Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches.
Haley J. Abel,Eric J. Duncavage +1 more
TLDR
In the past several years, there have been considerable advances in methods used to detect structural variation, and a full range of variants from SNVs to balanced translocations to CNV can now be detected with reasonable sensitivity from either whole genome or targeted NGS data.About:
This article is published in Cancer Genetics and Cytogenetics.The article was published on 2013-12-01 and is currently open access. It has received 140 citations till now. The article focuses on the topics: Massive parallel sequencing & Hybrid genome assembly.read more
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Prognostic and predictive biomarkers in breast cancer: Past, present and future
TL;DR: Current research is focusing on tumor and circulating DNA and RNA and mutational status of ER (ESR1) for predicting the emergence of resistance to aromatase inhibitors and circulating tumor cells.
Journal ArticleDOI
Clinical next-generation sequencing in patients with non-small cell lung cancer.
Ian S. Hagemann,Siddhartha Devarakonda,Christina M. Lockwood,David H. Spencer,Kalin Guebert,Andrew J. Bredemeyer,Hussam Al-Kateb,TuDung T. Nguyen,Eric J. Duncavage,Catherine E. Cottrell,Shashikant Kulkarni,Rakesh Nagarajan,Karen Seibert,Maria Q. Baggstrom,Saiama N. Waqar,John D. Pfeifer,Daniel Morgensztern,Ramaswamy Govindan +17 more
TL;DR: The feasibility and diagnostic yield of this assay in 381 consecutive patients with non–small cell lung cancer (NSCLC) is described.
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Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software.
TL;DR: A comprehensive benchmarking analysis comparing 10 general-purpose callers is performed and recommendations for both users and methods developers are provided.
Journal ArticleDOI
Whole-genome CNV analysis: advances in computational approaches.
TL;DR: A review of recent advances in CNV detection from whole genome sequencing will assist researchers and analysts in choosing the most suitable tools for CNV analysis as well as provide suggestions for new directions in future development.
Journal ArticleDOI
Guide and Position of the International Society of Nutrigenetics/Nutrigenomics on Personalised Nutrition: Part 1 - Fields of Precision Nutrition
Lynnette R. Ferguson,Raffaele De Caterina,Ulf Görman,Hooman Allayee,Martin Kohlmeier,Chandan Prasad,Myung-Sook Choi,Rui Curi,D.A. de Luis,Angel Gil,Jing X. Kang,Ron L. Martin,Fermín I. Milagro,Carolina Ferreira Nicoletti,Carla Barbosa Nonino,Jose M. Ordovas,Jose M. Ordovas,Virginia R. Parslow,María P. Portillo,José Luis Santos,Charles N. Serhan,Artemis P. Simopoulos,Antonio Velázquez-Arellano,Maria Angeles Zulet,J. Alfredo Martínez,J. Alfredo Martínez +25 more
TL;DR: A scientific society, such as the International Society of Nutrigenetics/Nutrigenomics (ISNN), internationally devoted to the study of nutrigenetically-based studies can indeed serve the commendable roles of promoting science and favoring scientific communication and permanently working as a ‘clearing house' to prevent disqualifying logical jumps, correct or stop unwarranted claims, and prevent the creation of unwarranted expectations in patients and in the general public.
References
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The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
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Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
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A framework for variation discovery and genotyping using next-generation DNA sequencing data
Mark A. DePristo,Eric Banks,Ryan Poplin,Kiran V. Garimella,Jared Maguire,Christopher Hartl,Anthony A. Philippakis,Anthony A. Philippakis,Anthony A. Philippakis,Guillermo del Angel,Manuel A. Rivas,Manuel A. Rivas,Matt Hanna,Aaron McKenna,Timothy Fennell,Andrew Kernytsky,Andrey Sivachenko,Kristian Cibulskis,Stacey Gabriel,David Altshuler,David Altshuler,Mark J. Daly,Mark J. Daly +22 more
TL;DR: A unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs is presented.
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Identification of the transforming EML4–ALK fusion gene in non-small-cell lung cancer
Manabu Soda,Young Lim Choi,Munehiro Enomoto,Shuji Takada,Yoshihiro Yamashita,Shunpei Ishikawa,Shin-ichiro Fujiwara,Hideki Watanabe,Kentaro Kurashina,Hisashi Hatanaka,Masashi Bando,Shoji Ohno,Yuichi Ishikawa,Hiroyuki Aburatani,Toshiro Niki,Yasunori Sohara,Yukihiko Sugiyama,Hiroyuki Mano +17 more
TL;DR: It is shown that a small inversion within chromosome 2p results in the formation of a fusion gene comprising portions of the echinoderm microtubule-associated protein-like 4 (EML4) gene and the anaplastic lymphoma kinase (ALK) gene in non-small-cell lung cancer (NSCLC) cells.
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Letter: A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining.
TL;DR: An unsuspected abnormality in all cells from the nine patients with chronic myelogenous leukaemia has been detected with quinacrine fluorescence and various Giemsa staining techniques, suggesting that there may be a hitherto undetected translocation between the long arm of 22 and thelong arm of 9, producing the 9q+ chromosome.
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