Jonathan R. Adkins

Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies

The paper establishes reference samples with high-coverage whole-genome sequencing to create truth sets for somatic mutation and germline variant detection using NGS technologies.

Genomic Basis of Multiple Myeloma Subtypes from the MMRF CoMMpass Study

The paper identifies genomic subtypes of multiple myeloma using the MMRF CoMMpass study and finds that 25.5% of patients transition to a high-risk expression subtype at progression, which expresses immunotherapy targets.

ACValidator: a novel assembly-based approach for in silico validation of circular RNAs

ACValidator validates circRNAs by assembling reads around junctions and aligning contigs to detect back-spliced junctions, achieving high sensitivity and specificity in simulated and experimental datasets.

Tumor cell phenotype and heterogeneity differences in IDH1 mutant vs wild-type gliomas

This study compares tumor cell phenotype and heterogeneity differences between IDH1 mutant and wild-type gliomas using integrated multi-omics data.

Joint analysis of matched tumor samples with varying tumor contents improves somatic variant calling in the absence of a germline sample

LumosVar 2.0 improves somatic variant calling by jointly analyzing tumor and adjacent normal samples without a germline reference.

Circular RNA expression and regulatory network prediction in posterior cingulate astrocytes in elderly subjects

The paper identifies circRNAs and their regulatory networks in posterior cingulate astrocytes from elderly subjects, finding enriched immune response pathways.