Archival single-cell genomics reveals persistent subclones during DCIS progression

[1]  Jacco,et al.  Genomic analysis defines clonal relationships of ductal carcinoma in situ and recurrent invasive breast cancer , 2022, Nature Genetics.

[2]  Evan Z. Macosko,et al.  Spatial genomics enables multi-modal study of clonal heterogeneity in tissues , 2021, Nature.

[3]  N. Navin,et al.  MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution , 2021, bioRxiv.

[4]  King-Jen Chang,et al.  Evolutionary Trajectories and Genomic Divergence in Localized Breast Cancers after Ipsilateral Breast Tumor Recurrence , 2021, Cancers.

[5]  Thomas O. McDonald,et al.  Breast Tumors Maintain a Reservoir of Subclonal Diversity During Expansion , 2021, Nature.

[6]  K. Chin,et al.  Genomic Alterations during the In Situ to Invasive Ductal Breast Carcinoma Transition Shaped by the Immune System , 2020, Molecular Cancer Research.

[7]  Tonje G. Lien,et al.  Contrasting DCIS and invasive breast cancer by subtype suggests basal-like DCIS as distinct lesions , 2020, npj Breast Cancer.

[8]  J. Reis-Filho,et al.  Whole-Exome Sequencing Analysis of the Progression from Non–Low-Grade Ductal Carcinoma In Situ to Invasive Ductal Carcinoma , 2020, Clinical Cancer Research.

[9]  Guangchuang Yu,et al.  Using ggtree to Visualize Data on Tree‐Like Structures , 2020, Current protocols in bioinformatics.

[10]  William Stafford Noble,et al.  High-Throughput Single-Cell Sequencing with Linear Amplification. , 2019, Molecular cell.

[11]  Richard A. Moore,et al.  Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing , 2019, Cell.

[12]  Michael Hahsler,et al.  dbscan: Fast Density-Based Clustering with R , 2019, Journal of Statistical Software.

[13]  Nicholas J. Wang,et al.  Genomic landscape of ductal carcinoma in situ and association with progression , 2019, Breast Cancer Research and Treatment.

[14]  Zemin Zhang,et al.  Understanding tumor ecosystems by single-cell sequencing: promises and limitations , 2018, Genome biology.

[15]  Mary E. Edgerton,et al.  Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing , 2018, Cell.

[16]  Leonard D. Goldstein,et al.  Massively parallel nanowell-based single-cell gene expression profiling , 2017, BMC Genomics.

[17]  Gouri Nanjangud,et al.  Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples , 2017, Nature Medicine.

[18]  Andrew C. Adey,et al.  Sequencing thousands of single-cell genomes with combinatorial indexing , 2017, Nature Methods.

[19]  Samuel Aparicio,et al.  Scalable whole-genome single-cell library preparation without preamplification , 2017, Nature Methods.

[20]  N. Navin,et al.  Genome evolution in ductal carcinoma in situ: invasion of the clones , 2017, The Journal of pathology.

[21]  Roland Eils,et al.  Complex heatmaps reveal patterns and correlations in multidimensional genomic data , 2016, Bioinform..

[22]  M. Schmidt,et al.  Subsequent risk of ipsilateral and contralateral invasive breast cancer after treatment for ductal carcinoma in situ: incidence and the effect of radiotherapy in a population-based cohort of 10,090 women , 2016, Breast Cancer Research and Treatment.

[23]  Funda Meric-Bernstam,et al.  Punctuated Copy Number Evolution and Clonal Stasis in Triple-Negative Breast Cancer , 2016, Nature Genetics.

[24]  W. Koh,et al.  Single-cell genome sequencing: current state of the science , 2016, Nature Reviews Genetics.

[25]  N. Navin,et al.  Highly multiplexed targeted DNA sequencing from single nuclei , 2016, Nature Protocols.

[26]  Brian L. Frey,et al.  Formaldehyde Crosslinking: A Tool for the Study of Chromatin Complexes* , 2015, The Journal of Biological Chemistry.

