Sheila Dodge

Structural variant discovery and diagnostic impact in rare diseases from short-read and long-read sequencing

This study evaluates the diagnostic yield of short-read and long-read sequencing in rare diseases, finding limited added value from long-read sequencing despite increased variant discovery.

Sequencing of over 100,000 individuals identifies multiple genes and rare variants associated with Crohns disease susceptibility

The paper identifies ten new genes with coding variants linked to Crohn's disease risk using sequencing data from over 30,000 patients and 80,000 controls.

Cost-efficient whole genome-sequencing using novel mostly natural sequencing-by-synthesis chemistry and open fluidics platform

Open flow cell on a circular wafer with mostly natural nucleotides and no reversible terminators: about 300 bp reads at $1/Gb, 99.6% SNP accuracy on reference human genomes.

Exome sequencing identifies rare coding variants in 10 genes which confer substantial risk for schizophrenia

Exomes of 24,248 schizophrenia cases and 97,322 controls implicate ultra-rare damaging variants in 10 genes, including GRIN2A and GRIA3, with odds ratios of 3 to 50.

Neptune: An environment for the delivery of genomic medicine

Neptune delivers structured genomic data to EHR systems through customizable reports and variant reanalysis, supporting over 15,000 clinical reports.

Low-coverage sequencing cost-effectively detects known and novel variation in underrepresented populations

This study shows low-coverage sequencing is more accurate and cost-effective than GWAS arrays for detecting genetic variation in diverse African populations.

Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

The paper characterizes index swapping on Illumina sequencers and proposes dual indexing to mitigate its effects, showing varying swap rates across methods and sequencers.