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  1. Home
  2. Browse by Author

Browsing by Author "Garrison, Erik"

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    High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
    (Cold Spring Harbor Laboratory Press, 2024) Gustafson, Jonas A.; Gibson, Sophia B.; Damaraju, Nikhita; Zalusky, Miranda P. G.; Hoekzema, Kendra; Twesigomwe, David; Yang, Lei; Snead, Anthony A.; Richmond, Phillip A.; Coster, Wouter De; Olson, Nathan D.; Guarracino, Andrea; Li, Qiuhui; Miller, Angela L.; Goffena, Joy; Anderson, Zachary B.; Storz, Sophie H. R.; Ward, Sydney A.; Sinha, Maisha; Gonzaga-Jauregui, Claudia; Clarke, Wayne E.; Basile, Anna O.; Corvelo, André; Reeves, Catherine; Helland, Adrienne; Musunuri, Rajeeva Lochan; Revsine, Mahler; Patterson, Karynne E.; Paschal, Cate R.; Zakarian, Christina; Goodwin, Sara; Jensen, Tanner D.; Robb, Esther; Consortium, The 1000 Genomes ONT Sequencing; Research (UW-CRDR), University of Washington Center for Rare Disease; Consortium, Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR); McCombie, William Richard; Sedlazeck, Fritz J.; Zook, Justin M.; Montgomery, Stephen B.; Garrison, Erik; Kolmogorov, Mikhail; Schatz, Michael C.; McLaughlin, Richard N.; Dashnow, Harriet; Zody, Michael C.; Loose, Matt; Jain, Miten; Eichler, Evan E.; Miller, Danny E.
    Fewer than half of individuals with a suspected Mendelian or monogenic condition receive a precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using long-read sequencing (LRS) to streamline clinical genomic testing, but the absence of control data sets for variant filtering and prioritization has made tertiary analysis of LRS data challenging. To address this, the 1000 Genomes Project (1KGP) Oxford Nanopore Technologies Sequencing Consortium aims to generate LRS data from at least 800 of the 1KGP samples. Our goal is to use LRS to identify a broader spectrum of variation so we may improve our understanding of normal patterns of human variation. Here, we present data from analysis of the first 100 samples, representing all 5 superpopulations and 19 subpopulations. These samples, sequenced to an average depth of coverage of 37× and sequence read N50 of 54 kbp, have high concordance with previous studies for identifying single nucleotide and indel variants outside of homopolymer regions. Using multiple structural variant (SV) callers, we identify an average of 24,543 high-confidence SVs per genome, including shared and private SVs likely to disrupt gene function as well as pathogenic expansions within disease-associated repeats that were not detected using short reads. Evaluation of methylation signatures revealed expected patterns at known imprinted loci, samples with skewed X-inactivation patterns, and novel differentially methylated regions. All raw sequencing data, processed data, and summary statistics are publicly available, providing a valuable resource for the clinical genetics community to discover pathogenic SVs.
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    Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation
    (Oxford University Press, 2023) Kille, Bryce; Garrison, Erik; Treangen, Todd J; Phillippy, Adam M
    The Jaccard similarity on k-mer sets has shown to be a convenient proxy for sequence identity. By avoiding expensive base-level alignments and comparing reduced sequence representations, tools such as MashMap can scale to massive numbers of pairwise comparisons while still providing useful similarity estimates. However, due to their reliance on minimizer winnowing, previous versions of MashMap were shown to be biased and inconsistent estimators of Jaccard similarity. This directly impacts downstream tools that rely on the accuracy of these estimates.To address this, we propose the minmer winnowing scheme, which generalizes the minimizer scheme by use of a rolling minhash with multiple sampled k-mers per window. We show both theoretically and empirically that minmers yield an unbiased estimator of local Jaccard similarity, and we implement this scheme in an updated version of MashMap. The minmer-based implementation is over 10 times faster than the minimizer-based version under the default ANI threshold, making it well-suited for large-scale comparative genomics applications.MashMap3 is available at https://github.com/marbl/MashMap.
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