Population Genomics and the Statistical Values of Race: An Interdisciplinary Perspective on the Biological Classification of Human Populations and Implications for Clinical Genetic Epidemiological Research

The search for powerful optimizers has led to the development of a multitude of metaheuristic algorithms inspired from all areas. This work focuses on the animal kingdom as a source of inspiration and performs an extensive, yet not exhaustive, review of the animal inspired metaheuristics proposed in the 2006–2021 period. The review is organized considering the biological classification of living things, with a breakdown of the simulated behavior mechanisms. The centralized data indicated that 61.6% of the animal-based algorithms are inspired from vertebrates and 38.4% from invertebrates. In addition, an analysis of the mechanisms used to ensure diversity was performed. The results obtained showed that the most frequently used mechanisms belong to the niching category.

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Biological Systematics

10.7591/cornell/9781501752773.001.0001 ◽

2021 ◽

Author(s):

Andrew V. Z. Brower ◽

Randall T. Schuh

Keyword(s):

Phylogenetic Inference ◽

Molecular Clocks ◽

Practical Application ◽

Character Analysis ◽

Biological Classification ◽

Living Things ◽

Biological Systematics ◽

Desk Reference ◽

Systematic Biology

Understanding the history and philosophy of biological systematics (phylogenetics, taxonomy and classification of living things) is key to successful practice of the discipline. In this thoroughly revised third edition, the authors provide an updated account of cladistic principles and techniques, emphasizing their empirical and epistemological clarity. The book covers the history and philosophy of systematics; the mechanics and methods of character analysis, phylogenetic inference, and evaluation of results; the practical application of systematic results to biological classification, adaptation and coevolution, biodiversity, and conservation; along with new chapters on species and molecular clocks. The book is both a textbook for students studying systematic biology and a desk reference for practicing systematists. Part explication of concepts and methods, part exploration of the underlying epistemology of systematics, the edition addresses why some methods are more empirically sound than others.

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Management of vascular anomalies: Review of institutional management algorithm

Indian Journal of Plastic Surgery ◽

10.4103/ijps.ijps_245_15 ◽

2017 ◽

Vol 50 (02) ◽

pp. 193-200 ◽

Cited By ~ 1

Author(s):

Lalit K. Makhija ◽

Sameek Bhattacharya

Keyword(s):

Multidisciplinary Approach ◽

Vascular Malformations ◽

Treatment Protocol ◽

Vascular Anomalies ◽

Algorithmic Approach ◽

Institutional Management ◽

Management Algorithm ◽

Biological Classification ◽

Functional Consequences

ABSTRACT Introduction: Vascular anomalies are congenital lesions broadly categorised into vascular tumour (haemangiomas) and vascular dysmorphogenesis (vascular malformation). The management of these difficult problems has lately been simplified by the biological classification and multidisciplinary approach. To standardise the treatment protocol, an algorithm has been devised. The study aims to validate the algorithm in terms of its utility and presents our experience in managing vascular anomalies. Materials and Methods: The biological classification of Mulliken and Glowacki was followed. A detailed algorithm for management of vascular anomalies has been devised in the department. The protocol is being practiced by us since the past two decades. The data regarding the types of lesions and treatment modality used were maintained. Results and Conclusion: This study was conducted from 2002 to 2012. A total of 784 cases of vascular anomalies were included in the study of which 196 were haemangiomas and 588 were vascular malformations. The algorithmic approach has brought an element of much-needed objectivity in the management of vascular anomalies. This has helped us to define the management of particular lesion considering its pathology, extent and aesthetic and functional consequences of ablation to a certain extent.

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Genotype-Phenotype Features of Germline Variants of the TMEM127 Pheochromocytoma Susceptibility Gene: A 10-Year Update

The Journal of Clinical Endocrinology & Metabolism ◽

10.1210/clinem/dgaa741 ◽

2020 ◽

Vol 106 (1) ◽

pp. e350-e364

Author(s):

Gustavo Armaiz-Pena ◽

Shahida K Flores ◽

Zi-Ming Cheng ◽

Xhingyu Zhang ◽

Emmanuel Esquivel ◽

...

Keyword(s):

Transmembrane Protein ◽

Susceptibility Gene ◽

Causal Link ◽

Outcome Analysis ◽

Clinical Genetic ◽

Germline Variants ◽

Clinical Presentations ◽

Transmembrane Regions ◽

Function Integration

Abstract Purpose This work aimed to evaluate genotype-phenotype associations in individuals carrying germline variants of transmembrane protein 127 gene (TMEM127), a poorly known gene that confers susceptibility to pheochromocytoma (PHEO) and paraganglioma (PGL). Design Data were collected from a registry of probands with TMEM127 variants, published reports, and public databases. Main Outcome Analysis Clinical, genetic, and functional associations were determined. Results The cohort comprised 110 index patients (111 variants) with a mean age of 45 years (range, 21-84 years). Females were predominant (76 vs 34, P < .001). Most patients had PHEO (n = 94; 85.5%), although PGL (n = 10; 9%) and renal cell carcinoma (RCC, n = 6; 5.4%) were also detected, either alone or in combination with PHEO. One-third of the cases had multiple tumors, and known family history was reported in 15.4%. Metastatic PHEO/PGL was rare (2.8%). Epinephrine alone, or combined with norepinephrine, accounted for 82% of the catecholamine profiles of PHEO/PGLs. Most variants (n = 63) occurred only once and 13 were recurrent (2-12 times). Although nontruncating variants were less frequent than truncating changes overall, they were predominant in non-PHEO clinical presentations (36% PHEO-only vs 69% other, P < .001) and clustered disproportionately within transmembrane regions (P < .01), underscoring the relevance of these domains for TMEM127 function. Integration of clinical and previous experimental data supported classification of variants into 4 groups based on mutation type, localization, and predicted disruption. Conclusions Patients with TMEM127 variants often resemble sporadic nonmetastatic PHEOs. PGL and RCC may also co-occur, although their causal link requires further evaluation. We propose a new classification to predict variant pathogenicity and assist with carrier surveillance.

