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Comparing variant calling algorithms for target-exon sequencing in a large sample

Yancy Lo, Hyun M Kang, Matthew R Nelson, Mohammad I Othman, Stephanie L Chissoe, Margaret G Ehm, Gonçalo R Abecasis, Sebastian Zöllner
2015 BMC Bioinformatics  
With high coverage and large sample size, these studies tend to apply simple variant calling algorithms.  ...  We evaluate the potential benefits of different calling strategies by performing a comparative analysis of variant calling methods on exonic data from 202 genes sequenced at 24x in 7,842 individuals.  ...  We thank the co-principal investigators of the CoLaus study, Gerard Waeber and Peter Vollenweider, for sharing samples which enabled validation of variant calls.  ... 
doi:10.1186/s12859-015-0489-0 pmid:25884587 pmcid:PMC4359451 fatcat:dpztsvrqwba35asdhrfd2oolbu

Validation of a Custom Next-Generation Sequencing Assay for Cystic Fibrosis Newborn Screening

Robert J. Sicko, Colleen F. Stevens, Erin E. Hughes, Melissa Leisner, Helen Ling, Carlos A. Saavedra-Matiz, Michele Caggana, Denise M. Kay
2021 International Journal of Neonatal Screening  
bioinformatic assessment of deletions/duplications in a subset of samples requiring third-tier analysis.  ...  After full gene sequencing, a tiered strategy is used to first analyze only a specific panel of 338 clinically relevant CFTR variants (second-tier), followed by unblinding of all sequence variants and  ...  In addition to full gene sequence analysis, algorithms are used to impute large del/dup typically not detectable by sequencing.  ... 
doi:10.3390/ijns7040073 pmid:34842611 pmcid:PMC8628990 fatcat:lgi6kaj6ljgl3drp55ujij7lk4

An enhanced method for targeted next generation sequencing copy number variant detection using ExomeDepth

Andrew Parrish, Richard Caswell, Garan Jones, Christopher M. Watson, Laura A. Crinnion, Sian Ellard
2017 Wellcome Open Research  
In addition, the algorithms used favour the detection of multi-exon CNVs, and rely on suitably matched normal dosage samples for comparison.  ...  We developed a calling strategy that subdivides target intervals, and uses pools of historical control samples to overcome these limitations in a clinical diagnostic laboratory.  ...  Acknowledgements The authors would like to acknowledge the contribution of the technical and bioinformatics staff involved in the sample preparation, in particular A. Bussell, M. Johnson, and M.  ... 
doi:10.12688/wellcomeopenres.11548.1 fatcat:6i63clkth5fuzlfs3zxmhfmiqu

The functional spectrum of low-frequency coding variation

Gabor T Marth, Fuli Yu, Amit R Indap, Kiran Garimella, Simon Gravel, Wen Leong, Chris Tyler-Smith, Matthew Bainbridge, Tom Blackwell, Xiangqun Zheng-Bradley, Yuan Chen, Danny Challis (+24 others)
2011 Genome Biology  
Results: The 1000 Genomes Exon Pilot Project has collected deep-coverage exon-capture data in roughly 1,000 human genes, for nearly 700 samples.  ...  Although medical whole-exome projects are currently afoot, this is still the deepest reported sampling of a large number of human genes with next-generation technologies.  ...  The higher performance in detecting rare damaging variants in the Exon Pilot compared to the Low Coverage Pilot underlines the utility of targeted exome sequencing for disease studies.  ... 
doi:10.1186/gb-2011-12-9-r84 pmid:21917140 pmcid:PMC3308047 fatcat:eiaz3dat6rgfvnkgk52hw3foxa

Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels

Maria Zanti, Kyriaki Michailidou, Maria A Loizidou, Christina Machattou, Panagiota Pirpa, Kyproula Christodoulou, George M Spyrou, Kyriacos Kyriacou, Andreas Hadjisavvas
2021 BMC Bioinformatics  
We also recommend the BWA-MEM algorithm for sequence alignment, whereas variant calling should be performed using a combination of variant calling algorithms; GATK-HaplotypeCaller and SAMtools for the  ...  Fourteen germline DNA samples from breast cancer patients were sequenced using a targeted NGS panel approach and subjected to data analysis.  ...  Acknowledgements We would like to thank all the patients and their families for participating in this study.  ... 
doi:10.1186/s12859-021-04144-1 pmid:33910496 fatcat:jw7w2t5m4bfwxkimjuvkagdi6u

Comparison of insertion/deletion calling algorithms on human next-generation sequencing data

