 6 aberrations and the support for their families by increasing the available information about these rare aberrations. This parent-driven research project makes use of information collected directly from parents via a multilingual online questionnaire. Here, we report our findings on 93 individuals with terminal 6q deletions and 11 individuals with interstitial 6q26q27 deletions, a cohort that includes 38 newly identified individuals. RESULTS: Using this cohort, we can identify a common terminal 6q deletion phenotype that includes microcephaly, dysplastic outer ears, hypertelorism, vision problems, abnormal eye movements, dental abnormalities, feeding problems, recurrent infections, respiratory problems, spinal cord abnormalities, abnormal vertebrae, scoliosis, joint hypermobility, brain abnormalities (ventriculomegaly/hydrocephaly, corpus callosum abnormality and cortical dysplasia), seizures, hypotonia, ataxia, torticollis, balance problems, developmental delay, sleeping problems and hyperactivity. Other frequently reported clinical characteristics are congenital heart defects, kidney problems, abnormalities of the female genitalia, spina bifida, anal abnormalities, positional foot deformities, hypertonia and self-harming behaviour. The phenotypes were comparable up to a deletion size of 7.1 Mb, and most features could be attributed to the terminally located gene DLL1. Larger deletions that include QKI (> 7.1 Mb) lead to a more severe phenotype that includes additional clinical characteristics. CONCLUSIONS: Terminal 6q deletions cause a common but highly variable phenotype. Most clinical characteristics can be linked to the smallest terminal 6q deletions that include the gene DLL1 (> 500 kb). Based on our findings, we provide recommendations for clinical follow-up and surveillance of individuals with terminal 6q deletions.


Asunto(s)
Anomalías Múltiples , Malformaciones del Sistema Nervioso , Medios de Comunicación Sociales , Femenino , Humanos , Anomalías Múltiples/genética , Deleción Cromosómica , Cromosomas Humanos Par 6 , Malformaciones del Sistema Nervioso/genética , Fenotipo , Convulsiones/genética
2.
Orphanet J Rare Dis ; 18(1): 60, 2023 03 19.
Artículo en Inglés | MEDLINE | ID: mdl-36935495

RESUMEN

BACKGROUND: Even with the introduction of new genetic techniques that enable accurate genomic characterization, knowledge about the phenotypic spectrum of rare chromosomal disorders is still limited, both in literature and existing databases. Yet this clinical information is of utmost importance for health professionals and the parents of children with rare diseases. Since existing databases are often hampered by the limited time and willingness of health professionals to input new data, we collected phenotype data directly from parents of children with a chromosome 6 disorder. These parents were reached via social media, and the information was collected via the online Chromosome 6 Questionnaire, which includes 115 main questions on congenital abnormalities, medical problems, behaviour, growth and development. METHODS: Here, we assess data consistency by comparing parent-reported phenotypes to phenotypes based on copies of medical files for the same individual (n = 20) and data availability by comparing the data available on specific characteristics reported by parents (n = 34) to data available in existing literature (n = 39). RESULTS: The reported answers to the main questions on phenotype characteristics were 85-95% consistent, and the consistency of answers to subsequent more detailed questions was 77-96%. For all but two main questions, significantly more data was collected from parents via the Chromosome 6 Questionnaire than was currently available in literature. For the topics developmental delay and brain abnormalities, no significant difference in the amount of available data was found. The only feature for which significantly more data was available in literature was a sub-question on the type of brain abnormality present. CONCLUSION: This is the first study to compare phenotype data collected directly from parents to data extracted from medical files on the same individuals. We found that the data was highly consistent, and phenotype data collected via the online Chromosome 6 Questionnaire resulted in more available information on most clinical characteristics when compared to phenotypes reported in literature reports thus far. We encourage active patient participation in rare disease research and have shown that parent-reported phenotypes are reliable and contribute to our knowledge of the phenotypic spectrum of rare chromosomal disorders.


