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Literature DB >> 28989557

ALLELE-SPECIFIC COPY NUMBER ESTIMATION BY WHOLE EXOME SEQUENCING.

Hao Chen¹, Yuchao Jiang², Kara N Maxwell², Katherine L Nathanson², Nancy Zhang².

Abstract

Whole exome sequencing is currently a technology of choice in large-scale cancer genomics studies, where the priority is to identify cancer-associated variants in coding regions. We describe a method for estimating allele-specific copy number using whole exome sequencing data from tumor and matched normal.

Entities: Chemical Disease Gene Species

Keywords: Allele-specific copy number; tumor-normal pair; whole exome sequencing

Year: 2017 PMID： 28989557 PMCID： PMC5627665 DOI： 10.1214/17-AOAS1043

Source DB: PubMed Journal: Ann Appl Stat ISSN： 1932-6157 Impact factor: 2.083

22 in total

1. A modified Bayes information criterion with applications to the analysis of comparative genomic hybridization data.

Authors: Nancy R Zhang; David O Siegmund
Journal: Biometrics Date: 2007-03 Impact factor: 2.571

Review 2. Computational methods for discovering structural variation with next-generation sequencing.

Authors: Paul Medvedev; Monica Stanciu; Michael Brudno
Journal: Nat Methods Date: 2009-11 Impact factor: 28.547

3. Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth.

Authors: Menachem Fromer; Jennifer L Moran; Kimberly Chambert; Eric Banks; Sarah E Bergen; Douglas M Ruderfer; Robert E Handsaker; Steven A McCarroll; Michael C O'Donovan; Michael J Owen; George Kirov; Patrick F Sullivan; Christina M Hultman; Pamela Sklar; Shaun M Purcell
Journal: Am J Hum Genet Date: 2012-10-05 Impact factor: 11.025

4. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.

Authors: Geraldine A Van der Auwera; Mauricio O Carneiro; Christopher Hartl; Ryan Poplin; Guillermo Del Angel; Ami Levy-Moonshine; Tadeusz Jordan; Khalid Shakir; David Roazen; Joel Thibault; Eric Banks; Kiran V Garimella; David Altshuler; Stacey Gabriel; Mark A DePristo
Journal: Curr Protoc Bioinformatics Date: 2013

5. Allele-specific copy number profiling by next-generation DNA sequencing.

Authors: Hao Chen; John M Bell; Nicolas A Zavala; Hanlee P Ji; Nancy R Zhang
Journal: Nucleic Acids Res Date: 2014-12-03 Impact factor: 16.971

6. Copy number variation detection and genotyping from exome sequence data.

Authors: Niklas Krumm; Peter H Sudmant; Arthur Ko; Brian J O'Roak; Maika Malig; Bradley P Coe; Aaron R Quinlan; Deborah A Nickerson; Evan E Eichler
Journal: Genome Res Date: 2012-05-14 Impact factor: 9.043

7. Reconstructing DNA copy number by joint segmentation of multiple sequences.

Authors: Zhongyang Zhang; Kenneth Lange; Chiara Sabatti
Journal: BMC Bioinformatics Date: 2012-08-16 Impact factor: 3.169

8. Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data.

Authors: F Favero; T Joshi; A M Marquard; N J Birkbak; M Krzystanek; Q Li; Z Szallasi; A C Eklund
Journal: Ann Oncol Date: 2014-10-15 Impact factor: 32.976

9. SomatiCA: identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing data.

Authors: Mengjie Chen; Murat Gunel; Hongyu Zhao
Journal: PLoS One Date: 2013-11-12 Impact factor: 3.240

ALLELE-SPECIFIC COPY NUMBER ESTIMATION BY WHOLE EXOME SEQUENCING.

1. A modified Bayes information criterion with applications to the analysis of comparative genomic hybridization data.

Review 2. Computational methods for discovering structural variation with next-generation sequencing.

3. Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth.

4. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.

5. Allele-specific copy number profiling by next-generation DNA sequencing.

6. Copy number variation detection and genotyping from exome sequence data.

7. Reconstructing DNA copy number by joint segmentation of multiple sequences.

8. Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data.

9. SomatiCA: identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing data.

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

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

2. Copy Number Variation Detection by Single-Cell DNA Sequencing with SCOPE.

3. Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny.

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