Untitled

Funder

Organizational Unit

Publications

Exclusion of inv(2)(p16.1;q14.3) as the cause of a severe congenital disease by Next-Generation Sequencing

Publication . Pinto Cardoso, Manuela; Talkowski, Michael E.; Freixo, João; Gonçalves, Rui; Morton, Cynthia C.; David, Dezső

Introduction: Congenital anomalies, a leading cause of infant mortality in developed countries, are usually caused by genomic and/or chromosome rearrangements. Such rearrangements, like inversions, disrupt the genomic architecture at the breakpoint regions and can be either subclinical or pathogenic. Currently, the lack of a fully annotated genome hinders the prediction of phenotypical consequences of these anomalies. Methods: We report a familial pericentric inversion, inv(2)(p16.1;q14.3), in a proband presenting multiple psychomotor and developmental anomalies, dismorphism and autistic features, with phenotypically normal parents. Traditional analysis methods are labor intensive and of low resolution. Here we employed Next-Generation Sequencing (NGS) to identify breakpoints at nucleotide resolution in the proband, followed by familial segregation analysis by Sanger sequencing. Genomic and transcriptome array analysis were performed, for exclusion of further genomic alterations and for gene expression profiling. Results: The inversion breakpoints, at chr2:55,707,929 and chr2:123,010,109 (GRCh38), did not disrupt any gene or regulatory element and are flanked by PNPT1 and EFEMP1, and TSN and CNTNAP5, respectively. No significant alteration in the expression level of possible candidate genes were observed. Aside from a polymorphic duplication, inherited from his father, no other pathogenic genomic imbalances were identified in the proband. Discussion: Based on these data, the causal relationship between clinical phenotype and the inversion is most likely excluded, as the inversion probably is nonpathogenic. It was yet not possible to establish the cause of the observed phenotype. The introduction of NGS represents a hallmark in the characterization of congenital disorders associated with chromosomal rearrangements.

2015-11Conference object

Open access

Next-Gen Cytogenetics and the Hidden Complexity of Genomic or Chromosomal Rearrangements

Publication . David, Dezső; Freixo, João; Carvalho, Inês; Tkachenko, Natalia; Oliva Teles, Natália; Marques, Bárbara; Alves, Ana Cristina; Fortuna, Ana; Sofia, Dória; Pinto de Moura, Carla; Gaspar, Isabel; Marques Carreira, Isabel; Sá, Joaquim; Gonçalves, Rui; Lavinha, João; Kay, Teresa; Correia, Hildeberto; Talkowski, Michael E.; Morton, Cynthia C.

Human developmental abnormalities are devastating conditions that account for almost half of all full-term neonatal deaths in developed countries. For individuals who survive, congenital anomalies often confer lifelong disability and their impact on public health is profound. However, the genetic etiology and genomic architecture contributing to the vast majority of these conditions remain unknown. Separately, and in addition, the genetic etiologies of recurrent infertility remain to be elucidated. The current low resolution diagnostic techniques are insensitive to the full mutational spectrum contributing to human developmental abnormalities and infertility, the poor understanding of the molecular alterations introduced by genomic rearrangements, and the lack of a fully annotated human genome hinders predictive diagnostics. This study results from collaboration between a Portuguese Consortium including clinical geneticists and the Developmental Genome Anatomy Project (DGAP) from Harvard Medical School. First, a group of cases were comparatively analyzed using genomic array and Next-Generation Sequencing (NGS). Subsequently, NGS of whole-genome large-insert libraries was applied for the identification of genomic or chromosomal rearrangements at nucleotide resolution in a series of cases, including two prenatal samples. Presently, this high-throughput technology is the only approach able to identify the full spectrum of structural variants, in a time frame that allows its application even for prenatal samples.The introduction of NGS into clinical cytogenetics surely will create a high-throughput, sequence-based Next-Gen Cytogenetics that will catalyze a dramatic advancement in clinical diagnostics. Therefore the understanding of the molecular pathology of these chromosome rearrangement-associated developmental disorders and infertilities will contribute to an improved prediction of the phenotypic consequences of these rearrangements.

2015Conference object

Open access