Asunto(s)
Encefalopatías , Cromosomas Humanos Par 6 , Humanos , Aberraciones Cromosómicas , Proyectos de Investigación , Encuestas y Cuestionarios , Fenotipo , Padres
3.
Eur J Pediatr ; 182(6): 2683-2692, 2023 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-36997769

RESUMEN

The introduction of rapid exome sequencing (rES) for critically ill neonates admitted to the neonatal intensive care unit has made it possible to impact clinical decision-making. Unbiased prospective studies to quantify the impact of rES over routine genetic testing are, however, scarce. We performed a clinical utility study to compare rES to conventional genetic diagnostic workup for critically ill neonates with suspected genetic disorders. In a multicenter prospective parallel cohort study involving five Dutch NICUs, we performed rES in parallel to routine genetic testing for 60 neonates with a suspected genetic disorder and monitored diagnostic yield and the time to diagnosis. To assess the economic impact of rES, healthcare resource use was collected for all neonates. rES detected more conclusive genetic diagnoses than routine genetic testing (20% vs. 10%, respectively), in a significantly shorter time to diagnosis (15 days (95% CI 10-20) vs. 59 days (95% CI 23-98, p < 0.001)). Moreover, rES reduced genetic diagnostic costs by 1.5% (€85 per neonate). CONCLUSION:  Our findings demonstrate the clinical utility of rES for critically ill neonates based on increased diagnostic yield, shorter time to diagnosis, and net healthcare savings. Our observations warrant the widespread implementation of rES as first-tier genetic test in critically ill neonates with disorders of suspected genetic origin. WHAT IS KNOWN: • Rapid exome sequencing (rES) enables diagnosing rare genetic disorders in a fast and reliable manner, but retrospective studies with neonates admitted to the neonatal intensive care unit (NICU) indicated that genetic disorders are likely underdiagnosed as rES is not routinely used. • Scenario modeling for implementation of rES for neonates with presumed genetic disorders indicated an expected increase in costs associated with genetic testing. WHAT IS NEW: • This unique prospective national clinical utility study of rES in a NICU setting shows that rES obtained more and faster diagnoses than conventional genetic tests. • Implementation of rES as replacement for all other genetic tests does not increase healthcare costs but in fact leads to a reduction in healthcare costs.


Asunto(s)
Enfermedad Crítica , Pruebas Genéticas , Recién Nacido , Humanos , Secuenciación del Exoma , Estudios Prospectivos , Estudios Retrospectivos , Países Bajos , Estudios de Cohortes , Pruebas Genéticas/métodos
4.
Orphanet J Rare Dis ; 18(1): 68, 2023 03 24.
Artículo en Inglés | MEDLINE | ID: mdl-36964621

RESUMEN

BACKGROUND: Terminal 6p deletions are rare, and information on their clinical consequences is scarce, which impedes optimal management and follow-up by clinicians. The parent-driven Chromosome 6 Project collaborates with families of affected children worldwide to better understand the clinical effects of chromosome 6 aberrations and to support clinical guidance. A microarray report is required for participation, and detailed phenotype information is collected directly from parents through a multilingual web-based questionnaire. Information collected from parents is then combined with case data from literature reports. Here, we present our findings on 13 newly identified patients and 46 literature cases with genotypically well-characterised terminal and subterminal 6p deletions. We provide phenotype descriptions for both the whole group and for subgroups based on deletion size and HI gene content. RESULTS: The total group shared a common phenotype characterised by ocular anterior segment dysgenesis, vision problems, brain malformations, congenital defects of the cardiac septa and valves, mild to moderate hearing impairment, eye movement abnormalities, hypotonia, mild developmental delay and dysmorphic features. These characteristics were observed in all subgroups where FOXC1 was included in the deletion, confirming a dominant role for this gene. Additional characteristics were seen in individuals with terminal deletions exceeding 4.02 Mb, namely complex heart defects, corpus callosum abnormalities, kidney abnormalities and orofacial clefting. Some of these additional features may be related to the loss of other genes in the terminal 6p region, such as RREB1 for the cardiac phenotypes and TUBB2A and TUBB2B for the cerebral phenotypes. In the newly identified patients, we observed previously unreported features including gastrointestinal problems, neurological abnormalities, balance problems and sleep disturbances. CONCLUSIONS: We present an overview of the phenotypic characteristics observed in terminal and subterminal 6p deletions. This reveals a common phenotype that can be highly attributable to haploinsufficiency of FOXC1, with a possible additional effect of other genes in the 6p25 region. We also delineate the developmental abilities of affected individuals and report on previously unrecognised features, showing the added benefit of collecting information directly from parents. Based on our overview, we provide recommendations for clinical surveillance to support clinicians, patients and families.


