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Campbell IM, Gambin T, Jhangiani S, Grove ML, Veeraraghavan N, Muzny DM, Shaw CA, Gibbs RA, Boerwinkle E, Yu F, Lupski JR. Multiallelic Positions in the Human Genome: Challenges for Genetic Analyses. Hum Mutat 2015; 37:231-234. [PMID: 26670213 DOI: 10.1002/humu.22944] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/03/2015] [Indexed: 11/11/2022]
Abstract
As the amount of human genomic sequence available from personal genomes and exomes has increased, so too has the observation of genomic positions having two or more alternative alleles, so-called multiallelic sites. For portions of the haploid genome that are present in more than one copy, including segmental duplications, variation at such multisite variant positions becomes even more complex. Despite the frequency of multiallelic variants, a number of commonly used resources and tools in genomic research and diagnostics do not support these multiallelic variants all together or require special modifications. Here, we explore the frequency of multiallelic sites in large samples with whole exome sequencing and discuss potential outcomes of failing to account for multiple variant alleles. We also briefly discuss some commonly utilized resources that fully support multiallelic sites.
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Affiliation(s)
- Ian M Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Megan L Grove
- Human Genetics Center, University of Texas Health Sciences Center at Houston, Houston, TX 77030, USA
| | | | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genetics Center, University of Texas Health Sciences Center at Houston, Houston, TX 77030, USA
| | - Fuli Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.,Texas Children's Hospital, Houston, TX 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
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Iriemenam NC, Pandey JP, Williamson J, Blackstock AJ, Yesupriya A, Namboodiri AM, Rocca KM, van Eijk AM, Ayisi J, Oteino J, Lal RB, ter Kuile FO, Steketee R, Nahlen B, Slutsker L, Shi YP. Association between immunoglobulin GM and KM genotypes and placental malaria in HIV-1 negative and positive women in western Kenya. PLoS One 2013; 8:e53948. [PMID: 23326546 PMCID: PMC3543394 DOI: 10.1371/journal.pone.0053948] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 12/06/2012] [Indexed: 01/24/2023] Open
Abstract
Immunoglobulin (Ig) GM and KM allotypes, genetic markers of γ and κ chains, are associated with humoral immune responsiveness. Previous studies have shown the relationships between GM6-carrying haplotypes and susceptibility to malaria infection in children and adults; however, the role of the genetic markers in placental malaria (PM) infection and PM with HIV co-infection during pregnancy has not been investigated. We examined the relationship between the gene polymorphisms of Ig GM6 and KM allotypes and the risk of PM infection in pregnant women with known HIV status. DNA samples from 728 pregnant women were genotyped for GM6 and KM alleles using polymerase chain reaction-restriction fragment length polymorphism method. Individual GM6 and KM genotypes and the combined GM6 and KM genotypes were assessed in relation to PM in HIV-1 negative and positive women, respectively. There was no significant effect of individual GM6 and KM genotypes on the risk of PM infection in HIV-1 negative and positive women. However, the combination of homozygosity for GM6(+) and KM3 was associated with decreased risk of PM (adjusted OR, 0.25; 95% CI, 0.08-0.8; P = 0.019) in HIV-1 negative women while in HIV-1 positive women the combination of GM6(+/-) with either KM1-3 or KM1 was associated with increased risk of PM infection (adjusted OR, 2.10; 95% CI, 1.18-3.73; P = 0.011). Hardy-Weinberg Equilibrium (HWE) tests further showed an overall significant positive F(is) (indication of deficit in heterozygotes) for GM6 while there was no deviation for KM genotype frequency from HWE in the same population. These findings suggest that the combination of homozygous GM6(+) and KM3 may protect against PM in HIV-1 negative women while the HIV-1 positive women with heterozygous GM6(+/-) combined with KM1-3 or KM1 may be more susceptible to PM infection. The deficit in heterozygotes for GM6 further suggests that GM6 could be under selection likely by malaria infection.
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Affiliation(s)
- Nnaemeka C. Iriemenam
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Janardan P. Pandey
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, United States of America
- * E-mail: (YPS); (JPP)
| | - John Williamson
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Anna J. Blackstock
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Atlanta Research and Education Foundation/VA Medical Center, Decatur, Georgia, United States of America
| | - Ajay Yesupriya
- National Office of Public Health Genomics, Coordinating Center for Health Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Aryan M. Namboodiri
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Keith M. Rocca
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Anna Maria van Eijk
- Centre for Vector Biology and Control Research, Kenyan Medical Research Institute, Kisumu, Kenya
| | - John Ayisi
- Centre for Vector Biology and Control Research, Kenyan Medical Research Institute, Kisumu, Kenya
| | - Juliana Oteino
- New Nyanza Provincial General Hospital, Ministry of Health, Kisumu, Kenya
| | - Renu B. Lal
- Division of AIDS, STD, TB Laboratory Research, National Center for HIV, STD, TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Feiko O. ter Kuile
- Child and Reproductive Health Group, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Richard Steketee
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Bernard Nahlen
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Laurence Slutsker
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Ya Ping Shi
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail: (YPS); (JPP)
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Huchard E, Albrecht C, Schliehe-Diecks S, Baniel A, Roos C, Kappeler PM, Peter PMK, Brameier M. Large-scale MHC class II genotyping of a wild lemur population by next generation sequencing. Immunogenetics 2012; 64:895-913. [PMID: 22948859 PMCID: PMC3496554 DOI: 10.1007/s00251-012-0649-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Accepted: 08/13/2012] [Indexed: 12/23/2022]
Abstract
The critical role of major histocompatibility complex (MHC) genes in disease resistance, along with their putative function in sexual selection, reproduction and chemical ecology, make them an important genetic system in evolutionary ecology. Studying selective pressures acting on MHC genes in the wild nevertheless requires population-wide genotyping, which has long been challenging because of their extensive polymorphism. Here, we report on large-scale genotyping of the MHC class II loci of the grey mouse lemur (Microcebus murinus) from a wild population in western Madagascar. The second exons from MHC-DRB and -DQB of 772 and 672 individuals were sequenced, respectively, using a 454 sequencing platform, generating more than 800,000 reads. Sequence analysis, through a stepwise variant validation procedure, allowed reliable typing of more than 600 individuals. The quality of our genotyping was evaluated through three independent methods, namely genotyping the same individuals by both cloning and 454 sequencing, running duplicates, and comparing parent-offspring dyads; each displaying very high accuracy. A total of 61 (including 20 new) and 60 (including 53 new) alleles were detected at DRB and DQB genes, respectively. Both loci were non-duplicated, in tight linkage disequilibrium and in Hardy-Weinberg equilibrium, despite the fact that sequence analysis revealed clear evidence of historical selection. Our results highlight the potential of 454 sequencing technology in attempts to investigate patterns of selection shaping MHC variation in contemporary populations. The power of this approach will nevertheless be conditional upon strict quality control of the genotyping data.
