Low-pass whole genome sequencing as a cost-effective alternative to chromosomal microarray analysis for low- and middle-income countries.

Low-pass whole genome sequencing (LP-WGS) has been applied as alternative method to detect copy number variants (CNVs) in the clinical setting. Compared with chromosomal microarray analysis (CMA), the sequencing-based approach provides a similar resolution of CNV detection at a lower cost. In this study, we assessed the efficiency and reliability of LP-WGS as a more affordable alternative to CMA. A total of 1363 patients with unexplained neurodevelopmental delay/intellectual disability, autism spectrum disorders, and/or multiple congenital anomalies were enrolled. Those patients were referred from 15 nonprofit organizations and university centers located in different states in Brazil. The analysis of LP-WGS at 1x coverage (>50kb) revealed a positive testing result in 22% of the cases (304/1363), in which 219 and 85 correspond to pathogenic/likely pathogenic (P/LP) CNVs and variants of uncertain significance (VUS), respectively. The 16% (219/1363) diagnostic yield observed in our cohort is comparable to the 15%-20% reported for CMA in the literature. The use of commercial software, as demonstrated in this study, simplifies the implementation of the test in clinical settings. Particularly for countries like Brazil, where the cost of CMA presents a substantial barrier to most of the population, LP-WGS emerges as a cost-effective alternative for investigating copy number changes in cytogenetics.

Low-pass whole genome sequencing is a reliable and cost-effective approach for copy number variant analysis in the clinical setting.

INTRODUCTION: Next generation sequencing technology has greatly reduced the cost and time required for sequencing a genome. An approach that is rapidly being adopted as an alternative method for CNV analysis is the low-pass whole genome sequencing (LP-WGS). Here, we evaluated the performance of LP-WGS to detect copy number variants (CNVs) in clinical cytogenetics. MATERIALS AND METHODS: DNA samples with known CNVs detected by chromosomal microarray analyses (CMA) were selected for comparison and used as positive controls; our panel included 44 DNA samples (12 prenatal and 32 postnatal), comprising a total of 55 chromosome imbalances. The selected cases were chosen to provide a wide range of clinically relevant CNVs, the vast majority being associated with intellectual disability or recognizable syndromes. The chromosome imbalances ranged in size from 75 kb to 90.3 Mb, including aneuploidies and two cases of mosaicism. RESULTS: All CNVs were successfully detected by LP-WGS, showing a high level of consistency and robust performance of the sequencing method. Notably, the size of chromosome imbalances detected by CMA and LP-WGS were compatible between the two different platforms, which indicates that the resolution and sensitivity of the LP-WGS approach are at least similar to those provided by CMA. DISCUSSION: Our data show the potential use of LP-WGS to detect CNVs in clinical diagnosis and confirm the method as an alternative for chromosome imbalances detection. The diagnostic effectiveness and feasibility of LP-WGS, in this technical validation study, were evidenced by a clinically representative dataset of CNVs that allowed a systematic assessment of the detection power and the accuracy of the sequencing approach. Further, since the software used in this study is commercially available, the method can easily be tested and implemented in a routine diagnostic setting.

Diagnóstico prenatal de malformaciones del tracto urinario: evaluación posnatal y resultado clínico / Prenatal diagnosis of urinary tract malformations: postnatal evaluation and clinical outcome

Resumen Antecedentes: Las malformaciones del tracto urinario representan el 15-20% de las anomalías por ecografía prenatal; la prevalencia oscila entre 3 y 6 por cada 1,000 nacimientos. Objetivo: Conocer el desenlace clínico de los recién nacidos diagnosticados prenatalmente con malformación del tracto urinario. Material y métodos: Observacional, analítico, ambispectivo. Recién nacidos con diagnóstico prenatal de malformación urinaria. Evaluación posnatal con pruebas diagnósticas, analizamos días de estancia hospitalaria, intervención quirúrgica y seguimiento. Resultados: 45 pacientes, 55% varones, 65% de término, 77% cesárea. El diagnóstico prenatal más frecuente fue hidronefrosis, 100% se realizó ultrasonido renal posnatal, 27% cistograma miccional, 42% gammagrama renal; 60% requirió estancia hospitalaria prolongada, 27% intervención quirúrgica, 60% seguimiento. 89% de los casos diagnosticados prenatalmente se corroboró algún tipo de malformación del tracto urinario, solo en el 75% de los casos fue el mismo diagnóstico. Conclusión: La evaluación posnatal siempre requiere la realización de un ultrasonido renal y no en todos los casos realización de cistograma miccional o gammagrama renal.

Abstract Background: Urinary tract malformations represent 15-20% of abnormalities in prenatal ultrasound; the prevalence oscillates between 3-6 per 1000 births. Objective: To know the clinical outcome of newborns diagnosed prenatally with some malformation of the urinary tract. Material and methods: Observational, analytical, ambispective. Newborns with prenatal diagnosis of malformation urinary. Postnatal evaluation diagnostic tests performed, we analyzed the days of hospital stay, surgical intervention, follow-up. Results: 45 children, 55% male, 65% term, 77% c-section. Prenatal diagnosis with higher frequency was hydronephrosis. In all cases postnatal renal ultrasound was performed, 27% voiding cystogram, 42% renal gammagram. A 60% of the cases required prolonged hospital stay, 27% required a surgical intervention, 60% were follow-up. 89% of the cases diagnosed prenatally corroborated some type of malformation of the urinary tract, only in 75% of the cases was the same diagnosis. Conclusion: Postnatal evaluation always requires the performance of a renal ultrasound and not in all cases the performance of voiding cystogram or renal gammagram.

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.

Incidencia y tratamiento de las cardiopatías congénitas en San Miguel del Padrón / Incidence and treatment of congenital heart disease in San Miguel del Padrón

Introducción: los defectos congénitos cardiovasculares son en la actualidad con frecuencia, la causa de muerte en los primeros años de vida, y la detección de estos en la etapa fetal, les proporciona a los futuros padres, los conocimientos que les permite tomar una decisión, con respecto a continuar o no con el embarazo. Objetivo: analizar la incidencia y tratamiento de las cardiopatías congénitas, en el municipio San Miguel del Padrón, en el periodo entre enero de 2007 y diciembre de 2010. Métodos: se realizó un estudio descriptivo acerca del diagnóstico prenatal y postnatal de las cardiopatías congénitas, en el municipio San Miguel del Padrón, entre el 1ro de enero de 2007 y el 31 de diciembre de 2010. ..

Introduction: Nowadays, cardiovascular birth defects are often the cause of death in the first years of life, and the detection of these in the fetal stage, provides prospective parents, the knowledge that enables them to make a decision, regarding whether to continue pregnancy. Objective: To analyze incidence and treatment of congenital heart disease in the municipality of San Miguel del Padrón, from January 2007 to December 2010. Methods: We carried out a descriptive study on the prenatal and postnatal diagnosis of congenital heart disease in the municipality of San Miguel del Padrón, from 1st January 2007 to December 31st, 2010. ..