Author

John Penn

Regeneron (United States)

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 3 Bioinformatics· 2

Signature Assays, Organisms & Methods

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Approach:statistical model· 5 Assay:whole-exome sequencing· 5 Organism:human· 4 Research Focus:variant calling· 4 Research Focus:GWAS / association mapping· 2 Research Focus:benchmarking· 1 Research Focus:database / resource· 1 Assay:electronic health records· 1

Frequent Co-Authors

Jeffrey G. ReidiD· 5 shared Alexander E. LopeziD· 4 shared Aris BarasiD· 4 shared Claudia G. Gonzaga-JaureguiiD· 4 shared Evan K. MaxwelliD· 4 shared Jeffrey C. StaplesiD· 4 shared John D. OvertoniD· 4 shared Lukas Habegger· 4 shared

Activity by Year

2017-2019 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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5 shared papersGenomics

Jeffrey G. ReidORCID

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Author profile →

5 papers

Recent·Most cited

Whole exome sequencing and characterization of coding variation in 49,960 individuals in the UK Biobank

Cristopher V. Van Hout, Ioanna Tachmazidou, Joshua Backman, Joshua X. Hoffman, Bin Ye, Ashutosh K. Pandey, Claudia G. Gonzaga-Jauregui, Shareef Khalid, Daren Liu, Nilanjana Banerjee, Alexander H. Li, O’Dushlaine Colm, Anthony Marcketta, Jeffrey C. Staples, Claudia Schurmann, , Aris Baras

Exomes of 49,960 UK Biobank participants reveal 231,631 predicted loss-of-function variants (>10-fold more than imputed data); burden tests implicate PIEZO1, MEPE, and COL6A1 in disease traits.

bioRxiv · Mar 9, 2019 · PreprintGenomics✦ In-depth digest

GLnexus: joint variant calling for large cohort sequencing

Michael F. Lin, Ohad Rodeh, John Penn, Xiaodong Bai, Jeffrey G. Reid, Olga A. Krasheninina, William J. Salerno

GLnexus, a joint variant caller backed by an incrementally growable gVCF database, largely matched GATK on 50,000 exomes while keeping more rare indels and using 3.8–6.6-fold fewer core-hours.

bioRxiv · Jun 11, 2018 · PreprintBioinformatics✦ In-depth digest

Profiling and leveraging relatedness in a precision medicine cohort of 92,455 exomes

Jeffrey C. Staples, Evan K. Maxwell, Nehal Gosalia, Claudia G. Gonzaga-Jauregui, Christopher Snyder, Alicia C. Hawes, John Penn, Ricardo H. Ulloa, Xiaodong Bai, Alexander E. Lopez, Cristopher V. Van Hout, Colm T. O’Dushlaine, Tanya M. Teslovich, Shane McCarthy, Suganthi Balasubramanian, , Jeffrey G. Reid

The paper analyzes cryptic relatedness in a large exome cohort, identifies numerous close relationships, reconstructs pedigrees, and demonstrates their utility in improving mutation phasing and identifying de novo mutations.

The American Journal of Human Genetics · May 1, 2018Peer-reviewedGenomics

KaryoScan: abnormal karyotype detection from whole-exome sequence

Evan K. Maxwell, Claudia G. Gonzaga-Jauregui, Shane McCarthy, Colm T. O’Dushlaine, Jeffrey C. Staples, Alexander E. Lopez, Xiaodong Bai, John Penn, Rick H. Ulloa, Omri Gottesman, Aris Baras, Frederick E. Dewey, John D. Overton, Erik G. Puffenberger, Lukas Habegger, Jeffrey G. Reid

KaryoScan detects chromosomal anomalies from whole-exome sequencing, identifying aneuploidies and complex rearrangements in large cohorts.

bioRxiv · Oct 17, 2017 · PreprintBioinformatics

Profiling copy number variation and disease associations from 50,726 DiscovEHR Study exomes

Evan K. Maxwell, Jonathan S. Packer, Colm T. O’Dushlaine, Shane McCarthy, Abby E. Hare-Harris, Jeffrey C. Staples, Claudia G. Gonzaga-Jauregui, Samantha N. Fetterolf, W. Andrew Faucett, Joseph B. Leader, Andrés Moreno-De-Luca, Giusy Della Gatta, Margaret E. Scollan, Trikaldarshi Persaud, John Penn, , Jeffrey G. Reid

The paper identifies and analyzes exonic copy number variants (CNVs) in 50,726 DiscovEHR participants, linking them to clinical traits and phenotypes.

bioRxiv · Mar 22, 2017 · PreprintGenomics