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  • Articles  (22)
  • Oxford University Press  (19)
  • Society of Geomagnetism and Earth, Planetary and Space Sciences  (3)
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  • Articles  (22)
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  • 1
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    Component-wise gradient boosting and false discovery control in survival analysis with high-dimensional covariates (2015)
    Oxford University Press
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    Publication Date: 2015-12-18
    Description: Motivation: Technological advances that allow routine identification of high-dimensional risk factors have led to high demand for statistical techniques that enable full utilization of these rich sources of information for genetics studies. Variable selection for censored outcome data as well as control of false discoveries (i.e. inclusion of irrelevant variables) in the presence of high-dimensional predictors present serious challenges. This article develops a computationally feasible method based on boosting and stability selection. Specifically, we modified the component-wise gradient boosting to improve the computational feasibility and introduced random permutation in stability selection for controlling false discoveries. Results: We have proposed a high-dimensional variable selection method by incorporating stability selection to control false discovery. Comparisons between the proposed method and the commonly used univariate and Lasso approaches for variable selection reveal that the proposed method yields fewer false discoveries. The proposed method is applied to study the associations of 2339 common single-nucleotide polymorphisms (SNPs) with overall survival among cutaneous melanoma (CM) patients. The results have confirmed that BRCA2 pathway SNPs are likely to be associated with overall survival, as reported by previous literature. Moreover, we have identified several new Fanconi anemia (FA) pathway SNPs that are likely to modulate survival of CM patients. Availability and implementation: The related source code and documents are freely available at https://sites.google.com/site/bestumich/issues . Contact: yili@umich.edu
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    A Bayesian framework for de novo mutation calling in parents-offspring trios (2015)
    Oxford University Press
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    Publication Date: 2015-04-28
    Description: Motivation: Spontaneous ( de novo ) mutations play an important role in the disease etiology of a range of complex diseases. Identifying de novo mutations (DNMs) in sporadic cases provides an effective strategy to find genes or genomic regions implicated in the genetics of disease. High-throughput next-generation sequencing enables genome- or exome-wide detection of DNMs by sequencing parents-proband trios. It is challenging to sift true mutations through massive amount of noise due to sequencing error and alignment artifacts. One of the critical limitations of existing methods is that for all genomic regions the same pre-specified mutation rate is assumed, which has a significant impact on the DNM calling accuracy. Results: In this study, we developed and implemented a novel Bayesian framework for DNM calling in trios (TrioDeNovo), which overcomes these limitations by disentangling prior mutation rates from evaluation of the likelihood of the data so that flexible priors can be adjusted post-hoc at different genomic sites. Through extensively simulations and application to real data we showed that this new method has improved sensitivity and specificity over existing methods, and provides a flexible framework to further improve the efficiency by incorporating proper priors. The accuracy is further improved using effective filtering based on sequence alignment characteristics. Availability and implementation: The C++ source code implementing TrioDeNovo is freely available at https://medschool.vanderbilt.edu/cgg . Contact: bingshan.li@vanderbilt.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 3
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    A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis (2015)
    Oxford University Press
    Details
    Publication Date: 2015-04-28
    Description: Motivation: A major focus of current sequencing studies for human genetics is to identify rare variants associated with complex diseases. Aside from reduced power of detecting associated rare variants, controlling for population stratification is particularly challenging for rare variants. Transmission/disequilibrium tests (TDT) based on family designs are robust to population stratification and admixture, and therefore provide an effective approach to rare variant association studies to eliminate spurious associations. To increase power of rare variant association analysis, gene-based collapsing methods become standard approaches for analyzing rare variants. Existing methods that extend this strategy to rare variants in families usually combine TDT statistics at individual variants and therefore lack the flexibility of incorporating other genetic models. Results: In this study, we describe a haplotype-based framework for group-wise TDT (gTDT) that is flexible to encompass a variety of genetic models such as additive, dominant and compound heterozygous (CH) (i.e. recessive) models as well as other complex interactions. Unlike existing methods, gTDT constructs haplotypes by transmission when possible and inherently takes into account the linkage disequilibrium among variants. Through extensive simulations we showed that type I error was correctly controlled for rare variants under all models investigated, and this remained true in the presence of population stratification. Under a variety of genetic models, gTDT showed increased power compared with the single marker TDT. Application of gTDT to an autism exome sequencing data of 118 trios identified potentially interesting candidate genes with CH rare variants. Availability and implementation: We implemented gTDT in C++ and the source code and the detailed usage are available on the authors’ website ( https://medschool.vanderbilt.edu/cgg ). Contact: bingshan.li@vanderbilt.edu or wei.chen@chp.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 4
