scholarly journals Copy number motifs expose genome instability type and predict driver events and disease outcome in breast cancer

2019 ◽  
Author(s):  
Arne V. Pladsen ◽  
Gro Nilsen ◽  
Oscar M. Rueda ◽  
Miriam R. Aure ◽  
Ørnulf Borgan ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Copy Number ◽  
Genome Instability ◽  
Prognostic Index ◽  
Tumor Evolution ◽  
Cancer Specific Survival ◽  
Allele Specific ◽  
Low Dimensional ◽  
Genomic Regions ◽  
Tumor Genome

AbstractTumor evolution is dependent on and constrained by the genotypes emerging from genome instability. We hypothesized that non-site-specific copy number motifs would correlate with underlying replication defects and also with tumor and patient fate. Six feature detectors were defined to characterize and score the local spatial behaviour of a copy number profile. By accumulating scores across genomic regions, a low-dimensional representation of the tumor genome was obtained. The proposed Copy Aberration Regional Mapping Analysis (CARMA) algorithm was applied to 2384 breast tumors from three breast cancer cohorts, revealing distinct copy number motifs in established molecular subtypes. A prognostic index combining the features predicted breast cancer specific survival better than both the genomic instability index (GII) and all commonly used clinical stratifications. CARMA offers effective comparison of tumor subgroups and extracts biologically and clinically relevant features from allele-specific copy number profiles.

scholarly journals Reconstructing mutational lineages in breast cancer by multi-patient-targeted single cell DNA sequencing

2021 ◽  
Author(s):  
Nicholas Navin ◽  
Jake Leighton ◽  
Min Hu ◽  
Emi Sei ◽  
Funda Meric-Bernstam
Keyword(s):  
Breast Cancer ◽  
Dna Sequencing ◽  
Single Cell ◽  
Copy Number ◽  
Somatic Mutations ◽  
Single Cells ◽  
Tumor Evolution ◽  
Sequencing Method ◽  
Genomic Regions ◽  
Microfluidics Platform

Single cell DNA sequencing (scDNA-seq) methods are powerful tools for profiling mutations in cancer cells, however most genomic regions characterized in single cells are non-informative. To overcome this issue, we developed a Multi-Patient-Targeted (MPT) scDNA-seq sequencing method. MPT involves first performing bulk exome sequencing across a cohort of cancer patients to identify somatic mutations, which are then pooled together to develop a single custom targeted panel for high-throughput scDNA-seq using a microfluidics platform. We applied MPT to profile 330 mutations across 23,500 cells from 5 TNBC patients, which showed that 3 tumors were monoclonal and 2 tumors were polyclonal. From this data, we reconstructed mutational lineages and identified early mutational and copy number events, including early TP53 mutations that occurred in all five patients. Collectively, our data suggests that MPT can overcome technical obstacles for studying tumor evolution using scDNA-seq by profiling information-rich mutation sites.

scholarly journals Characterizing the allele- and haplotype-specific copy number landscape of cancer genomes at single-cell resolution with CHISEL

2019 ◽  
Author(s):  
Simone Zaccaria ◽  
Benjamin J. Raphael
Keyword(s):  
Breast Cancer ◽  
Single Cell ◽  
Copy Number ◽  
Single Cells ◽  
Neutral Loss ◽  
Tumor Evolution ◽  
Whole Genome ◽  
Copy Numbers ◽  
Allele Specific ◽  
Total Copy Number

