[Genetic testing in neurological diseases: a practical guide]. / Pruebas genéticas en enfermedades neurológicas: guía práctica.

During the last decades, genomic medicine has made it possible to bring the knowledge of molecular genetics to the field of medical consultation. There are several studies that contribute to the diagnosis, the definition of prognoses, as well as the possibility of providing genetic counseling based on accurate scientific data. Advances in genomic sequencing have promoted the reclassification of entities according to an etiological criterion. Such is the case of epileptic encephalopathies, ataxias, dystonias, among many other neurological conditions. Its implementation requires strategies aimed at achieving the best diagnostic yield. This requires a greater understanding of the molecular bases of each of these practices, as well as their scope. They allow reducing the time until a certain diagnosis is made and the possibility, in some cases, of improving the quality of life of those affected with the use of tailored treatments. The objective of this article was to describe current laboratory studies, their scope and emphasize the algorithms for the study of genetic diseases in general, focusing the attention on those specific to neuropediatrics, in order to promote good practices, avoiding confusion, errors, and unnecessary expenditures of money and shortening the so-called "diagnostic odyssey".

Durante las últimas décadas la medicina genómica ha llevado al ámbito de la consulta médica los conocimientos de la genética molecular. Existe un número de estudios que contribuyen en el diagnóstico, la definición de pronósticos y posibilitan un asesoramiento genético basado en datos científicos certeros. En algunas enfermedades, los avances en la secuenciación genómica, ha promovido la reclasificación de entidades según un criterio etiológico, como las encefalopatías epilépticas, las ataxias, las distonías, entre muchas condiciones médicas. Su implementación requiere, por parte de los médicos, de estrategias tendientes a alcanzar el mejor rédito diagnóstico. Es necesario para ello, una mayor comprensión de las bases moleculares de estas prácticas, así como sus alcances. Permiten reducir los tiempos hasta la concreción de un diagnóstico de certeza y la posibilidad, en algunos casos, de mejorar la calidad de vida de los afectados con la utilización de tratamientos a la medida. El objetivo de este artículo fue describir las técnicas de laboratorio actuales, sus alcances y enfatizar los algoritmos de estudio de las enfermedades genéticas, haciendo hincapié en aquellas propias de la neuropediatría, a fin de propiciar las buenas prácticas, evitando confusiones, errores, erogaciones innecesarias de dinero y acortando la llamada "odisea diagnóstica".

Diagnostic yield of chromosomal microarray in the largest Latino clinical cohort.

Copy number variants (CNVs) remain a major etiological cause of neurodevelopmental delay and congenital malformations. Chromosomal microarray analysis (CMA) represents the gold standard for CNVs molecular characterization. We applied CMA throughout the patient's clinical diagnostic workup, as the patient's medical provider requested. We collected CMA results of 3380 patients enrolled for 5 years (2016-2021). We found 830 CNVs in 719 patients with potential clinical significance, that is, (i) pathogenic, (ii) likely pathogenic, and (iii) variants of uncertain significance (VUS), from which 10.6% (predominantly involving chromosomes 15 and 22) were most likely the final cause underpinning the patients' clinical phenotype. For those associated with neurodevelopmental phenotypes, the rate of pathogenic or likely pathogenic findings among the patients with CNVs was 60.75%. When considering epileptic phenotypes, it was 59%. Interestingly, our protocol identified two gains harbored in 17q21.31 and 9q34.3, internationally classified initially as VUS. However, because of their high frequency, we propose that these two VUS be reclassified as likely benign in this widely heterogeneous phenotypic population. These results support the diagnostic yield efficiency of CMA in characterizing CNVs to define the final molecular cause of genetic diseases in this cohort of Colombian patients, the most significant sample of patients from a Latino population, and define new benign polymorphic CNVs.

Overlapping Spectrum of Craniofacial Microsomia Phenotype in Cat-Eye Syndrome.

This study reports three patients with Cat-eye Syndrome (CES), two of which present a previous clinical diagnosis of Craniofacial microsomia (CFM). Chromosomal microarray analysis (CMA) revealed a tetrasomy of 1,7 Mb at the 22q11.2q11.21 region, which is the typical region triplicated in the CES, in all patients. The most frequent craniofacial features found in individuals with CFM and CES are preauricular tags and/or pits and mandibular hypoplasia. We reinforce that the candidate genes for CFM features, particularly ear malformation, preauricular tags/pits, and facial asymmetry, can be in the proximal region of the 22q11.2 region.

