Whole-exome sequencing of pancreatic cancer defines genetic diversity and therapeutic targets
Nature Communications, 2015 Pancreatic ductal adenocarcinoma (PDA) has a dismal prognosis and insights into both disease etiology and targeted intervention are needed. A total of 109 micro-dissected PDA cases were subjected to whole-exome sequencing. Microdissection enriches tumour
A. Witkiewicz +14 more
semanticscholar +1 more source
Learning from Data-Rich Problems: A Case Study on Genetic Variant Calling [PDF]
arXiv, 2019 Next Generation Sequencing can sample the whole genome (WGS) or the 1-2% of the genome that codes for proteins called the whole exome (WES). Machine learning approaches to variant calling achieve high accuracy in WGS data, but the reduced number of training examples causes training with WES data alone to achieve lower accuracy.
arxiv
Exome sequencing supports a de novo mutational paradigm for schizophrenia [PDF]
, 2011 Bin Xu +7 more
openalex +1 more source
Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing
Nature Biotechnology, 2021 Wenming Xiao +89 more
semanticscholar +1 more source
Diagnostic Cytopathology, Volume 51, Issue 1, Page 83-94, January 2023., 2023 Abstract Molecular diagnostics has expanded to become the standard of care for a variety of solid tumor types. With limited diagnostic material, it is often desirable to use cytological preparations to provide rapid and accurate molecular results. This review covers important pre‐analytic considerations and limitations, and a description of common ...
Scott A. Turner +2 more
wiley +1 more source
SlopMap: a software application tool for quick and flexible identification of similar sequences using exact k-mer matching [PDF]
arXiv, 2013 With the advent of Next-Generation (NG) sequencing, it has become possible to sequence an entire genome quickly and inexpensively. However, in some experiments one only needs to extract and assembly a portion of the sequence reads, for example when performing transcriptome studies, sequencing mitochondrial genomes, or characterizing exomes.
arxiv
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV [PDF]
, 2011 J. Fah Sathirapongsasuti +7 more
openalex +1 more source
Inference on High-Dimensional Sparse Count Data [PDF]
arXiv, 2015 In a variety of application areas, there is a growing interest in analyzing high dimensional sparse count data, with sparsity exhibited by an over-abundance of zeros and small non-zero counts. Existing approaches for analyzing multivariate count data via Poisson or negative binomial log-linear hierarchical models with zero-inflation cannot flexibly ...
arxiv
Unlocking Mendelian disease using exome sequencing [PDF]
, 2011 Christian Gilissen +3 more
openalex +1 more source
TFisher Tests: Optimal and Adaptive Thresholding for Combining $p$-Values [PDF]
arXiv, 2018 For testing a group of hypotheses, tremendous $p$-value combination methods have been developed and widely applied since 1930's. Some methods (e.g., the minimal $p$-value) are optimal for sparse signals, and some others (e.g., Fisher's combination) are optimal for dense signals.
arxiv