[27]  Kylie L. Gorringe,et al.  Copy number analysis of ductal carcinoma in situ with and without recurrence , 2015, Modern Pathology.

[28]  N. Navin,et al.  Advances and applications of single-cell sequencing technologies. , 2015, Molecular cell.

[29]  Tae-Min Kim,et al.  Genomic differences between pure ductal carcinoma in situ and synchronous ductal carcinoma in situ with invasive breast cancer , 2015, Oncotarget.

[30]  Edwin Cuppen,et al.  Sambamba: fast processing of NGS alignment formats , 2015, Bioinform..

[31]  N. Navin.  Cancer genomics: one cell at a time , 2014, Genome Biology.

[32]  B. Chua,et al.  A review of the management of ductal carcinoma in situ following breast conserving surgery. , 2013, Breast.

[33]  J. Reis-Filho,et al.  Progression from ductal carcinoma in situ to invasive breast cancer: Revisited , 2013, Molecular oncology.

[34]  Z. Baloch,et al.  Archived formalin-fixed paraffin-embedded (FFPE) blocks: A valuable underexploited resource for extraction of DNA, RNA, and protein. , 2013, Biopreservation and biobanking.

[35]  X. Xie,et al.  Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell , 2012, Science.

[36]  L. Shepherd,et al.  Differential copy number aberrations in novel candidate genes associated with progression from in situ to invasive ductal carcinoma of the breast , 2012, Genes, chromosomes & cancer.

[37]  A. Bleyer,et al.  Effect of three decades of screening mammography on breast-cancer incidence. , 2012, The New England journal of medicine.

[38]  Stephen R. Quake,et al.  Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm , 2012, Cell.

[39]  Steven J. M. Jones,et al.  Comprehensive molecular portraits of human breast tumors , 2012, Nature.

[40]  Samantha E. Boyle,et al.  Identification of copy number alterations associated with the progression of DCIS to invasive ductal carcinoma , 2012, Breast Cancer Research and Treatment.

[41]  J. Reis-Filho,et al.  Genomic and mutational profiling of ductal carcinomas in situ and matched adjacent invasive breast cancers reveals intra‐tumour genetic heterogeneity and clonal selection , 2012, The Journal of pathology.

[42]  F. Markowetz,et al.  The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups , 2012, Nature.

[43]  Jorge S Reis-Filho,et al.  Genetic heterogeneity and cancer drug resistance. , 2012, The Lancet. Oncology.

[44]  Charles Swanton,et al.  Intratumor Heterogeneity: Seeing the Wood for the Trees , 2012, Science Translational Medicine.

[45]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[46]  J. Troge,et al.  Tumour evolution inferred by single-cell sequencing , 2011, Nature.

[47]  D. Hunter,et al.  mixtools: An R Package for Analyzing Mixture Models , 2009 .

[48]  Adrian V. Lee,et al.  Molecular profiles of progesterone receptor loss in human breast tumors , 2009, Breast Cancer Research and Treatment.

[49]  M. Wigler,et al.  Circular binary segmentation for the analysis of array-based DNA copy number data. , 2004, Biostatistics.

[50]  S. Devries,et al.  Patterns of Chromosomal Alterations in Breast Ductal Carcinoma In situ , 2004, Clinical Cancer Research.

[51]  S. Kingsmore,et al.  Comprehensive human genome amplification using multiple displacement amplification , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[52]  S. Devries,et al.  Chromosomal alterations in ductal carcinomas in situ and their in situ recurrences. , 2000, Journal of the National Cancer Institute.

[53]  N. Carter,et al.  Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. , 1992, Genomics.

[54]  Annapurna Poduri,et al.  Single-cell, genome-wide sequencing identifies clonal somatic copy-number variation in the human brain. , 2015, Cell reports.

[55]  Ira M. Hall,et al.  BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..

[56]  M. Feldman,et al.  Reactions of nucleic acids and nucleoproteins with formaldehyde. , 1973, Progress in nucleic acid research and molecular biology.