Pisces: an accurate and versatile variant caller for somatic and germline next-generation sequencing data.

MOTIVATION: Next-generation sequencing technology is transitioning quickly from research labs to clinical settings. The diagnosis and treatment selection for many acquired and autosomal conditions necessitate a method for accurately detecting somatic and germline variants. RESULTS: We have developed Pisces, a rapid, versatile and accurate small-variant calling suite designed for somatic and germline amplicon sequencing applications. Accuracy is achieved by four distinct modules, each incorporating a number of novel algorithmic strategies. AVAILABILITY AND IMPLEMENTATION: Pisces is distributed under an open source license and can be downloaded from https://github.com/Illumina/Pisces. Pisces is available on the BaseSpace™ SequenceHub. It is distributed on Illumina sequencing platforms such as the MiSeq™ and is included in the Praxis™ Extended RAS Panel test which was recently approved by the FDA. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me).

Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms.

SUMMARY: An ultrafast DNA sequence aligner (Isaac Genome Alignment Software) that takes advantage of high-memory hardware (>48 GB) and variant caller (Isaac Variant Caller) have been developed. We demonstrate that our combined pipeline (Isaac) is four to five times faster than BWA + GATK on equivalent hardware, with comparable accuracy as measured by trio conflict rates and sensitivity. We further show that Isaac is effective in the detection of disease-causing variants and can easily/economically be run on commodity hardware. AVAILABILITY: Isaac has an open source license and can be obtained at https://github.com/sequencing.

Expression divergence measured by transcriptome sequencing of four yeast species.

BACKGROUND: The evolution of gene expression is a challenging problem in evolutionary biology, for which accurate, well-calibrated measurements and methods are crucial. RESULTS: We quantified gene expression with whole-transcriptome sequencing in four diploid, prototrophic strains of Saccharomyces species grown under the same condition to investigate the evolution of gene expression. We found that variation in expression is gene-dependent with large variations in each gene's expression between replicates of the same species. This confounds the identification of genes differentially expressed across species. To address this, we developed a statistical approach to establish significance bounds for inter-species differential expression in RNA-Seq data based on the variance measured across biological replicates. This metric estimates the combined effects of technical and environmental variance, as well as Poisson sampling noise by isolating each component. Despite a paucity of large expression changes, we found a strong correlation between the variance of gene expression change and species divergence (R² = 0.90). CONCLUSION: We provide an improved methodology for measuring gene expression changes in evolutionary diverged species using RNA Seq, where experimental artifacts can mimic evolutionary effects.GEO Accession Number: GSE32679.

A comprehensive map of mobile element insertion polymorphisms in humans.

As a consequence of the accumulation of insertion events over evolutionary time, mobile elements now comprise nearly half of the human genome. The Alu, L1, and SVA mobile element families are still duplicating, generating variation between individual genomes. Mobile element insertions (MEI) have been identified as causes for genetic diseases, including hemophilia, neurofibromatosis, and various cancers. Here we present a comprehensive map of 7,380 MEI polymorphisms from the 1000 Genomes Project whole-genome sequencing data of 185 samples in three major populations detected with two detection methods. This catalog enables us to systematically study mutation rates, population segregation, genomic distribution, and functional properties of MEI polymorphisms and to compare MEI to SNP variation from the same individuals. Population allele frequencies of MEI and SNPs are described, broadly, by the same neutral ancestral processes despite vastly different mutation mechanisms and rates, except in coding regions where MEI are virtually absent, presumably due to strong negative selection. A direct comparison of MEI and SNP diversity levels suggests a differential mobile element insertion rate among populations.

BamTools: a C++ API and toolkit for analyzing and managing BAM files.

MOTIVATION: Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging, sorting, etc.). However, the enormous amount of data produced by current sequencing technologies is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research. RESULTS: We introduce a software suite for programmers and end users that facilitates research analysis and data management using BAM files. BamTools provides both the first C++ API publicly available for BAM file support as well as a command-line toolkit. AVAILABILITY: BamTools was written in C++, and is supported on Linux, Mac OSX and MS Windows. Source code and documentation are freely available at http://github.org/pezmaster31/bamtools.

Mapping copy number variation by population-scale genome sequencing.

Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies.

Rapid whole-genome mutational profiling using next-generation sequencing technologies.

Forward genetic mutational studies, adaptive evolution, and phenotypic screening are powerful tools for creating new variant organisms with desirable traits. However, mutations generated in the process cannot be easily identified with traditional genetic tools. We show that new high-throughput, massively parallel sequencing technologies can completely and accurately characterize a mutant genome relative to a previously sequenced parental (reference) strain. We studied a mutant strain of Pichia stipitis, a yeast capable of converting xylose to ethanol. This unusually efficient mutant strain was developed through repeated rounds of chemical mutagenesis, strain selection, transformation, and genetic manipulation over a period of seven years. We resequenced this strain on three different sequencing platforms. Surprisingly, we found fewer than a dozen mutations in open reading frames. All three sequencing technologies were able to identify each single nucleotide mutation given at least 10-15-fold nominal sequence coverage. Our results show that detecting mutations in evolved and engineered organisms is rapid and cost-effective at the whole-genome level using new sequencing technologies. Identification of specific mutations in strains with altered phenotypes will add insight into specific gene functions and guide further metabolic engineering efforts.

