Curated variation benchmarks for challenging medically relevant autosomal genes
The repetitive nature and complexity of some medically relevant genes poses a challenge
for their accurate analysis in a clinical setting. The Genome in a Bottle Consortium has …
for their accurate analysis in a clinical setting. The Genome in a Bottle Consortium has …
[PDF][PDF] Benchmarking challenging small variants with linked and long reads
Genome in a Bottle benchmarks are widely used to help validate clinical sequencing pipelines
and develop variant calling and sequencing methods. Here we use accurate linked and …
and develop variant calling and sequencing methods. Here we use accurate linked and …
[HTML][HTML] A diploid assembly-based benchmark for variants in the major histocompatibility complex
…, C Xiao, WJ Rowell, C Markello, J Farek… - Nature …, 2020 - nature.com
Most human genomes are characterized by aligning individual reads to the reference genome,
but accurate long reads and linked reads now enable us to construct accurate, phased …
but accurate long reads and linked reads now enable us to construct accurate, phased …
[HTML][HTML] FixItFelix: improving genomic analysis by fixing reference errors
The current version of the human reference genome, GRCh38, contains a number of errors
including 1.2 Mbp of falsely duplicated and 8.04 Mbp of collapsed regions. These errors …
including 1.2 Mbp of falsely duplicated and 8.04 Mbp of collapsed regions. These errors …
[HTML][HTML] Epigenome-wide DNA methylation association study of circulating IgE levels identifies novel targets for asthma
Background Identifying novel epigenetic signatures associated with serum immunoglobulin
E (IgE) may improve our understanding of molecular mechanisms underlying asthma and IgE…
E (IgE) may improve our understanding of molecular mechanisms underlying asthma and IgE…
[PDF][PDF] Exome variant discrepancies due to reference-genome differences
Despite release of the GRCh38 human reference genome more than seven years ago, GRCh37
remains more widely used by most research and clinical laboratories. To date, no study …
remains more widely used by most research and clinical laboratories. To date, no study …
xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments
J Farek, D Hughes, W Salerno, Y Zhu, A Pisupati… - …, 2023 - academic.oup.com
Background The growing volume and heterogeneity of next-generation sequencing (NGS)
data complicate the further optimization of identifying DNA variation, especially considering …
data complicate the further optimization of identifying DNA variation, especially considering …
[HTML][HTML] Author Correction: Clonal haematopoiesis and risk of chronic liver disease
… Eric Boerwinkle, Adithya Balasubramanian, Huyen Dinh, Harsha Doddapaneni,
Shannon Dugan-Perez, Jesse Farek, Richard Gibbs, Yi Han, Jianhong Hu, Ziad Khan …
Shannon Dugan-Perez, Jesse Farek, Richard Gibbs, Yi Han, Jianhong Hu, Ziad Khan …
[HTML][HTML] Author Correction: A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response
In the version of this Article initially published, the author list and affiliations were incomplete.
Karl Heilbron and Adam Auton, both with 23andMe, Inc., have been added to the author list…
Karl Heilbron and Adam Auton, both with 23andMe, Inc., have been added to the author list…
[HTML][HTML] GLnexus: joint variant calling for large cohort sequencing
As ever-larger cohorts of human genomes are collected in pursuit of genotype/phenotype
associations, sequencing informatics must scale up to yield complete and accurate genotypes …
associations, sequencing informatics must scale up to yield complete and accurate genotypes …