Asunto(s)
Anomalías del Ojo , Cardiopatías Congénitas , Medios de Comunicación Sociales , Humanos , Fenotipo , Aberraciones Cromosómicas , Anomalías del Ojo/genética , Cardiopatías Congénitas/genética , Deleción Cromosómica , Cromosomas Humanos Par 6/genética
6.
Clin Genet ; 101(1): 127-133, 2022 01.
Artículo en Inglés | MEDLINE | ID: mdl-34612517

RESUMEN

Only two families have been reported with biallelic TMEM260 variants segregating with structural heart defects and renal anomalies syndrome (SHDRA). With a combination of genome, exome sequencing and RNA studies, we identified eight individuals from five families with biallelic TMEM260 variants. Variants included one multi-exon deletion, four nonsense/frameshifts, two splicing changes and one missense change. Together with the published cases, analysis of clinical data revealed ventricular septal defects (12/12), mostly secondary to truncus arteriosus (10/12), elevated creatinine levels (6/12), horse-shoe kidneys (1/12) and renal cysts (1/12) in patients. Three pregnancies were terminated on detection of severe congenital anomalies. Six patients died between the ages of 6 weeks and 5 years. Using a range of stringencies, carrier frequency for SHDRA was estimated at 0.0007-0.007 across ancestries. In conclusion, this study confirms the genetic basis of SHDRA, expands its known mutational spectrum and clarifies its clinical features. We demonstrate that SHDRA is a severe condition associated with substantial mortality in early childhood and characterised by congenital cardiac malformations with a variable renal phenotype.


Asunto(s)
Alelos , Cardiopatías Congénitas/diagnóstico , Cardiopatías Congénitas/genética , Enfermedades Renales/diagnóstico , Enfermedades Renales/genética , Proteínas de la Membrana/genética , Tronco Arterial/anomalías , Anomalías Múltiples/diagnóstico , Anomalías Múltiples/genética , Sustitución de Aminoácidos , Familia , Estudios de Asociación Genética , Predisposición Genética a la Enfermedad , Genotipo , Heterocigoto , Humanos , Fenotipo
7.
Eur J Hum Genet ; 29(11): 1669-1676, 2021 11.
Artículo en Inglés | MEDLINE | ID: mdl-34456334

RESUMEN

Deletions that include the gene TAB2 and TAB2 loss-of-function variants have previously been associated with congenital heart defects and cardiomyopathy. However, other features, including short stature, facial dysmorphisms, connective tissue abnormalities and a variable degree of developmental delay, have only been mentioned occasionally in literature and thus far not linked to TAB2. In a large-scale, social media-based chromosome 6 study, we observed a shared phenotype in patients with a 6q25.1 deletion that includes TAB2. To confirm if this phenotype is caused by haploinsufficiency of TAB2 and to delineate a TAB2-related phenotype, we subsequently sequenced TAB2 in patients with matching phenotypes and recruited patients with pathogenic TAB2 variants detected by exome sequencing. This identified 11 patients with a deletion containing TAB2 (size 1.68-14.31 Mb) and 14 patients from six families with novel truncating TAB2 variants. Twenty (80%) patients had cardiac disease, often mitral valve defects and/or cardiomyopathy, 18 (72%) had short stature and 18 (72%) had hypermobility. Twenty patients (80%) had facial features suggestive for Noonan syndrome. No substantial phenotypic differences were noted between patients with deletions and those with intragenic variants. We then compared our patients to 45 patients from the literature. All literature patients had cardiac diseases, but syndromic features were reported infrequently. Our study shows that the phenotype in 6q25.1 deletions is caused by haploinsufficiency of TAB2 and that TAB2 is associated not just with cardiac disease, but also with a distinct phenotype, with features overlapping with Noonan syndrome. We propose the name "TAB2-related syndrome".