Whole-genome sequencing and variant discovery in C. elegans.

Massively parallel sequencing instruments enable rapid and inexpensive DNA sequence data production. Because these instruments are new, their data require characterization with respect to accuracy and utility. To address this, we sequenced a Caernohabditis elegans N2 Bristol strain isolate using the Solexa Sequence Analyzer, and compared the reads to the reference genome to characterize the data and to evaluate coverage and representation. Massively parallel sequencing facilitates strain-to-reference comparison for genome-wide sequence variant discovery. Owing to the short-read-length sequences produced, we developed a revised approach to determine the regions of the genome to which short reads could be uniquely mapped. We then aligned Solexa reads from C. elegans strain CB4858 to the reference, and screened for single-nucleotide polymorphisms (SNPs) and small indels. This study demonstrates the utility of massively parallel short read sequencing for whole genome resequencing and for accurate discovery of genome-wide polymorphisms.

Pyrobayes: an improved base caller for SNP discovery in pyrosequences.

Previously reported applications of the 454 Life Sciences pyrosequencing technology have relied on deep sequence coverage for accurate polymorphism discovery because of frequent insertion and deletion sequence errors. Here we report a new base calling program, Pyrobayes, for pyrosequencing reads. Pyrobayes permits accurate single-nucleotide polymorphism (SNP) calling in resequencing applications, even in shallow read coverage, primarily because it produces more confident base calls than the native base calling program.

The effect of cocaine on the expression of motor activity and conditioned place preference in high and low alcohol-preferring Wistar rats.

Outbred rats show significant variability in their propensity to consume alcohol. These experiments were designed to examine the effect of cocaine on the expression of motor activation or place preference in outbred Wistar rats that consumed either high or low quantities of alcohol. These rats were exposed to a 2-bottle limited access procedure and dichotomized into 2 groups, high (mean 0.91 g/kg/h) and low alcohol consumption (0.36 g/kg/h), and then exposed to repeated daily cocaine, 10 or 20 mg/kg, or saline injections. The low alcohol-consuming rats showed a significant increase in motor behavior to a cocaine challenge across both doses of cocaine, which did not differ from each other. The high alcohol-consuming rats showed a significant increase in motor behavior only at the high dose of cocaine. In Experiment 2 both high and low alcohol-consuming rats were exposed to a conditioned place preference procedure using cocaine 10 mg/kg. High alcohol-consuming rats showed a significant place preference to the cocaine-paired side while low consuming rats did not. The differential effects of cocaine on motor activating behavior and reward obtained in these experiments suggest that those factors determining whether an outbred Wistar rat will consume high or low amounts of alcohol are related, in part, to differential sensitivity of those neural systems underlying the effects of those drugs.

SNP discovery using advanced algorithms and neural networks.

UNLABELLED: Forage is an application which uses two neural networks for detecting single nucleotide polymorphisms (SNPs). Potential SNP candidates are identified in multiple alignments. Each candidate is then represented by a vector of features, which is classified as SNP or monomorphic by the networks. A validated dataset of SNPs was constructed from experimentally verified SNP data and used for network training and method evalutation. AVAILABILITY: The package is available at biobase.biotech.kth.se/forage/

The effect of baclofen alone and in combination with naltrexone on ethanol consumption in the rat.

Naltrexone has been evaluated in preclinical animal models of ethanol consumption and found to be effective in most reports. In clinical use, naltrexone has not proved to be as efficacious in preventing relapse. While naltrexone targets opioid receptors, many other neurotransmitter systems are targeted by ethanol and, to a greater or lesser extent, contribute to modulating ethanol's reinforcing effects. There has been indication that drugs active at the gamma amino butyric acid B (GABAB) receptors can affect the self-administration of many drugs with abuse potential. The experiments reported here evaluated the effect of three doses of baclofen (2.5, 5.0, or 7.5 mg/kg), a GABAB agonist, administered alone or in combination with a single dose of naltrexone (1.0 mg/kg). In Experiment 1, both naltrexone and baclofen, at the two higher doses tested, significantly reduced ethanol consumption in Wistar rats using a limited access procedure on Drug Days 1 and 2. When combined on Drug Days 3 and 4, baclofen/naltrexone was significantly more effective in reducing ethanol consumption than did either drug alone. Neither drug, alone or in combination, had an effect on water consumption. In Experiment 2, both baclofen and naltrexone again significantly reduced ethanol consumption, with no evidence that chronic administration across Drug Days 3 and 4 further reduced consumption compared with Drug Days 1 and 2. The clinical use of multiple pharmacotherapeutic agents in combination may allow for the use of lower doses of individual components, thereby reducing the negative side effects that contribute to lower compliance and higher relapse.

Effect of the combination of naltrexone and acamprosate on alcohol intake in mice.

