scholarly journals Emergent populations derived with unsupervised learning of human whole genomes

2018 ◽  
Author(s):  
eMalick G. Njie
Keyword(s):  
Genetic Background ◽  
Disease Gene ◽  
Feature Space ◽  
Gene Identification ◽  
Great Promise ◽  
Whole Genome ◽  
Essential Step ◽  
Whole Genomes ◽  
Human Ancestry ◽  
Uniform Population

AbstractArtificial intelligence (AI) holds great promise to precisely classify human ancestry and the genetic causes of complex diseases. I have constructed an unsupervised machine learning paradigm that examines the whole genome as a hyper-dense, nonlinear, multidimensional feature space. The AI system culminates in 26 neural network neurons each sensitive to a specific heritage that can identify an individual’s component genetic heritages with a top-5 error of <0.5%. Importantly, I observed some populations previously thought to belong to single stratum are composed of multiple strata – for instance Japan is defined as a uniform population using previous methods. I found that the Japanese individuals segregate to two very distinct populations. This work represents an essential step towards understanding the genetic background of patients to enable precision medicine causal disease gene identification.

scholarly journals Patterns of relatedness and genetic diversity inferred from whole genome sequencing of archival blood fluke miracidia (Schistosoma japonicum)

2021 ◽  
Vol 15 (1) ◽  
pp. e0009020
Author(s):  
Zachary L. Nikolakis ◽  
Nicole R. Hales ◽  
Blair W. Perry ◽  
Drew R. Schield ◽  
Laura E. Timm ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Amplification ◽  
Neglected Tropical Diseases ◽  
Genomic Data ◽  
Population Level ◽  
Great Promise ◽  
Whole Genome ◽  
Whole Genomes ◽  
The Cost ◽  
Insight Into

Genomic approaches hold great promise for resolving unanswered questions about transmission patterns and responses to control efforts for schistosomiasis and other neglected tropical diseases. However, the cost of generating genomic data and the challenges associated with obtaining sufficient DNA from individual schistosome larvae (miracidia) from mammalian hosts have limited the application of genomic data for studying schistosomes and other complex macroparasites. Here, we demonstrate the feasibility of utilizing whole genome amplification and sequencing (WGS) to analyze individual archival miracidia. As an example, we sequenced whole genomes of 22 miracidia from 11 human hosts representing two villages in rural Sichuan, China, and used these data to evaluate patterns of relatedness and genetic diversity. We also down-sampled our dataset to test how lower coverage sequencing could increase the cost effectiveness of WGS while maintaining power to accurately infer relatedness. Collectively, our results illustrate that population-level WGS datasets are attainable for individual miracidia and represent a powerful tool for ultimately providing insight into overall genetic diversity, parasite relatedness, and transmission patterns for better design and evaluation of disease control efforts.

Human Gene Mapping and Disease Gene Identification

2007 ◽  
pp. 207-230
Author(s):  
Robert L. Nussbaum ◽  
Roderick R. McInnes ◽  
Huntington F. Willard ◽  
Ada Hamosh
Keyword(s):  
Gene Mapping ◽  
Disease Gene ◽  
Human Gene ◽  
Gene Identification ◽  
Human Gene Mapping

scholarly journals Disease gene identification by using graph kernels and Markov random fields

2014 ◽  
Vol 57 (11) ◽  
pp. 1054-1063 ◽  
Author(s):  
BoLin Chen ◽  
Min Li ◽  
JianXin Wang ◽  
Fang-Xiang Wu
Keyword(s):  
Random Fields ◽  
Markov Random Fields ◽  
Disease Gene ◽  
Gene Identification ◽  
Graph Kernels ◽  
Markov Random

Techniques for the Identification of Genes Involved in Psychiatric Disorders

2005 ◽  
Vol 39 (7) ◽  
pp. 542-549 ◽  
Author(s):  
Ian P. Blair ◽  
Philip B. Mitchell ◽  
Peter R. Schofield
Keyword(s):  
Psychiatric Disorders ◽  
Susceptibility Genes ◽  
Genome Project ◽  
Mental Illnesses ◽  
Gene Identification ◽  
Great Promise ◽  
Psychiatric Genetics ◽  
Biochemical Basis ◽  
Genetic Traits ◽  
The Future

