Memory-efficient Alignment Research Articles

Cancer genomics: new software tools making sequencing more accessible.

Next-generation sequencing transforms today’s cancer research Next-generation sequencing (NGS) technologies can parallelize sequencing processes and produce millions of short-read sequences concurrently. The advent of NGS technologies has transformed today’s cancer genome research by providing an unbiased and comprehensive method of detecting somatic genome alterations [1]. The application of NGS technologies, through whole-genome, -exome and -transcriptome approaches has led to the discovery of mutated genes that drive oncogenic phenotypes in tumors. In a recent The Cancer Genome Atlas (TCGA) Pan-Cancer effort [2], 127 mutated driver genes were identified from 3281 tumors across 12 tumor types. These cancer drivers converged on several well-known pathways such as cell cycle and MAPK pathways. Interestingly, these drivers are also involved in cellular processes in cancers that have previously been less well characterized such as histone modification, RNA splicing, cellular metabolism and proteolysis. Mutations in transcription factors are more tissue specific, whereas mutations in histone modifiers are shared among multiple cancer types. The average number of driver mutations varies across tumor types and most individual tumors have two to six mutations [2]. Generally, larger numbers of driver mutations are involved in tumors with high levels of background mutations [3]. For example, most squamous cell lung carcinomas are attributed to life-long tobacco exposure. Carcinogens from tobacco exposure can cause a broad spectrum of DNA lesions on the genome, and this increases the chance that mutations conferring a small growth advantage to cells are selected in the lung microenvironment. Many such mutations with small effects can accumulate in a specific group of cells over time and collectively lead to carcinogenesis. This is in contrast to hematologic cancers, where fewer driver mutations (with potentially large effects) are observed in tumors with low background mutations. Driver genes are promising drug targets and their discovery has the potential to revolutionize personalized gene-targeted treatments that guide patient therapy according to the genomic profile of the tumor. The battle of Dr Lukas Wartman at Washington University in St Louis (WUSTL; MO, USA) against leukemia is a prime example of the promise of personalized medicine [4]. When Wartman had relapsed a second time, his colleagues at WUSTL sequenced the entire genome of DNA and RNA from his cancerous cells. His RNA sequencing showed that a gene called FLT3 was unexpectedly overproduced by his cancer cells. It so happens that the drug Sutent, previously approved for treating advanced kidney cancer, effectively inhibits FLT3. Sutent was prescribed to Wartman, and his leukemia was in remission 2 weeks later. In next decade, we will witness many such cases come to the forefront of cancer treatment and soon realize the promise of personalized medicines purred by advances in cancer genomics and associated drug development. part of Editorial

Zinc Deficiency Impacts CO2 Assimilation and Disrupts Copper Homeostasis in Chlamydomonas reinhardtii

Zinc is an essential nutrient because of its role in catalysis and in protein stabilization, but excess zinc is deleterious. We distinguished four nutritional zinc states in the alga Chlamydomonas reinhardtii: toxic, replete, deficient, and limited. Growth is inhibited in zinc-limited and zinc-toxic cells relative to zinc-replete cells, whereas zinc deficiency is visually asymptomatic but distinguished by the accumulation of transcripts encoding ZIP family transporters. To identify targets of zinc deficiency and mechanisms of zinc acclimation, we used RNA-seq to probe zinc nutrition-responsive changes in gene expression. We identified genes encoding zinc-handling components, including ZIP family transporters and candidate chaperones. Additionally, we noted an impact on two other regulatory pathways, the carbon-concentrating mechanism (CCM) and the nutritional copper regulon. Targets of transcription factor Ccm1 and various CAH genes are up-regulated in zinc deficiency, probably due to reduced carbonic anhydrase activity, validated by quantitative proteomics and immunoblot analysis of Cah1, Cah3, and Cah4. Chlamydomonas is therefore not able to grow photoautotrophically in zinc-limiting conditions, but supplementation with 1% CO2 restores growth to wild-type rates, suggesting that the inability to maintain CCM is a major consequence of zinc limitation. The Crr1 regulon responds to copper limitation and is turned on in zinc deficiency, and Crr1 is required for growth in zinc-limiting conditions. Zinc-deficient cells are functionally copper-deficient, although they hyperaccumulate copper up to 50-fold over normal levels. We suggest that zinc-deficient cells sequester copper in a biounavailable form, perhaps to prevent mismetallation of critical zinc sites.

G-SNPM - A GPU-based SNP mapping tool

G-SNPM - A GPU-based SNP mapping tool

Filtering with alignment free distances for high throughput DNA reads assembly

Filtering with alignment free distances for high throughput DNA reads assembly

A strategy to reduce technical variability and bias in RNA sequencing data

A strategy to reduce technical variability and bias in RNA sequencing data

A Missense Mutation in Myelin Oligodendrocyte Glycoprotein as a Cause of Familial Narcolepsy with Cataplexy

Narcolepsy is a rare sleep disorder characterized by excessive daytime sleepiness and cataplexy. Familial narcolepsy accounts for less than 10% of all narcolepsy cases. However, documented multiplex families are very rare and causative mutations have not been identified to date. To identify a causative mutation in familial narcolepsy, we performed linkage analysis in the largest ever reported family, which has 12 affected members, and sequenced coding regions of the genome (exome sequencing) of three affected members with narcolepsy and cataplexy. We successfully mapped a candidate locus on chromosomal region 6p22.1 (LOD score ¼ 3.85) by linkage analysis. Exome sequencing identified a missense mutation in the second exon of MOG within the linkage region. A c.398C>G mutation was present in all affected family members but absent in unaffected members and 775 unrelated control subjects. Transient expression of mutant myelin oligodendrocyte glycoprotein (MOG) in mouse oligodendrocytes showed abnormal subcellular localization, suggesting an altered function of the mutant MOG. MOG has recently been linked to various neuropsychiatric disorders and is considered as a key autoantigen in multiple sclerosis and in its animal model, experimental autoimmune encephalitis. Our finding of a pathogenic MOG mutation highlights a major role for myelin and oligodendrocytes in narcolepsy and further emphasizes glial involvement in neurodegeneration and neurobehavioral disorders. [corrected].

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Bowtie: a new ultrafast memory-efficient tool for the alignment of short DNA sequence reads to large genomes.

Memory efficient alignment between RNA sequences and stochastic grammar models of pseudoknots

Stochastic Context-Free Grammars (SCFG) has been shown to be effective in modelling RNA secondary structure for searches. Our previous work (Cai et al., 2003) in Stochastic Parallel Communicating Grammar Systems (SPCGS) has extended SCFG to model RNA pseudoknots. However, the alignment algorithm requires O(n4) memory for a sequence of length n. In this paper, we develop a memory efficient algorithm for sequence-structure alignments including pseudoknots. This new algorithm reduces the memory space requirement from O(n4) to O(n2) without increasing the computation time. Our experiments have shown that this novel approach can achieve excellent performance on searching for RNA pseudoknots.