Computational methods for detecting copy number variations in cancer genome using next generation sequencing: principles and challenges (Q26864808)

Carl D. Morrison

2

1 reference

Candace S. Johnson

3

1 reference

Donald L. Trump

4

1 reference

Maochun Qin

5

1 reference

Jeffrey C. Conroy

6

1 reference

Jianmin Wang

7

1 reference

Song Liu

8

1 reference

language of work or name

1 reference

November 2013

1 reference

1 November 2013

9 references

3 April 2019

19 June 2019

30 June 2019

14 September 2019

19 September 2019

25 November 2020

8 February 2021

30 April 2021

25 October 2022

10 references

3 April 2019

19 June 2019

30 June 2019

14 September 2019

19 September 2019

25 November 2020

8 February 2021

30 April 2021

25 October 2022

4

1 reference

issue

11

1 reference

page(s)

1868-81

1 reference

Creative Commons Attribution 2.5 Generic

copyright license

9 references

3 April 2019

19 June 2019

30 June 2019

14 September 2019

19 September 2019

25 November 2020

8 February 2021

30 April 2021

describes a project that uses

25 October 2022

massive parallel sequencing

1 reference

based on heuristic

inferred from title

on focus list of Wikimedia project

ScienceSource

0 references

cites work

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Global variation in copy number in the human genome

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Structural variation in the human genome

21 March 2017

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An analysis of the feasibility of short read sequencing

21 March 2017

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A census of human cancer genes

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Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

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Sequencing technologies - the next generation

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21 March 2017

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Subgroup-specific structural variation across 1,000 medulloblastoma genomes

21 March 2017

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

21 March 2017

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Genome remodelling in a basal-like breast cancer metastasis and xenograft

21 March 2017

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21 March 2017

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Next-generation DNA sequencing methods

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21 March 2017

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21 March 2017

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21 March 2017

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21 March 2017

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7 April 2017

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7 April 2017

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7 April 2017

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Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

7 April 2017

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Relative impact of nucleotide and copy number variation on gene expression phenotypes

7 April 2017

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7 April 2017

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7 April 2017

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7 April 2017

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Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma

7 April 2017

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Characterizing and measuring bias in sequence data

9 May 2017

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Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue.

28 September 2017

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28 September 2017

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28 September 2017

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Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes

28 September 2017

1 reference

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Extensive genetic variation in somatic human tissues

28 September 2017

1 reference

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Statistical challenges associated with detecting copy number variations with next-generation sequencing.

28 September 2017

1 reference

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Novel mutations target distinct subgroups of medulloblastoma.

28 September 2017

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

28 September 2017

1 reference

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Copy number variation detection and genotyping from exome sequence data

28 September 2017

1 reference

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28 September 2017

1 reference

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Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor

28 September 2017

1 reference

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Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm

28 September 2017

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28 September 2017

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cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3875755

Fast computation and applications of genome mappability

28 September 2017

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28 September 2017

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28 September 2017

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28 September 2017

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28 September 2017

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

28 September 2017

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

28 September 2017

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28 September 2017

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Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV

28 September 2017

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Copy number and SNP arrays in clinical diagnostics

28 September 2017

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Parent-specific copy number in paired tumor-normal studies using circular binary segmentation

28 September 2017

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28 September 2017

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Genome structural variation discovery and genotyping

28 September 2017

1 reference

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Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

28 September 2017

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

28 September 2017

1 reference

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ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads

28 September 2017

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Overcoming bias and systematic errors in next generation sequencing data

28 September 2017

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

28 September 2017

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28 September 2017

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28 September 2017

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Copy number variations and cancer

28 September 2017

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

28 September 2017

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The new cytogenetics: blurring the boundaries with molecular biology

28 September 2017

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A survey of homozygous deletions in human cancer genomes

28 September 2017

1 reference

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What is a hidden Markov model?

28 September 2017

1 reference

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Chromosome aberrations in solid tumors

28 September 2017

1 reference

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A census of amplified and overexpressed human cancer genes

28 September 2017

1 reference

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

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3875755

Integrated study of copy number states and genotype calls using high-density SNP arrays

31 May 2018

1 reference

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Results of two open-label, multicenter phase II studies of docetaxel, platinum salts, and trastuzumab in HER2-positive advanced breast cancer.

31 May 2018

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OncoSNP-SEQ: a statistical approach for the identification of somatic copy number alterations from next-generation sequencing of cancer genomes

31 May 2018

1 reference

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pIRS: Profile-based Illumina pair-end reads simulator

28 November 2018

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Randomized phase III study of trastuzumab, paclitaxel, and carboplatin compared with trastuzumab and paclitaxel in women with HER-2-overexpressing metastatic breast cancer

28 November 2018

1 reference

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inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.18632/ONCOTARGET.1537

1 reference

4022581

4022581

1 reference

1 reference

1 reference