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Your search keyword '"Rollat-Farnier, Pierre-Antoine"' showing total 3 results
Start Over Author "Rollat-Farnier, Pierre-Antoine" Topic dna copy number variations
3 results on '"Rollat-Farnier, Pierre-Antoine"'

1. Development of a new expanded next-generation sequencing panel for genetic diseases involved in dyslipidemia.

Author

Marmontel O, Rollat-Farnier PA, Wozny AS, Charrière S, Vanhoye X, Simonet T, Chatron N, Collin-Chavagnac D, Nony S, Dumont S, Mahl M, Jacobs C, Janin A, Caussy C, Poinsot P, Tauveron I, Bardel C, Millat G, Peretti N, Moulin P, Marçais C, and Di Filippo M

Subjects
Dyslipidemias diagnosis, Dyslipidemias pathology, Female, Genetic Diseases, Inborn genetics, Genetic Diseases, Inborn pathology, Genetic Testing, Humans, Male, Sequence Analysis, DNA methods, DNA Copy Number Variations genetics, Dyslipidemias genetics, Genetic Diseases, Inborn diagnosis, High-Throughput Nucleotide Sequencing methods
Abstract

The aim of this study was to provide an efficient tool: reliable, able to increase the molecular diagnosis performance, to facilitate the detection of copy number variants (CNV), to assess genetic risk scores (wGRS) and to offer the opportunity to explore candidate genes. Custom SeqCap EZ libraries, NextSeq500 sequencing and a homemade pipeline enable the analysis of 311 dyslipidemia-related genes. In the training group (48 DNA from patients with a well-established molecular diagnosis), this next-generation sequencing (NGS) workflow showed an analytical sensitivity >99% (n = 532 variants) without any false negative including a partial deletion of one exon. In the prospective group, from 25 DNA from patients without prior molecular analyses, 18 rare variants were identified in the first intention panel genes, allowing the diagnosis of monogenic dyslipidemia in 11 patients. In six other patients, the analysis of minor genes and wGRS determination provided a hypothesis to explain the dyslipidemia. Remaining data from the whole NGS workflow identified four patients with potentially deleterious variants. This NGS process gives a major opportunity to accede to an enhanced understanding of the genetic of dyslipidemia by simultaneous assessment of multiple genetic determinants., (© 2020 John Wiley & Sons A/S . Published by John Wiley & Sons Ltd.)

Published
2020
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2. Molecular investigation, using chromosomal microarray and whole exome sequencing, of six patients affected by Williams Beuren syndrome and Autism Spectrum Disorder.

Author

Masson J, Demily C, Chatron N, Labalme A, Rollat-Farnier PA, Schluth-Bolard C, Gilbert-Dussardier B, Giuliano F, Touraine R, Tordjman S, Verloes A, Testa G, Sanlaville D, Edery P, Lesca G, and Rossi M

Subjects
Adolescent, Adult, Child, Chromosome Deletion, Female, Humans, Male, Phenotype, Young Adult, Autism Spectrum Disorder genetics, DNA Copy Number Variations genetics, Exome Sequencing methods, Williams Syndrome genetics
Abstract

Williams Beuren syndrome (WBS) is a multiple malformations/intellectual disability (ID) syndrome caused by 7q11.23 microdeletion and clinically characterized by a typical neurocognitive profile including excessive talkativeness and social disinhibition, often defined as "overfriendliness" and "hyersociability". WBS is generally considered as the polar opposite phenotype to Autism Spectrum Disorder (ASD). Surprisingly, the prevalence of ASD has been reported to be significantly higher in WBS (12%) than in general population (1%). Our study aims to investigate the molecular basis of the peculiar association of ASD and WBS. We performed chromosomal microarray analysis and whole exome sequencing in six patients presenting with WBS and ASD, in order to evaluate the possible presence of chromosomal or gene variants considered as pathogenic.Our study shows that the presence of ASD in the recruited WBS patients is due to i) neither atypically large deletions; ii) nor the presence of pathogenic variants in genes localized in the non-deleted 7q11.23 allele which would unmask recessive conditions; iii) moreover, we did not identify a second, indisputable independent genetic diagnosis, related to pathogenic Copy Number Variations or rare pathogenic exonic variants in known ID/ASD causing genes, although several variants of unknown significance were found. Finally, imprinting effect does not appear to be the only cause of autism in WBS patients, since the deletions occurred in alleles of both maternal and paternal origin.The social disinhibition observed in WBS does not follow common social norms and symptoms overlapping with ASD, such as restricted interests and repetitive behavior, can be observed in "typical" WBS patients: therefore, the terms "overfriendliness" and "hypersociability" appear to be a misleading oversimplification.The etiology of ASD in WBS is likely to be heterogeneous. Further studies on large series of patients are needed to clarify the observed variability in WBS social communication, ranging from excessive talkativeness and social disinhibition to absence of verbal language and social deficit.

Published
2019
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3. Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization.

Author

Uguen, Kévin, Jubin, Claire, Duffourd, Yannis, Bardel, Claire, Malan, Valérie, Dupont, Jean‐Michel, El Khattabi, Laila, Chatron, Nicolas, Vitobello, Antonio, Rollat‐Farnier, Pierre‐Antoine, Baulard, Céline, Lelorch, Marc, Leduc, Aurélie, Tisserant, Emilie, Tran Mau‐Them, Frédéric, Danjean, Vincent, Delepine, Marc, Till, Marianne, Meyer, Vincent, and Lyonnet, Stanislas

Subjects
NUCLEOTIDE sequencing, DNA copy number variations, CYTOGENETICS, CHROMOSOMAL rearrangement
Abstract

Background: Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base‐pair resolution, but the use of short‐read sequencing is limited by repetitive sequences, and long‐read approaches are not yet validated for diagnosis. Recently, 10X Genomics proposed Chromium, a technology providing linked‐reads to reconstruct long DNA fragments and which could represent a good alternative. No study has compared short‐read to linked‐read technologies to detect SVs in a constitutional diagnostic setting yet. The aim of this work was to determine whether the 10X Genomics technology enables better detection and comprehension of SVs than short‐read WGS. Methods: We included 13 patients carrying various SVs. Whole genome analyses were performed using paired‐end HiSeq X sequencing with (linked‐read strategy) or without (short‐read strategy) Chromium library preparation. Two different bioinformatic pipelines were used: Variants are called using BreakDancer for short‐read strategy and LongRanger for long‐read strategy. Variant interpretations were first blinded. Results: The short‐read strategy allowed diagnosis of known SV in 10/13 patients. After unblinding, the linked‐read strategy identified 10/13 SVs, including one (patient 7) missed by the short‐read strategy. Conclusion: In conclusion, regarding the results of this study, 10X Genomics solution did not improve the detection and characterization of SV. [ABSTRACT FROM AUTHOR]

Published
2020
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