Next Generation Sequencing (NGS) Strategies for Genetic Testing of Cerebral Cavernous Malformation (CCM) Disease

2020 ◽  
pp. 59-75
Author(s):  
Valerio Benedetti ◽  
Elisa Pellegrino ◽  
Alfredo Brusco ◽  
Roberto Piva ◽  
Saverio Francesco Retta
Keyword(s):  
Genetic Testing ◽  
Next Generation Sequencing ◽  
Cavernous Malformation ◽  
Cerebral Cavernous Malformation ◽  
Next Generation ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

scholarly journals Targeted next-generation sequencing detects rare genetic events in pheochromocytoma and paraganglioma

2019 ◽  
Vol 56 (8) ◽  
pp. 513-520 ◽  
Author(s):  
Laurène Ben Aim ◽  
Pascal Pigny ◽  
Luis Jaime Castro-Vega ◽  
Alexandre Buffet ◽  
Laurence Amar ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Next Generation Sequencing ◽  
Retrospective Cohort ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Genetic Mechanisms ◽  
Large Rearrangements ◽  
Next Generation Sequencing Ngs ◽  
Genetic Events ◽  
Generation Sequencing

BackgroundKnowing the genetic status of patients affected by paragangliomas and pheochromocytomas (PPGL) is important for the guidance of their management and their relatives. Our objective was to improve the diagnostic performances of PPGL genetic testing by next-generation sequencing (NGS).MethodsWe developed a custom multigene panel, which includes 17 PPGL genes and is compatible with both germline and tumour DNA screening. The NGS assay was first validated in a retrospective cohort of 201 frozen tumour DNAs and then applied prospectively to 623 DNAs extracted from leucocytes, frozen or paraffin-embedded PPGL tumours.ResultsIn the retrospective cohort, the sensitivity of the NGS assay was evaluated at 100% for point and indels mutations and 86% for large rearrangements. The mutation rate was re-evaluated from 65% (132/202) to 78% (156/201) after NGS analysis. In the prospective cohort, NGS detected not only germline and somatic mutations but also co-occurring variants and mosaicism. A mutation was identified in 74% of patients for whom both germline and tumour DNA were available.ConclusionThe analysis of 824 DNAs from patients with PPGL demonstrated that NGS assay significantly improves the performances of PPGL genetic testing compared with conventional methods, increasing the rate of identified mutations and identifying rare genetic mechanisms.

scholarly journals Preimplantation Genetic Testing for Thalassemia Through Next- Generation Sequencing of Affected-embryos

2021 ◽  
Author(s):  
Zhanhui Ou ◽  
Yu Deng ◽  
Yunhao Liang ◽  
Zhiheng Chen ◽  
Ling Sun
Keyword(s):  
Prenatal Diagnosis ◽  
Genetic Testing ◽  
Next Generation Sequencing ◽  
Birth Rate ◽  
Normal Karyotype ◽  
Live Birth Rate ◽  
Next Generation ◽  
Preimplantation Genetic Testing ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Background: To evaluate the ability of next-generation sequencing (NGS) to conduct preimplantation genetic testing (PGT) for thalassemia using affected embryos. Methods: This study included data from 36 couples who underwent PGT for thalassemia without proband and relative pedigrees. NGS results were compared with prenatal diagnosis results.Results: Thirty-six couples (29 α-thalassemia and 7 β-thalassemia) underwent 41 PGT cycles (31 α-thalassemia and 10 β-thalassemia). All biopsied blastocysts received conclusive results from NGS analysis (100%, 217/217). One hundred and sixty (73.7%, 160/217) were determined to be unaffected by thalassemia. PGT-A (PGT for aneuploidy) results showed that 112 (70.0%, 112/160) were euploid. Thirty-four couples were transferred with a single blastocyst (53 frozen embryo transfer (FET) cycles). Thirty-two cycles resulted in clinical pregnancies, and the clinical pregnancy rate was 60.1% (32/53) per FET cycle. Twenty-two cycles (22 couples) resulted in 23 live births and the live birth rate was 43.4% (23/53, 3 cycles were ongoing pregnancy). All 25 cycles’ prenatal diagnosis results and/or thalassemia gene analysis after the delivery were concordant with the NGS-PGT results. Seven cycles were miscarried before 12 weeks’ gestation, and the abortion villus in four cycles showed a normal karyotype and thalassemia results consistent with the NGS-PGT results. Aborted fetus samples from 3 cycles were not available because the pregnancy was less than 5 weeks.Conclusion: NGS can be used to conduct PGT for thalassemia using affected embryos as a reference.Trial registration: Retrospectively registered.

scholarly journals Novel PAX6 variant in a family with ophthalmologic, pancreatic, and olfactory features

2021 ◽  
pp. mcs.a006149
Author(s):  
Kristen Lee Buehne ◽  
Sarah Hart ◽  
Bradley Williams ◽  
Jennifer L Cohen
Keyword(s):  
Genetic Testing ◽  
Next Generation Sequencing ◽  
Family Members ◽  
Clinical Findings ◽  
Young Age ◽  
Next Generation ◽  
Congenital Cataracts ◽  
Novel Variant ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Variants in the PAX6 gene have been associated with ophthalmologic, neurologic, and pancreatic differences. We report on a proband, mother, and affected brother who presented with congenital cataracts and glaucoma at a young age. Non-ocular findings are also reported among these family members. After a congenital cataracts next generation sequencing (NGS) gene panel was found to be non-diagnostic in 2016, a more expanded panel in 2020 revealed a novel variant: c.178T>A; p.Tyr60Asn in exon 6 of the PAX6 gene in the proband. The variant is also present in the affected mother and affected brother; it is absent in an unaffected brother. The clinical findings of these three relatives, in conjunction with their genetic testing and the associated PAX6 features reported in the literature, suggest that this novel familial variant may be an underlying etiology for these individuals' ophthalmologic, pancreatic, and olfactory symptoms.

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