cfDNA Tumor Fraction and CNAs in Mets

[PMID: 29298117] [Journal of Clinical Oncology]

Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer

“low-coverage genome-wide sequencing of cfDNA from plasma.”



[PMID: 29474557] [Bioinformatics]

PennDiff: Detecting Differential Alternative Splicing and Transcription by RNA Sequencing

“Differential alternative splicing and transcription (DAST), which describe different usage of transcript isoforms across different conditions, can complement differential expression in characterizing gene regulation. However, the analysis of DAST is challenging because only a small fraction of RNA-seq reads is informative for isoforms. Several methods have been developed to detect exon-based and gene-based DAST, but they suffer from power loss for genes with many isoforms.” “PennDiff, a novel statistical method that makes use of information on gene structures and pre-estimated isoform relative abundances, to detect DAST from RNA-seq data. PennDiff has several advantages. First, grouping exons avoids multiple testing for “exons” originated from the same isoform(s). Second, it utilizes all available reads in exon-inclusion level estimation, which is different from methods that only use junction reads. Third, collapsing isoforms sharing the same alternative exons reduces the impact of isoform expression estimation uncertainty. PennDiff is able to detect DAST at both exon and gene levels, thus offering more flexibility than existing methods. “


[PMID: 29182778] [Nucleic Acids Research]

Jointly aligning a group of DNA reads improves accuracy of identifying large deletions

“a method to jointly align reads to a genome, whereby alignment ambiguity of one read can be disambiguated by other reads. We show this leads to a significant improvement in the accuracy of identifying large deletions (≥20 bases)”


GATK on Cloud for $5 per Genome

Run the germline GATK Best Practices Pipeline for $5 per genome

$45 iin 2016, $13.5 in 2017, and now $5.


The Human Transcription Factors

[PMID: 29425488] [Cell]

The Human Transcription Factors




[PMID: 29385401] [Bioinformatics]

Accurity: Accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants

“infers tumor purity, tumor cell ploidy, and absolute allelic copy numbers for somatic copy number alterations (SCNAs) from tumor-normal WGS data by jointly modelling SCNAs and heterozygous germline single-nucleotide-variants (HGSNVs).”



[PMID: 29348365] [Science]

Detection and localization of surgically resectable cancers with a multi-analyte blood test

“Here we describe a blood test that can detect eight common cancer types through assessment of the levels of circulating proteins and mutations in cell-free DNA. We applied this test, called CancerSEEK, to 1,005 patients with non-metastatic, clinically detected cancers of the ovary, liver, stomach, pancreas, esophagus, colorectum, lung, or breast. “