Characterization of Associated Nonclassical Phenotypes in Patients with Deletion in the WAGR Region Identified by Chromosomal Microarray: New Insights and Literature Review.

WAGR syndrome (Wilms' tumor, aniridia, genitourinary changes, and intellectual disability) is a contiguous gene deletion syndrome characterized by the joint deletion of PAX6 and WT1 genes, located in the short arm of chromosome 11. However, most deletions include other genes, leading to multiple associated phenotypes. Therefore, understanding how genes deleted together can contribute to other clinical phenotypes is still considered a challenge. In order to establish genotype-phenotype correlation in patients with interstitial deletions of the short arm of chromosome 11, we selected 17 patients with deletions identified by chromosomal microarray analysis: 4 new subjects and 13 subjects previously described in the literature with detailed clinical data. Through the analysis of deleted regions and the phenotypic changes, it was possible to suggest the contribution of specific genes to several nonclassical phenotypes, contributing to the accuracy of clinical characterization of the syndrome and emphasizing the broad phenotypic spectrum found in the patients. This study reports the first patient with a PAX6 partial deletion who does not present any eye anomaly thus opening a new set of questions about the functional activity of PAX6.

Congenital chromoanagenesis in the routine postnatal chromosomal microarray analyses.

Chromosomal microarray analyses (CMA) have greatly increased both the yield and diagnostic accuracy of postnatal analysis; it has been used as a first-tier cytogenetic test in patients with intellectual disability, autism spectrum disorder, and multiple congenital abnormalities. During the last 15 years, we performed CMA in approximately 8,000 patients with neurodevelopmental and/or congenital disorders, of which 13 (0.16%) genetically catastrophic complex chromosomal rearrangements were identified. These ultrarare rearrangements showed clustering of breakpoints, characteristic of chromoanagenesis events. Al1 13 complex events display underlying formation mechanisms, originating either by a synchronization of the shattering of clustered chromosome regions in which regional asynchrony of DNA replication may be one of the main causes of disruption. We provide an overview of the copy number profiling in these patients. Although several previous studies have suggested that chromoanagenesis is often a genetic disease source in postnatal diagnostic screening, due to either the challenge of clinical interpretation of these complex rearrangements or the limitation of microarray resolution relative to the small size and complexity of chromogenic induced chromosome abnormalities, bringing further attention and to study its occurrence in the clinical setting is extremely important.

Avances genómicos de la última década y su influencia en el enfoque diagnóstico de la discapacidad intelectual / Genomic advances in the last decade and their influence in the diagnosis of intellectual disability

RESUMEN La inteligencia humana es un rasgo poligénico (~1000 genes) con una influencia de cada gen aproximadamente ascendente al 0,1%. Es un atributo indispensable para el desarrollo personal, familiar, social y económico y tiene, además, una relación directamente proporcional al mantenimiento de la salud y a una mayor esperanza de vida. La discapacidad intelectual, consecuentemente, afecta todas estas áreas y constituye un problema de salud pública en varios países de Latinoamérica en los que exhibe una prevalencia mayor al 10%. La etiología de la discapacidad intelectual sea aislada o sindrómica, es genética hasta en un 85% de los casos; se diagnostica mediante las nuevas tecnologías de búsqueda en el genoma, tales como la secuenciación masiva y el análisis cromosómico por micromatrices. El diagnóstico etiológico de la discapacidad intelectual permite la selección de terapias específicas, la determinación del pronóstico y de riesgos de recurrencia familiar e individual.

SUMMARY Human intelligence is a polygenic trait (~1000 genes), with an approximate influence of 0.1% per every individual gen. It is an indispensable attribute for personal, familial, social, and economic development; furthermore, it is directly proportional to health maintenance and a longer life expectancy. Consequently, intellectual disability affects all these areas, and constitutes a public health problem in several Latin American countries where it shows a >10%. In ~85% of the patients, the etiology of intellectual disability, be that isolated or syndromic; it is mostly diagnosed through the new technological search studies of the genome, such as new generation sequencing and/or chromosomal microarray analysis. The clinical and etiological diagnosis of intellectual disability, when duly confirmed, allows the choice of specific treatment modalities, the precise determination of prognosis, and the estimation of individual or familial recurrence risks.

