Erin N. Smith

Effective filtering strategies to improve data quality from population-based whole exome sequencing studies.

Published in BMC Bioinformatics

miR-150 influences B-cell receptor signaling in chronic lymphocytic leukemia by regulating expression of GAB1 and FOXP1....

Published in Blood

We examined the microRNAs (miRNAs) expressed in chronic lymphocytic leukemia (CLL) and identified miR-150 as the most abundant, but with leukemia cell expression levels that varied among patients. CLL cells that expressed ζ-chain-associated protein of 70 kDa (ZAP-70) or that used unmutated immunoglobulin heavy chain variable (IGHV) genes, each had ...

Genetic ancestry of participants in the National Children s Study.

Published in Genome Biology

Whole Transcriptome Sequencing Enables Discovery and Analysis of Viruses in Archived Primary Central Nervous System Lymp...

Primary central nervous system lymphomas (PCNSL) have a dramatically increased prevalence among persons living with AIDS and are known to be associated with human Epstein Barr virus (EBV) infection. Previous work suggests that in some cases, co-infection with other viruses may be important for PCNSL pathogenesis. Viral transcription in tumor sample...

High-resolution mutational profiling suggests the genetic validity of glioblastoma patient-derived pre-clinical models.

Recent advances in the ability to efficiently characterize tumor genomes is enabling targeted drug development, which requires rigorous biomarker-based patient selection to increase effectiveness. Consequently, representative DNA biomarkers become equally important in pre-clinical studies. However, it is still unclear how well these markers are mai...

Consanguinity and rare mutations outside of MCCC genes underlie nonspecific phenotypes of MCCD.

Published in Genetics in Medicine

Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens.

Published in Nucleic Acids Research

The utilization of archived, formalin-fixed paraffin-embedded (FFPE) tumor samples for massive parallel sequencing has been challenging due to DNA damage and contamination with normal stroma. Here, we perform whole genome sequencing of DNA isolated from two triple-negative breast cancer tumors archived for >11 years as 5 µm FFPE sections and matche...

Genetic and epigenetic profiling of CLL disease progression reveals limited somatic evolution and suggests a relationshi...

Published in Blood Cancer Journal

We examined genetic and epigenetic changes that occur during disease progression from indolent to aggressive forms of chronic lymphocytic leukemia (CLL) using serial samples from 27 patients. Analysis of DNA mutations grouped the leukemia cases into three categories: evolving (26%), expanding (26%) and static (47%). Thus, approximately three-quarte...

Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experi...

Published in Genome Biology

Accurate allele frequencies are important for measuring subclonal heterogeneity and clonal evolution. Deep-targeted sequencing data can contain PCR duplicates, inflating perceived read depth. Here we adapted the Illumina TruSeq Custom Amplicon kit to include single molecule tagging (SMT) and show that SMT-identified duplicates arise from PCR. We de...