Waved aCGH: to smooth or not to smooth

Leprêtre, Frédéric; Villenet, Céline; Quief, Sabine; Nibourel, Olivier; Jacquemin, Christian; Troussard, Xavier; Jardin, Fabrice; Gibson, Fernando; Kerckaert, Jean‐Pierre; Roumier, Christophe; Figeac, Martin

doi:10.1093/nar/gkp1215

Cited by 27 publications

(23 citation statements)

References 16 publications

(37 reference statements)

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“…The Waves array comparative genomic hybridization Correction Algorithm (WACA), based on GC content and fragment size adjustment was applied in several cases. 18 WACA efficiently removes the wave artifact, thereby greatly improving the accuracy of array comparative genomic hybridization data analysis. Copy number variations/polymorphisms were identified and excluded from further analyses.…”

Section: Dna Extraction and Array Comparative Genomic Hybridizationmentioning

confidence: 99%

Genomic and immunohistochemical profiles of enteropathy-associated T-cell lymphoma in Japan

et al. 2015

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Enteropathy-associated T-cell lymphoma (EATL) is a rare primary T-cell lymphoma of the digestive tract. EATL is classified as either Type I, which is frequently associated with and thought to arise from celiac disease and is primarily observed in Northern Europe, and Type II, which occurs de novo and is distributed all over the world with predominance in Asia. The pathogenesis of EATL in Asia is unknown. We aimed to clarify the histological and genomic profiles of EATL in Japan in a homogeneous series of 20 cases. The cases were characterized by immunohistochemistry, high-resolution oligonucleotide microarray, and fluorescence in situ hybridization (FISH) at five different loci: 1q21.3 (CKS1B), 6q16.3 (HACE1), 7p22.3 (MAFK), 9q33.3 (PPP6C), and 9q34.3 (ASS1, CARD9) using formalin-fixed paraffin-embedded sections. The histological appearance of EATL ranged from medium-to large-sized cells in 13 cases (65%), small-to medium-sized cells in five cases (25%), and medium-sized in two cases (10%). The immunophenotype was CD2 + (60%), CD3e + (100%), CD4 + (10%), CD7 + (95%), CD8 + (80%), CD56 + (85%), TIA-1 + (100%), Granzyme B + (25%), T-cell receptor (TCR)β + (10%), TCRγ + (35%), TCRγδ + (50%), and double negative for TCR (six cases, 30%). All cases were EBER − . The genomic profile showed recurrent copy number gains of 1q32. 3, 4p15.1, 5q34, 7q34, 8p11.23, 9q22.31, 9q33.2, 9q34.13, and 12p13.31, and losses of 7p14.1. FISH showed 15 patients (75%) with a gain of 9q34.3 with good correlation with array comparative genomic hybridization. EATL in Japan is characterized by non-monomorphic cells with a cytotoxic CD8 + CD56 + phenotype similar to EATL Type II. The genomic profile is comparable to EATL of Western countries, with more similarity to Type I (gain of 1q and 5q) rather than Type II (gain of 8q24, including MYC). The 9q34.3 gain was the most frequent change confirmed by FISH irrespective of the cell origin of αβ-T-cells and γδ-T-cells.

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Section: Dna Extraction and Array Comparative Genomic Hybridizationmentioning

confidence: 99%

Genomic and immunohistochemical profiles of enteropathy-associated T-cell lymphoma in Japan

et al. 2015

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“…The WACA (waves aCGH correction algorithm) noise-reduction algorithm was applied post-analysis in order to determine if the complex profile observed in a subgroup of tumors was due to a "wave" artefact. 35 Data are available in the ArrayExpress database (Accession no. E-MEXP-3604).…”

Section: High Density Oligonucleotide Array Cgh (Hd-acgh)mentioning

confidence: 99%

“…As intragenic genomic rearrangements of the PTEN gene have been previously reported in breast carcinomas 35 and cannot be detected through BAC-aCGH analysis due to their relatively small size compared with the BAC covering the PTEN locus, we used a custom HD-CGH array focused on the PTEN locus to confirm and characterize PTEN large deletions. Forty-eight tumors were analyzed which included all but one (lack of DNA) of the tumors shown to have a 10q23 loss and/or absence of PTEN expression (i.e., 32 tumors) and the additional 16 tumors for which a large deletion had been identified through SQMP.…”

Section: Pten Large Genomic Rearrangement Analysismentioning

confidence: 99%

“…The persistence of PTEN expression in the 11 tumors of the complex PTEN status subgroup is surprising given the HD-CGH array profile at the PTEN locus but may be explained by the presence of remaining PTEN wild-type alleles necessary for tumorigenic progression. We do not believe that this complex PTEN profile is an artifact, as it was identified using two different techniques and the characteristic PTEN profile and genomic rearrangement persists following correction for CGH array "wave" artifacts 35 (Supporting Information Figs. 5 and 6).…”

Section: Pten Loss Of Function Can Be Accurately Identified By Ihc Anmentioning

confidence: 99%

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Comprehensive analysis of PTEN status in breast carcinomas