Genomic imbalances in craniofacial microsomia.

The aim of this study was to perform 22q11.2 deletion screening and chromosomal microarray analysis (CMA) in individuals clinically diagnosed with craniofacial microsomia (CFM) and review previously published cases of CFM with genomic imbalances. It included 54 individuals who were evaluated by a clinical geneticist. Copy number variants (CNVs) in the 22q11.2 region were investigated by multiplex ligation-dependent probe amplification (MLPA) for all individuals. The CMA was performed only for individuals with additional major features. MLPA revealed pathogenic CNVs at the 22q11 region in 3/54 (5.6%) individuals. CMA revealed pathogenic CNVs in 4/17 (23.5%) individuals, including the three CNVs at the 22q11 region also detected by MLPA, and CNVs classified as variants of unknown significance (VOUS) in 4/17 (23.5%) individuals. Pathogenic alterations were found at the 2p12, 5p15, 13q13, and 22q11 regions. VOUS were found at 3q29, 5q22.2, 5q22.1, and 9p22 regions. All individuals with pathogenic alterations presented additional major features, including congenital heart disease (CHD). The literature review revealed pathogenic CNVs in 17/193 (8.8%) individuals and most of them also presented additional major features, such as CHD, renal anomalies, or developmental delay. In conclusion, CNVs should be investigated in patients with CFM and additional major features.

Brazil's Craniofacial Project: Different approaches on orofacial clefts and 22q11.2 deletion syndrome.

This article reports the present situation of Brazilian health care in genetics for Orofacial Cleft (OFC) and 22q11.2 Deletions Syndrome (22q11.2 DS) based on research conducted by Brazil's Craniofacial Project (BCFP). Established in 2003, BCFP is a voluntary and cooperative network aiming to investigate the health care of people with these diseases and other craniofacial anomalies. The initiatives and research results are presented in four sections: (a) a comprehensive report of the Brazilian public health system in craniofacial genetics; (b) multicentric studies developed on OFC and 22q11.2 DS; (c) education strategies focused on addressing these conditions for both population and health-care professionals; and (d) the nosology through the Brazilian Database on Craniofacial Anomalies (BDCA). Since 2006, BDCA uses a standardized method with detailed clinical data collection, which allows for conducting studies on nosology, genotype-phenotype correlations, and natural history; data can also contribute to public policies. Currently, the BDCA stores data on 1,724 individuals, including 1,351 (78.36%) who were primarily admitted due to OFC and 373 (21.63%) with clinical suspicion of 22q11.2 DS. Chromosomal abnormalities/genomic imbalances were represented by 92/213 (43.19%) individuals with syndromic OFC, including 43 with 22q11.2 DS, which indicates the need for chromosomal microarray analysis in this group. The nosologic diversity reinforces that monitoring clinical is the best strategy for etiological investigation. BCFP's methodology has introduced the possibility of increasing scientific knowledge and genetic diagnosis of OFC and 22q11.2 DS to in turn improve health care and policies for this group of diseases.

Copy Number Gain at Xq28 in a Child with Global Developmental Delay Associated with a Variant Form of Hoyeraal-Hreidarsson Syndrome.

We report the case of a child from Central Brazil with global developmental delay (GDD), syndromic features, and absence of abnormal skin pigmentation, nail dystrophy, and leukoplakia of the oral mucosa, with a rearrangement at Xq28 harboring the DKC1 gene. GTC-banding revealed a male karyotype (46,XY) with no visible numerical or structural alterations. Chromosomal microarray analysis (CMA) showed a 0.36-Mb gain at Xq28 of maternal origin, encompassing 22 genes, including DKC1. Rearrangements and mutations involving this gene have been associated with dyskeratosis congenita, X-linked (OMIM 305000) and Hoyeraal-Hreidarsson syndrome. CMA was a powerful and efficient approach to identify a gain at Xq28 harboring the DKC1 gene in our patient with GDD syndromic features and no cutaneous alterations, suggesting that this variant is associated with the Hoyeraal-Hreidarsson syndrome.

