Somatic variants can be used as lineage markers for the phylogenetic reconstruction of cancer evolution. Since somatic phylogenetics is complicated by sample heterogeneity, novel specialized tree-building methods are required for cancer phylogeny reconstruction. We present LICHeE (Lineage Inference for Cancer Heterogeneity and Evolution), a novel method that automates the phylogenetic inference of cancer progression from multiple somatic samples. LICHeE uses variant allele frequencies of somatic single nucleotide variants obtained by deep sequencing to reconstruct multi-sample cell lineage trees and infer the subclonal composition of the samples. LICHeE is open source and available at http://viq854.github.io/lichee.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0647-8) contains supplementary material, which is available to authorized users.

Summary: The increasing availability of high-throughput sequencing technologies has led to thousands of human genomes having been sequenced in the past years. Efforts such as the 1000 Genomes Project further add to the availability of human genome variation data. However, to date, there is no method that can map reads of a newly sequenced human genome to a large collection of genomes. Instead, methods rely on aligning reads to a single reference genome. This leads to inherent biases and lower accuracy. To tackle this problem, a new alignment tool BWBBLE is introduced in this article. We (i) introduce a new compressed representation of a collection of genomes, which explicitly tackles the genomic variation observed at every position, and (ii) design a new alignment algorithm based on the Burrows–Wheeler transform that maps short reads from a newly sequenced genome to an arbitrary collection of two or more (up to millions of) genomes with high accuracy and no inherent bias to one specific genome.Availability: http://viq854.github.com/bwbble.Contact: serafim@cs.stanford.edu

Alternative splicing is a core biological process that enables profound and essential diversification of gene function. Short-read RNA sequencing approaches fail to resolve RNA isoforms and therefore primarily enable gene expression measurements -an isoform unaware representation of the transcriptome. Conversely, full-length RNA sequencing using long-read technologies are able to capture complete transcript isoforms, but their utility is deeply constrained due to throughput limitations. Here, we introduce MAS-ISO-seq, a technique for programmably concatenating cDNAs into single molecules optimal for long-read sequencing, boosting the throughput >15 fold to nearly 40 million cDNA reads per run on the Sequel IIe sequencer. We validated unambiguous isoform assignment with MAS-ISO-seq using a synthetic RNA isoform library and applied this approach to single-cell RNA sequencing of tumor-infiltrating T cells. Results demonstrated a >30 fold boosted discovery of differentially spliced genes and robust cell clustering, as well as canonical PTPRC splicing patterns across T cell subpopulations and the concerted expression of the associated hnRNPLL splicing factor. Methods such as MAS-ISO-seq will drive discovery of novel isoforms and the transition from gene expression to transcript isoform expression analyses. MainWhile RNA sequencing has dramatically accelerated our understanding of biology, accurate quantification and discovery of RNA isoforms, especially at single-cell resolution, remains a steep challenge 1 . Alternative splicing is a core regulatory process that modulates the structure, expression, and localization of proteins through differential exon and/or UTR splicing during transcript maturation in eukaryotes. Beyond being an integral component of cellular/organismal development and homeostatic maintenance, alternative splicing is implicated in a wide range of pathologies with hallmark isoforms being linked to cardiovascular, neurological, and immunological diseases 2,3 . Additionally, mutated and/or dysregulated splicing factors make up a major class of phenotypic alterations associated with tumor progression and therapeutic resistance 4 .

Programmers who need high performance currently rely on low-level, architecture-specific programming models (e.g. OpenMP for CMPs, CUDA for GPUs, MPI for clusters). Performance optimization with these frameworks usually requires expertise in the specific programming model and a deep understanding of the target architecture. Domain-specific languages (DSLs) are a promising alternative, allowing compilers to map problem-specific abstractions directly to low-level architecture-specific programming models. However, developing DSLs is difficult, and using multiple DSLs together in a single application is even harder because existing compiled solutions do not compose together. In this paper, we present four new performance-oriented DSLs developed with Delite, an extensible DSL compilation framework. We demonstrate new techniques to compose compiled DSLs embedded in a common backend together in a single program and show that generic optimizations can be applied across the different DSL sections. Our new DSLs are implemented with a small number of reusable components (less than 9 parallel operators total) and still achieve performance up to 125x better than library implementations and at worst within 30% of optimized stand-alone DSLs. The DSLs retain good performance when composed together, and applying cross-DSL optimizations results in up to an additional 1.82x improvement.

Alternative splicing is a core biological process that enables profound and essential diversification of gene function. Short-read RNA sequencing approaches fail to resolve RNA isoforms and therefore primarily enable gene expression measurements - an isoform unaware representation of the transcriptome. Conversely, full-length RNA sequencing using long-read technologies are able to capture complete transcript isoforms, but their utility is deeply constrained due to throughput limitations. Here, we introduce MAS-ISO-seq, a technique for programmably concatenating cDNAs into single molecules optimal for long-read sequencing, boosting the throughput >15 fold to nearly 40 million cDNA reads per run on the Sequel IIe sequencer. We validated unambiguous isoform assignment with MAS-ISO-seq using a synthetic RNA isoform library and applied this approach to single-cell RNA sequencing of tumor-infiltrating T cells. Results demonstrated a >30 fold boosted discovery of differentially spliced genes and robust cell clustering, as well as canonical PTPRC splicing patterns across T cell subpopulations and the concerted expression of the associated hnRNPLL splicing factor. Methods such as MAS-ISO-seq will drive discovery of novel isoforms and the transition from gene expression to transcript isoform expression analyses.