Declarative symbolic pure-logic model checking

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.Includes bibliographical references (p. 173-181).Model checking, a technique for findings errors in systems, involves building a formal model that describes possible system behaviors and correctness conditions, and using a tool to search for model behaviors violating correctness properties. Existing model checkers are well-suited for analyzing control-intensive algorithms (e.g. network protocols with simple node state). Many important analyses, however, fall outside the capabilities of existing model checkers. Examples include checking algorithms with complex state, distributed algorithms over all network topologies, and highly declarative models. This thesis addresses the problem of building an efficient model checker that overcomes these limitations. The work builds on Alloy, a relational modeling language. Previous work has defined the language and shown that it can be analyzed by translation to SAT. The primary contributions of this thesis include: a modeling paradigm for describing complex structures in Alloy; significant improvements in scalability of the analyzer; and improvements in usability of the analyzer via addition of a debugger for over constraints. Together, these changes make model-checking practical for important new classes of analyses. While the work was done in the context of Alloy, some techniques generalize to other verification tools.by Ilya A. Shlyakhter.S.M

Identification and Functional Validation of the Novel Antimalarial Resistance Locus PF10_0355 in Plasmodium falciparum

The Plasmodium falciparum parasite's ability to adapt to environmental pressures, such as the human immune system and antimalarial drugs, makes malaria an enduring burden to public health. Understanding the genetic basis of these adaptations is critical to intervening successfully against malaria. To that end, we created a high-density genotyping array that assays over 17,000 single nucleotide polymorphisms (~1 SNP/kb), and applied it to 57 culture-adapted parasites from three continents. We characterized genome-wide genetic diversity within and between populations and identified numerous loci with signals of natural selection, suggesting their role in recent adaptation. In addition, we performed a genome-wide association study (GWAS), searching for loci correlated with resistance to thirteen antimalarials; we detected both known and novel resistance loci, including a new halofantrine resistance locus, PF10_0355. Through functional testing we demonstrated that PF10_0355 overexpression decreases sensitivity to halofantrine, mefloquine, and lumefantrine, but not to structurally unrelated antimalarials, and that increased gene copy number mediates resistance. Our GWAS and follow-on functional validation demonstrate the potential of genome-wide studies to elucidate functionally important loci in the malaria parasite genome.Bill & Melinda Gates FoundationEllison Medical FoundationExxon Mobil FoundationFogarty International CenterNational Institute of Allergy and Infectious Diseases (U.S.)Burroughs Wellcome FundDavid & Lucile Packard FoundationNational Science Foundation (U.S.). Graduate Research Fellowship Progra

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.Organismic and Evolutionary Biolog

ALLPATHS: De novo assembly of whole-genome shotgun microreads

New DNA sequencing technologies deliver data at dramatically lower costs but demand new analytical methods to take full advantage of the very short reads that they produce. We provide an initial, theoretical solution to the challenge of de novo assembly from whole-genome shotgun “microreads.” For 11 genomes of sizes up to 39 Mb, we generated high-quality assemblies from 80× coverage by paired 30-base simulated reads modeled after real Illumina-Solexa reads. The bacterial genomes of Campylobacter jejuni and Escherichia coli assemble optimally, yielding single perfect contigs, and larger genomes yield assemblies that are highly connected and accurate. Assemblies are presented in a graph form that retains intrinsic ambiguities such as those arising from polymorphism, thereby providing information that has been absent from previous genome assemblies. For both C. jejuni and E. coli, this assembly graph is a single edge encompassing the entire genome. Larger genomes produce more complicated graphs, but the vast majority of the bases in their assemblies are present in long edges that are nearly always perfect. We describe a general method for genome assembly that can be applied to all types of DNA sequence data, not only short read data, but also conventional sequence reads