Syndromic Oral Clefts: Challenges of Genetic Assessment in Brazil and Suggestions to Improve Health Policies.

Addressing the unmet health needs of persons living with congenital anomalies in low- and middle-income countries (LMIC) is a major challenge. Registries and databases are exemplary tools capable to link research data with health programs. Since 2009, Brazil's Craniofacial Project, a multicenter and voluntary research initiative, collects socioeconomic, medical, and genetic information on individuals with craniofacial anomalies through the Brazilian Database on Craniofacial Anomalies (BDCA). This article discusses challenges to the provision of genetic assessment and counselling for individuals with syndromic oral clefts (SOC) through public health services in LMIC, such as Brazil. Subjects were selected using methods of the BDCA as described elsewhere. Among 800 records, 66 assigned as SOC with no etiologic diagnosis were preselected for genomic imbalance screening. Only 28 have timely completed basic protocol using public health services, and 22 were able to perform chromosomal microarray analysis. Pathogenic genomic imbalances were identified in 4 (18.18%) and a copy number variation of uncertain clinical significance was detected in one. Results exemplify barriers faced by the majority of the population of Brazil to reach whole genetic assessment either through public genetic services or in research settings. In this unfavorable scenario, BDCA has allowed the recognition of individuals with similar needs, optimizing the scarce genetic laboratory facilities in Brazil. Ultimately, BDCA has facilitated the translation of research into care. This experience may be successfully extended to other congenital anomalies and to LMIC with similar characteristics. A set of suggestions focusing on oral clefts is provided.

Testing criteria for 22q11.2 deletion syndrome: preliminary results of a low cost strategy for public health.

BACKGROUND: The clinical heterogeneity of the 22q11.2 Deletion Syndrome (22q11.2DS - OMIM, #188400 and #192430) is a universal challenge leading to diagnostic delay. The aim of this study was to evaluate a low cost strategy for the diagnosis of this condition based upon clinical criteria previously reported. Health professionals, who collected clinical data, from twelve centers were trained in those criteria, which were summed through an online application (CranFlow). RESULTS: Clinical and laboratorial data of 347 individuals registered from 2008 to 2017 in the Brazilian Database on Craniofacial Anomalies/22q11.2 Deletion Syndrome, were reviewed. They were divided in two groups: (I) 168 individuals investigated before the definition of the criteria and (II) 179 individuals investigated after the criteria application. All of them were investigated for 22q11.2DS by Fluorescent in situ Hybridization (FISH) and/or Multiplex Ligation Probe-dependent Amplification (MLPA), detecting 98 cases with 22q11.2DS. Among the individuals with 22q11.2DS in Group II, 42/53 (79.25%) fulfilled the proposed criteria against 11/53 (20.75%) who did not fulfill them (p < .0001). The association of congenital heart diseases with high predictive value for 22q11.2DS and hypernasal voice were significantly associated to the presence of 22q11.2DS (p = 0.0172 and p < .0001, respectively). In addition, 22q11.2DS was confirmed 3.82 more times when the individuals fulfilled the proposed criteria. Of the 249 cases negative for the typical deletion in 22q11.2, Chromosomal Microarray Analysis (CMA) was performed in 132 individuals and detected pathogenic alterations at other genomic regions in 19 individuals, and variants of uncertain clinical significance in 31 cases. CONCLUSIONS: Therefore, a locus-specific approach could be used to individuals with positive criteria as a cost-effective alternative for 22q11.2DS diagnosis. The authors discuss advantages and suggest ways of implementing this approach to investigate 22q11.2DS in a public health system.

Phenotype comparison among individuals with developmental delay/intellectual disability with or without genomic imbalances.