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The subtypes of human immunodeficiency virus in Australia and Asia

Sexual Health ◽

10.1071/sh03002 ◽

2004 ◽

Vol 1 (1) ◽

pp. 1 ◽

Cited By ~ 6

Author(s):

Robert Oelrichs

Keyword(s):

Human Immunodeficiency Virus ◽

Genetic Variability ◽

Distribution Patterns ◽

Human Populations ◽

Regional Diversity ◽

Subtype B ◽

Immunodeficiency Virus ◽

Australasian Region ◽

Hiv 1

Worldwide, the human immunodeficiency virus exhibits a great genetic variability, with multiple circulating subtypes of the virus. This variability allows study of the movement of HIV strains within and between human populations but also has implications for diagnosis, treatment and monitoring. The type of HIV causing the epidemic in Australia is changing from being homogeneous subtype B, reflecting a greater regional diversity. In this paper the classification of HIV-1 subtypes and their distribution within the Australasian region are reviewed and the implications of these distribution patterns discussed.

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Is the biological classification of benthic diatom communities concordant with ecotypes?

Hydrobiologia ◽

10.1007/s10750-012-1119-8 ◽

2012 ◽

Vol 695 (1) ◽

pp. 43-55 ◽

Cited By ~ 10

Author(s):

Elisabet Tornés ◽

Manel Leira ◽

Sergi Sabater

Keyword(s):

Benthic Diatom ◽

Biological Classification ◽

Diatom Communities

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Harnessing population-specific protein truncating variants to improve the annotation of loss-of-function alleles

10.1101/2020.08.17.254904 ◽

2020 ◽

Author(s):

Rostislav K. Skitchenko ◽

Julia S. Kornienko ◽

Evgeniia M. Maksiutenko ◽

Andrey S. Glotov ◽

Alexander V. Predeus ◽

...

Keyword(s):

Population Genomics ◽

False Positive Rate ◽

Threshold Value ◽

Specific Protein ◽

Human Populations ◽

Loss Of Function ◽

Human Genes ◽

Strong Negative Selection ◽

Disease Penetrance ◽

Positive Rate

AbstractAccurate annotation of putative loss-of-function (pLoF) variants is an important problem in human genomics and disease, which recently drew substantial attention. Since such variants in disease-related genes are under strong negative selection, their frequency across major ancestral groups is expected to be highly similar. In this study, we tested this assumption by systematically assessing the presence of highly population-specific protein-truncating variants (PTVs) in human genes using latest population-scale data. We discovered an unexpectedly high incidence of population-specific PTVs in all major ancestral groups. This does not conform to a recently proposed model, indicating either systemic differences in disease penetrance in different human populations, or a failure of current annotation criteria to accurately predict the loss-of-function potential of PTVs. We show that low-confidence pLoF variants are enriched in genes with non-uniform PTV count distribution, and developed a computational tool called LoFfeR that can efficiently predict tolerated pLoF variants. To evaluate the performance of LoFfeR, we use a set of known pathogenic and benign PTVs from the ClinVar database, and show that LoFfeR allows for a more accurate annotation of low-confidence pLoF variants compared to existing methods. Notably, only 4.4% of protein-truncating gnomAD SNPs in canonical transcripts can be filtered out using a recommended threshold value of the recently proposed pext score, while up to 10.9% of such variants are filtered using LoFfeR with the same false positive rate. Hence, we believe that LoFfeR can be used for additional filtering of low-confidence pLoF variants in population genomics and medical genetics studies.

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A novel framework for classification of selection mechanisms in epidemiological research

10.21203/rs.2.16849/v1 ◽

2019 ◽

Author(s):

Jonas Bjork ◽

Anton Nilsson ◽

Carl Bonander ◽

Ulf Strömberg

Keyword(s):

General Framework ◽

Empirical Studies ◽

Population Level ◽

Epidemiological Studies ◽

Three Dimensions ◽

Epidemiological Research ◽

Selection Processes ◽

Selection Mechanisms

Abstract Background: Non-participation, losses to follow up and other types of study-specific selection mechanisms can be serious concerns in epidemiological studies. There are also selection processes that result in non-random groupings and changes in the composition of populations. These are continuously on-going irrespectively of whether they are subject to sampling in empirical studies. Such population selections are often overlooked, but may lead to lack of comparability of exposed and unexposed populations or decrease study validity in other ways. The overall aim of this study was to develop a simple but general framework for classifying various types of selection mechanisms of relevance for epidemiological research. Methods: We classify selection mechanisms in three dimensions: i) selection at the population level vs. selection that is study-specific, ii) type of mechanism (selection causing exposure vs. selection in population at risk), iii) timing of the selection (pre-exposure, during exposure or post-outcome). Results: Examples from the epidemiological literature of selection mechanisms are discussed and classified according to the three dimensions of the proposed framework. Conclusions: Increased mechanistic understanding of when, how, and why confusion of effects can occur because of selection is an important step towards improved validity of epidemiological research.

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