MUTATION ANALYSIS AND CHARACTERIZATION OF COL7A1 C.4531_4564-42DEL FROM TROPHECTODERM (TE) BIOPSIES USING NEXT GENERATION SEQUENCING (NGS) SIMULTANEOUSLY WITH PRE-IMPLANTATION GENETIC TESTING FOR ANEUPLOIDY (PGT-A)

2020 ◽  
Vol 114 (3) ◽  
pp. e434
Author(s):  
Xin Tao ◽  
Li Ma ◽  
Yiping Zhan ◽  
Heather Garnsey ◽  
Richard Thomas Scott ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Next Generation Sequencing ◽  
Mutation Analysis ◽  
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 Characterization of Novel Reoviruses Wad Medani Virus (Orbivirus) and Kundal Virus (Coltivirus) Collected fromHyalomma anatolicumTicks in India during Surveillance for Crimean Congo Hemorrhagic Fever

2019 ◽  
Vol 93 (13) ◽  
Author(s):  
Pragya D. Yadav ◽  
Shannon L. M. Whitmer ◽  
Prasad Sarkale ◽  
Terry Fei Fan Ng ◽  
Cynthia S. Goldsmith ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Common Ancestor ◽  
Hemorrhagic Fever ◽  
Fever Virus ◽  
Hyalomma Anatolicum ◽  
Next Generation ◽  
Crimean Congo Hemorrhagic Fever ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

ABSTRACTIn 2011, ticks were collected from livestock following an outbreak of Crimean Congo hemorrhagic fever (CCHF) in Gujarat state, India. CCHF-negativeHyalomma anatolicumtick pools were passaged for virus isolation, and two virus isolates were obtained, designated Karyana virus (KARYV) and Kundal virus (KUNDV), respectively. Traditional reverse transcription-PCR (RT-PCR) identification of known viruses was unsuccessful, but a next-generation sequencing (NGS) approach identified KARYV and KUNDV as viruses in theReoviridaefamily,OrbivirusandColtivirusgenera, respectively. Viral genomes werede novoassembled, yielding 10 complete segments of KARYV and 12 nearly complete segments of KUNDV. The VP1 gene of KARYV shared a most recent common ancestor with Wad Medani virus (WMV), strain Ar495, and based on nucleotide identity we demonstrate that it is a novel WMV strain. The VP1 segment of KUNDV shares a common ancestor with Colorado tick fever virus, Eyach virus, Tai Forest reovirus, and Tarumizu tick virus from theColtivirusgenus. Based on VP1, VP6, VP7, and VP12 nucleotide and amino acid identities, KUNDV is proposed to be a new species ofColtivirus. Electron microscopy supported the classification of KARYV and KUNDV as reoviruses and identified replication morphology consistent with other orbi- and coltiviruses. The identification of novel tick-borne viruses carried by the CCHF vector is an important step in the characterization of their potential role in human and animal pathogenesis.IMPORTANCETicks and mosquitoes, as wellCulicoides, can transmit viruses in theReoviridaefamily. With the help of next-generation sequencing (NGS), previously unreported reoviruses such as equine encephalosis virus, Wad Medani virus (WMV), Kammavanpettai virus (KVPTV), and, with this report, KARYV and KUNDV have been discovered and characterized in India. The isolation of KUNDV and KARYV fromHyalomma anatolicum, which is a known vector for zoonotic pathogens, such as Crimean Congo hemorrhagic fever virus,Babesia,Theileria, andAnaplasmaspecies, identifies arboviruses with the potential to transmit to humans. Characterization of KUNDV and KARYV isolated fromHyalommaticks is critical for the development of specific serological and molecular assays that can be used to determine the association of these viruses with disease in humans and livestock.

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