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Multiplexed DNA high throughput genotyping study to determine the mutational status of transient (TAM) and acute myeloid leukaemic (ML-DS) Down syndrome individuals.

ABSTRACT: Multiplexed DNA high throughput genotyping study to determine the mutational status of transient (TAM) and acute myeloid leukaemic (ML-DS) Down syndrome individuals.

PROVIDER: PRJEB31641 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3210530_1.fastq.gz	Fastqsanger.gz
	ERR3210530_2.fastq.gz	Fastqsanger.gz
	ERR3210540_1.fastq.gz	Fastqsanger.gz
	ERR3210540_2.fastq.gz	Fastqsanger.gz
	ERR3210550_1.fastq.gz	Fastqsanger.gz

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Multiplexed DNA high throughput genotyping study to determine the mutational status of transient (TAM) and acute myeloid leukaemic (ML-DS) Down syndrome individuals.

Project description:We used a 48.48 Fluidigm Access Array approach (1070 Amplicons spanning 62 genes: 157kB coverage) of genomic DNA from over 100 samples to genotype individuals with transient abnormal myelopoiesis (TAM) and acute myeloid leukemia of Down syndrome (ML-DS). Individually barcoded patient samples were subjected to paired-end 150bp sequencing (Illumina MiSeq), including paired GATA1 variant negative controls (including Post treatment) and 8 known reference GATA1- controls. Samples were mapped to build 37 of the human reference genome and subject to bioinformatic analysis (Varscan, Pindel, GATK) to facilitate the characterisation of known gene mutations in cancer as well as the identification / validation of potentially novel variants.

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Project description:Transient abnormal myelopoiesis (TAM) is a clonal pre-leukemic disorder that progresses to myeloid leukemia of Down syndrome (ML-DS) through the accumulation of genetic alterations. To investigate the mechanism of leukemogenesis in this disorder, a xenograft model of TAM was established using NOD/Shi-scid, IL-2Rγnull mice. In serial transplantations, engrafted TAM-derived cells showed the emergence of divergent subclones with another GATA1 mutation and various CNAs, including a 16q deletion and 1q gain, which are clinically associated with ML-DS. These results suggest that genetically heterogeneous subclones with varying leukemia-initiating potential already exist in the neonatal TAM phase, and ML-DS may develop from a pool of such minor clones through clonal selection. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from murine bone marrow (hCD45 sorted) or human peripheral blood samples. Copy number analysis of Affymetrix 500K SNP arrays was performed for xenografted TAM samples of 3 patients. There are also 3 samples from TAM patients in remission, which were used as references for copy number inference.

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