Objective: Most psychiatric disorders are complex genetic traits involving both genetic and environmental risk factors. This paper aims to review the gene identification strategies being applied bymolecular geneticists in their efforts to elucidate the genetic and molecular basis of psychiatric disorders. Future strategies will also be canvassed. Method: The psychiatric genetic literature was reviewed to identify current strategies applied to gene identification, with examples provided where available. The future strategies and applications that will arise from genome projects, including the International Haplotype Mapping Project, are also discussed. Results: Many advances in the techniques of gene discovery, and the increasing resources available, are rapidly being adopted by researchers and applied to the complex problem of identifying susceptibility genes for mental illnesses. Perhaps the single most important advance to date is the Human Genome Project and all that has stemmed from the vast quantity of information that this endeavour has provided. With these technological advances and the massive increase of publicly available genetic resources, several genes have recently been implicated in the susceptibility to psychiatric illnesses including schizophrenia and depression. After many years of fruitless endeavours, these recent reports indicate that the labours of researchers in psychiatric genetics are beginning to show exciting results. Conclusions: Identification of these susceptibility genes holds great promise, with the unravelling of the molecular and biochemical basis of some conditions now being a more realistic and tangible goal. The increasing number of genes being identified augers well for the future treatment of psychiatric disorders. The genes identified, and the pathways of genes and proteins that they implicate, will provide potential novel targets for new therapeutic drugs. Psychiatric genetics appears to be poised for significant advances in our knowledge and understanding of the molecular genetic basis of mental illness.

scholarly journals Whole Genome Shotgun Phylogenomics Resolves the Pattern and Timing of Swallowtail Butterfly Evolution

2019 ◽  
Vol 69 (1) ◽  
pp. 38-60 ◽  
Author(s):  
Rémi Allio ◽  
Céline Scornavacca ◽  
Benoit Nabholz ◽  
Anne-Laure Clamens ◽  
Felix AH Sperling ◽  
...  
Keyword(s):  
Missing Data ◽  
Shotgun Sequencing ◽  
Whole Genome Shotgun ◽  
Amino Acid Sequences ◽  
Molecular Dating ◽  
Whole Genome ◽  
Gene Trees ◽  
Data Set ◽  
Whole Genomes ◽  
Bayesian Mixture Models

Abstract Evolutionary relationships have remained unresolved in many well-studied groups, even though advances in next-generation sequencing and analysis, using approaches such as transcriptomics, anchored hybrid enrichment, or ultraconserved elements, have brought systematics to the brink of whole genome phylogenomics. Recently, it has become possible to sequence the entire genomes of numerous nonbiological models in parallel at reasonable cost, particularly with shotgun sequencing. Here, we identify orthologous coding sequences from whole-genome shotgun sequences, which we then use to investigate the relevance and power of phylogenomic relationship inference and time-calibrated tree estimation. We study an iconic group of butterflies—swallowtails of the family Papilionidae—that has remained phylogenetically unresolved, with continued debate about the timing of their diversification. Low-coverage whole genomes were obtained using Illumina shotgun sequencing for all genera. Genome assembly coupled to BLAST-based orthology searches allowed extraction of 6621 orthologous protein-coding genes for 45 Papilionidae species and 16 outgroup species (with 32% missing data after cleaning phases). Supermatrix phylogenomic analyses were performed with both maximum-likelihood (IQ-TREE) and Bayesian mixture models (PhyloBayes) for amino acid sequences, which produced a fully resolved phylogeny providing new insights into controversial relationships. Species tree reconstruction from gene trees was performed with ASTRAL and SuperTriplets and recovered the same phylogeny. We estimated gene site concordant factors to complement traditional node-support measures, which strengthens the robustness of inferred phylogenies. Bayesian estimates of divergence times based on a reduced data set (760 orthologs and 12% missing data) indicate a mid-Cretaceous origin of Papilionoidea around 99.2 Ma (95% credibility interval: 68.6–142.7 Ma) and Papilionidae around 71.4 Ma (49.8–103.6 Ma), with subsequent diversification of modern lineages well after the Cretaceous-Paleogene event. These results show that shotgun sequencing of whole genomes, even when highly fragmented, represents a powerful approach to phylogenomics and molecular dating in a group that has previously been refractory to resolution.

