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Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations

Zhifu Sun, Aditya Bhagwate, Naresh Prodduturi, Ping Yang, Jean-Pierre A. Kocher
2016 Briefings in Bioinformatics  
The aim is to develop strategies for accurate indel detection.  ...  This study evaluates commonly used RNA-seq analysis programs along with variant and somatic mutation callers in a series of data sets with simulated and known indels.  ...  for accurate indel detection in RNA-seq using different aligners Our evaluation demonstrated that intermediate indel detection from RNA-seq highly hinged on aligners and callers.  ... 
doi:10.1093/bib/bbw069 pmid:27473065 fatcat:pkn2e4cfynbmplh3ayfddhpxie

RNA-SSNV: A Reliable Somatic Single Nucleotide Variant Identification Framework for Bulk RNA-Seq Data

Qihan Long, Yangyang Yuan, Miaoxin Li
2022 Frontiers in Genetics  
However, accurately calling mutations from RNA-seq data is difficult due to confounding factors such as RNA-editing, reverse transcription, and gap alignment.  ...  In sum, RNA-SSNV will be a useful approach to accurately call expressed somatic mutations for a more insightful analysis of cancer drive genes and carcinogenic mechanisms.  ...  For cancer research involving both WES and RNA-seq data, the conventional analysis strategy uses WES data to call somatic mutations and then validates whether somatic mutations exist in RNA-seq data.  ... 
doi:10.3389/fgene.2022.865313 pmid:35846154 pmcid:PMC9279659 fatcat:pje5waci5jhexfrc3ms5a577f4

A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data

Jennifer D. Hintzsche, William A. Robinson, Aik Choon Tan
2016 International Journal of Genomics  
Understanding the exomes of individuals at single base resolution allows the identification of actionable mutations for disease treatment and management.  ...  These tools range from the alignment of raw sequencing reads all the way to linking variants to actionable therapeutics.  ...  This work is partly supported by the National Institutes of Health P50CA058187, Cancer League of Colorado, the David F. and Margaret T.  ... 
doi:10.1155/2016/7983236 pmid:28070503 pmcid:PMC5192301 fatcat:qtlmgypwxjbv7ewg5wskhqxs4a

Computational Methods for the Pharmacogenetic Interpretation of Next Generation Sequencing Data

Yitian Zhou, Kohei Fujikura, Souren Mkrtchian, Volker M. Lauschke
2018 Frontiers in Pharmacology  
Here, we review concepts and important progress in the development of computational prediction methods that allow to evaluate the effect of amino acid sequence alterations in drug metabolizing enzymes  ...  A substantial fraction of these inter-individual differences is due to heritable factors and a growing number of associations between genetic variations and drug response phenotypes have been identified  ...  AUTHOR CONTRIBUTIONS All authors listed have made a substantial, direct and intellectual contribution to the work, and approved it for publication.  ... 
doi:10.3389/fphar.2018.01437 pmid:30564131 pmcid:PMC6288784 fatcat:w5z2qrm47fh25nannvs6h7zqfe

A primer on precision medicine informatics

Andrea Sboner, Olivier Elemento
2015 Briefings in Bioinformatics  
, privacy requirements, prioritization and interpretation of results to report based on clinical needs, rapidly evolving knowledge base of genomic alterations and clinical treatments and return of results  ...  In this review, we describe key components of a computational infrastructure for a precision medicine program that is based on clinical-grade genomic sequencing.  ...  Acknowledgments We are grateful to all members of Weill Cornell Medical College's Institute for Precision Medicine for discussion and insights.  ... 
doi:10.1093/bib/bbv032 pmid:26048401 fatcat:e4kiblelezdvtmsswwobcamydi

Advances in the Molecular Analysis of Soft Tissue Tumors and Clinical Implications

Adrian Marino-Enriquez
2015 Surgical Pathology Clinics  
Most clinical molecular data will be likely generated by high-throughput genomic technologies, and reporting clinically actionable somatic mutations will be part of the routine pathology workflow, informing  ...  In soft tissue tumor pathology, accurate interpretation of comprehensive genomic data provides useful diagnostic and prognostic information, and informs therapeutic decisions.  ...  Acknowledgments Financial support: Adrian Marino-Enriquez is supported by a Career Development Award from The Sarcoma Alliance for Research through Collaboration.  ... 
doi:10.1016/j.path.2015.06.001 pmid:26297069 pmcid:PMC4920057 fatcat:zmgbj2n3xjho3ohd3xkyjbocde

