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Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays

A. A. Morgan, R. Chen, A. J. Butte
2012 JAMIA Journal of the American Medical Informatics Association  
Objective We investigated the common-disease relevant information obtained from sequencing compared with that reported from genotyping arrays.  ...  Results We show that the model risk predictions derived from sequencing differ substantially from those obtained from the SNPs measured on commercially available genotyping arrays for several different  ...  Acknowledgments We thank Optra Systems of Pune, India for geneedisease variant data curation.  ... 
doi:10.1136/amiajnl-2011-000737 pmid:22718036 pmcid:PMC3392859 fatcat:komitbxzebcy7db7wmlo5zcxvy

Genotyping Performance between Saliva and Blood-Derived Genomic DNAs on the DMET Array: A Comparison

Yueshan Hu, Erik A. Ehli, Kelly Nelson, Krista Bohlen, Christophina Lynch, Patty Huizenga, Julie Kittlelsrud, Timothy J. Soundy, Gareth E. Davies, Tatjana Adamovic
2012 PLoS ONE  
In conclusion, when compared with blood DNA and tested on the DMET array, salivaderived DNA provided adequate genotyping quality with a significant lower number of SNP calls.  ...  Genomic DNA extractions from saliva samples produced an ample quantity of genomic DNA for DMET arrays, however when human amplifiable DNA was measured, it was determined that a large percentage of this  ...  We would also like to thank all of the excellent staff at the Avera Research Institute. Author Contributions  ... 
doi:10.1371/journal.pone.0033968 pmid:22448283 pmcid:PMC3309006 fatcat:xx4pw4uk5zfpxpjxqclt7hizqi

PGRNseq

Adam S. Gordon, Robert S. Fulton, Xiang Qin, Elaine R. Mardis, Deborah A. Nickerson, Steve Scherer
2016 Pharmacogenetics & Genomics  
Additionally, the high accuracy associated with genotypes from PGRNseq highlight its utility as a clinical test.  ...  Conclusion-PGRNseq is an ideal platform for performing sequencing-based analyses of pharmacogenetic variation in large cohorts.  ...  the Genome Institute at Washington University and Richard Gibbs and Donna Muzny from the Human Genome Sequencing Center at Baylor College of Medicine.  ... 
doi:10.1097/fpc.0000000000000202 pmid:26736087 pmcid:PMC4935646 fatcat:7vlt72wn7ncxtomklditsqqetm

Low coverage whole genome sequencing enables accurate assessment of common variants and calculation of genome-wide polygenic scores

Julian R Homburger, Cynthia L Neben, Gilad Mishne, Alicia Y Zhou, Sekar Kathiresan, Amit V Khera
2019 Genome Medicine  
We assessed the feasibility and accuracy of using low coverage whole genome sequencing (lcWGS) as an alternative to genotyping arrays to calculate GPSs.  ...  The traditional approach requires two distinct genetic testing technologies-high coverage sequencing of known genes to detect monogenic variants and a genome-wide genotyping array followed by imputation  ...  Consent for publication All individuals in the technical concordance cohort and clinical cohort gave electronic informed consent that Color may author publications  ... 
doi:10.1186/s13073-019-0682-2 pmid:31771638 pmcid:PMC6880438 fatcat:6rciwplqhzh2vgwt4ehhx2w4ru

Assessing the capability of massively parallel sequencing for opportunistic pharmacogenetic screening

David Ng, Celine S. Hong, Larry N. Singh, Jennifer J. Johnston, James C. Mullikin, Leslie G. Biesecker
2016 Genetics in Medicine  
ACKNOWLEDGMENTS The authors are grateful for the contributions of the staff at the NIH Intramural Sequencing Center and NIH Clinical Center and of the ClinSeq ® study participants.  ...  This study was funded by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health.  ...  The second is that the extraction of PGx variants from ES/GS data is part of a larger effort to maximize the utility of ES/GS testing results.  ... 
doi:10.1038/gim.2016.105 pmid:27537706 pmcid:PMC5316383 fatcat:gcbmwp55zzb6pjhmms4k3cyzde

Clinical utility of the low-density Infinium QC genotyping Array in a genomics-based diagnostics laboratory