Asunto(s)
Proteínas Adaptadoras Transductoras de Señales/genética , Cardiomiopatías/genética , Enanismo/genética , Enfermedades de las Válvulas Cardíacas/genética , Inestabilidad de la Articulación/genética , Fenotipo , Cardiomiopatías/patología , Cromosomas Humanos Par 6/genética , Enanismo/patología , Eliminación de Gen , Enfermedades de las Válvulas Cardíacas/patología , Humanos , Inestabilidad de la Articulación/patología , Válvula Mitral/patología , Síndrome
8.
Front Pediatr ; 9: 600556, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34136434

RESUMEN

Background: Genetic disorders are a substantial cause of infant morbidity and mortality and are frequently suspected in neonatal intensive care units. Non-specific clinical presentation or limitations to physical examination can result in a plethora of genetic testing techniques, without clear strategies on test ordering. Here, we review our 2-years experiences of rapid genetic testing of NICU patients in order to provide such recommendations. Methods: We retrospectively included all patients admitted to the NICU who received clinical genetic consultation and genetic testing in our University hospital. We documented reasons for referral for genetic consultation, presenting phenotypes, differential diagnoses, genetic testing requested and their outcomes, as well as the consequences of each (rapid) genetic diagnostic approach. We calculated diagnostic yield and turnaround times (TATs). Results: Of 171 included infants that received genetic consultation 140 underwent genetic testing. As a result of testing as first tier, 13/14 patients received a genetic diagnosis from QF-PCR; 14/115 from SNP-array; 12/89 from NGS testing, of whom 4/46 were diagnosed with a small gene panel and 8/43 with a large OMIM-morbid based gene panel. Subsequent secondary or tertiary analysis and/or additional testing resulted in five more diagnoses. TATs ranged from 1 day (QF-PCR) to a median of 14 for NGS and SNP-array testing, with increasing TAT in particular when many consecutive tests were performed. Incidental findings were detected in 5/140 tested patients (3.6%). Conclusion: We recommend implementing a broad NGS gene panel in combination with CNV calling as the first tier of genetic testing for NICU patients given the often unspecific phenotypes of ill infants and the high yield of this large panel.

9.
Orphanet J Rare Dis ; 16(1): 137, 2021 03 19.
Artículo en Inglés | MEDLINE | ID: mdl-33741030

RESUMEN

We report five patients with lung disease immuno-deficiency and chromosome breakage syndrome (LICS) but without recurrent infections and severe immunodeficiency. One patient had extended survival to 6.5 years. Hematopoietic stem-cell transplantation failed to cure another patient. Our findings suggest that the immunological abnormalities can be limited and do not fully explain the LICS phenotype.


Asunto(s)
Trasplante de Células Madre Hematopoyéticas , Enfermedades Pulmonares , Síndrome de Dificultad Respiratoria , Rotura Cromosómica , Humanos , Fenotipo , Estudios Retrospectivos
10.
Genome Med ; 12(1): 75, 2020 08 24.
Artículo en Inglés | MEDLINE | ID: mdl-32831124

RESUMEN

Exome sequencing is now mainstream in clinical practice. However, identification of pathogenic Mendelian variants remains time-consuming, in part, because the limited accuracy of current computational prediction methods requires manual classification by experts. Here we introduce CAPICE, a new machine-learning-based method for prioritizing pathogenic variants, including SNVs and short InDels. CAPICE outperforms the best general (CADD, GAVIN) and consequence-type-specific (REVEL, ClinPred) computational prediction methods, for both rare and ultra-rare variants. CAPICE is easily added to diagnostic pipelines as pre-computed score file or command-line software, or using online MOLGENIS web service with API. Download CAPICE for free and open-source (LGPLv3) at https://github.com/molgenis/capice .


Asunto(s)
Biología Computacional/métodos , Exoma , Variación Genética , Programas Informáticos , Frecuencia de los Genes , Estudios de Asociación Genética/métodos , Humanos , Mutación INDEL , Aprendizaje Automático , Técnicas de Diagnóstico Molecular , Anotación de Secuencia Molecular , Polimorfismo de Nucleótido Simple , Curva ROC , Reproducibilidad de los Resultados
11.
Am J Med Genet A ; 182(9): 2152-2160, 2020 09.
Artículo en Inglés | MEDLINE | ID: mdl-32618121

RESUMEN

The etiology of nonimmune hydrops fetalis is extensive and includes genetic disorders. We describe a term-born female neonate with late onset extensive nonimmune hydrops, that is, polyhydramnios, edema, and congenital bilateral chylothorax. This newborn was successfully treated with repetitive thoracocentesis, total parenteral feeding, octreotide intravenously and finally surgical pleurodesis and corticosteroids. A genetic cause seemed plausible as the maternal history revealed a fatal nonimmune hydrops fetalis. A homozygous truncating variant in GDF2 (c.451C>T, p.(Arg151*)) was detected with exome sequencing. Genetic analysis of tissue obtained from the deceased fetal sibling revealed the same homozygous variant. The parents and two healthy siblings were heterozygous for the GDF2 variant. Skin and lung biopsies in the index patient, as well as the revised lung biopsy of the deceased fetal sibling, showed lymphatic dysplasia and lymphangiectasia. To the best of our knowledge, this is the first report of an association between a homozygous variant in GDF2 with lymphatic dysplasia, hydrothorax and nonimmune hydrops fetalis.