BACKGROUND: The chromosomal microarray analysis (CMA) is recommended as a first-tier test for individuals with developmental delay (DD)/intellectual disability (ID) and/or multiple congenital anomalies. However, owing to high costs, this technique is not widely performed for diagnostic purposes in several countries. The aim of this study was to identify clinical features that could favour the hypothesis of genomic imbalances (GIs) in individuals with DD/ID. METHODS: The sample consisted of 63 individuals, and all of them underwent a detailed evaluation by a clinical geneticist and were investigated by the CMA. They were divided into two groups. Group A composed of 20 individuals with pathogenic copy number variants (CNVs); and group B composed of 43 individuals with normal CMA results or variants of uncertain clinical significance (VUS). RESULTS: Pathogenic GIs were found in 20 cases (32%), including 11 individuals with an abnormal karyotype, VUS was found in five individuals (8%) and the results were normal in 38 individuals (60%). Major anomalies were found in 15/20 (75%) individuals in group A against 35/43 (81%) in group B. Dysmorphisms (≥5) were found in 17/20 (85%) in group A and 41/43 (95%) in group B. The most frequent major anomalies detected in group A were congenital heart disease, epilepsy and renal malformation; and in group B, they were malformations of central nervous system, congenital heart disease, microcephaly, epilepsy and hearing impairment. There was no significant statistical difference among the frequencies in groups A and B. CONCLUSIONS: Evidences point that every individual with DD/ID, with no specific clinical suspicion, should have screening for GIs as a first-tier test, regardless of the presence or absence of additional major anomalies or dysmorphisms. Future studies with a similar design would be helpful, especially in countries where the access to new technologies is still limited.

A recognizable phenotype related to 19p13.12 microdeletion.

Submicroscopic deletions in chromosome 19 have been rarely reported. We reported a male patient presenting with neurodevelopmental delay and facial dysmorphisms with a de novo 19p13.11p13.12 deletion of approximately 1.4 Mb. To date, there are seven cases with deletions overlapping the 19p13.11-p13.12 region described in the literature. A region of 800 kb for branchial arch defects in the proximal region of 19p13.12, and another minimal critical region of 305 kb for hypertrichosis, synophrys, and protruding front teeth have been proposed previously. We suggest that the shortest region of overlap could be refined to an approximately 53 kb region shared within all patients, encompassing part of BRD4 and AKAP8L genes and the AKAP8 gene. Based on the genotype-phenotype correlation of the present case and cases with overlapping deletions described in the literature, it was possible to recognize a consistent phenotype characterized by microcephaly, ear abnormalities, rounded face, synophrys, arched or upwardly angulated eyebrows, short nose, anteverted nares, prominent cheeks, teeth abnormalities, and developmental delay.

Utility of Genetic Testing in Fetal Alcohol Spectrum Disorder.

OBJECTIVE: To study the utility of genetic evaluation and testing in patients with suspected fetal alcohol spectrum disorder (FASD). STUDY DESIGN: We performed a retrospective chart review of all patients (n = 36) referred for evaluation for suspected FASD to the genetics clinic at Boston Children's Hospital between January 2006 and January 2013. Records of all patients were reviewed to obtain the medical history, family history, examination findings, and investigations, including genetic testing. RESULTS: Of the 36 patients, definite prenatal exposure was documented in 69%. Eight patients did not fulfill clinical criteria for FASD. Chromosomal microarray analysis (CMA) detected 19 copy number variants (CNVs) in 14 patients. Among patients who fulfilled criteria for FASD and underwent CMA, pathogenic CNVs were detected in 3 patients (2q37del, 22q11.22dup, and 4q31.21del syndromes), giving a yield of 14.3%. All 3 patients had overlapping features between FASD and the genetic syndrome. CONCLUSION: Genetic testing, especially CMA, should be considered in patients referred for evaluation of FASD, as a significant proportion have a clinically significant CNV even when they fulfill diagnostic criteria for FASD spectrum.

Molecular Characterization of Koolen De Vries Syndrome in Two Girls with Idiopathic Intellectual Disability from Central Brazil.

