Nathan D. Olson
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View article: Aardvark: Sifting through differences in a mound of variants
Aardvark: Sifting through differences in a mound of variants Open
Variant benchmarking is critical in assessing the accuracy of genomic secondary pipelines. However, traditional benchmarking tools that require exact genotype matches inject biases from variant representation and are ill-suited for tandem …
View article: A complete diploid human genome benchmark for personalized genomics
A complete diploid human genome benchmark for personalized genomics Open
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and structurally polymorphic regions of the…
View article: Small variant benchmark from a complete assembly of X and Y chromosomes
Small variant benchmark from a complete assembly of X and Y chromosomes Open
The sex chromosomes contain complex, important genes impacting medical phenotypes, but differ from the autosomes in their ploidy and large repetitive regions. To enable technology developers along with research and clinical laboratories to…
View article: A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material.
A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material. Open
Somatic mosaicism is an important cause of disease, but mosaic and somatic variants are often challenging to detect because they exist in only a fraction of cells. To address the need for benchmarking subclonal variants in normal cell popu…
View article: StratoMod: predicting sequencing and variant calling errors with interpretable machine learning
StratoMod: predicting sequencing and variant calling errors with interpretable machine learning Open
Despite the variety in sequencing platforms, mappers, and variant callers, no single pipeline is optimal across the entire human genome. Therefore, developers, clinicians, and researchers need to make tradeoffs when designing pipelines for…
View article: The Platinum Pedigree: A long-read benchmark for genetic variants
The Platinum Pedigree: A long-read benchmark for genetic variants Open
Recent advances in genome sequencing have improved variant calling in complex regions of the human genome. However, it is difficult to quantify variant calling performance since existing standards often focus on specificity, neglecting com…
View article: High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation Open
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 l…
View article: Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair
Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair Open
The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first to be explicitly consented for public dissemination of genomic data an…
View article: Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation
Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation Open
Less than half of individuals with a suspected Mendelian condition receive a precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using long-read seque…
View article: Editorial: Methods in computational genomics
Editorial: Methods in computational genomics Open
EDITORIAL article Front. Genet., 25 January 2024Sec. Computational Genomics Volume 15 - 2024 | https://doi.org/10.3389/fgene.2024.1367531
View article: Small variant benchmark from a complete assembly of X and Y chromosomes
Small variant benchmark from a complete assembly of X and Y chromosomes Open
The sex chromosomes contain complex, important genes impacting medical phenotypes, but differ from the autosomes in their ploidy and large repetitive regions. To evaluate variant detection on chromosomes X and Y, we created an 111,725 vari…
View article: Benchmarking of small and large variants across tandem repeats
Benchmarking of small and large variants across tandem repeats Open
Tandem repeats (TRs) are highly polymorphic in the human genome, have thousands of associated molecular traits, and are linked to over 60 disease phenotypes. However, their complexity often excludes them from at-scale studies due to challe…
View article: The GIAB genomic stratifications resource for human reference genomes
The GIAB genomic stratifications resource for human reference genomes Open
Stratification of the genome into different genomic contexts is useful when developing bioinformatics software like variant callers, to assess performance in difficult regions in the human genome. Here we describe a set of genomic stratifi…
View article: The GIAB genomic stratifications resource for human reference genomes
The GIAB genomic stratifications resource for human reference genomes Open
Stratification of the genome into different genomic contexts is useful when developing bioinformatics software like variant callers, to assess performance in different types of difficult regions in the human genome. Here we describe a set …
View article: Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome
Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome Open
The human pangenome, a new reference sequence, addresses many limitations of the current GRCh38 reference. The first release is based on 94 high-quality haploid assemblies from individuals with diverse backgrounds. We employed a k-mer inde…
View article: Increased mutation and gene conversion within human segmental duplications
Increased mutation and gene conversion within human segmental duplications Open
Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations of mapping short-read sequencing data 1,2 . Here we constructed 1:1 unambiguous alignments spanning high-ide…
View article: Emergency Medicine In-Training Examination Scores are Not Associated with Burnout and Not Affected by the Introduction of a Wellness Curriculum
Emergency Medicine In-Training Examination Scores are Not Associated with Burnout and Not Affected by the Introduction of a Wellness Curriculum Open
Introduction: There is little research examining the relationship between burnout and medical knowledge. Study Objectives: The authors sought to determine if emergency medicine (EM) resident performance on the In-Training Examination (EM-I…
View article: Precision engineering of biological function with large-scale measurements and machine learning
Precision engineering of biological function with large-scale measurements and machine learning Open
As synthetic biology expands and accelerates into real-world applications, methods for quantitatively and precisely engineering biological function become increasingly relevant. This is particularly true for applications that require progr…