Clinical validation of the tempus xT next-generation targeted oncology sequencing assay

Nike Beaubier, Robert Tell, Denise Lau, Jerod R. Parsons, Stephen Bush, Jason Perera, Shelly Sorrells, Timothy Baker, Alan Chang, Jackson Michuda, Catherine Iguartua, Shelley MacNeil (+10 others)
2019 OncoTarget  
This targeted oncology assay utilizes tumornormal matched samples for highly accurate somatic alteration calling and whole transcriptome RNA sequencing for unbiased identification of gene fusion events  ...  The assay was validated with a combination of clinical specimens and cell lines, and recorded a sensitivity of 99.1% for single nucleotide variants, 98.1% for indels, 99.9% for gene rearrangements, 98.4%  ...  Alexandria Bobe for critical review of the entire manuscript and Matthew Kase for proofreading the manuscript. We also thank Bri Santacaterina and Anna Sheals for help with assembly of the figures.  ... 
doi:10.18632/oncotarget.26797 fatcat:7pzihvqgsfdt3pj72d5hrx7wma

Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines

Xing Yi Woo, Anuj Srivastava, Joel H. Graber, Vinod Yadav, Vishal Kumar Sarsani, Al Simons, Glen Beane, Stephen Grubb, Guruprasad Ananda, Rangjiao Liu, Grace Stafford, Jeffrey H. Chuang (+4 others)
2019 BMC Medical Genomics  
mouse and human sequence reads and accurately identifying somatic mutations and copy number alterations when paired non-tumor DNA from the patient is not available for comparison.  ...  Patient-derived xenograft (PDX) models are in vivo models of human cancer that have been used for translational cancer research and therapy selection for individual patients.  ...  Acknowledgements The genomic data for PDX tumors used in this work were generated by The Jackson Laboratory (JAX) Genome Technologies and Single Cell Biology Scientific Service.  ... 
doi:10.1186/s12920-019-0551-2 pmid:31262303 pmcid:PMC6604205 fatcat:zfywxialabbclpm3ffvudhtxpq

ClinSeK: a targeted variant characterization framework for clinical sequencing

Wanding Zhou, Hao Zhao, Zechen Chong, Routbort J Mark, Agda K Eterovic, Funda Meric-Bernstam, Ken Chen
2015 Genome Medicine  
Further, the approach must be sufficiently robust as to be able to detect multiple and potentially rare variants from heterogeneous samples.  ...  ClinSeK is designed for efficient targeted short read alignment and is capable of characterizing a wide spectrum of genetic variants from single nucleotide variation to large-scale genomic rearrangement  ...  Acknowledgements We thank Kenna Shaw, Gordon Mills and John Mendelsohn for leadership, members of the IPCT for providing targeted exome-sequencing data, members of the Molecular Diagnostic Laboratory for  ... 
doi:10.1186/s13073-015-0155-1 pmid:25918555 pmcid:PMC4410453 fatcat:jqqlisbsnffqdf7y3fspvk53fa

Application of third-generation sequencing in cancer research

Zhiao Chen, Xianghuo He
2021 Medical Review  
In addition, these platforms enable structural variation characterization at a previously unparalleled resolution and direct detection of epigenetic marks in native DNA and RNA.  ...  Furthermore, we discuss the impact of the newly developed nanopore direct RNA sequencing (RNA-Seq) approach in advancing epitranscriptome research in cancer.  ...  Research funding: The National Natural Science Foundation of China played a role in the collection and interpretation of data, as well as in the writing of the manuscript.  ... 
doi:10.1515/mr-2021-0013 fatcat:r64zejp3knel3isccbqia254fe

Latest Developed Strategies to Minimize the Off-Target Effects in CRISPR-Cas-Mediated Genome Editing