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    p73 G4C14-to-A4T14 gene polymorphism and interaction with p53 exon 4 Arg72Pro on cancer susceptibility: a meta-analysis of the literature (2012)
    Oxford University Press
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    Publication Date: 2012-04-25
    Description: The p 73 gene (1p36–33) is involved in cancer development through cell growth inhibition by inducing apoptosis in a p 53-like manner. The p 73 G4C14-to-A4T14 dinucleotide polymorphism, consisting of two single-nucleotide polymorphisms in the non-coding region of exon 2 that are in complete linkage disequilibrium, has been extensively studied in association with cancer risk. We performed a meta-analysis of published studies that examined the association between this p 73 G4C14-to-A4T14 polymorphism and cancer by searching for relevant studies on Medline and Embase up to February 28, 2010. Pooling data from 19 case–control studies that included 6510 cancer cases and 5711 controls, we found that carriers of the p 73 G4C14-to-A4T14 homozygous variant genotype (AT/AT) had an increased global risk of cancer [odds ratio (OR) = 1.30, 95% confidence interval (CI), 1.03–1.65]. There was no evidence of an effect modification of p 73 AT/AT by age, gender, ethnicity or smoking status in subgroup analyses; however, a 1.35-fold statistically significant increased risk was found among individuals 〈55 years old. In case-only analysis, the homozygous p 73 G4C14-to-A4T14 variant of p 73 genotype was associated with the presence of the p 53 exon 4 Arg72Pro allele (OR = 1.30, 95% CI, 1.02–1.64), which is suggestive of a biological interaction between the two genes in carcinogenesis. In conclusion, the p 73 G4C14-to-A4T14 homozygous variant genotype might be a risk factor for cancer, especially in combination with the p 53 exon 4 Arg72Pro polymorphism. Further studies looking at p 73 G4C14-to-A4T14 and p 53 exon 4 Arg72Pro interaction are required to support our findings.
    Print ISSN: 0267-8357
    Electronic ISSN: 1464-3804
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 5
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    Global regulation of gene expression by OxyR in an important human opportunistic pathogen (2012)
    Oxford University Press
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    Publication Date: 2012-05-23
    Description: Most bacteria control oxidative stress through the H 2 O 2 -responsive transactivator OxyR, a member of the LTTR family (LysR Type Transcriptional Regulators), which activates the expression of defensive genes such as those encoding catalases, alkyl hydroperoxide reductases and superoxide dismutases. In the human opportunistic pathogen Pseudomonas aeruginosa , OxyR positively regulates expression of the oxidative stress response genes katA , katB , ahpB and ahpCF . To identify additional targets of OxyR in P . aeruginosa PAO1, we performed chromatin immunoprecipitation in combination with whole genome tiling array analyses (ChIP-chip). We detected 56 genes including all the previously identified defensive genes and a battery of novel direct targets of OxyR. Electrophoretic mobility shift assays (EMSAs) for selected newly identified targets indicated that ~70% of those were bound by purified oxidized OxyR and their regulation was confirmed by quantitative real-time polymerase chain reaction. Furthermore, a thioredoxin system was identified to enzymatically reduce OxyR under oxidative stress. Functional classification analysis showed that OxyR controls a core regulon of oxidative stress defensive genes, and other genes involved in regulation of iron homeostasis ( pvdS ), quorum-sensing ( rsaL ), protein synthesis ( rpsL ) and oxidative phosphorylation ( cyoA and snr1 ). Collectively, our results indicate that OxyR is involved in oxidative stress defense and regulates other aspects of cellular metabolism as well.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Rapid Creation of Forward-Genetics Tools for C. briggsae Using TALENs: Lessons for Nonmodel Organisms (2014)
    Oxford University Press
    Details
    Publication Date: 2014-01-23
    Description: Although evolutionary studies of gene function often rely on RNA interference, the ideal approach would use reverse genetics to create null mutations for cross-species comparisons and forward genetics to identify novel genes in each species. We have used transcription activator-like effector nucleases (TALENs) to facilitate both approaches in Caenorhabditis nematodes. First, by combining golden gate cloning and TALEN technology, we can induce frameshifting mutations in any gene. Second, by combining this approach with bioinformatics we can predict and create the resources needed for forward genetic analysis in species like Caenorhabditis briggsae . Although developing genetic model organisms used to require years to isolate marker mutations, balancers, and tools, with TALENs, these reagents can now be produced in months. Furthermore, the analysis of nonsense mutants in related model organisms allows a directed approach for making these markers and tools. When used together, these methods could simplify the adaptation of other organisms for forward and reverse genetics.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    A New and Effective Approach to GML Documents Compression (2014)
    Oxford University Press
