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ABSTRACT: NGS for balanced chromosomal translocation

PROVIDER: PRJNA779115 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16895022.fastq.gz	Fastqsanger.gz
	SRR16895023.fastq.gz	Fastqsanger.gz
	SRR16895024.fastq.gz	Fastqsanger.gz
	SRR16895025.fastq.gz	Fastqsanger.gz
	SRR16895026.fastq.gz	Fastqsanger.gz

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Non-allelic homologous recombination between retrotransposable elements is a major driver of de novo unbalanced translocations.

Project description:Large scale analysis of balanced chromosomal translocation breakpoints has shown nonhomologous end joining and microhomology-mediated repair to be the main drivers of interchromosomal structural aberrations. Breakpoint sequences of de novo unbalanced translocations have not yet been investigated systematically. We analyzed 12 de novo translocations and mapped the breakpoints in 9. Surprisingly, in contrast to balanced translocations, we identify non-allelic homologous recombination (NAHR) between (retro)transposable elements and especially long interspersed elements (LINEs) as the main mutational mechanism. This finding implicates (retro)transposons to be a major driver of genomic rearrangements and exposes a profoundly different mutational mechanism compared to balanced chromosomal translocations. Furthermore, we show the existence of compound maternal/paternal derivative chromosomes, reinforcing the hypothesis that human cleavage stage embryogenesis is a cradle of chromosomal rearrangements.

2012-07-13 | GSE39303 | GEO

Expression data from MLL-AF6 positive leukemia cells

2013-04-03 | GSE43067 | GEO

Non-allelic homologous recombination between retrotransposable elements is a major driver of de novo unbalanced translocations.

2012-07-12 | E-GEOD-39303 | biostudies-arrayexpress

Altered chromatin topologies caused by balanced chromosomal translocation lead to central iris hypoplasia [Cut & Tag]

Project description:Altered chromatin topologies caused by balanced chromosomal translocation lead to central iris hypoplasia [Cut & Tag]

| PRJNA1107487 | ENA

Altered chromatin topologies caused by balanced chromosomal translocation lead to central iris hypoplasia [Hi-C]

Project description:Altered chromatin topologies caused by balanced chromosomal translocation lead to central iris hypoplasia [Hi-C]

| PRJNA1107486 | ENA

Altered chromatin topologies caused by balanced chromosomal translocation lead to central iris hypoplasia [RNA-Seq]

Project description:Altered chromatin topologies caused by balanced chromosomal translocation lead to central iris hypoplasia [RNA-Seq]

| PRJNA1107490 | ENA

Expression data from a human MLL-AF6 positive AML cell line

Project description:The MLL gene on chromosome 11 fuses to the AF6 gene on chromosome 6 in a balanced chromosomal translocation that is characetristic of certain adult and pediatric human leukemias. We established a murine leukemia model of MLL-AF6 using the retroviral MLL-AF6 contruct in a bone marrow transplantation system. The ML2 human MLL-AF6 positive leukemia cell line was used for gene expression profiling to assess the transctiptional profile in MLL-AF6 leukemias.

2013-04-03 | GSE43068 | GEO

The Effect of Translocation-Induced Nuclear Re-organization on Gene Expression

Project description:To study the effect of balanced chromosomal rearrangements on gene expression, we compared the transcriptomes of cell lines from control and t(11;22)(q23;q11) individuals. This translocation between chromosomes 11 and 22 is the only recurrent constitutional non-Robertsonian translocation in humans. The number of differentially expressed transcripts between the translocated and control cohort is significantly higher than that observed between control samples alone, suggesting that balanced rearrangements have a greater effect on gene expression than normal variation. Altered expression is not limited to genes close to the translocation breakpoint suggesting that a long-range effect is operating. Indeed we show that the nuclear position of the derivative chromosome is altered compared to the normal chromosomes. Our results are consistent with recent studies that indicate a functional role for nuclear position in regulating the expression of some genes in mammalian cells. They may also have implications on reproductive separation, as we show that reciprocal translocations not only provide partial isolation for speciation but also significant changes in transcriptional regulation through alteration of nuclear chromosomes territories. Keywords: Genetic modification

2010-03-05 | GSE13122 | GEO

Expression data from MLL-AF6 positive leukemia cells

Project description:The MLL gene on chromosome 11 fuses to the AF6 gene on chromosome 6 in a balanced chromosomal translocation that is characetristic of certain adult and pediatric human leukemias. We established a murine leukemia model of MLL-AF6 using the retroviral MLL-AF6 contruct in a bone marrow transplantation system. Leukemic bone marrow cells from a sacrificed moribund mouse were thawed and RNA was extracted using TRIZOL (Invitrogen) and purified further using the RNAeasy kit (Qiagen) under standard conditions and and hybridized onto Affymetrix arrays.

2013-04-03 | E-GEOD-43067 | biostudies-arrayexpress

Use of single nucleotide polymorphism microarrays to distinguish between balanced and normal chromosomes in embryos from a translocation carrier

Project description:Objective: To prove the ability to distinguish between balanced and normal chromosomes in embryos from a translocation carrier. Design: Case report. Setting: Academic center for reproductive medicine. Patient: A female with a balanced translocation causing Alagille Syndrome seeking preimplantation genetic diagnosis (PGD). Interventions: Blastocyst biopsy for PGD. Main outcome measures: Consistency of 3 methods of embryo genetic analysis (real-time PCR, SNP microarray, and FISH) and normalcy in the newborn derived from PGD. Results: PGD was applied to 48 embryos. Real-time PCR, SNP microarray, and FISH demonstrated 100% consistency, although FISH failed to detect aneuploidies observed by comprehensive SNP microarray based analyses. Two blastocysts were identified to be normal for all 3 factors using SNP microarray technology alone. The two normal embryos were transferred back to the patient resulting in the delivery of a healthy baby boy with a normal karyotype. Conclusions: This is the first report of validation and successful clinical application of microarray based PGD to distinguish between balanced and normal chromosomes in embryos from a translocation carrier.

2011-05-18 | GSE21732 | GEO

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