Two distinct mechanisms underlie estrogen-receptor-negative breast cancer susceptibility at the 2p23.2 locus

Mendoza-Fandiño, Gustavo; Lyra, Paulo C.; Nepomuceno, Thales C.; Harro, Carly M.; Woods, Nicholas T.; Li, Xueli; Rangel, L.B.A.; Carvalho, Marcelo A.; Couch, Fergus J.; Monteiro, Alvaro N.A.

doi:10.1038/s41431-021-01005-6

Cited by 3 publications

(2 citation statements)

References 42 publications

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“…We performed a literature search and also consulted the Sanger Cancer Data Base (COSMIC) [ 38 ]. In the Basal subtype, cytoband 1q21.1-q25.2 contains cancer genes HORMAD1, LOC92312, SNG5, TMEM79, CCT3, IQGAP3, HDGF, PRCC in [ 39 ], cytoband 2p23.2-p16.3 contains cancer genes PLB1 and WDR43 [ 40 , 41 ] and cytoband 23q26.2-q28 contains the cancer genes ISR4 and FLNA [ 42 , 43 ]. In the case of the Luminal A subtype, cytoband 2q12.1-q21.1 contains gene ECRG4 [ 44 ].…”

Section: Discussionmentioning

confidence: 99%

TAaCGH Suite for Detecting Cancer—Specific Copy Number Changes Using Topological Signatures

Aslam

Ardanza-Trevijano

Xiong

et al. 2022

Entropy

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Copy number changes play an important role in the development of cancer and are commonly associated with changes in gene expression. Persistence curves, such as Betti curves, have been used to detect copy number changes; however, it is known these curves are unstable with respect to small perturbations in the data. We address the stability of lifespan and Betti curves by providing bounds on the distance between persistence curves of Vietoris–Rips filtrations built on data and slightly perturbed data in terms of the bottleneck distance. Next, we perform simulations to compare the predictive ability of Betti curves, lifespan curves (conditionally stable) and stable persistent landscapes to detect copy number aberrations. We use these methods to identify significant chromosome regions associated with the four major molecular subtypes of breast cancer: Luminal A, Luminal B, Basal and HER2 positive. Identified segments are then used as predictor variables to build machine learning models which classify patients as one of the four subtypes. We find that no single persistence curve outperforms the others and instead suggest a complementary approach using a suite of persistence curves. In this study, we identified new cytobands associated with three of the subtypes: 1q21.1-q25.2, 2p23.2-p16.3, 23q26.2-q28 with the Basal subtype, 8p22-p11.1 with Luminal B and 2q12.1-q21.1 and 5p14.3-p12 with Luminal A. These segments are validated by the TCGA BRCA cohort dataset except for those found for Luminal A.

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Section: Discussionmentioning

confidence: 99%

TAaCGH Suite for Detecting Cancer—Specific Copy Number Changes Using Topological Signatures

Aslam

Ardanza-Trevijano

Xiong

et al. 2022

Entropy

View full text Add to dashboard Cite

show abstract

“…For most loci identified in Genome-Wide Association Studies, the mechanisms of disease susceptibility are unclear. A study of the 2p23.2 ER-negative breast cancer susceptibility locus identifies potential candidate genes [4]. Genotype-phenotype correlations can also help in clinical practice, Moualed and colleagues describe the effect of NF2 pathogenic variants on tumour progression [5].…”

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confidence: 99%

No April fools in clinical genomics

McNeill

2022

Eur J Hum Genet

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A review on CRISPR/Cas: a versatile tool for cancer screening, diagnosis, and clinic treatment

Yang

Zhang

2023

Funct Integr Genomics

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Two distinct mechanisms underlie estrogen-receptor-negative breast cancer susceptibility at the 2p23.2 locus

Cited by 3 publications

References 42 publications

TAaCGH Suite for Detecting Cancer—Specific Copy Number Changes Using Topological Signatures

TAaCGH Suite for Detecting Cancer—Specific Copy Number Changes Using Topological Signatures

No April fools in clinical genomics

A review on CRISPR/Cas: a versatile tool for cancer screening, diagnosis, and clinic treatment

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