AbstractSingle-cell barcoding technologies have recently been used to perform whole-genome sequencing of thousands of individual cells in parallel. These technologies provide the opportunity to characterize genomic heterogeneity at single-cell resolution, but their extremely low sequencing coverage (<0.05X per cell) has thus far restricted their use to identification of the total copy number of large multi-megabase segments in individual cells. However, total copy numbers do not distinguish between the two homologous chromosomes in humans, and thus provide a limited view of tumor heterogeneity and evolution missing important events such as copy-neutral loss-of-heterozygosity (LOH). We introduce CHISEL, the first method to infer allele- and haplotype-specific copy numbers in single cells and subpopulations of cells by aggregating sparse signal across thousands of individual cells. We applied CHISEL to 10 single-cell sequencing datasets from 2 breast cancer patients, each dataset containing ≈2000 cells. We identified extensive allele-specific copy-number aberrations (CNAs) in these samples including copy-neutral LOH, whole-genome duplications (WGDs), and mirrored-subclonal CNAs in subpopulations of cells. These allele-specific CNAs alter the copy number of genomic regions containing well-known breast cancer genes including TP53, BRCA2, and PTEN but are invisible to total copy number analysis. We utilized CHISEL’s allele- and haplotype-specific copy numbers to derive a more refined reconstruction of tumor evolution: timing allele-specific CNAs before and after WGDs, identifying low-frequency subclones distinguished by unique CNAs, and uncovering evidence of convergent evolution. This reconstruction is supported by orthogonal analysis of somatic single-nucleotide variants (SNVs) obtained by pooling barcoded reads across clones defined by CHISEL.

scholarly journals Single Cell Genetic Profiling of Tumors of Breast Cancer Patients Aged 50 Years and Older Reveals Enormous Intratumor Heterogeneity Independent of Individual Prognosis

Cancers ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 3366
Author(s):  
Anna-Sophie Liegmann ◽  
Kerstin Heselmeyer-Haddad ◽  
Annette Lischka ◽  
Daniela Hirsch ◽  
Wei-Dong Chen ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Patients ◽  
Copy Number ◽  
Genome Instability ◽  
Single Cells ◽  
Gene Mutations ◽  
Intratumor Heterogeneity ◽  
Breast Cancer Patients ◽  
Luminal A ◽  
Pik3ca Mutations

Purpose: Older breast cancer patients are underrepresented in cancer research even though the majority (81.4%) of women dying of breast cancer are 55 years and older. Here we study a common phenomenon observed in breast cancer which is a large inter- and intratumor heterogeneity; this poses a tremendous clinical challenge, for example with respect to treatment stratification. To further elucidate genomic instability and tumor heterogeneity in older patients, we analyzed the genetic aberration profiles of 39 breast cancer patients aged 50 years and older (median 67 years) with either short (median 2.4 years) or long survival (median 19 years). The analysis was based on copy number enumeration of eight breast cancer-associated genes using multiplex interphase fluorescence in situ hybridization (miFISH) of single cells, and by targeted next-generation sequencing of 563 cancer-related genes. Results: We detected enormous inter- and intratumor heterogeneity, yet maintenance of common cancer gene mutations and breast cancer specific chromosomal gains and losses. The gain of COX2 was most common (72%), followed by MYC (69%); losses were most prevalent for CDH1 (74%) and TP53 (69%). The degree of intratumor heterogeneity did not correlate with disease outcome. Comparing the miFISH results of diploid with aneuploid tumor samples significant differences were found: aneuploid tumors showed significantly higher average signal numbers, copy number alterations (CNAs) and instability indices. Mutations in PIKC3A were mostly restricted to luminal A tumors. Furthermore, a significant co-occurrence of CNAs of DBC2/MYC, HER2/DBC2 and HER2/TP53 and mutual exclusivity of CNAs of HER2 and PIK3CA mutations and CNAs of CCND1 and PIK3CA mutations were revealed. Conclusion: Our results provide a comprehensive picture of genome instability profiles with a large variety of inter- and intratumor heterogeneity in breast cancer patients aged 50 years and older. In most cases, the distribution of chromosomal aneuploidies was consistent with previous results; however, striking exceptions, such as tumors driven by exclusive loss of chromosomes, were identified.

scholarly journals Human rDNA Copy Number Is Unstable in Metastatic Breast Cancers

2019 ◽  
Author(s):  
Virginia Valori ◽  
Katalin Tus ◽  
Christina Laukaitis ◽  
David T. Harris ◽  
Lauren LeBeau ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Copy Number Variation ◽  
Copy Number ◽  
Genome Instability ◽  
Gene Clusters ◽  
Genome Rearrangements ◽  
Epigenetic Silencing ◽  
Healthy Tissue ◽  
Gene Promoters ◽  
Number Variation

