Mark Fleharty

TL;DR: It is shown that incomplete XCI affects at least 23% of X-chromosomal genes, identified seven genes that escape XCI with support from multiple lines of evidence and demonstrated that escape from XCI results in sex biases in gene expression, establishing incomplete X CI as a mechanism that is likely to introduce phenotypic diversity.

TL;DR: This work provides guidance on how to match variant calls with different representations, define standard performance metrics, and stratify performance by variant type and genome context, and describes limitations of high-confidence calls and regions that can be used as truth sets.

TL;DR: It is demonstrated that escape from XCI results in sex biases in gene expression, thus establishing incomplete XCI as a likely mechanism introducing phenotypic diversity6,7 and this updated catalogue of XCI across human tissues informs the understanding of the extent and impact of the incompleteness.

TL;DR: An in-depth characterization of the mechanism of sequencer-induced sample contamination due to the phenomenon of index swapping that impacts Illumina sequencers employing patterned flow cells with Exclusion Amplification chemistry is presented and methods for eliminating sample data cross contamination are provided.

TL;DR: The synthetic-diploid (Syndip) benchmark dataset, constructed from two fully homozygous long-read assemblies, provides more accurate assessments of error rates in small-variant-calling algorithms than existing benchmarks.