Petr Ponomarenko, Alex Ryutov, Dennis T. Maglinte, Ancha Baranova, Tatiana V. Tatarinova, Xiaowu Gai
2017 BMC Medical Genomics  
Methods: We evaluated accuracy and reproducibility of Infinium QC genotyping calls by comparing them with genotyping data of the same samples from other genotyping platforms, whole genome/exome sequencing  ...  Conclusions: Our results indicate that the Infinium QC Array-24 chip is suitable for cost-efficient, independent QC assaying in the settings of an NGS-based molecular diagnostic laboratory; hence, we recommend  ...  Ethics approval and consent to participate The samples used in this study were de-identified DNA samples from CHLA patients; 33 of the samples were used for validation of our Clinical Exome Sequencing  ... 
doi:10.1186/s12920-017-0297-7 pmid:28985730 pmcid:PMC5639583 fatcat:lhf74dsngvaapa2efxorcqfizq

Viral and microbial genotyping by a combination of multiplex competitive hybridization and specific extension followed by hybridization to generic tag arrays

B. Gharizadeh
2003 Nucleic Acids Research  
By introducing an innovative technique, we show a robust, reliable and accurate microarray-based method for identi®cation of microbial pathogens.  ...  The technique utilizes a unique combination of multiplex competitive hybridization, which enhances hybridization accuracy of oligonucleotides to the speci®c target, and apyrase-mediated allele-speci®c  ...  ACKNOWLEDGEMENTS This work was supported by grants from the Swedish Research Council and Cancerfonden.  ... 
doi:10.1093/nar/gng147 pmid:14602939 pmcid:PMC275583 fatcat:35zdaubp4zekzitxwvik5a4e2u

Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken

Guiyan Ni, Tim M. Strom, Hubert Pausch, Christian Reimer, Rudolf Preisinger, Henner Simianer, Malena Erbe
2015 BMC Genomics  
Genotype concordance (GC) defined as the proportion of individuals whose array-derived genotypes are the same as the sequence-derived genotypes over all non-missing SNPs on the array were 0.98 (GATK),  ...  Methods: First, we compared the sets of variants detected with different variant callers, namely GATK, freebayes and SAMtools, and checked the quality of genotypes of the called variants in a set of 50  ...  Acknowledgements We thank Annett and Steffen Weigend (Friedrich-Loeffler-Institut Mariensee) for the management and DNA extraction of the samples.  ... 
doi:10.1186/s12864-015-2059-2 pmid:26486989 pmcid:PMC4618161 fatcat:iow2fzskszhgroz5c2lgbhvlju

Diversity and microevolution of CRISPR loci in Helicobacter cinaedi

Junko Tomida, Yuji Morita, Keigo Shibayama, Ken Kikuchi, Tomohiro Sawa, Takaaki Akaike, Yoshiaki Kawamura, Wolfgang R. Hess
2017 PLoS ONE  
Analysis of the organization and sequence similarity of the spacers of the H. cinaedi strains showed that CRISPR arrays could be divided into 7 different genotypes.  ...  Spacer polymorphisms of conserved arrays across the strains were instrumental for differentiating closely-related strains collected from the same hospital.  ...  used in this study: Keita Yamakawa, Kumamoto Orthopedic Hospital; Koichi Hashimoto, Kumamoto City Medical Association; Shunji Takahashi, Sapporo City General Hospital; Emiko Rimbara, National Institute of  ... 
doi:10.1371/journal.pone.0186241 pmid:29028814 pmcid:PMC5640232 fatcat:h7g2psguurcfjgczxkygst5iei

Evaluation of low-pass genome sequencing in polygenic risk score calculation for Parkinson's disease

Sungjae Kim, Jong-Yeon Shin, Nak-Jung Kwon, Chang-Uk Kim, Changhoon Kim, Chong Sik Lee, Jeong-Sun Seo
2021 Human Genomics  
Genotype imputation of array and downsampled LPS were conducted using a population-specific reference panel, and we calculated risk scores based on the PD-associated SNPs from an East Asian meta-GWAS.  ...  Additionally, comparing imputation accuracies between LPS and simulated array illustrated that LPS had higher accuracies particularly at rare frequencies.  ...  Informed consents were obtained from all participants in this study. Consent for publication Not applicable. 1  ... 
doi:10.1186/s40246-021-00357-w pmid:34454617 pmcid:PMC8403377 fatcat:2pqs7d6vafg55dqpmbtp6zb3vu