AbstractEpigenetic silencing, including the formation of heterochromatin, silent chromosome territories, and repressed gene promoters, acts to stabilize patterns of gene regulation and the physical structure of the genome. Reduction of epigenetic silencing can result in genome rearrangements, particularly at intrinsically unstable regions of the genome such as transposons, satellite repeats, and repetitive gene clusters including the rRNA gene clusters (rDNA). It is thus expected that mutational or environmental conditions that compromise heterochromatin function might cause genome instability, and diseases associated with decreased epigenetic stability might exhibit genome changes as part of their etiology. We find support of this hypothesis in invasive ductal breast carcinoma, in which reduced epigenetic silencing has been previously described, by using a facile method to quantify rDNA copy number in biopsied breast tumors and pair-matched healthy tissue. We found that rDNA and satellite DNA sequences had significant copy number variation – both losses and gains of copies – compared to healthy tissue, arguing that these genome rearrangements are common in developing breast cancer. Thus, any proposed etiology onset or progression of breast cancer should consider alterations to the epigenome, but must also accommodate concomitant changes to genome sequence at heterochromatic loci.Authors’ StatementOne of the common hallmarks of cancer is genome instability, including hypermutation and changes to chromosome structure. Using tumor tissues obtained from women with invasive ductal carcinoma, we find that a sensitive area of the genome – the ribosomal DNA gene repeat cluster – shows hypervariability in copy number. The patterns we observe as not consistent with an adaptive loss leading to increased tumor growth, but rather we conclude that copy number variation at repeat DNA is a general consequence of reduced heterochromatin function in cancer progression.

822 Allele-specific aberrations and two dimensional disparity of copy number alterations in breast cancer

2010 ◽  
Vol 8 (5) ◽  
pp. 207
Author(s):  
F. Kaveh ◽  
H. Edvardsen ◽  
A.L. Børresen-Dale ◽  
V.N. Kristensen ◽  
H.K. Solvang
Keyword(s):  
Breast Cancer ◽  
Copy Number ◽  
Two Dimensional ◽  
Copy Number Alterations ◽  
Allele Specific

Estrogen receptor alpha (ESR1) gene amplification status and clinical outcome in tamoxifen-treated postmenopausal patients with endocrine-responsive early breast cancer: An analysis of the prospective ABCSG-6 trial.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 10501-10501 ◽  
Author(s):  
Christian F. Singer ◽  
Frederik Holst ◽  
Stefan Steurer ◽  
E C Burandt ◽  
Hellmut Samonigg ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Estrogen Receptor ◽  
Clinical Outcome ◽  
Copy Number ◽  
Estrogen Receptor Alpha ◽  
Distant Recurrence ◽  
Breast Cancer Specific Survival ◽  
Cancer Specific Survival ◽  
Esr1 Gene

10501 Background: Estrogen receptor alpha (ERα) expression is a prognostic parameter in breast cancer and predicts response to endocrine therapy. One of the factors important for protein expression is amplification of its encoding gene ESR1. We have investigated the value of ESR1 amplification in predicting the long-term clinical outcome in tamoxifen-treated postmenopausal women with endocrine-responsive breast cancer. Methods: 394 patients who had been randomized into the tamoxifen-only arm of the prospectively designed endocrine ABCSG-06 trial and in whom FFPE tumor tissue was available were included in this analysis. Immunohistochemical ERα expression was evaluated both locally and centrally using the Allred score, while ESR1 gene amplification status was evaluated by FISH analysis using the ESR1/CEN6 ratio. Results: ESR1 copy number gains were detected in 187 of 394 (47%) tumor specimen and was associated with favorable clinical outcome. At a median follow-up of 10 years, women with intratumoral ESR1 copy number gains had a significantly longer distant recurrence-free survival (adjusted HR for relapse 0.48; 95% CI 0.28-0.83; p=0.009) and breast cancer-specific survival (adjusted HR for death 0.46; CI 0.46-0.71; p=0.006) when compared to women with normal ESR1 copy numbers. Immunohistochemical ERα protein expression, evaluated by Allred score, was significantly correlated with ESR1 copy number alterations (p<0.0001; Chi-Square test), but did itself not allow to discriminate between patients with poor and good prognosis. Conclusions: ESR1 amplification status is an independent and powerful predictor for long-term distant recurrence-free and breast cancer-specific survival in postmenopausal women with endocrine-responsive early-stage breast cancer who received 5 years of tamoxifen.

