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Methods for Copy Number Aberration Detection from Single-cell DNA Sequencing Data

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Probability Distributions on Cladograms

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The MM Algorithm

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Degenerate oligonucleotide-primed PCR: General amplification of target DNA by a single degenerate primer

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Determination of the Beta distribution form its Lorenz curve

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Focal chromosomal copy number aberrations in cancer—Needles in a genome haystack

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Tumor evolution: Linear, branching, neutral or punctuated?

inferredcites →https://doi.org/10.1016/j.cell.2018.03.041openalex-snapshot

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing

inferredcites →https://doi.org/10.1016/j.cell.2018.06.001openalex-snapshot

Universal Patterns of Selection in Cancer and Somatic Tissues

inferredcites →https://doi.org/10.1016/j.cels.2020.03.005openalex-snapshot

SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing

inferredcites →https://doi.org/10.1016/j.mam.2017.08.005openalex-snapshot

High-dimension single-cell analysis applied to cancer

inferredcites →https://doi.org/10.1038/nature07517openalex-snapshot

Accurate whole human genome sequencing using reversible terminator chemistry

inferredcites →https://doi.org/10.1038/nature08822openalex-snapshot

The landscape of somatic copy-number alteration across human cancers

inferredcites →https://doi.org/10.1038/nature09807openalex-snapshot

Tumour evolution inferred by single-cell sequencing

inferredcites →https://doi.org/10.1038/nature13600openalex-snapshot

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

inferredcites →https://doi.org/10.1038/ng.2760openalex-snapshot

Pan-cancer patterns of somatic copy number alteration

inferredcites →https://doi.org/10.1038/ng.3641openalex-snapshot

Punctuated copy number evolution and clonal stasis in triple-negative breast cancer

inferredcites →https://doi.org/10.1038/ng2028openalex-snapshot

Methods and strategies for analyzing copy number variation using DNA microarrays

inferredcites →https://doi.org/10.1038/nm.4279openalex-snapshot

Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples

inferredcites →https://doi.org/10.1038/nm.4369openalex-snapshot

An approach to suppress the evolution of resistance in BRAFV600E-mutant cancer

inferredcites →https://doi.org/10.1038/nmeth.1276openalex-snapshot

High-resolution mapping of copy-number alterations with massively parallel sequencing

inferredcites →https://doi.org/10.1038/nmeth.3578openalex-snapshot

Interactive analysis and assessment of single-cell copy-number variations

inferredcites →https://doi.org/10.1038/nmeth.4140openalex-snapshot

Scalable whole-genome single-cell library preparation without preamplification

inferredcites →https://doi.org/10.1038/nmeth.4154openalex-snapshot

Sequencing thousands of single-cell genomes with combinatorial indexing

inferredcites →https://doi.org/10.1038/nprot.2012.039openalex-snapshot

Genome-wide copy number analysis of single cells

inferredcites →https://doi.org/10.1038/nprot.2016.138openalex-snapshot

Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq

inferredcites →https://doi.org/10.1038/nrg1767openalex-snapshot

Structural variation in the human genome

inferredcites →https://doi.org/10.1038/s41467-019-13779-xopenalex-snapshot

CaSpER identifies and visualizes CNV events by integrative analysis of single-cell or bulk RNA-sequencing data

inferredcites →https://doi.org/10.1038/s41598-018-22323-8openalex-snapshot

MSeq-CNV: accurate detection of Copy Number Variation from Sequencing of Multiple samples

inferredcites →https://doi.org/10.1056/nejmcibr067658openalex-snapshot

Structural Variation in the Human Genome

inferredcites →https://doi.org/10.1073/pnas.1110574108openalex-snapshot

Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion

inferredcites →https://doi.org/10.1073/pnas.93.25.14800openalex-snapshot

The mutation rate and cancer

inferredcites →https://doi.org/10.1080/10635150600889625openalex-snapshot

Which Random Processes Describe the Tree of Life? A Large-Scale Study of Phylogenetic Tree Imbalance

