Percorrer por autor "Morton, Cynthia C."
A mostrar 1 - 6 de 6
Resultados por página
Opções de ordenação
- Array and NGS based characterization of translocation breakpoints of the t(2:7)(q23;q32),t(5;6)(q23,q26)dnPublication . Marques, Mariana; Talkowski, Michael E.; Freixo, João; Rui, Gonçalves; Morton, Cynthia C.; David, DezsőIntroduction: Congenital anomalies, namely caused by chromosome rearrangements, are a leading cause of infant mortality in European countries. The elucidation of the causal relationship between rearrangements and clinical phenotypes requires an efficient approach for identification of breakpoints at nucleotide resolution. Methods: In the last decade we went from conventional FISH based positional mapping of chromosomal breakpoints to sorting and amplification of derivative (der) chromosomes followed by array painting based mapping. Currently we are moving towards the application of Next-Generation Sequencing (NGS) for the identification of chromosome rearrangement breakpoints at nucleotide resolution. By means of these comprehensive molecular techniques we unveil the structural chromosomal alterations at nucleotide resolution in a proband with t(2:7)(q23;q32),t(5;6)(q23,q26)dn. Expression profiling of the proband’s LCLs was also carried out. Results: Array painting identified the breakpoints of two balanced chromosome translocations. The disruption of the PRPF40A and SND1 genes by the t(2;7) was identified both by array and NGS analysis. While array analysis identified only t(5;6) breakpoints and the affected PACRG gene, NGS revealed further complexity of the breakpoint region. Indeed, der(6) is a complex chromosomal rearrangement (CCR) with three additional breakpoints resulting from an inversion and a PTPRK gene excision/insertion. Discussion: Because of the complexity of this rearrangement we are not yet able to establish the candidate genes for the observed clinical phenotype. As shown by the CCR, NGS is currently the only methodology able to identify the full spectrum of balanced structural alterations. Thus, the introduction of NGS technology for high-throughput delineation of chromosomal rearrangements is presently underway.
- Chromosome structural variants: Epidemiology, identification and contribution to human diseasesPublication . Dong, Zirui; David, Dezso; Gonzaga-Jauregui, Claudia; Morton, Cynthia C.; Zepeda-Mendoza, Cinthya J.Human chromosome structural variants (SVs) are balanced/unbalanced genomic abnormalities that include translocation, inversion, insertion, and deletion/duplication (also known as copy-number variants, CNVs) events with a size of >50 bp. Currently, the capability of genome sequencing in the research and clinical fields has increased our capacity to detect cryptic SVs and further delineate the complexity of karyotypically/microarray detectable SVs. This has increased our knowledge of pathogenicity mechanisms by considering dysregulation of gene expression through position effects and complex interactions between gene dosage and mutational burden. However, much of the contribution of SVs to human disease is left to explore, as the incidence of SVs is still underestimated owing to limitations of current sequencing technologies and analytical pipelines, and few studies have comprehensively integrated SV information with single nucleotide variants in congenital diseases. Rigorous investigation of SV pathogenicity is warranted for clinical applications. The Research Topic in this issue is divided into three main sections: three articles demonstrate methodologies in SV identification and pathogenicity annotation; five papers discuss the spectrum of SVs in individuals with different indications; and two reports characterize sequence complexity of SVs [...].
- Comprehensive clinically oriented workflow for nucleotide level resolution and interpretation in prenatal diagnosis of de novo apparently balanced chromosomal translocations in their genomic landscapePublication . David, Dezső; Freixo, João P.; Fino, Joana; Carvalho, Inês; Marques, Mariana; Cardoso, Manuela; Piña-Aguilar, Raul E.; Morton, Cynthia C.We present a comprehensive clinically oriented workflow for large-insert genome sequencing (liGS)-based nucleotide level resolution and interpretation of de novo (dn) apparently balanced chromosomal abnormalities (BCA) in prenatal diagnosis (PND). Retrospective or concomitant with conventional PND and liGS, molecular and newly developed clinically inspired bioinformatic tools (TAD-GConTool and CNV-ConTool) are applied to analyze and assess the functional and phenotypic outcome of dn structural variants (dnSVs). Retrospective analysis of four phenotype-associated dnSVs identified during conventional PND precisely reveal the genomic elements disrupted by the translocation breakpoints. Identification of autosomal dominant disease due to the disruption of ANKS1B and WDR26 by t(12;17)(q23.1;q21.33)dn and t(1;3)(q24.11;p25.3)dn breakpoints, respectively, substantiated the proposed workflow. We then applied this workflow to two ongoing prenatal cases with apparently balanced dnBCAs: 46,XX,t(16;17)(q24;q21.3)dn referred for increased risk on combined first trimester screening and 46,XY,t(2;19)(p13;q13.1)dn referred due to a previous trisomy 21 pregnancy. Translocation breakpoints in the t(16;17) involve ANKRD11 and WNT3 and disruption of ANKRD11 resulted in KBG syndrome confirmed in postnatal follow-up. Breakpoints in the t(2;19) are within ATP6V1B1 and the 3' UTR of CEP89, and are not interpreted to cause disease. Genotype-phenotype correlation confirms the causative role of WDR26 in the Skraban-Deardorff and 1q41q42 microdeletion phenocopy syndromes, and that disruption of ANKS1B causes ANKS1B haploinsufficiency syndrome. In sum, we show that an liGS-based approach can be realized in PND care providing additional information concerning clinical outcomes of dnBCAs in patients with such rearrangements.