Muhammad Naeem, Saman Majeed, Mubasher Zahir Hoque, Irshad Ahmad
2020 Cells  
tools, including zinc finger nucleases (ZFNs) and Transcription activator-like effector nucleases (TALENs).  ...  Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 emerged as a substantial tool due to its simplicity in use, less cost and extraordinary efficiency than the conventional gene-editing  ...  Acknowledgments: We acknowledges the King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, 31261, Saudi Arabia for financial support for the APC of this work.  ... 
doi:10.3390/cells9071608 pmid:32630835 fatcat:dg2zegpqovhyvfkadkqp2iqeme

Diagnosis of fusion genes using targeted RNA sequencing

Erin E. Heyer, Ira W. Deveson, Danson Wooi, Christina I. Selinger, Ruth J. Lyons, Vanessa M. Hayes, Sandra A. O'Toole, Mandy L. Ballinger, Devinder Gill, David M. Thomas, Tim R. Mercer, James Blackburn
2019 Nature Communications  
Fusion genes are a major cause of cancer. Their rapid and accurate diagnosis can inform clinical action, but current molecular diagnostic assays are restricted in resolution and throughput.  ...  Next, we analyse a clinical patient cohort and improve the overall fusion gene diagnostic rate from 63% with conventional approaches to 76% with targeted RNAseq while demonstrating high concordance for  ...  Tian Chi, Pei Hui and Keji Zhao for reading the manuscript and for valuable comments.  ... 
doi:10.1038/s41467-019-09374-9 pmid:30918253 pmcid:PMC6437215 fatcat:wwfqnb7azffjhpanmiyjazucjm

Timing chromosomal abnormalities using mutation data

Steffen Durinck, Christine Ho, Nicholas J Wang, Wilson Liao, Lakshmi R Jakkula, Eric A Collisson, Jennifer Pons, Sai-Wing Chan, Ernest T Lam, Catherine Chu, Kyunghee Park, Sung-woo Hong (+20 others)
2011 Genome Biology  
We analyzed exome data from 2,440 individuals of European and African ancestry as part of the National Heart, Lung, and Blood Institute's Exome Project, the aim of which is to discover novel genes and  ...  purifying selection in shaping patterns of proteincoding variation and the diff erential signatures of population structure from rare and common variation.  ...  novo copy number variation, de novo point mutations of large eff ect could explain the majority of all mental retardation cases in the population.  ... 
doi:10.1186/gb-2011-12-s1-p39 fatcat:4ta4lsp5g5bbfecj7vbwba6cny

Circulating tumor DNA: a noninvasive biomarker for tracking ovarian cancer

Fang Yang, Jun Tang, Zihao Zhao, Chunling Zhao, Yuancai Xiang
2021 Reproductive Biology and Endocrinology  
A wide variety of ctDNA applications are being elucidated in multiple studies for tracking ovarian carcinoma during diagnostic and prognostic evaluations of patients and are being integrated into clinical  ...  Certain intrinsic features of ctDNA that may enhance its utility as a biomarker are problematic for its detection, including ctDNA lengths, copy number variations, and methylation.  ...  Acknowledgements We would like to thank Editage (www. edita ge. cn) for English language editing.  ... 
doi:10.1186/s12958-021-00860-8 pmid:34861867 pmcid:PMC8641226 fatcat:awx7p3fgjndeteoi2gvsvgu4wq

Genomics pipelines and data integration: challenges and opportunities in the research setting

Jeremy Davis-Turak, Sean M. Courtney, E. Starr Hazard, W. Bailey Glen, Willian A. da Silveira, Timothy Wesselman, Larry P. Harbin, Bethany J. Wolf, Dongjun Chung, Gary Hardiman
2017 Expert Review of Molecular Diagnostics  
Areas covered-The very success of this industry also translates into daunting big data challenges for researchers and institutions that extend beyond the traditional academic focus of algorithms and tools  ...  that incorporate data tracking and auditing, enabling greater consistency and reproducibility for basic research, translational or clinical settings.  ...  Specialized variant callers are also in development for special cases, such as detection of large insertions and deletions and the detection of copy number variants ie. Amplicon Indel Hunter [74] .  ... 
doi:10.1080/14737159.2017.1282822 pmid:28092471 pmcid:PMC5580401 fatcat:2jmdazejqva5nez26l2fmcwov4
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