Both naltrexone and acamprosate have been utilized clinically in recovering alcoholics with varying success. In the experiment reported here the combination of naltrexone and acamprosate was examined in a limited access alcohol model using C57BL/6 mice to determine if there was evidence of additive or synergistic effects. The results of this experiment demonstrate that naltrexone, at the higher dose but not the lower dose, significantly reduced alcohol consumption. When combined with naltrexone, acamprosate reduced alcohol consumption across both doses of naltrexone. This effect was sensitive to both dose and number of days of exposure to the naltrexone/acamprosate combination.

Ethanol consumption improves avoidance learning in rats: role of deprivation interval.

Voluntary oral self-administration of ethanol in rats has been used to model ethanol consumption and abuse in human beings, with contradictory results. The purpose of the current study was to assess the effect of voluntary ethanol consumption on acquisition of a lever press escape/avoidance task in rats. Male Wistar rats were exposed to ethanol in a limited-access procedure, and either 1 day or 10 days after their last ethanol exposure, animals received a 4-h lever press escape/avoidance session. Control animals were not exposed to ethanol at any time. Animals in the 1-day ethanol-deprivation group performed significantly better than did the other two groups with respect to avoidance responding. There were no group differences in number of lever presses during a safety period, a measure of anxiety. Further, we obtained a significant negative correlation between behavioral performance and change in ethanol consumption after the escape/avoidance session, as well as a significant positive correlation between baseline ethanol consumption and avoidance performance. Results are discussed in terms of the potential neural mediators of the improved avoidance effect in animals in the 1-day ethanol-deprivation group.

The relationship between cocaine-induced increases in NAC1 and behavioral sensitization.

Repeated exposure to cocaine can cause long-term behavioral changes in mammals, including an augmented locomotor response known as behavioral sensitization. A major goal of research is the identification of molecules associated with these behaviors. NAC1, a member of the POZ/BTB transcription factor family, exhibited increased mRNA levels in the nucleus accumbens of the rat weeks after cocaine use. NAC1 exists as two isoforms, each demonstrating the ability to inhibit transcription, but to different extents. The present experiments examined the time course for both NAC1 isoforms after five consecutive days of systemic cocaine administration in male rats. Tissues were collected from several central nervous system regions and underwent Western blot analysis. There was significantly greater expression of the long isoform, lNAC1 (cocaine 1.341+/-0.641; saline 1+/-0.321; P=.044), and the short isoform, sNAC1 (cocaine 3.038+/-2.816; saline 1+/-0.720; P=.001), in the nucleus accumbens of cocaine-treated rats. The olfactory tubercle also showed a significant increase, but only in sNAC1 expression and at only one time period. No other significant differences were observed for either isoform of NAC1 in any other brain region. The expression of lNAC1 exhibited an inverse relationship with behavioral sensitization in rats 1-3 months following repeated cocaine injections predicting approximately 40% of the variance in the behavior variables (R(2)=.387; and P=.031 for distance and P=.025 for ambulatory count). These results indicate that NAC1 expression is increased for a period of several months after chronic cocaine exposure. Furthermore, these data suggest that NAC1 may function as an endogenous inhibitor of behavioral sensitization. NAC1 represents a target for future studies examining cocaine-induced behavioral changes.

A comparison of the effects of 6-beta naltrexol and naltrexone on the consumption of ethanol or sucrose using a limited-access procedure in rats.

We recently reported that 6-beta naltrexol, the major metabolite of naltrexone in humans, reduced ethanol consumption in rats. Two new experiments were designed to compare 6-beta naltrexol and naltrexone across three dose levels on an ethanol or sucrose baseline using a limited-access procedure in Wistar rats. The results of Experiment 1 showed that both 6-beta naltrexol and naltrexone reduced ethanol consumption across a range of doses. An in vivo assay showed that naltrexone was approximately 25 times more potent than 6-beta naltrexol at comparable ED50 doses. In addition, there was no indication of systematic development of tolerance to the effect of either drug across the 4 days of drug administration. In Experiment 2, both 6-beta naltrexol and naltrexone reduced the consumption of a sucrose solution using a limited-access procedure. The implications of these data for the development of pharmacotherapeutic agents capable of reducing drinking in recovering alcoholics are discussed.

Effect of naltrexone on oral consumption of concurrently available ethanol and cocaine in the rat.

Comorbid abuse of and dependency on multiple drugs is a common occurrence clinically. We have developed an animal model that provides rats with the opportunity to choose, through oral consumption, between concurrently available ethanol and cocaine with water also available. This provides the ability to screen for the effectiveness of potential pharmacotherapeutic agents on the baseline consumption of both drugs. We used this animal model to evaluate the effects of naltrexone, at doses of 0, 1.0, 3.0, and 10.0 mg/kg, on concurrent oral consumption of ethanol and cocaine solutions. Naltrexone at all doses significantly reduced both consumption of and preference for ethanol. Consumption of both cocaine and water was unaffected by naltrexone, supporting the suggestion that the effects of naltrexone were selective for ethanol. These findings support the suggestion that ethanol and cocaine act on different central reward pathways. The implications of these findings for the clinical use of naltrexone in populations with comorbid ethanol and cocaine abuse are discussed.