Asunto(s)
Anomalías Craneofaciales/genética , Factor 2 de Diferenciación de Crecimiento/genética , Hidropesía Fetal/genética , Linfangiectasia Intestinal/genética , Linfedema/genética , Polihidramnios/genética , Anomalías Craneofaciales/diagnóstico , Anomalías Craneofaciales/patología , Femenino , Homocigoto , Humanos , Hidropesía Fetal/diagnóstico , Hidropesía Fetal/patología , Recién Nacido , Linfangiectasia Intestinal/diagnóstico , Linfangiectasia Intestinal/patología , Linfedema/diagnóstico , Linfedema/patología , Polihidramnios/diagnóstico , Polihidramnios/patología , Embarazo , Toracocentesis , Ultrasonografía Prenatal , Secuenciación del Exoma
12.
J Pediatr ; 225: 65-73.e5, 2020 10.
Artículo en Inglés | MEDLINE | ID: mdl-32502478

RESUMEN

OBJECTIVE: To describe the prevalence of pulmonary arterial hypertension (PAH)-associated gene mutations, and other genetic characteristics in a national cohort of children with PAH from the Dutch National registry and to explore genotype-phenotype associations and outcomes. STUDY DESIGN: Children (n = 70) diagnosed with idiopathic PAH, heritable PAH, PAH associated with congenital heart disease with coincidental shunt (PAH-congenital heart disease group 3), PAH after closure of a cardiac shunt (PAH-congenital heart disease group 4), or PAH associated with other noncardiac conditions were enrolled. Targeted next-generation sequencing was performed on PAH-associated genes (BMPR2, ACVRL1, EIF2AK4, CAV1, ENG, KCNK3, SMAD9, and TBX4). Also, children were tested for specific genetic disorders in case of clinical suspicion. Additionally, children were tested for copy number variations. RESULTS: Nineteen children (27%) had a PAH-associated gene mutation/variant: BMPR2 n = 7, TBX4 n = 8, ACVRL1 n = 1, KCNK3 n = 1, and EIF2AK4 n = 2. Twelve children (17%) had a genetic disorder with an established association with PAH (including trisomy 21 and cobalamin C deficiency). In another 16 children (23%), genetic disorders without an established association with PAH were identified (including Noonan syndrome, Beals syndrome, and various copy number variations). Survival rates differed between groups and was most favorable in TBX4 variant carriers. CONCLUSIONS: Children with PAH show a high prevalence of genetic disorders, not restricted to established PAH-associated genes. Genetic architecture could play a role in risk-stratified care management in pediatric PAH.


Asunto(s)
Cardiopatías Congénitas/epidemiología , Cardiopatías Congénitas/genética , Mutación , Hipertensión Arterial Pulmonar/epidemiología , Hipertensión Arterial Pulmonar/genética , Receptores de Activinas Tipo II/genética , Adolescente , Aracnodactilia/complicaciones , Aracnodactilia/epidemiología , Aracnodactilia/genética , Receptores de Proteínas Morfogenéticas Óseas de Tipo II/genética , Niño , Preescolar , Contractura/complicaciones , Contractura/epidemiología , Contractura/genética , Síndrome de Down/epidemiología , Síndrome de Down/genética , Femenino , Dosificación de Gen , Estudios de Asociación Genética , Predisposición Genética a la Enfermedad , Variación Genética , Humanos , Lactante , Masculino , Proteínas del Tejido Nervioso/genética , Países Bajos/epidemiología , Síndrome de Noonan/complicaciones , Síndrome de Noonan/epidemiología , Síndrome de Noonan/genética , Canales de Potasio de Dominio Poro en Tándem/genética , Estudios Prospectivos , Proteínas Serina-Treonina Quinasas/genética , Sistema de Registros , Proteínas de Dominio T Box/genética , Vitamina B 12/metabolismo , Deficiencia de Vitamina B 12/epidemiología , Deficiencia de Vitamina B 12/genética
13.
Am J Hum Genet ; 106(6): 779-792, 2020 06 04.
Artículo en Inglés | MEDLINE | ID: mdl-32413283