- Exclusion of inv(2)(p16.1;q14.3) as the cause of a severe congenital disease by Next-Generation SequencingPublication . Pinto Cardoso, Manuela; Talkowski, Michael E.; Freixo, João; Gonçalves, Rui; Morton, Cynthia C.; David, DezsőIntroduction: 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.
- Next-Gen Cytogenetics and the Hidden Complexity of Genomic or Chromosomal RearrangementsPublication . 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.
- The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomaliesPublication . Redin, Claire; Brand, Harrison; Collins, Ryan L.; Kammin, Tammy; Mitchell, Elyse; Hodge, Jennelle C.; Hanscom, Carrie; Pillalamarri, Vamsee; Seabra, Catarina M.; Abbott, Mary-Alice; Abdul-Rahman, Omar A.; de Vries, Bert B A.; Earl, Dawn L.; Ferguson, Heather L.; Harris, David J.; Fisher, Heather; FitzPatrick, David R.; Gerrol, Pamela; Giachino, Daniela; Glessner, Joseph T.; Gliem, Troy; Margolin, Lauren; Grady, Margo; Graham, Brett H.; Griffis, Cristin; Hayden, Mark A.; Hill, Rosamund; Hochstenbach, Ron; Hoffman, Jodi D.; Hopkin, Robert J.; Hubshman, Monika W.; Moya, Graciela; Mason, Tamara; Innes, A Micheil; Irons, Mira; Irving, Melita; Jacobsen, Jessie C.; Janssens, Sandra; Jewett, Tamison; Johnson, John P.; Jongmans, Marjolijn C.; Kahler, Stephen G.; Koolen, David A.; Masser-Frye, Diane; Nieuwint, Aggie W.; Korzelius, Jerome; Kroisel, Peter M.; Lacassie, Yves; Lawless, William; Lemyre, Emmanuelle; Leppig, Kathleen; Levin, Alex V.; Li, Haibo; Li, Hong; Parkash, Sandhya; Liao, Eric C.; Ordulu, Zehra; Lim, Cynthia; Lose, Edward J.; Lucente, Diane; Macera, Michael J.; Manavalan, Poornima; Mandrile, Giorgia; Marcelis, Carlo L.; McClellan, Michael W.; Mendoza, Cinthya J. Zepeda; Menten, Björn; Middelkamp, Sjors; Mikami, Liya R.; Moe, Emily; Wiley, Susan; Mohammed, Shehla; Mononen, Tarja; Mortenson, Megan E.; Pauker, Susan P.; Pereira, Shahrin; Perrin, Danielle; Phelan, Katy; Aguilar, Raul E Piña; Poddighe, Pino J.; Aberg, Erika; Wilson, Anna; Pregno, Giulia; Raskin, Salmo; Reis, Linda; Rhead, William; Rita, Debra; Renkens, Ivo; Roelens, Filip; Ruliera, Jayla; Rump, Patrick; Schilit, Samantha L.P.; Yerena-de Vega, Maria de la Concepcion A.; Adley, Rhett; Shaheen, Ranad; Sparkes, Rebecca; Spiegel, Erica; Stevens, Blair; Stone, Matthew R.; Tagoe, Julia; Thakuria, Joseph V.; van Bon, Bregje W.; van de Kamp, Jiddeke; Alkuraya, Fowzan S.; van Der Burgt, Ineke; Alcaraz-Estrada, Sofia L.; van Essen, Ton; van Ravenswaaij-Arts, Conny M.; van Roosmalen, Markus J.; Vergult, Sarah; Volker-Touw, Catharina M.L.; Warburton, Dorothy P.; Waterman, Matthew J.; Zori, Roberto T.; Levy, Brynn; Brunner, Han G.; de Leeuw, Nicole; Kloosterman, Wigard P.; Thorland, Erik C.; Gripp, Karen W.; Morton, Cynthia C.; Gusella, James F.; Talkowski, Michael E.; An, Yu; Anderson, Mary-Anne; Antolik, Caroline; Anyane-Yeboa, Kwame; Atkin, Joan F.; Bartell, Tina; Bernstein, Jonathan A.; Gropman, Andrea L.; Beyer, Elizabeth; Blumenthal, Ian; Bongers, Ernie M.H.F.; Brilstra, Eva H.; Brown, Chester W.; Brüggenwirth, Hennie T.; Callewaert, Bert; Chiang, Colby; Corning, Ken; Cox, Helen; Hanson-Kahn, Andrea; Cuppen, Edwin; Currall, Benjamin B.; Cushing, Tom; David, Dezső; Deardorff, Matthew A.; Dheedene, Annelies; D'Hooghe, MarcDespite the clinical significance of balanced chromosomal abnormalities (BCAs), their characterization has largely been restricted to cytogenetic resolution. We explored the landscape of BCAs at nucleotide resolution in 273 subjects with a spectrum of congenital anomalies. Whole-genome sequencing revised 93% of karyotypes and demonstrated complexity that was cryptic to karyotyping in 21% of BCAs, highlighting the limitations of conventional cytogenetic approaches. At least 33.9% of BCAs resulted in gene disruption that likely contributed to the developmental phenotype, 5.2% were associated with pathogenic genomic imbalances, and 7.3% disrupted topologically associated domains (TADs) encompassing known syndromic loci. Remarkably, BCA breakpoints in eight subjects altered a single TAD encompassing MEF2C, a known driver of 5q14.3 microdeletion syndrome, resulting in decreased MEF2C expression. We propose that sequence-level resolution dramatically improves prediction of clinical outcomes for balanced rearrangements and provides insight into new pathogenic mechanisms, such as altered regulation due to changes in chromosome topology.