inferredcites →https://doi.org/10.1093/bib/bbx004openalex-snapshot

DNA copy number profiling using single-cell sequencing

inferredcites →https://doi.org/10.1093/bioinformatics/btl238openalex-snapshot

Integrating copy number polymorphisms into array CGH analysis using a robust HMM

inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btq587openalex-snapshot

CNAseg—a novel framework for identification of copy number changes in cancer from second-generation sequencing data

inferredcites →https://doi.org/10.1093/bioinformatics/btq635openalex-snapshot

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization

inferredcites →https://doi.org/10.1093/bioinformatics/btr593openalex-snapshot

Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data

inferredcites →https://doi.org/10.1093/bioinformatics/btr670openalex-snapshot

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

inferredcites →https://doi.org/10.1093/bioinformatics/btz174openalex-snapshot

Multiresolution correction of GC bias and application to identification of copy number alterations

inferredcites →https://doi.org/10.1093/biomet/asq025openalex-snapshot

Detecting simultaneous changepoints in multiple sequences

inferredcites →https://doi.org/10.1093/biostatistics/kxh008openalex-snapshot

Circular binary segmentation for the analysis of array-based DNA copy number data

inferredcites →https://doi.org/10.1093/nar/gkr068openalex-snapshot

Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm

inferredcites →https://doi.org/10.1098/rsos.160016openalex-snapshot

A Beta-splitting model for evolutionary trees

inferredcites →https://doi.org/10.1101/411058openalex-snapshot

Resource: Scalable whole genome sequencing of 40,000 single cells identifies stochastic aneuploidies, genome replication states and clonal repertoires

inferredcites →https://doi.org/10.1101/gr.092981.109openalex-snapshot

Sensitive and accurate detection of copy number variants using read depth of coverage

inferredcites →https://doi.org/10.1101/gr.106344.110openalex-snapshot

Detecting copy number variation with mated short reads

inferredcites →https://doi.org/10.1101/gr.114876.110openalex-snapshot

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

inferredcites →https://doi.org/10.1101/gr.137570.112openalex-snapshot

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer

inferredcites →https://doi.org/10.1101/gr.198937.115openalex-snapshot

Assessment of megabase-scale somatic copy number variation using single-cell sequencing

inferredcites →https://doi.org/10.1101/gr.6861907openalex-snapshot

PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data

inferredcites →https://doi.org/10.1101/pdb.prot4919openalex-snapshot

Whole-Genome Amplification by Degenerate Oligonucleotide Primed PCR (DOP-PCR)

inferredcites →https://doi.org/10.1109/tcbb.2019.2920889openalex-snapshot

CNV_IFTV: An Isolation Forest and Total Variation-Based Detection of CNVs from Short-Read Sequencing Data

inferredcites →https://doi.org/10.1111/j.1541-0420.2006.00662.xopenalex-snapshot

A Modified Bayes Information Criterion with Applications to the Analysis of Comparative Genomic Hybridization Data

inferredcites →https://doi.org/10.1126/science.959840openalex-snapshot

The Clonal Evolution of Tumor Cell Populations

inferredcites →https://doi.org/10.1146/annurev-genet-102209-163544openalex-snapshot

Human Copy Number Variation and Complex Genetic Disease

inferredcites →https://doi.org/10.1146/annurev.ge.16.120182.000321openalex-snapshot

DOUBLE MINUTES AND HOMOGENEOUSLY STAINING REGIONS: Gene Amplification in Mammalian Cells

inferredcites →https://doi.org/10.1146/annurev.genom.7.080505.115618openalex-snapshot

Structural Variation of the Human Genome

inferredcites →https://doi.org/10.1152/physiolgenomics.00082.2012openalex-snapshot