Jones

Bonnet

Sfar

et al. 2013

Intl Journal of Cancer

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PTEN plays a well-established role in the negative regulation of the PI3K pathway, which is frequently activated in several cancer types, including breast cancer. A nuclear function in the maintenance of chromosomal stability has been proposed for PTEN but is yet to be clearly defined. In order to improve understanding of the role of PTEN in mammary tumorigenesis in terms of a possible gene dosage effect, its PI3K pathway function and its association with p53, we undertook comprehensive analysis of PTEN status in 135 sporadic invasive ductal carcinomas. Four PTEN status groups were defined; complete loss (19/ 135, 14%), reduced copy number (19/135, 14%), normal (86/135, 64%) and complex (11/135, 8%). Whereas the PTEN complete loss status was significantly associated with estrogen receptor (ER) negativity (p50.006) and in particular the basal-like phenotype (p<0.0001), a reduced PTEN copy number was not associated with hormone receptor status or a particular breast cancer subtype. Overall, PI3K pathway alteration was suggested to be involved in 59% (79/134) of tumors as assessed by human epidermal growth factor receptor 2 overexpression, PIK3CA mutation or a complete loss of PTEN. A complex PTEN status was identified in a tumor subgroup which displayed a specific, complex DNA profile at the PTEN locus with a strikingly similar highly rearranged pan-genomic profile. All of these tumors had relapsed and were associated with a poorer prognosis in the context of node negative disease (p51.4 3 10 213 ) thus may represent a tumor subgroup with a common molecular alteration which could be targeted to improve clinical outcome.Alterations in phosphatidylinositol 3-kinase (PI3K) pathway components have been described in breast cancer and can lead to hyperactivation of the pathway. Human epidermal growth factor receptor 2 (HER2) overexpression is observed in 15% of breast cancers. 1,2 Activating mutations in PIK3CA, which encodes the PI3K catalytic subunit, have been reported in approximately a quarter of breast tumors 3 and copy number gain of this gene has been identified in 1-14% of breast cancers. [4][5][6] Approximately one fifth of breast cancers are described as having loss of phosphatase and tensin homologue deleted on chromosome 10 (PTEN) expression (range 4-48%) 6-15 and epigenetic silencing of the PTEN gene through promoter hypermethylation has been reported in 34% 16 and 48% 17 of breast cancers. Loss of heterozygosity at the PTEN locus is observed in 40% of invasive breast carcinomas 18,19 but mutations in this gene have only been identified in 2-9% of breast cancers 3,7,[20][21][22] suggesting that PTEN haploinsufficiency may have tumorigenic consequences. 23,24 Indeed, complete loss of Pten has been reported to oppose tumor progression in vitro and in a prostate-specific mouse model through induction of p53-dependant cellular senescence. 25 In addition to its function as a negative regulator of the PI3K pathway, a nuclear role for PTEN has been proposed. It has been reported to control chromosomal integrity t...

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“…The aCGH experiment utilized a customized high-definition microarray consisting of 105,000 probes (105K, Agilent Technologies, Santa Clara, CA). All arrays were treated by the WACA algorithm that removes all false aberrations without modifying real aberrations, allowing efficient further analysis [18]. Experimental methods and data analysis were performed according to the manufacturer's instructions, using CGH Analytics TM Agilent software v3.4 and the Human Genome Browser build 19 (February 2009).…”

Section: Cytogenetic Analysismentioning

confidence: 99%

Neurofibromatosis‐1 gene deletions and mutations in de novo adult acute myeloid leukemia

et al. 2013

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On behalf of the French ALFA groupGermline heterozygous alterations of the tumor-suppressor gene neurofibromatosis-1 (NF1) lead to neurofibromatosis type 1, a genetic disorder characterized by a higher risk to develop juvenile myelomonocytic leukemia and/or acute myeloid leukemia (AML). More recently, somatic 17q11 deletions encompassing NF1 have been described in many adult myeloid malignancies. In this context, we aimed to define NF1 involvement in AML. We screened a total of 488 previously untreated de novo AML patients for the NF1 deletion using either array comparative genomic hybridization (aCGH) or real-time quantitative PCR/fluorescence in situ hybridization approaches. We also applied massively parallel sequencing for in depth mutation analysis of NF1 in 20 patients including five NF1-deleted patients. We defined a small~0.3 Mb minimal deleted region involving NF1 by aCGH and an overall frequency of NF1 deletion of 3.5% (17/485). NF1 deletion is significantly associated with unfavorable cytogenetics and with monosomal karyotype notably. We discovered six NF1 variants of unknown significance in 7/20 patients of which only one out of four disappeared in corresponding complete remission sample. In addition, only one out of five NF1-deleted patients has an acquired coding mutation in the remaining allele. In conclusion, direct NF1 inactivation is infrequent in de novo AML and may be a secondary event probably involved in leukemic progression. Am. J.

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Waved aCGH: to smooth or not to smooth

Cited by 27 publications

References 16 publications

Genomic and immunohistochemical profiles of enteropathy-associated T-cell lymphoma in Japan

Genomic and immunohistochemical profiles of enteropathy-associated T-cell lymphoma in Japan

Comprehensive analysis of PTEN status in breast carcinomas

Neurofibromatosis‐1 gene deletions and mutations in de novo adult acute myeloid leukemia

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