Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Candidate driver genes in SÑzary syndrome

ABSTRACT: Illumina human Omni5Exome arrays were used to investigate CNVs in SÑzary syndrome tumours as part of a larger study involving whole exome sequencing of the same samples and targeted resequencing of a further cohort. 16 Samples underwent SNP array including 10 tumour/gDNA matched samples that also underwent whole exome sequencing, public databases were used as further control data for calling CNVs.

ORGANISM(S): Homo sapiens

SUBMITTER: Venu Pullabhatla

PROVIDER: E-GEOD-80650 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Candidate driver genes involved in genome maintenance and DNA repair in Sézary syndrome.

Woollard Wesley J WJ Pullabhatla Venu V Lorenc Anna A Patel Varsha M VM Butler Rosie M RM Bayega Anthony A Begum Nelema N Bakr Farrah F Dedhia Kiran K Fisher Joshua J Aguilar-Duran Silvia S Flanagan Charlotte C Ghasemi Aria A AA Hoffmann Ricarda M RM Castillo-Mosquera Nubia N Nuttall Elisabeth A EA Paul Arisa A Roberts Ceri A CA Solomonidis Emmanouil G EG Tarrant Rebecca R Yoxall Antoinette A Beyers Carl Z CZ Ferreira Silvia S Tosi Isabella I Simpson Michael A MA de Rinaldis Emanuele E Mitchell Tracey J TJ Whittaker Sean J SJ

Blood 20160427 26

Sézary syndrome (SS) is a leukemic variant of cutaneous T-cell lymphoma (CTCL) and represents an ideal model for study of T-cell transformation. We describe whole-exome and single-nucleotide polymorphism array-based copy number analyses of CD4(+) tumor cells from untreated patients at diagnosis and targeted resequencing of 101 SS cases. A total of 824 somatic nonsynonymous gene variants were identified including indels, stop-gain/loss, splice variants, and recurrent gene variants indicative of c ...[more]

PMID: 27121473

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Project description:Highly specific amplification of complex DNA pools without bias or template-independent products (TIPs) remains a challenge. We have developed a procedure using phi29 DNA polymerase and trehalose and optimized control of amplification to create micrograms of specific amplicons without TIPs from down to sub-femtograms of DNA. The amplicons from 5 ng and 0.5 ng DNA, which were from originally good quality of gDNA (05-050), or partially degraded gDNA (04-018), faithfully demonstrated all previously known heterozygous segmental duplications and deletions (3 Mb to 18 kb) located on chromosome 22 and even a homozygous deletion smaller than 1 kb with high resolution chromosome-wide CGH. Specifically, HR-CGH with 5 ng-input gDNA-derived amplicon detected all previously known chromosomal segmental aberrations in chromosome 22 in samples from two different probands, and was indistinguishable from the HR-CGH result with native gDNA from the same probands (Fig. 4, Fig. S3 and S4). The break points were also precisely demonstrated. These include a heterozygous genomic segmental duplication (3 copies, 3 Mb in size, sample 05-050, Fig. 4) and 2 different heterozygous deletions (1 copy, 1.4 Mb and 18 kb respectively, sample 04-018, Fig. S4), all of which are located in or bounded by regions of low copy repeats (LCRs). In addition, a previous known homozygous deletion of 975 bp (in 04-018 and 05-050) was again accurately demonstrated (05-050 data showed in Fig. 4c), although sometimes (04-018) the data was a little noisier than with unamplified DNA (Fig. S4d). In contrast, the Wpa-40oC resulted in abundant signal noise and failed in detection of these copy number aberrations (Fig. 4, Fig. S3, S4). Impressively, HR-CGH with 0.5 ng gDNA-derived amplicons via Wpa also clearly detected the known CNVs, although noisier (Fig. S4). The 0.1ng gDNA derived amplicons via Wpa could not unambiguously show CNVs because of higher variability of signals, but the CNVs’ patterns were mostly well maintained (Fig. S4 for 04-018). We did also notice some locus-imbalance in the amplicon, however this was minimized, and was reproducible when the input was above a certain threshold amount, and it could be well compensated if the same amplified reference sample was applied in parallel as showed above. Keywords: Whole-pool amplification, high resolution comparative genome hybridization (HR-CGH)

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Candidate driver genes in SÑzary syndrome

Publications

Candidate driver genes involved in genome maintenance and DNA repair in Sézary syndrome.

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OmicsDI is part of the ELIXIR infrastructure

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Dataset Information

Candidate driver genes in SÑzary syndrome

Publications

Candidate driver genes involved in genome maintenance and DNA repair in Sézary syndrome.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Candidate driver genes in SÑzary syndrome