A global reference for human genetic variation

The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.Wellcome Trust (London, England) (Core Award 090532/Z/09/Z)Wellcome Trust (London, England) (Senior Investigator Award 095552/Z/11/Z )Wellcome Trust (London, England) (WT095908)Wellcome Trust (London, England) (WT109497)Wellcome Trust (London, England) (WT098051)Wellcome Trust (London, England) (WT086084/Z/08/Z)Wellcome Trust (London, England) (WT100956/Z/13/Z )Wellcome Trust (London, England) (WT097307)Wellcome Trust (London, England) (WT0855322/Z/08/Z )Wellcome Trust (London, England) (WT090770/Z/09/Z )Wellcome Trust (London, England) (Major Overseas program in Vietnam grant 089276/Z.09/Z)Medical Research Council (Great Britain) (grant G0801823)Biotechnology and Biological Sciences Research Council (Great Britain) (grant BB/I02593X/1)Biotechnology and Biological Sciences Research Council (Great Britain) (grant BB/I021213/1)Zhongguo ke xue ji shu qing bao yan jiu suo. Office of 863 Programme of China (2012AA02A201)National Basic Research Program of China (2011CB809201)National Basic Research Program of China (2011CB809202)National Basic Research Program of China (2011CB809203)National Natural Science Foundation of China (31161130357)Shenzhen Municipal Government of China (grant ZYC201105170397A)Canadian Institutes of Health Research (grant 136855)Quebec Ministry of Economic Development, Innovation, and Exports (PSR-SIIRI-195)Germany. Bundesministerium für Bildung und Forschung (0315428A)Germany. Bundesministerium für Bildung und Forschung (01GS08201)Germany. Bundesministerium für Bildung und Forschung (BMBF-EPITREAT grant 0316190A)Deutsche Forschungsgemeinschaft (Emmy Noether Grant KO4037/1-1)Beatriu de Pinos Program (2006 BP-A 10144)Beatriu de Pinos Program (2009 BP-B 00274)Spanish National Institute for Health (grant PRB2 IPT13/0001-ISCIII-SGEFI/FEDER)Japan Society for the Promotion of Science (fellowship number PE13075)Marie Curie Actions Career Integration (grant 303772)Fonds National Suisse del la Recherche, SNSF, Scientifique (31003A_130342)National Center for Biotechnology Information (U.S.) (U54HG3067)National Center for Biotechnology Information (U.S.) (U54HG3273)National Center for Biotechnology Information (U.S.) (U01HG5211)National Center for Biotechnology Information (U.S.) (U54HG3079)National Center for Biotechnology Information (U.S.) (R01HG2898)National Center for Biotechnology Information (U.S.) (R01HG2385)National Center for Biotechnology Information (U.S.) (RC2HG5552)National Center for Biotechnology Information (U.S.) (U01HG6513)National Center for Biotechnology Information (U.S.) (U01HG5214)National Center for Biotechnology Information (U.S.) (U01HG5715)National Center for Biotechnology Information (U.S.) (U01HG5718)National Center for Biotechnology Information (U.S.) (U01HG5728)National Center for Biotechnology Information (U.S.) (U41HG7635)National Center for Biotechnology Information (U.S.) (U41HG7497)National Center for Biotechnology Information (U.S.) (R01HG4960)National Center for Biotechnology Information (U.S.) (R01HG5701)National Center for Biotechnology Information (U.S.) (R01HG5214)National Center for Biotechnology Information (U.S.) (R01HG6855)National Center for Biotechnology Information (U.S.) (R01HG7068)National Center for Biotechnology Information (U.S.) (R01HG7644)National Center for Biotechnology Information (U.S.) (DP2OD6514)National Center for Biotechnology Information (U.S.) (DP5OD9154)National Center for Biotechnology Information (U.S.) (R01CA166661)National Center for Biotechnology Information (U.S.) (R01CA172652)National Center for Biotechnology Information (U.S.) (P01GM99568)National Center for Biotechnology Information (U.S.) (R01GM59290)National Center for Biotechnology Information (U.S.) (R01GM104390)National Center for Biotechnology Information (U.S.) (T32GM7790)National Center for Biotechnology Information (U.S.) (P01GM99568)National Center for Biotechnology Information (U.S.) (R01HL87699)National Center for Biotechnology Information (U.S.) (R01HL104608)National Center for Biotechnology Information (U.S.) (T32HL94284)National Center for Biotechnology Information (U.S.) (HHSN268201100040C)National Center for Biotechnology Information (U.S.) (HHSN272201000025C)Lundbeck Foundation (grant R170-2014-1039Simons Foundation (SFARI award SF51)National Science Foundation (U.S.) (Research Fellowship DGE-1147470