RESUMEN

The evolutionarily conserved hedgehog (Hh) pathway is essential for organogenesis and plays critical roles in postnatal tissue maintenance and renewal. A unique feature of the vertebrate Hh pathway is that signal transduction requires the primary cilium (PC) where major pathway components are dynamically enriched. These factors include smoothened (SMO) and patched, which constitute the core reception system for sonic hedgehog (SHH) as well as GLI transcription factors, the key mediators of the pathway. Here, we report bi-allelic loss-of-function variations in SMO in seven individuals from five independent families; these variations cause a wide phenotypic spectrum of developmental anomalies affecting the brain (hypothalamic hamartoma and microcephaly), heart (atrioventricular septal defect), skeleton (postaxial polydactyly, narrow chest, and shortening of long bones), and enteric nervous system (aganglionosis). Cells derived from affected individuals showed normal ciliogenesis but severely altered Hh-signal transduction as a result of either altered PC trafficking or abnormal activation of the pathway downstream of SMO. In addition, Hh-independent GLI2 accumulation at the PC tip in cells from the affected individuals suggests a potential function of SMO in regulating basal ciliary trafficking of GLI2 when the pathway is off. Thus, loss of SMO function results in abnormal PC dynamics of key components of the Hh signaling pathway and leads to a large continuum of malformations in humans.


Asunto(s)
Alelos , Discapacidades del Desarrollo/genética , Proteínas Hedgehog/metabolismo , Transducción de Señal , Receptor Smoothened/genética , Secuencia de Bases , Niño , Preescolar , Cilios/fisiología , Femenino , Humanos , Lactante , Masculino , Modelos Moleculares , Neoplasias/genética , Proteínas del Tejido Nervioso , Proteínas Nucleares , Linaje , Proteína Gli2 con Dedos de Zinc , Proteína Gli3 con Dedos de Zinc
14.
Curr Opin Pulm Med ; 26(3): 277-284, 2020 05.
Artículo en Inglés | MEDLINE | ID: mdl-32195678

RESUMEN

PURPOSE OF REVIEW: In 2013, the association between T-Box factor 4 (TBX4) variants and pulmonary arterial hypertension (PAH) has first been described. Now - in 2020 - growing evidence is emerging indicating that TBX4 variants associate with a wide spectrum of lung disorders. RECENT FINDINGS: TBX4 variants are enriched in both children and adults with PAH. The clinical phenotype associated with a TBX4 variant seems to be milder than that in other PAH-associated gene mutations. Further, TBX4 variants have increasingly been associated with a variety of clinical and histopathological phenotypes, including lethal developmental parenchymal lung diseases such as not only acinar dysplasia in neonates, but also less outspoken parenchymal lung diseases in children and adults. SUMMARY: The clinical phenotype of a TBX4 variant has recently been recognised to expand from bone disorders to different types of lung diseases. Recent data suggest that variants of TBX4, a transcription factor known to be an important regulator in embryonic development, are not rare in both children and adults with PAH and/or developmental parenchymal lung diseases.


Asunto(s)
Enfermedades Pulmonares/genética , Enfermedades Pulmonares/patología , Proteínas de Dominio T Box/genética , Desarrollo Embrionario/genética , Hipertensión Pulmonar Primaria Familiar/genética , Regulación de la Expresión Génica , Humanos , Mutación , Fenotipo , Hipertensión Arterial Pulmonar/genética , Hipertensión Arterial Pulmonar/patología
16.
Nat Commun ; 10(1): 2837, 2019 06 28.
Artículo en Inglés | MEDLINE | ID: mdl-31253775

RESUMEN

The diagnostic yield of exome and genome sequencing remains low (8-70%), due to incomplete knowledge on the genes that cause disease. To improve this, we use RNA-seq data from 31,499 samples to predict which genes cause specific disease phenotypes, and develop GeneNetwork Assisted Diagnostic Optimization (GADO). We show that this unbiased method, which does not rely upon specific knowledge on individual genes, is effective in both identifying previously unknown disease gene associations, and flagging genes that have previously been incorrectly implicated in disease. GADO can be run on www.genenetwork.nl by supplying HPO-terms and a list of genes that contain candidate variants. Finally, applying GADO to a cohort of 61 patients for whom exome-sequencing analysis had not resulted in a genetic diagnosis, yields likely causative genes for ten cases.