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    Publication Date: 2014-10-28
    Description: Geography Markup Language (GML) has become a de facto standard for encoding and exchanging geographic data. Usually, GML documents are of huge size due to its verbose structures and textual data, hence it is very costly to store and transit them. In this paper, we propose an effective pattern-based approach to compressing GML documents. First, a tree-structured pattern from the GML document under compression is extracted. Then, a tree automaton for matching the document against the extracted pattern is constructed. While doing compression, the GML document is matched against the pattern to generate a bits-stream that represents the difference between the document's structure and the extracted pattern. Meanwhile, we separate document structure from document content and group document content into different streams according to the tags. Spatial coordinate data are compressed by delta encoding. Finally, the extracted pattern, all streams and encodings are forwarded to a text compressor gzip. Extensive experiments on real GML documents show that the proposed approach outperforms the existing XML and GML compression approaches in compression ratio, while keeping an acceptable compression efficiency.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 8
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    Human interactome resource and gene set linkage analysis for the functional interpretation of biologically meaningful gene sets (2013)
    Oxford University Press
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    Publication Date: 2013-07-26
    Description: Motivation: A molecular interaction network can be viewed as a network in which genes with related functions are connected. Therefore, at a systems level, connections between individual genes in a molecular interaction network can be used to infer the collective functional linkages between biologically meaningful gene sets. Results: We present the human interactome resource and the gene set linkage analysis (GSLA) tool for the functional interpretation of biologically meaningful gene sets observed in experiments. GSLA determines whether an observed gene set has significant functional linkages to established biological processes. When an observed gene set is not enriched by known biological processes, traditional enrichment-based interpretation methods cannot produce functional insights, but GSLA can still evaluate whether those genes work in concert to regulate specific biological processes, thereby suggesting the functional implications of the observed gene set. The quality of human interactome resource and the utility of GSLA are illustrated with multiple assessments. Availability: http://www.cls.zju.edu.cn/hir/ Contact: xinchen@zju.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 9
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    Genome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-25
    Description: Aiming to identify novel genetic loci for pigmentation and skin cancer, we conducted a series of genome-wide association studies on hair color, eye color, number of sunburns, tanning ability and number of non-melanoma skin cancers (NMSCs) among 10 183 European Americans in the discovery stage and 4504 European Americans in the replication stage (for eye color, 3871 males in the discovery stage and 2496 males in the replication stage). We targeted novel chromosome regions besides the known ones for replication. As a result, we identified a new region downstream of the EDNRB gene on 13q22 associated with hair color and the strongest association was the single-nucleotide polymorphism (SNP) rs975739 ( P = 2.4 x 10 –14 ; P = 5.4 x 10 –9 in the discovery set and P = 1.2 x 10 –6 in the replication set). Using blue, intermediate (including green) and brown eye colors as co-dominant outcomes, we identified the SNP rs3002288 in VASH2 on 1q32.3 associated with brown eye ( P = 7.0 x 10 –8 ; P = 5.3 x 10 –5 in the discovery set and P = 0.02 in the replication set). Additionally, we identified a significant interaction between the SNPs rs7173419 and rs12913832 in the OCA2 gene region on brown eye color ( P -value for interaction = 3.8 x 10 –3 ). As for the number of NMSCs, we identified two independent SNPs on chr6 and one SNP on chromosome 14: rs12203592 in IRF4 ( P = 7.2 x 10 –14 ; P = 1.8 x 10 –8 in the discovery set and P = 6.7 x 10 –7 in the replication set), rs12202284 between IRF4 and EXOC2 ( P = 5.0 x 10 –8 ; P = 6.6 x 10 –7 in the discovery set and P = 3.0 x 10 –3 in the replication set) and rs8015138 upstream of GNG2 ( P = 6.6 x 10 –8 ; P = 5.3 x 10 –7 in the discovery set and P = 0.01 in the replication set).
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 10
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    PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualization tool (2015)
    Oxford University Press
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    Publication Date: 2015-01-10
    Description: : Protein function prediction (PFP) is an automated function prediction method that predicts Gene Ontology (GO) annotations for a protein sequence using distantly related sequences and contextual associations of GO terms. Extended similarity group (ESG) is another GO prediction algorithm that makes predictions based on iterative sequence database searches. Here, we provide interactive web servers for the PFP and ESG algorithms that are equipped with an effective visualization of the GO predictions in a hierarchical topology. Availability : PFP/ESG servers are freely available at http://kiharalab.org/web/pfp.php and http://kiharalab.org/web/esg.php , or access both at http://kiharalab.org/pfp_esg.php Contact : dkihara@purdue.edu Supplementary information : Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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