Dalia H Ghoneim, Jason R Myers, Emily Tuttle, Alex R Paciorkowski
2014 BMC Research Notes  
Pindel's low validation rate of indel calls made in targeted exon sequencing suggests that HaplotypeCaller is better suited for short indels and multi-sample runs in targets with very high read depth.  ...  Identification of indels in next generation sequencing data is a challenge, and algorithms commonly used for indel detection have not been compared on a research cohort of human subject genomic data.  ...  We also wish to thank the Center for Integrated Research Computing at the University of Rochester Medical Center for computational resources used in this work.  ... 
doi:10.1186/1756-0500-7-864 pmid:25435282 pmcid:PMC4265454 fatcat:w6nwvqhchzgsro55h64pihxlou

DNA Sequence Capture and Enrichment by Microarray Followed by Next-Generation Sequencing for Targeted Resequencing: Neurofibromatosis Type 1 Gene as a Model

L.-S. Chou, C.-S. J. Liu, B. Boese, X. Zhang, R. Mao
2009 Clinical Chemistry  
METHODS: In this study, we investigated a process for enriching DNA samples that uses a customized highdensity oligonucleotide microarray to enrich a targeted 280-kb region of the NF1 (neurofibromin 1)  ...  RESULTS: Targeted microarray capture may also capture sequences from nontargeted regions in the genome. The capture specificity estimated for the targeted NF1 region was approximately 60%.  ...  Acknowledgments: We thank Jacquelyn McCowen-Rose and Alison Millson for critical review of this manuscript.  ... 
doi:10.1373/clinchem.2009.132639 pmid:19910506 fatcat:uizam6gusvh3xnqjmv6pdomy5e

Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis

Tejasvi S Niranjan, Abby Adamczyk, Héctor Bravo, Margaret A Taub, Sarah J Wheelan, Rafael Irizarry, Tao Wang
2011 Genome Biology  
Sequencing targeted DNA regions in large samples is necessary to discover the full spectrum of rare variants.  ...  Validation by Sanger sequencing revealed an excellent combination of sensitivity and specificity for variant detection in pooled samples of both cohorts as compared to publicly available algorithms.  ...  Acknowledgements We thank Dr David Valle of Johns Hopkins University for critical reading of this manuscript, Autism Genetics Research Exchange (AGRE) and Greenwood Genetic Center (GGC) for DNA samples  ... 
doi:10.1186/gb-2011-12-9-r93 pmid:21955804 pmcid:PMC3308056 fatcat:yeoz4jdhtvcipeb7te3kxto4pe

Effective detection of rare variants in pooled DNA samples using cross-pool tail-curve analysis

Tejasvi S Niranjan, Abby Adamczyk, Hector Bravo, Margaret A Taub, Sarah J Wheelan, Rafael Irizarry, Tao Wang
2011 Genome Biology  
Sequencing targeted DNA regions in large samples is necessary to discover the full spectrum of rare variants.  ...  Validation by Sanger sequencing revealed an excellent combination of sensitivity and specificity for variant detection in pooled samples of both cohorts as compared to publicly available algorithms.  ...  Acknowledgements We thank Dr David Valle of Johns Hopkins University for critical reading of this manuscript, Autism Genetics Research Exchange (AGRE) and Greenwood Genetic Center (GGC) for DNA samples  ... 
doi:10.1186/1465-6906-12-s1-p45 fatcat:7e2vqx4ntng3xmx2hopk3hnxyy

Detection of Mutations in Myeloid Malignancies through Paired-Sample Analysis of Microdroplet-PCR Deep Sequencing Data

Donavan T. Cheng, Janice Cheng, Talia N. Mitchell, Aijazuddin Syed, Ahmet Zehir, Nana Yaa T. Mensah, Alifya Oultache, Khedoudja Nafa, Ross L. Levine, Maria E. Arcila, Michael F. Berger, Cyrus V. Hedvat
2014 Journal of Molecular Diagnostics  
Amplicon-based methods for targeted resequencing of cancer genes have gained traction in the clinic as a strategy for molecular diagnostic testing.  ...  Variant calling using an unmatched Hapmap DNA control removed a substantial number of artifactual calls regardless of algorithm used or variant class.  ...  We compare differences in variants called in single-sample analysis (tumor samples considered alone) versus paired-sample analysis (tumor samples compared against a Hapmap DNA sample, used as a generic  ... 
doi:10.1016/j.jmoldx.2014.05.006 pmid:25017477 pmcid:PMC5707185 fatcat:glwqhcrceve33dqyteya3uf4je

Comprehensive Mutation Analysis for Congenital Muscular Dystrophy: A Clinical PCR-Based Enrichment and Next-Generation Sequencing Panel