Asunto(s)
Regulación de la Expresión Génica/fisiología , Predisposición Genética a la Enfermedad , Análisis de Secuencia de ARN/métodos , Transcriptoma , Bases de Datos de Ácidos Nucleicos , Humanos , Modelos Genéticos , Análisis de Componente Principal , Programas Informáticos , Interfaz Usuario-Computador
17.
Int J Cardiol ; 258: 243-248, 2018 05 01.
Artículo en Inglés | MEDLINE | ID: mdl-29452988

RESUMEN

BACKGROUND: Thoracic aortic aneurysm (TAA) is a potentially life-threatening disorder with a strong genetic component. The number of genes implicated in TAA has increased exponentially over the last decade. Approximately 20% of patients with TAA have a positive family history. As most TAA remain asymptomatic for a long time, screening of at risk relatives is warranted to prevent complications. Existing international guidelines lack detailed instructions regarding genetic evaluation and family screening of TAA patients. We aimed to develop a consensus document to provide medical guidance for all health care professionals involved in the recognition, diagnosis and treatment of patients with thoracic aortic disease and their relatives. METHODS: A multidisciplinary panel of experts including cardiologists, cardiothoracic surgeons, clinical geneticists and general practitioners, convened to review and discuss the current literature, guidelines and clinical practice on genetic testing and family screening in TAA. RESULTS: There is a lack of high-quality evidence in the literature. This consensus statement, based on the available literature and expert opinions, summarizes our recommendations in order to standardize and optimize the cardiogenetic care for patients and families with thoracic aortic disease. In particular, we provide criteria to identify those patients most likely to have a genetic predisposition, and discuss the preferred modality and frequency of screening in their relatives. CONCLUSIONS: Age, family history, aortic size and syndromic features determine who is advised to have genetic testing as well as screening of first-degree relatives. There is a need for more prospective multicenter studies to optimize current recommendations.


Asunto(s)
Aneurisma de la Aorta Torácica/genética , Consenso , Testimonio de Experto/normas , Familia , Predisposición Genética a la Enfermedad/genética , Atención al Paciente/normas , Aneurisma de la Aorta Torácica/epidemiología , Aneurisma de la Aorta Torácica/terapia , Testimonio de Experto/métodos , Predisposición Genética a la Enfermedad/epidemiología , Humanos , Países Bajos/epidemiología , Atención al Paciente/métodos
18.
Pediatrics ; 140(4)2017 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-28939701

RESUMEN

BACKGROUND: Rapid diagnostic whole-genome sequencing has been explored in critically ill newborns, hoping to improve their clinical care and replace time-consuming and/or invasive diagnostic testing. A previous retrospective study in a research setting showed promising results with diagnoses in 57%, but patients were highly selected for known and likely Mendelian disorders. The aim of our prospective study was to assess the speed and yield of rapid targeted genomic diagnostics for clinical application. METHODS: We included 23 critically ill children younger than 12 months in ICUs over a period of 2 years. A quick diagnosis could not be made after routine clinical evaluation and diagnostics. Targeted analysis of 3426 known disease genes was performed by using whole-genome sequencing data. We measured diagnostic yield, turnaround times, and clinical consequences. RESULTS: A genetic diagnosis was obtained in 7 patients (30%), with a median turnaround time of 12 days (ranging from 5 to 23 days). We identified compound heterozygous mutations in the EPG5 gene (Vici syndrome), the RMND1 gene (combined oxidative phosphorylation deficiency-11), and the EIF2B5 gene (vanishing white matter), and homozygous mutations in the KLHL41 gene (nemaline myopathy), the GFER gene (progressive mitochondrial myopathy), and the GLB1 gene (GM1-gangliosidosis). In addition, a 1p36.33p36.32 microdeletion was detected in a child with cardiomyopathy. CONCLUSIONS: Rapid targeted genomics combined with copy number variant detection adds important value in the neonatal and pediatric intensive care setting. It led to a fast diagnosis in 30% of critically ill children for whom the routine clinical workup was unsuccessful.


