Author

Stephen E. Lincoln

Invitae (United States)ORCID 0000-0002-0966-5282Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genetics· 2 Genetic & Genomic Medicine· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Research Focus:variant calling· 3 Research Focus:benchmarking· 2 Organism:human· 2 Approach:statistical model· 2 Assay:whole-exome sequencing· 2 Assay:whole-genome sequencing· 2 Approach:benchmark study· 1 Approach:experimental assay· 1

Frequent Co-Authors

Justin M. ZookiD· 4 shared Marc SalitiD· 3 shared Rebecca TrutyiD· 3 shared Robert Luke NussbaumiD· 3 shared ANDREW P. FELLOWESiD· 2 shared Brian H. ShirtsiD· 2 shared Catherine Huang· 2 shared Eric W. KleeiD· 2 shared

Activity by Year

2017-2022 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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4 shared papersGenetics

Justin M. ZookORCID

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4 papers

Recent·Most cited

GenomicsNature BiotechnologyPeer-reviewedFeb 7, 2022

Towards a Comprehensive Variation Benchmark for Challenging Medically-Relevant Autosomal Genes

Justin Wagner, Nathan D. Olson, Lindsay N. Harris…·Fritz Joachim Sedlazeck

This paper creates a comprehensive benchmark for challenging medically-relevant autosomal genes, improving variant recall from 8% to 100% by addressing reference-specific false duplications.

241 citationstop 1%

humanwhole-genome sequencing

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Genetic & Genomic MedicineGenetics in MedicinePeer-reviewedMay 18, 2021

One in seven pathogenic variants can be challenging to detect by NGS: An analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation

Stephen E. Lincoln, Tina M. Hambuch, Justin M. Zook…·Robert Luke Nussbaum

The paper evaluates the detection of technically challenging variants in NGS workflows using synthetic specimens and clinical data from 450,000 patients, finding significant variability in detection rates.

91 citationstop 1%

humanwhole-exome sequencing

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GeneticsJournal of Molecular DiagnosticsPeer-reviewedJan 2, 2019

A Rigorous Interlaboratory Examination of the Need to Confirm NGS-Detected Variants by an Orthogonal Method in Clinical Genetic Testing

Stephen E. Lincoln, Rebecca Truty, Chiao‐Feng Lin…·Matthew S. Lebo

The paper examines the need for orthogonal confirmation of NGS-detected variants in clinical testing and develops criteria to identify false positives with high accuracy.

71 citationstop 4%

whole-exome sequencingstatistical model

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GeneticsbioRxivPreprintNov 23, 2017

An interlaboratory study of complex variant detection

Stephen E. Lincoln, Justin M. Zook, Shimul Chowdhury…·Brian H. Shirts

This study evaluates synthetic specimens with challenging variants across 10 NGS workflows, finding limited variant detection consistency and highlighting bioinformatic limitations.

11 citations

whole-genome sequencingstatistical model

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