C. Alexander Valencia, Arunkanth Ankala, Devin Rhodenizer, Shruti Bhide, Martin Robert Littlejohn, Lisa Mari Keong, Anne Rutkowski, Susan Sparks, Carsten Bonnemann, Madhuri Hegde, Noam Shomron
2013 PLoS ONE  
Using a highly multiplexed PCR-based target enrichment method (RainDance) in conjunction with NGS, we performed mutation detection in all CMD genes of 26 samples and compared the results with Sanger sequencing  ...  The panel's limitation is the amplification failure of select gene-specific exons which require Sanger sequencing for test completion.  ...  Comparable low coverage (,106 coverage in 20% of exons) has also been observed in non-CMD genes as reported by a recent study of ataxia gene targets involving array-based enrichment and NGS sequencing  ... 
doi:10.1371/journal.pone.0053083 pmid:23326386 pmcid:PMC3543442 fatcat:p6kbzfivnbgrjmh6k2hezstjgy

Detailed comparison of two popular variant calling packages for exome and targeted exon studies

Charles D. Warden, Aaron W. Adamson, Susan L. Neuhausen, Xiwei Wu
2014 PeerJ  
Variant calling was performed on three datasets (1 targeted exon dataset and 2 exome datasets), each with approximately a dozen subjects.  ...  More broadly, we believe the metrics used for comparison in this study can be useful in assessing the quality of variant calls in the context of a specific experimental design.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.7717/peerj.600 pmid:25289185 pmcid:PMC4184249 fatcat:23sxjintnrhb3ach7jo4yi7zky

Homozygous and hemizygous CNV detection from exome sequencing data in a Mendelian disease cohort

Tomasz Gambin, Zeynep C. Akdemir, Bo Yuan, Shen Gu, Theodore Chiang, Claudia M.B. Carvalho, Chad Shaw, Shalini Jhangiani, Philip M. Boone, Mohammad K. Eldomery, Ender Karaca, Yavuz Bayram (+9 others)
2016 Nucleic Acids Research  
of 86.5% (82% for single-exonic and 88% for multiexonic calls) and precision of 78% (53% singleexonic and 96% for multi-exonic calls).  ...  HMZDelFinder was applied to 4866 samples in the Baylor-Hopkins Center for Mendelian Genomics (BHCMG) cohort and detected 773 HMZ deletion calls (567 homozygous or 206 hemizygous) with an estimated sensitivity  ...  ACKNOWLEDGEMENTS The authors thank the family members and the collaborators that participated in this study. FUNDING  ... 
doi:10.1093/nar/gkw1237 pmid:27980096 pmcid:PMC5389578 fatcat:jcxg5ddm65czbnikr5ainof4yy

EXCAVATOR: detecting copy number variants from whole-exome sequencing data

Alberto Magi, Lorenzo Tattini, Ingrid Cifola, Romina D'Aurizio, Matteo Benelli, Eleonora Mangano, Cristina Battaglia, Elena Bonora, Ants Kurg, Marco Seri, Pamela Magini, Betti Giusti (+5 others)
2013 Genome Biology  
We developed a novel software tool, EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data.  ...  EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomic regions into five copy number states.  ...  Acknowledgements We gratefully acknowledge the financial support of the Cariplo Foundation grant number 2006_0771 for genomic, epigenetic and transcriptional analysis of cancer by next-generation sequencing  ... 
doi:10.1186/gb-2013-14-10-r120 pmid:24172663 pmcid:PMC4053953 fatcat:sqwcrdwwvvgdlfwjjqe6cpxrxi

Exome Sequencing of a Multigenerational Human Pedigree

Dale Hedges, Dan Burges, Eric Powell, Cherylyn Almonte, Jia Huang, Stuart Young, Benjamin Boese, Mike Schmidt, Margaret A. Pericak-Vance, Eden Martin, Xinmin Zhang, Timothy T. Harkins (+2 others)
2009 PLoS ONE  
Applying the conservative genotype calling approach HCDiff, the average rate of detection of a variant allele based on Illumina 1 M BeadChips genotypes was 95.2% at $10x sequence.  ...  Recently, comprehensive exome capture arrays have become available for targeting approximately 33 Mb or ,180,000 coding exons across the human genome.  ...  As described below, this empirically determined variant calling approach improved the overall sensitivity to detect variants compared to the standard HCDiff variant detection algorithm, particularly at  ... 
doi:10.1371/journal.pone.0008232 pmid:20011588 pmcid:PMC2788131 fatcat:6nmoybxcmzhydcem2bujn25hci
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