Asunto(s)
Diagnóstico Tardío/prevención & control , Enfermedades Genéticas Congénitas/diagnóstico , Genómica/métodos , Cuidado Intensivo Neonatal/métodos , Análisis de Secuencia de ADN/métodos , Enfermedad Crítica , Femenino , Estudios de Seguimiento , Enfermedades Genéticas Congénitas/genética , Marcadores Genéticos , Humanos , Recién Nacido , Masculino , Mutación , Proyectos Piloto , Estudios Prospectivos , Factores de Tiempo
19.
Pharmacogenomics ; 18(10): 987-1001, 2017 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-28639488

RESUMEN

AIM: To explore the role of pharmacogenetics in determining the risk of congenital heart anomalies (CHA) with prenatal use of serotonin reuptake inhibitors. METHODS: We included 33 case-mother dyads and 2 mother-only (child deceased) cases of CHA in a case-only study. Ten genes important in determining fetal exposure to serotonin reuptake inhibitors were examined: CYP1A2, CYP2C9, CYP2C19, CYP2D6, ABCB1, SLC6A4, HTR1A, HTR1B, HTR2A and HTR3B. RESULTS: Among the exposed cases, polymorphisms that tended to be associated with an increased risk of CHA were SLC6A4 5-HTTLPR and 5-HTTVNTR, HTR1A rs1364043, HTR1B rs6296 and rs6298 and HTR3B rs1176744, but none reached statistical significance due to our limited sample sizes. CONCLUSION: We identified several polymorphisms that might potentially affect the risk of CHA among exposed fetuses, which warrants further investigation.


Asunto(s)
Cardiopatías Congénitas/inducido químicamente , Exposición Materna/efectos adversos , Variantes Farmacogenómicas , Polimorfismo de Nucleótido Simple , Efectos Tardíos de la Exposición Prenatal/inducido químicamente , Inhibidores Selectivos de la Recaptación de Serotonina/efectos adversos , Femenino , Desarrollo Fetal/efectos de los fármacos , Genotipo , Cardiopatías Congénitas/genética , Humanos , Recién Nacido , Masculino , Embarazo , Efectos Tardíos de la Exposición Prenatal/genética , Inhibidores Selectivos de la Recaptación de Serotonina/farmacocinética , Inhibidores Selectivos de la Recaptación de Serotonina/uso terapéutico
20.
BMC Pregnancy Childbirth ; 17(1): 120, 2017 04 14.
Artículo en Inglés | MEDLINE | ID: mdl-28410576

RESUMEN

BACKGROUND: Pharmacogenetics is an emerging field currently being implemented to improve safety when prescribing drugs. While many women who take drugs during pregnancy would likely benefit from such personalized drug therapy, data is lacking on the awareness towards pharmacogenetics among women. We aim to determine the level of knowledge and acceptance of formerly pregnant women in the Netherlands regarding pharmacogenetics and its implementation, and their interest in pharmacogenetic research. METHODS: A population-based survey using postal questionnaires was conducted among formerly pregnant women in the Northern parts of the Netherlands. A total of 986 women were invited to participate. RESULTS: Of the 219 women who returned completed questionnaires (22.2% response rate), only 22.8% had heard of pharmacogenetics, although the majority understood the concept (64.8%). Women who had experience with drug side-effects were more likely to know about pharmacogenetics [OR = 2.06, 95% CI 1.16, 3.65]. Of the respondents, 53.9% were positive towards implementing pharmacogenetics in their future drug therapy, while 46.6% would be willing to participate in pharmacogenetic research. Among those who were either not willing or undecided in this regard, their concerns were about the consequences of the pharmacogenetic test, including the privacy and anonymity of their genetic information. CONCLUSION: The knowledge and attitude regarding the concept of pharmacogenetics among our population of interest is good. Also, their interest in pharmacogenetic research provides opportunities for future research related to drug use during pregnancy and fetal outcome.


Asunto(s)
Conocimientos, Actitudes y Práctica en Salud , Aceptación de la Atención de Salud/estadística & datos numéricos , Farmacogenética , Salud de la Mujer , Adulto , Femenino , Humanos , Países Bajos/epidemiología , Satisfacción del Paciente , Atención Prenatal , Encuestas y Cuestionarios
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