A statistical method to estimate DNA copy number from Illumina high-density methylation arrays

Feng, Gang; Hobbs, Jennifer; Lu, Xin; Yu, Yue; Du, Pan; Kibbe, Warren A.; Chandler, James P.; Hou, Lifang; Lin, Simon

doi:10.4161/sysb.25896

Cited by 2 publications

(3 citation statements)

References 16 publications

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“…Herein, we propose a strategy for the statistical analysis of CNVs with data from methylation arrays using bioinformatics tools (conumee and ChAMP) ( 15 ). Previous publications have shown that they provide analogous results to the gold-standard technique for CNV analysis (CGH arrays) ( 26 , 27 ). Nevertheless, these tools focus on CNV representation ( 15 , 26 , 28 ) and are not designed for the statistical analysis of differences between different groups.…”

Section: Discussionmentioning

confidence: 83%

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DNA Copy Number Variation Associated with Anti-tumour Necrosis Factor Drug Response and Paradoxical Psoriasiform Reactions in Patients with Moderate-to-severe Psoriasis

Sanz-García¹,

Reolid²,

Fisas³

et al. 2021

Acta Derm Venereol

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Biological drugs targeting tumour necrosis factor are effective for psoriasis. However, 30–50% of patients do not respond to these drugs and may even develop paradoxical psoriasiform reactions. This study searched for DNA copy number variations that could predict anti-tumour necrotic factor drug response or the appearance of antitumour necrotic factor induced psoriasiform reactions. Peripheral blood samples were collected from 70 patients with anti-tumour necrotic factor drug-treated moderate-to-severe plaque psoriasis. Samples were analysed with an Illumina 450K methylation microarray. Copy number variations were obtained from raw methylation data using conumee and Chip Analysis Methylation Pipeline (ChAMP) R packages. One copy number variation was found, harbouring one gene ( CPM ) that was significantly associated with adalimumab response (Bonferroni-adjusted p -value < 0.05). Moreover, one copy number variation was identified harbouring 3 genes ( ARNT2 , LOC101929586 and MIR5572 ) related to the development of paradoxical psoriasiform reactions. In conclusion, this study has identified DNA copy number variations that could be good candidate markers to predict response to adalimumab and the development of anti-tumour necrotic factor paradoxical psoriasiform reactions.

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Section: Discussionmentioning

confidence: 83%

“…Susceptibility to psoriasis or disease severity has been associated with CNVs in certain genes such as CCL4/CCL4L ( 6 ), LCE3B and LCE3C ( 7 ) and DEFB ( 8 ). However, we have not found CNVs associated with anti-TNF drug response or with the appearance of psoriasiform reactions in the regions containing these genes.…”

Section: Discussionmentioning

confidence: 99%

DNA Copy Number Variation Associated with Anti-tumour Necrosis Factor Drug Response and Paradoxical Psoriasiform Reactions in Patients with Moderate-to-severe Psoriasis

Sanz-García¹,

Reolid²,

Fisas³

et al. 2021

Acta Derm Venereol

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“…This strategy allows for maximizing the information gathered with such an expensive technique as methylation microarrays. In addition, CNV determination from methylation arrays provides similar results to the gold-standard technique for CNV analysis (CGH arrays) [37,38]. Nevertheless, quantifying CNV differences between two groups is still very challenging since most of these tools are focused on CNV representation [37,39,40].…”

Section: Discussionmentioning

confidence: 99%

CNVs Associated with Different Clinical Phenotypes of Psoriasis and Anti-TNF-Induced Palmoplantar Pustulosis

Reolid

Sahuquillo‐Torralba

Sanz-García

et al. 2022

JPM

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Background: Psoriasis can present different phenotypes and could affect diverse body areas. In contrast to the high effectiveness of biological drugs in the treatment of trunk and extremities plaque psoriasis, in palmoplantar phenotypes and in plaque scalp psoriasis, these same drugs usually have reduced efficacy. Anti-TNF drugs could induce the appearance of palmoplantar pustulosis (PPP) in patients with other inflammatory diseases. The objective of this study is to identify if there are DNA Copy Number Variations (CNVs) associated with these different clinical phenotypes, which could justify the differences found in clinical practice. Moreover, we intend to elucidate if anti-TNF-induced PPP has a similar genetic background to idiopathic PPP. Methods: Skin samples were collected from 39 patients with different patterns of psoriasis and six patients with anti-TNF-induced PPP. The CNVs were obtained from methylation array data (Illumina Infinium Human Methylation) using the conumee R package. Results: No significant CNVs were found between the different phenotypes and the locations of psoriasis compared. Nevertheless, we found two significant bins harboring five different genes associated with anti-TNF-induced PPP in patients with a different background other than psoriasis. Conclusions: Our results may help to predict which patients could develop anti-TNF-induced PPP.

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A statistical method to estimate DNA copy number from Illumina high-density methylation arrays

Abstract: A statistical method to estimate DNA copy number from Illumina high-density methylation arrays, Systems Biomedicine, 1:2, 94-98,

Cited by 2 publications

References 16 publications

DNA Copy Number Variation Associated with Anti-tumour Necrosis Factor Drug Response and Paradoxical Psoriasiform Reactions in Patients with Moderate-to-severe Psoriasis

DNA Copy Number Variation Associated with Anti-tumour Necrosis Factor Drug Response and Paradoxical Psoriasiform Reactions in Patients with Moderate-to-severe Psoriasis

CNVs Associated with Different Clinical Phenotypes of Psoriasis and Anti-TNF-Induced Palmoplantar Pustulosis

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