Array-Based Karyotyping for Prognostic Assessment in Chronic Lymphocytic Leukemia

Hagenkord, Jill; Monzon, Federico A.; Kash, Shera; Lilleberg, Stan L.; Xie, Qingmei; Kant, Jeffrey A.

doi:10.2353/jmoldx.2010.090118

Cited by 52 publications

(20 citation statements)

References 39 publications

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“…40 Studies of chronic lymphocytic leukemia have indicated that there is an association between TP53 mutation and the LOH of 17p, where TP53 is localized. 10 Recently, somatic LOH at the neurofibromatosis type 1 (NF1) locus, caused predominantly by segmental UPD of large parts of chromosome arm 17q, was identified as the main mechanism in children with juvenile myelomonocytic leukemia and NF1. 41 Because BRCA1 mutation carriers tend to develop ER-negative tumors, 42 and because growing evidence supports the potentially critical role of BRCA1 in the arising of basal-like breast cancers, 24 it is likely that 17q LOH suggests the presence of a BRCA1 mutation.…”

Section: Discussionmentioning

confidence: 99%

“…8,9 Single-nucleotide polymorphism (SNP) arrays offer high-resolution fine mapping of CNAs and also uniquely allow for the identification of genomic regions of loss of heterozygosity (LOH) without copy number loss, also known as somatic or acquired uniparental disomy (aUPD). 10,11 This may arise from segmental deletions and subsequent replacement of the lost fragment through gene conversion or mitotic recombination during carcinogenesis. 11 LOH/aUPD in cancer can lead to duplication of an activating mutation, homozygosity for a cancer-prone minor allele, duplication or deletion of a methylation pattern that impacts gene expression, or duplication of an allele that carries a deleted region, thus obtaining a homozygous deletion.…”

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confidence: 99%

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Genomic differences between estrogen receptor (ER)‐positive and ER‐negative human breast carcinoma identified by single nucleotide polymorphism array comparative genome hybridization analysis

Fang

Toher

Morgan

et al. 2010

Cancer

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BACKGROUND Estrogen receptor (ER) remains one of the most important biomarkers for breast cancer subtyping and prognosis, and comparative genome hybridization has greatly contributed to the understanding of global genetic imbalance. The authors used single-nucleotide polymorphism (SNP) arrays to compare overall copy number aberrations (CNAs) as well as loss of heterozygosity (LOH) of the entire human genome in ER-positive and ER-negative breast carcinomas. METHODS DNA was extracted from frozen tumor sections of 21 breast carcinoma specimens and analyzed with a proprietary 50K XbaI SNP array. Copy number and LOH probability values were derived for each sample. Data were analyzed using bioinformatics and computational software, and permutation tests were used to estimate the significance of these values. RESULTS There was a global increase in CNAs and LOH in ER-negative relative to ER-positive cancers. Gain of the long arm of chromosome 1 (1q) and 8q were the most obvious changes common in both subtypes: An increase in the chromosome 1 short arm (1p)/1q ratio was observed in ER-negative samples, and an increased 16p/16q ratio was observed in ER-positive samples. Significant CNAs (adjusted P<.05) in ER-negative relative to ER-positive tumors included 5q deletion, loss of 15q, and gain of 2p and 21q. Copy-neutral LOH (cnLOH) common to both ER-positive and ER-negative samples included 9p21, the p16 tumor suppressor locus, and 4q13, the RCHY1 (ring finger and CHY zinc finger domain-containing 1) oncogene locus. Of particular interest was an enrichment of 17q LOH among the ER-negative tumors, potentially suggesting breast cancer 1 gene (BRCA1) mutations. CONCLUSIONS SNP array detected both genetic imbalances and cnLOH and was capable of discriminating ER-negative breast cancer from ER-positive breast cancer.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Genomic differences between estrogen receptor (ER)‐positive and ER‐negative human breast carcinoma identified by single nucleotide polymorphism array comparative genome hybridization analysis

Fang

Toher

Morgan

et al. 2010

Cancer

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“…Since the cost of the 250K array is lower, it is preferred for routine use. In contrast, the 10K array is not suitable for routine clinical use due to its low resolution (Hagenkord et al, 2010).…”

Section: Molecular Karyotypingmentioning

confidence: 99%

“…In Table 3 an overview of selected publications on array-applications in CLL is shown, describing known prognostically important lesions and new molecular cytogenetic findings (Grubor et al, 2009;Gunn et al, 2008;Gunn et al, 2009;Gunnarsson et al, 2008;Gunnarsson et al, 2010;Gunnarsson et al, 2011;Hagenkord et al, 2010;Kay et al, 2010;Kujawski et al, 2008;Lehmann et al, 2008;O'Malley et al, 2011;Ouillette et al, 2010;Ouillette et al, 2011;Pfeifer et al, 2007;Rinaldi et al, 2011). Other recent studies using array-platforms revealed new insights in the disease: i.e.…”

Section: Molecular Karyotypingmentioning

confidence: 99%

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Genetics of Chronic Lymphocytic Leukemia: Practical Aspects and Prognostic Significance

Put¹,

Włodarska²,

Vandenberghe³

et al. 2012

Chronic Lymphocytic Leukemia

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Chromosomal Aberrations in Cancer

Weele

McNerney

Beau

2017

Holland‐Frei Cancer Medicine

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Overview The malignant cells of most patients who have leukemia, lymphoma, or a solid tumor have acquired clonal chromosomal abnormalities, the identification of which can aid in establishing the correct diagnosis and prognosis and in the selection of therapy. Today, our arsenal of approaches to characterize an individual's malignant disease combines pathologic evaluation, cytogenetic analysis, and molecular studies, typically focused on a few key genes. The advent of high‐throughput methods, such as next‐generation sequencing, capable of surveying the entire genome or large panels of cancer‐related genes, presents new options for a revolutionary change in the way we diagnose, characterize, and treat cancer. The vision for the future entails an integrated molecular profile, that is, chromosomal pattern, gene/miRNA expression, DNA methylation/epigenomic pattern, gene mutation status, and chemosensitivity of each patient's tumor, as well as predisposition to disease, facilitating the development of an individualized treatment plan with decreased toxicities and prolonged survival.

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Array-Based Karyotyping for Prognostic Assessment in Chronic Lymphocytic Leukemia

Cited by 52 publications

References 39 publications

Genomic differences between estrogen receptor (ER)‐positive and ER‐negative human breast carcinoma identified by single nucleotide polymorphism array comparative genome hybridization analysis

Genomic differences between estrogen receptor (ER)‐positive and ER‐negative human breast carcinoma identified by single nucleotide polymorphism array comparative genome hybridization analysis

Genetics of Chronic Lymphocytic Leukemia: Practical Aspects and Prognostic Significance

Chromosomal Aberrations in Cancer

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