Koolen de Vries syndrome (KDVS; MIM 610443) is a genomic disorder caused by a recurrent microdeletion derived from nonallelic homologous recombination mediated by flanking segmental duplications. Clinical manifestations of this syndrome are characterized by intellectual disability, hypotonia, a friendly behavior, distinctive facial features, and epilepsy. Herein, we report a case of 2 girls who revealed global developmental delay, mild facial dysmorphisms, friendly behavior, and epileptic seizure with a de novo 17q21.31 microdeletion detected by chromosomal microarray analysis (CMA). Conventional cytogenetics analysis by GTG-banding showed a female karyotype 46,XX for both girls. CMA revealed a microdeletion spanning approximately 500 kb in 17q21.31 in both girls, encompassing the following genes: CRHR1, MGC57346, CRHR1-IT1, MAPT-AS1, SPPL2C, MAPT, MAPT-IT1, STH, and KANSL1. Haploinsufficiency of one or more of these genes within the deleted region is the most probable cause of the probands' phenotype and is responsible for the phenotype seen in KDVS. CMA is a powerful diagnostic tool and an effective method to identify the de novo 17q21.31 microdeletion associated with KDVS in our probands.

Partial trisomy 17q and partial monosomy 20q in a boy with craniosynostosis.

Craniosynostosis is defined as a premature fusion of at least one cranial suture, which can be accompanied by other findings. Of syndromic cases, 14-22% have been associated with chromosomal rearrangements. This report describes a Brazilian boy with syndromic craniosynostosis who also presented with intellectual disability, microcephaly, frontal bossing, bitemporal narrowing, short neck, syndactyly, and cardiac defects. Chromosome banding showed an apparently normal male karyotype. Subsequent chromosomal microarray analysis (CMA) using the Affymetrix CytoScan 750 K Array showed a duplication of 2.1 Mb on chromosome 17q and a deletion of 1.4 Mb on chromosome 20q. The data suggested an unbalanced translocation, which was confirmed by fluorescence in-situ hybridization analysis (FISH). While there are several reports in the literature of chromosome 17q duplication syndrome accompanied by partial monosomies of other chromosomes, this is the first case featuring partial monosomy of 20q. The patient́s phenotype is generally consistent with 17q duplication syndrome, however craniosynostosis has rarely been associated with this chromosomal anomaly.

Investigation of selected genomic deletions and duplications in a cohort of 338 patients presenting with syndromic obesity by multiplex ligation-dependent probe amplification using synthetic probes.

BACKGROUND: Certain rare syndromes with developmental delay or intellectual disability caused by genomic copy number variants (CNVs), either deletions or duplications, are associated with higher rates of obesity. Current strategies to diagnose these syndromes typically rely on phenotype-driven investigation. However, the strong phenotypic overlap between syndromic forms of obesity poses challenges to accurate diagnosis, and many different individual cytogenetic and molecular approaches may be required. Multiplex ligation-dependent probe amplification (MLPA) enables the simultaneous analysis of multiple targeted loci in a single test, and serves as an important screening tool for large cohorts of patients in whom deletions and duplications involving specific loci are suspected. Our aim was to design a synthetic probe set for MLPA analysis to investigate in a cohort of 338 patients with syndromic obesity deletions and duplications in genomic regions that can cause this phenotype. RESULTS: We identified 18 patients harboring copy number imbalances; 18 deletions and 5 duplications. The alterations in ten patients were delineated by chromosomal microarrays, and in the remaining cases by additional MLPA probes incorporated into commercial kits. Nine patients showed deletions in regions of known microdeletion syndromes with obesity as a clinical feature: in 2q37 (4 cases), 9q34 (1 case) and 17p11.2 (4 cases). Four patients harbored CNVs in the DiGeorge syndrome locus at 22q11.2. Two other patients had deletions within the 22q11.2 'distal' locus associated with a variable clinical phenotype and obesity in some individuals. The other three patients had a recurrent CNV of one of three susceptibility loci: at 1q21.1 'distal', 16p11.2 'distal', and 16p11.2 'proximal'. CONCLUSIONS: Our study demonstrates the utility of an MLPA-based first line screening test to the evaluation of obese patients presenting with syndromic features. The overall detection rate with the synthetic MLPA probe set was about 5.3% (18 out of 338). Our experience leads us to suggest that MLPA could serve as an effective alternative first line screening test to chromosomal microarrays for diagnosis of syndromic obesity, allowing for a number of loci (e.g., 1p36, 2p25, 2q37, 6q16, 9q34, 11p14, 16p11.2, 17p11.2), known to be clinically relevant for this patient population, to be interrogated simultaneously.