Christopher M. Grochowski

This study evaluates somatic variant calling in normal tissues using single-cell RNA and ATAC sequencing, showing Monopogen outperforms other tools in accuracy and sensitivity.

The paper introduces a data model and dataset for rare disease research, enabling interoperable multi-omic data integration across clinical sites.

The paper identifies an SLC30A9 deletion causing familial medullary thyroid carcinoma through translation reinitiation and shows its oncogenic effects.

The paper uses single-cell DNA sequencing to analyze somatic mosaicism in postmortem lung and colon tissues, revealing mutation heterogeneity, chromosomal abnormalities, and cellular ancestry.

This study uses whole-genome sequencing to analyze 9p deletion and duplication syndromes, identifying key genes and structural variants, and introduces a machine learning model for syndrome prediction.

The paper benchmarks somatic variant and indel detection at low allele fractions using short- and long-read data, finding sensitivity and precision around 80% at 300x coverage.

The paper benchmarks somatic structural variant detection at ultra-low allele fractions using synthetic data and evaluates 12 pipelines, finding long-read sequencing provides higher accuracy than short-read methods.

The paper investigates how different genome references affect inversion detection, showing that T2T-CHM13 and long-read sequencing improve resolution of challenging inversions.

The paper characterizes intrachromosomal repeats in three human genome assemblies, finding more repeats in the T2T-CHM13 assembly and identifying gene categories enriched for repeat-associated genomic disorders.

Sniffles2 improves SV detection accuracy and speed, enabling mosaic and population-level SV calling with applications in neurological disorders.

The paper investigates DUP-TRP/INV-DUP genomic rearrangements in neurodevelopmental disorders, identifying four SV haplotypes and refining template switching points using multiple sequencing technologies.

The paper describes the role of the Centers for Mendelian Genomics in advancing gene discovery through data sharing, collaboration, and resource development over the past decade.

This study performs exome sequencing in 100 patients with isolated biliary atresia to identify genetic variants, finding no common causal genes but a de novo mutation in STIP1.