NeuroX, a fast and efficient genotyping platform for investigation of neurodegenerative diseases

Mike A. Nalls, Jose Bras, Dena G. Hernandez, Margaux F. Keller, Elisa Majounie, Alan E. Renton, Mohamad Saad, Iris Jansen, Rita Guerreiro, Steven Lubbe, Vincent Plagnol, J. Raphael Gibbs (+22 others)
2015 Neurobiology of Aging  
Our objective was to design a genotyping platform that would allow rapid genetic characterization of samples in the context of genetic mutations and risk factors associated with common neurodegenerative  ...  derived data.  ...  There was a broad consensus that the design of an accessible array that could type variants of interest for all major neurodegenerative diseases would be of great utility; such an array had the potential  ... 
doi:10.1016/j.neurobiolaging.2014.07.028 pmid:25444595 pmcid:PMC4317375 fatcat:lrc53eyndnc6biyhbzvg6e5r3a

Microarray-Based Genomic DNA Profiling Technologies in Clinical Molecular Diagnostics

Y. Shen, B.-L. Wu
2009 Clinical Chemistry  
Although no standardized platform is expected to emerge soon, comprehensive oligonucleotide microarray platforms-both comparative genomic hybridization arrays and genotyping hybrid arrays-are rapidly becoming  ...  A broad survey of CNVs in the healthy population, combined with the data accumulated from the patient population in clinical laboratories, will provide a better understanding of the nature of CNVs and  ...  Gusella of Massachusetts General Hospital, and Li-Jun Ma of the Broad Institute of MIT & Harvard for their critical reading of the manuscript and for thoughtful discussion.  ... 
doi:10.1373/clinchem.2008.112821 pmid:19233918 fatcat:mns3pqc5obeptp2zuznshiknf4

Genetic profiles of 103,106 individuals in the Taiwan Biobank provide insights into the health and history of Han Chinese

Chun-Yu Wei, Jenn-Hwai Yang, Erh-Chan Yeh, Ming-Fang Tsai, Hsiao-Jung Kao, Chen-Zen Lo, Lung-Pao Chang, Wan-Jia Lin, Feng-Jen Hsieh, Saurabh Belsare, Anand Bhaskar, Ming-Wei Su (+9 others)
2021 npj Genomic Medicine  
The Taiwan Biobank (TWB) has generated high-coverage, whole-genome sequencing data from 1492 individuals and genome-wide SNP data from 103,106 individuals of Han Chinese ancestry using custom SNP arrays  ...  Principal components analysis of the genotyping data showed that the full range of Han Chinese genetic variation was found in the cohort.  ...  The data that support the findings of this study from "The Pan-Asian Population Genomics Initiative and the Taiwan Han Chinese Sequence Database" and the "Collaborative Study to Establish a Cell Bank and  ... 
doi:10.1038/s41525-021-00178-9 pmid:33574314 fatcat:l2ielzubtbbcdoqeket2k6omby

Page 553 of Cancer Science Vol. 98, Issue 4 [page]

2007 Cancer Science  
that the design of the Luminex array, with 100 sets of beads, was easily integrated into the Luminex HPV Genotyping.''”  ...  In other words, each oligonucleotide was hybridized to nucleotide sequences derived from a single HPV gene of the same type.  ... 

Design and characterization of an 87k SNP genotyping array for Arctic charr (Salvelinus alpinus)

Cameron M. Nugent, Jong S. Leong, Kris A. Christensen, Eric B. Rondeau, Matthew K. Brachmann, Anne A. Easton, Christine L. Ouellet-Fagg, Michelle T. T. Crown, William S. Davidson, Ben F. Koop, Roy G. Danzmann, Moira M. Ferguson (+1 others)
2019 PLoS ONE  
The concordance between sdY markers and known phenotypic sex indicated that the array can accurately determine the sex of individuals based on genotype alone.  ...  Cross validation of SNPs from various sources and comparison with previously published Arctic charr SNP data provided a set of candidate SNPs that generalize across populations.  ...  Rico Law, Amber Garber and Matthieu Renner provided invaluable assistance with obtaining and processing samples from Icy Water's Ltd.  ... 
doi:10.1371/journal.pone.0215008 pmid:30951561 pmcid:PMC6450613 fatcat:mo2ifbbsjnacbosk235va5qel4
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