scholarly journals Divergence-Based Introgression Polarization

2020 ◽  
Vol 12 (4) ◽  
pp. 463-478 ◽  
Author(s):  
Evan S Forsythe ◽  
Daniel B Sloan ◽  
Mark A Beilstein
Keyword(s):  
Genetic Material ◽  
Introgressive Hybridization ◽  
Sequence Divergence ◽  
Whole Genome ◽  
Major Area ◽  
Genome Data ◽  
Whole Genomes ◽  
Potential Sources ◽  
Introgression Event ◽  
Do So

Abstract Introgressive hybridization results in the transfer of genetic material between species, often with fitness implications for the recipient species. The development of statistical methods for detecting the signatures of historical introgression in whole-genome data has been a major area of focus. Although existing techniques are able to identify the taxa that exchanged genes during introgression using a four-taxon system, most methods do not explicitly distinguish which taxon served as donor and which as recipient during introgression (i.e., polarization of introgression directionality). Existing methods that do polarize introgression are often only able to do so when there is a fifth taxon available and that taxon is sister to one of the taxa involved in introgression. Here, we present divergence-based introgression polarization (DIP), a method for polarizing introgression using patterns of sequence divergence across whole genomes, which operates in a four-taxon context. Thus, DIP can be applied to infer the directionality of introgression when additional taxa are not available. We use simulations to show that DIP can polarize introgression and identify potential sources of bias in the assignment of directionality, and we apply DIP to a well-described hominin introgression event.

scholarly journals Occurrence and Molecular Characterization of Recombinant Potato virus YNTN Isolates from Sulawesi, Indonesia

Plant Disease ◽  
2016 ◽  
Vol 100 (2) ◽  
pp. 269-275 ◽  
Author(s):  
Mohamad Chikh-Ali ◽  
Nilsa A. Bosque-Pérez ◽  
Dalton Vander Pol ◽  
Dantje Sembel ◽  
Alexander V. Karasev
Keyword(s):  
Potato Virus ◽  
Potato Virus Y ◽  
Potato Cultivar ◽  
Whole Genome ◽  
Chain Reaction ◽  
Recombinant Type ◽  
Whole Genomes ◽  
Polymerase Chain ◽  
First Time

The importance of potato has increased dramatically in Indonesia over the last three decades. During this period, ‘Granola’, a potato cultivar originally from Germany, has become the most common cultivar for fresh consumption in Indonesia. In August 2014, a survey was conducted in Sulawesi, where potato fields cultivated with Granola and its selection, ‘Super John’, were sampled for Potato virus Y (PVY) presence. PVY was found in Sulawesi for the first time. Samples determined to be positive for PVY were subsequently typed to strain using reverse-transcription polymerase chain reaction assays. All PVY isolates sampled were identified as PVYNTN recombinants, with three recombination junctions in P3, VPg, and CP regions of the genome. Three local PVY isolates were subjected to whole-genome sequencing and subsequent sequence analysis. The whole genomes of the Indonesian PVYNTN isolates I-6, I-16, and I-17 were found to be closely related to the European PVYNTN-A. This recombinant type was shown previously to cause potato tuber necrotic ringspot disease (PTNRD) in susceptible potato cultivars. The dependence of potato farmers on mostly a single cultivar, Granola, may have given a competitive advantage to PVYNTN over other PVY strains, resulting in the predominance of the PVYNTN recombinant. The dominance of PVYNTN in Sulawesi, and possibly in Indonesia as a whole, represents a potential risk to any newly introduced potato cultivar to the country, especially cultivars susceptible to PTNRD.

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