scholarly journals A Single-Array-Based Method for Detecting Copy Number Variants Using Affymetrix High Density SNP Arrays and its Application to Breast Cancer

2014 ◽  
Vol 13s4 ◽  
pp. CIN.S15203
Author(s):  
Ming Li ◽  
Yalu Wen ◽  
Wenjiang Fu
Keyword(s):  
Breast Cancer ◽  
Copy Number ◽  
Copy Number Variants ◽  
High Density ◽  
Breast Cancer Dataset ◽  
Structural Variations ◽  
Cancer Dataset ◽  
Snp Arrays ◽  
Array Normalization ◽  
Genomic Regions

Cumulative evidence has shown that structural variations, due to insertions, deletions, and inversions of DNA, may contribute considerably to the development of complex human diseases, such as breast cancer. High-throughput genotyping technologies, such as Affymetrix high density single-nucleotide polymorphism (SNP) arrays, have produced large amounts of genetic data for genome-wide SNP genotype calling and copy number estimation. Meanwhile, there is a great need for accurate and efficient statistical methods to detect copy number variants. In this article, we introduce a hidden-Markov-model (HMM)-based method, referred to as the PICR-CNV, for copy number inference. The proposed method first estimates copy number abundance for each single SNP on a single array based on the raw fluorescence values, and then standardizes the estimated copy number abundance to achieve equal footing among multiple arrays. This method requires no between-array normalization, and thus, maintains data integrity and independence of samples among individual subjects. In addition to our efforts to apply new statistical technology to raw fluorescence values, the HMM has been applied to the standardized copy number abundance in order to reduce experimental noise. Through simulations, we show our refined method is able to infer copy number variants accurately. Application of the proposed method to a breast cancer dataset helps to identify genomic regions significantly associated with the disease.

scholarly journals Intra-tumor heterogeneity defines treatment-resistant HER2+ breast tumors

2018 ◽  
Author(s):  
Inga H. Rye ◽  
Anne Trinh ◽  
Anna Sætersdal ◽  
Daniel Nebdal ◽  
Ole Christian Lingjærde ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Protein Expression ◽  
Copy Number ◽  
Tumor Heterogeneity ◽  
Breast Tumors ◽  
Gene Copy ◽  
Tumor Evolution ◽  
Her2 Breast Cancer ◽  
The Impact

AbstractTargeted therapy for patients with HER2 positive (HER2+) breast cancer has improved the overall survival, but many patients still suffer relapse and death of the disease. Intra-tumor heterogeneity of both estrogen receptor (ER) and HER2 expression has been proposed to play a key role in treatment failure, but little work has been done to comprehensively study this heterogeneity at the single-cell level.In this study, we explored the clinical impact of intra-tumor heterogeneity of ER protein expression, HER2 protein expression, and HER2 gene copy number alterations. Using combined immunofluorescence and in situ hybridization on tissue sections followed by a validated computational approach, we analyzed more than 13,000 single tumor cells across 37 HER2+ breast tumors. The samples were taken both before and after neoadjuvant chemotherapy plus HER2-targeted treatment, enabling us to study tumor evolution as well.We found that intra-tumor heterogeneity for HER2 copy number varied substantially between patient samples. Highly heterogeneous tumors were associated with significantly shorter disease-free survival and fewer long-term survivors. Patients for which HER2 characteristics did not change during treatment had a significantly worse outcome.This work shows the impact of intra-tumor heterogeneity in molecular diagnostics for treatment selection in HER2+ breast cancer patients and the power of computational scoring methods to evaluate in situ molecular markers in tissue biopsies.

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