Current analysis platforms and methods for detecting copy number variation

inferredcites →https://doi.org/10.1186/1471-2105-10-80openalex-snapshot

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

inferredcites →https://doi.org/10.1186/1471-2105-11-432openalex-snapshot

rSW-seq: Algorithm for detection of copy number alterations in deep sequencing data

inferredcites →https://doi.org/10.1186/1471-2105-13-205openalex-snapshot

Reconstructing DNA copy number by joint segmentation of multiple sequences

inferredcites →https://doi.org/10.1186/1471-2105-15-109openalex-snapshot

Copy number variation detection using next generation sequencing read counts

inferredcites →https://doi.org/10.1186/1471-2164-13-591openalex-snapshot

Copynumber: Efficient algorithms for single- and multi-track copy number segmentation

inferredcites →https://doi.org/10.1186/1471-2164-15-178openalex-snapshot

seqCNA: an R package for DNA copy number analysis in cancer using high-throughput sequencing

inferredcites →https://doi.org/10.1186/s12859-016-1239-7openalex-snapshot

nbCNV: a multi-constrained optimization model for discovering copy number variants in single-cell sequencing data

inferredcites →https://doi.org/10.1186/s12885-017-3447-6openalex-snapshot

Precision oncology using a limited number of cells: optimization of whole genome amplification products for sequencing applications

inferredcites →https://doi.org/10.1186/s13059-014-0452-9openalex-snapshot

Cancer genomics: one cell at a time

inferredcites →https://doi.org/10.1186/s13059-016-0971-7openalex-snapshot

Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies

inferredcites →https://doi.org/10.1186/s13059-016-0976-2openalex-snapshot

Single-cell whole genome sequencing reveals no evidence for common aneuploidy in normal and Alzheimer’s disease neurons

inferredcites →https://doi.org/10.1186/s13059-018-1578-yopenalex-snapshot

CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing

inferredcites →https://doi.org/10.1186/s13073-018-0537-2openalex-snapshot

Sensitivity to sequencing depth in single-cell cancer genomics

inferredcites →https://doi.org/10.1186/s40169-017-0177-yopenalex-snapshot

Using single‐cell multiple omics approaches to resolve tumor heterogeneity

inferredcites →https://doi.org/10.1198/016214502760047131openalex-snapshot

Model-Based Clustering, Discriminant Analysis, and Density Estimation

inferredcites →https://doi.org/10.1214/11-aoas517openalex-snapshot

Change-point model on nonhomogeneous Poisson processes with application in copy number profiling by next-generation DNA sequencing

inferredcites →https://doi.org/10.1214/aoms/1177697196openalex-snapshot

A Maximization Technique Occurring in the Statistical Analysis of Probabilistic Functions of Markov Chains

inferredcites →https://doi.org/10.1214/aos/1176343001openalex-snapshot

On Tests for Detecting Change in Mean

inferredcites →https://doi.org/10.1371/journal.pone.0016327openalex-snapshot

ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads

inferredcites →https://doi.org/10.1371/journal.pone.0085907openalex-snapshot

Reliable Single Cell Array CGH for Clinical Samples

inferredcites →https://doi.org/10.1371/journal.pone.0181163openalex-snapshot

New library construction method for single-cell genomes

inferredcites →https://doi.org/10.3892/or.2018.6325openalex-snapshot

Single nucleotide variant profiles of viable single circulating tumour cells reveal CTC behaviours in breast cancer

inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot

Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

inferredcites →https://doi.org/10.7150/ijbs.19627openalex-snapshot

Current Progresses of Single Cell DNA Sequencing in Breast Cancer Research

inferredcites →https://doi.org/10.7554/elife.21615openalex-snapshot

TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24− cancer cells

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.cels.2020.03.005openalex-snapshot

SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing

inferred← citeshttps://doi.org/10.1186/s40478-019-0873-5openalex-snapshot

Investigation of somatic CNVs in brains of synucleinopathy cases using targeted SNCA analysis and single cell sequencing

inferred← citeshttps://doi.org/10.1371/journal.pone.0238996openalex-snapshot

Directionally dependent multi-view clustering using copula model

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