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Comparison of Agilent SureSelect Focussed Exome and TruSight One Mendeliome sequencing kits using NA12878 trio DNA

ABSTRACT: Comparison of Agilent SureSelect Focussed Exome and TruSight One Mendeliome sequencing kits using NA12878 trio DNA

PROVIDER: PRJEB34483 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3528870_1.fastq.gz	Fastqsanger.gz
	ERR3528870_2.fastq.gz	Fastqsanger.gz
	ERR3528880_1.fastq.gz	Fastqsanger.gz
	ERR3528880_2.fastq.gz	Fastqsanger.gz
	ERR3528890_1.fastq.gz	Fastqsanger.gz

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Comparison of Agilent SureSelect Focussed Exome and TruSight One Mendeliome sequencing kits using NA12878 trio DNA

Project description:A technical comparison of Agilent SureSelect Focussed Exome and TruSight One Mendeliome sequencing kits, by triplicate sequencing of the cell line DNA of NA12878, NA12891, NA12892 and NIST RM8395

2019-09-20 | E-MTAB-8349 | biostudies-arrayexpress

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Project description:Illumina methylation 27 array (Illumina) analysis was performed on 24 HapMap individuals including one CEU trio (family 1463 including NA12878, NA12891, NA12892) and one YRI trio (family Y117 including NA19240, NA19238, NA19239)

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Recurrent TRIO fusion in non-translocation-related sarcomas

Project description:We used NGS on a cohort of complex genetics sarcomas to study their transcriptomes (RNA-seq technology), looking for recurrent and specific gene fusions. We identified multiple TRIO fusions with different partners in our cohort. No TRIO fusions were reported in negative-control cells (normal tissues) and in simple genetics sarcomas.

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Trio-R: a script for assessing maternity and paternity in trio studies performed on Agilent chromosomal microarrays.

Project description:BackgroundTrio studies, which involve the testing of samples from a proband and both parents, are often used by clinical laboratories to help with the classification of genetic variants, including copy number variants. In order for the results of the trio study to be valid, the mother and father must be the true biological parents of the proband. As such, non-paternity and sample mix-ups are potential sources of error. To address these potential issues, we developed a computer script to accurately assess maternity and paternity using single nucleotide polymorphism (SNP) data generated by Agilent chromosomal microarrays, a platform-of-choice for clinical copy number testing.ResultsWe assessed the performance of the script on 10 putative trios tested at our laboratory, and found that the numbers and proportions of discordant SNPs were useful for determining parental relationships. The results of the assessment also confirmed maternity and paternity in the 10 trios tested, and by doing so essentially excluded pre-analytical sample switching in these 30 samples.ConclusionsComputational analysis of SNP data can be implemented as a quality control measure for trio testing performed on Agilent microarrays.

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Contribution of DNA methylation profiling in the classification of TRIO::TERT sarcomas

Project description:DNA methylation profiling has emerged as a valuable tool for tumor classification, exemplified by the German Cancer Research Center's creation of online classifiers for CNS tumors and sarcomas. Identification of rare molecular events, such as TRIO::TERT fusion in undifferentiated sarcomas, through DNA methylation profiling and transcriptome analysis aims to define distinct molecular subgroups within sarcomas of uncertain diagnosis, potentially improving classification and treatment strategies.In this study, we present 8 cases of sarcomas characterized by TRIO::TERT fusion, establishing it as a distinct molecular subtype of sarcomas. This fusion represents a consistent molecular feature across all analyzed tumors, suggesting its pivotal role in sarcomatogenesis. Identifying TRIO::TERT transcript sarcoma as a new tumor type may enhance diagnostic strategies for improved patient management.

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