Natural Selection in a Bangladeshi Population from the Cholera-Endemic Ganges River Delta

As an ancient disease with high fatality, cholera has likely exerted strong selective pressure on affected human populations. We performed a genome-wide study of natural selection in a population from the Ganges River Delta, the historic geographic epicenter of cholera. We identified 305 candidate selected regions using the composite of multiple signals (CMS) method. The regions were enriched for potassium channel genes involved in cyclic adenosine monophosphate–mediated chloride secretion and for components of the innate immune system involved in nuclear factor κB (NF-κB) signaling. We demonstrate that a number of these strongly selected genes are associated with cholera susceptibility in two separate cohorts. We further identify repeated examples of selection and association in an NF-κB/inflammasome–dependent pathway that is activated in vitro by Vibrio cholerae. Our findings shed light on the genetic basis of cholera resistance in a population from the Ganges River Delta and present a promising approach for identifying genetic factors influencing susceptibility to infectious diseases.Organismic and Evolutionary Biolog

Identifying Recent Adaptations in Large-Scale Genomic Data

Summary: Although several hundred regions of the human genome harbor signals of positive natural selection, few of the relevant adaptive traits and variants have been elucidated. Using full-genome sequence variation from the 1000 Genomes (1000G) Project and the composite of multiple signals (CMS) test, we investigated 412 candidate signals and leveraged functional annotation, protein structure modeling, epigenetics, and association studies to identify and extensively annotate candidate causal variants. The resulting catalog provides a tractable list for experimental follow-up; it includes 35 high-scoring nonsynonymous variants, 59 variants associated with expression levels of a nearby coding gene or lincRNA, and numerous variants associated with susceptibility to infectious disease and other phenotypes. We experimentally characterized one candidate nonsynonymous variant in Toll-like receptor 5 (TLR5) and show that it leads to altered NF-κB signaling in response to bacterial flagellin.Organismic and Evolutionary Biolog

Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum.

The Plasmodium falciparum parasite's ability to adapt to environmental pressures, such as the human immune system and antimalarial drugs, makes malaria an enduring burden to public health. Understanding the genetic basis of these adaptations is critical to intervening successfully against malaria. To that end, we created a high-density genotyping array that assays over 17,000 single nucleotide polymorphisms (∼ 1 SNP/kb), and applied it to 57 culture-adapted parasites from three continents. We characterized genome-wide genetic diversity within and between populations and identified numerous loci with signals of natural selection, suggesting their role in recent adaptation. In addition, we performed a genome-wide association study (GWAS), searching for loci correlated with resistance to thirteen antimalarials; we detected both known and novel resistance loci, including a new halofantrine resistance locus, PF10_0355. Through functional testing we demonstrated that PF10_0355 overexpression decreases sensitivity to halofantrine, mefloquine, and lumefantrine, but not to structurally unrelated antimalarials, and that increased gene copy number mediates resistance. Our GWAS and follow-on functional validation demonstrate the potential of genome-wide studies to elucidate functionally important loci in the malaria parasite genome

Identifying Recent Adaptations in Large-Scale Genomic Data

Although several hundred regions of the human genome harbor signals of positive natural selection, few of the relevant adaptive traits and variants have been elucidated. Using full-genome sequence variation from the 1000 Genomes (1000G) Project and the composite of multiple signals (CMS) test, we investigated 412 candidate signals and leveraged functional annotation, protein structure modeling, epigenetics, and association studies to identify and extensively annotate candidate causal variants. The resulting catalog provides a tractable list for experimental follow-up; it includes 35 high-scoring nonsynonymous variants, 59 variants associated with expression levels of a nearby coding gene or lincRNA, and numerous variants associated with susceptibility to infectious disease and other phenotypes. We experimentally characterized one candidate nonsynonymous variant in Toll-like receptor 5 (TLR5) and show that it leads to altered NF-κB signaling in response to bacterial flagellin.National Institute of General Medical Sciences (U.S.) (T32GM007753