Publications by authors named "David L Marron"

2 Publications

  • Page 1 of 1

The Prognostic Significance of Low-Frequency Somatic Mutations in Metastatic Cutaneous Melanoma.

Front Oncol 2018 4;8:584. Epub 2019 Jan 4.

Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.

Little is known about the prognostic significance of somatically mutated genes in metastatic melanoma (MM). We have employed a combined clinical and bioinformatics approach on tumor samples from cutaneous melanoma (SKCM) as part of The Cancer Genome Atlas project (TCGA) to identify mutated genes with potential clinical relevance. After limiting our DNA sequencing analysis to MM samples ( = 356) and to the CANCER CENSUS gene list, we filtered out mutations with low functional significance (snpEFF). We performed Cox analysis on 53 genes that were mutated in ≥3% of samples, and had ≥50% difference in incidence of mutations in deceased subjects versus alive subjects. Four genes were potentially prognostic [; false discovery rate (FDR) < 0.2]. We identified 18 additional genes (e.g., ) that were less likely to have prognostic value (FDR < 0.4). Most somatic mutations in these 22 genes were infrequent (< 10%), associated with high somatic mutation burden, and were evenly distributed across all exons, except for and . Mutations in only 9 of these 22 genes were also identified by RNA sequencing in >75% of the samples that exhibited corresponding DNA mutations. The low frequency, UV signature type and RNA expression of the 22 genes in MM samples were confirmed in a separate multi-institution validation cohort ( = 413). An underpowered analysis within a subset of this validation cohort with available patient follow-up ( = 224) showed that somatic mutations in and reached borderline prognostic significance [log-rank favorable ( = 0.09) and adverse ( = 0.07), respectively]. Somatic mutations in , and to a lesser extent , were not associated with definite gene copy number or RNA expression alterations. High (>2+) nuclear plus cytoplasmic expression intensity for SPEN was associated with longer melanoma-specific overall survival (OS) compared to lower (≤ 2+) nuclear intensity ( = 0.048). We conclude that expressed somatic mutations in infrequently mutated genes beyond the well-characterized ones (e.g., ), such as and , may have prognostic significance in MM.
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http://dx.doi.org/10.3389/fonc.2018.00584DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6329304PMC
January 2019

Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer.

Bioinformatics 2016 12 24;32(24):3729-3734. Epub 2016 Aug 24.

Lineberger Comprehensive Cancer Center.

Motivation: B-cell receptor (BCR) repertoire profiling is an important tool for understanding the biology of diverse immunologic processes. Current methods for analyzing adaptive immune receptor repertoires depend upon PCR amplification of VDJ rearrangements followed by long read amplicon sequencing spanning the VDJ junctions. While this approach has proven to be effective, it is frequently not feasible due to cost or limited sample material. Additionally, there are many existing datasets where short-read RNA sequencing data are available but PCR amplified BCR data are not.

Results: We present here V'DJer, an assembly-based method that reconstructs adaptive immune receptor repertoires from short-read RNA sequencing data. This method captures expressed BCR loci from a standard RNA-seq assay. We applied this method to 473 Melanoma samples from The Cancer Genome Atlas and demonstrate V'DJer's ability to accurately reconstruct BCR repertoires from short read mRNA-seq data.

Availability And Implementation: V'DJer is implemented in C/C ++, freely available for academic use and can be downloaded from Github: https://github.com/mozack/vdjer CONTACT: [email protected] or [email protected] information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btw526DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167060PMC
December 2016
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