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Affiliation(s)
- Elise Huchard
- Behavioral Ecology and Sociobiology Unit, German Primate Center, Kellnerweg 4, Göttingen, Germany.
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Multiallelic models of genetic effects and variance decomposition in non-equilibrium populations. Genetica 2011; 139:1119-34. [PMID: 22068562 PMCID: PMC3247674 DOI: 10.1007/s10709-011-9614-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 10/31/2011] [Indexed: 01/09/2023]
Abstract
Quantitative genetics stems from the theoretical models of genetic effects, which are re-parameterizations of the genotypic values into parameters of biological (genetic) relevance. Different formulations of genetic effects are adequate to address different subjects. We thus need to generalize and unify them under a common framework for enabling researchers to easily transform genetic effects between different biological meanings. The Natural and Orthogonal Interactions (NOIA) model of genetic effects has been developed to achieve this aim. Here, we further implement the statistical formulation of NOIA with multiple alleles under Hardy-Weinberg departures (HWD). We show that our developments are straightforwardly connected to the decomposition of the genetic variance and we point out several emergent properties of multiallelic quantitative genetic models, as compared to the biallelic ones. Further, NOIA entails a natural extension of one-locus developments to multiple epistatic loci under linkage equilibrium. Therefore, we present an extension of the orthogonal decomposition of the genetic variance to multiple epistatic, multiallelic loci under HWD. We illustrate this theory with a graphical interpretation and an analysis of published data on the human acid phosphatase (ACP1) polymorphism.
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Lonard DM, Kumar R, O'Malley BW. Minireview: the SRC family of coactivators: an entrée to understanding a subset of polygenic diseases? Mol Endocrinol 2009; 24:279-85. [PMID: 19846539 DOI: 10.1210/me.2009-0276] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In this perspective, we present the idea that SRC family coactivators are likely agents in human polygenic disease states based upon a number of interlocking aspects of their biology. We argue that their role as key integrators of environmental signals and their ability to regulate the expression of myriad downstream genes makes them likely candidates for strong positive evolutionary selection pressures. Based on the fact that they work as part of multiprotein coactivator complexes, we predict that individual coactivator alleles exist as weakly penetrant disease alleles, each contributing only a fraction of transcriptional activity to the whole coactivator complex. In this way, individual coactivator alleles are free to evolve in the absence of strong negative selection. Emerging genomic and proteomic approaches promise to advance the characterization of coactivator proteins and their physiological functions, allowing us to have a greater appreciation of their roles as master regulators at the nexus between genetics, reproduction, metabolism, cancer, other human diseases, and our environment.
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Affiliation(s)
- David M Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030.
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Lachance J. Detecting selection-induced departures from Hardy-Weinberg proportions. Genet Sel Evol 2009; 41:15. [PMID: 19284519 PMCID: PMC2660905 DOI: 10.1186/1297-9686-41-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 01/21/2009] [Indexed: 11/20/2022] Open
Abstract
Viability selection influences the genotypic contexts of alleles and leads to quantifiable departures from Hardy-Weinberg proportions. One measure of these departures is Wright's inbreeding coefficient (F), where observed heterozygosity is compared with expected heterozygosity. Here, I extend population genetics theory to describe post-selection genotype frequencies in terms of post-selection allele frequencies and fitness dominance. The resulting equations correspond to non-equilibrium populations, allowing the following questions to be addressed: When selection is present, how large a sample size is needed to detect significant departures from Hardy-Weinberg? How do selection-induced departures from Hardy-Weinberg vary with allele frequencies and levels of fitness dominance? For realistic selection coefficients, large sample sizes are required and departures from Hardy-Weinberg proportions are small.
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Affiliation(s)
- Joseph Lachance
- Graduate Program in Genetics, Department of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, NY 11794-5222, USA.
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Abstract
The set of possible postselection genotype frequencies in an infinite, randomly mating population is found. Geometric mean heterozygote frequency divided by geometric mean homozygote frequency equals two times the geometric mean heterozygote fitness divided by geometric mean homozygote fitness. The ratio of genotype frequencies provides a measure of genetic variation that is independent of allele frequencies. When this ratio does not equal two, either selection or population structure is present. Within-population HapMap data show population-specific patterns, while pooled data show an excess of homozygotes.
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