Structural variation discovery in the cancer genome using next generation sequencing: computational solutions and perspectives (Q26991436)

genomic structural variation

main subject

1 reference

14 September 2019

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19 September 2019

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25 November 2020

1 reference

8 February 2021

Biao Liu

1

1 reference

Jeffrey M. Conroy

2

1 reference

Carl D. Morrison

3

1 reference

Adekunle O. Odunsi

4

1 reference

Maochun Qin

5

1 reference

Lei Wei

6

1 reference

Donald L. Trump

7

1 reference

Candace S. Johnson

8

1 reference

Song Liu

9

1 reference

Jianmin Wang

10

1 reference

language of work or name

1 reference

20 March 2015

8 references

3 April 2019

19 June 2019

30 June 2019

14 September 2019

19 September 2019

25 November 2020

8 February 2021

8 references

3 April 2019

19 June 2019

30 June 2019

14 September 2019

19 September 2019

25 November 2020

8 February 2021

6

1 reference

issue

8

1 reference

page(s)

5477-89

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Creative Commons Attribution 2.5 Generic

copyright license

7 references

3 April 2019

19 June 2019

30 June 2019

14 September 2019

19 September 2019

25 November 2020

describes a project that uses

8 February 2021

massive parallel sequencing

1 reference

based on heuristic

inferred from title

on focus list of Wikimedia project

ScienceSource

0 references

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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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9 May 2017

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25 May 2017

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28 September 2017

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28 September 2017

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The evolution of the unstable cancer genome

28 September 2017

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ShatterProof: operational detection and quantification of chromothripsis

28 September 2017

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Sequencing depth and coverage: key considerations in genomic analyses

28 September 2017

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Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads.

28 September 2017

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Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma

28 September 2017

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28 September 2017

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Discovery of recurrent structural variants in nasopharyngeal carcinoma

28 September 2017

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28 September 2017

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Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia

28 September 2017

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28 September 2017

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BreakTrans: uncovering the genomic architecture of gene fusions

28 September 2017

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28 September 2017

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The mutational landscape of adenoid cystic carcinoma

28 September 2017

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Cancer genome-sequencing study design

28 September 2017

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Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas

28 September 2017

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Genome evolution during progression to breast cancer

28 September 2017

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Phenotypic impact of genomic structural variation: insights from and for human disease

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

A model-based clustering method for genomic structural variant prediction and genotyping using paired-end sequencing data

28 September 2017

1 reference

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An Inv(16)(p13.3q24.3)-encoded CBFA2T3-GLIS2 fusion protein defines an aggressive subtype of pediatric acute megakaryoblastic leukemia

28 September 2017

1 reference

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The genetic landscape of mutations in Burkitt lymphoma

28 September 2017

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Chromoanagenesis and cancer: mechanisms and consequences of localized, complex chromosomal rearrangements

28 September 2017

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Genomic landscape of non-small cell lung cancer in smokers and never-smokers

28 September 2017

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YAHA: fast and flexible long-read alignment with optimal breakpoint detection

28 September 2017

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Novel mutations target distinct subgroups of medulloblastoma.

28 September 2017

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The Pediatric Cancer Genome Project

28 September 2017

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An integrative probabilistic model for identification of structural variation in sequencing data

28 September 2017

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Association of age at diagnosis and genetic mutations in patients with neuroblastoma.

28 September 2017

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ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information

28 September 2017

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Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes

28 September 2017

1 reference

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A novel retinoblastoma therapy from genomic and epigenetic analyses

28 September 2017

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Performance comparison of whole-genome sequencing platforms

28 September 2017

1 reference

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SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data

28 September 2017

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Performance comparison of exome DNA sequencing technologies

28 September 2017

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Genetic evolution of pancreatic cancer: lessons learnt from the pancreatic cancer genome sequencing project

28 September 2017

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CREST maps somatic structural variation in cancer genomes with base-pair resolution.

28 September 2017

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Chromothripsis identifies a rare and aggressive entity among newly diagnosed multiple myeloma patients

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

Genome structural variation discovery and genotyping

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

Discovery and genotyping of genome structural polymorphism by sequencing on a population scale

28 September 2017

1 reference

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AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

Triggers for genomic rearrangements: insights into genomic, cellular and environmental influences

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

Clinical Implications of the Cancer Genome

28 September 2017

1 reference

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SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

A survey of sequence alignment algorithms for next-generation sequencing

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

Computational methods for discovering structural variation with next-generation sequencing

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

28 September 2017

1 reference

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A geometric approach for classification and comparison of structural variants

28 September 2017

1 reference

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A microhomology-mediated break-induced replication model for the origin of human copy number variation

28 September 2017

1 reference

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Chromosome aberrations in solid tumors

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

Targeting oxidative stress in embryonal rhabdomyosarcoma.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

Diverse mechanisms of somatic structural variations in human cancer genomes

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

Comparative analysis of algorithms for next-generation sequencing read alignment

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

Reference-free prediction of rearrangement breakpoint reads

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

PRISM: pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4467381

28 November 2018

Identifiers

DOI

10.18632/ONCOTARGET.3491

0 references

1 reference

PubMed publication ID

25849937

1 reference