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Agudo MM, Aanes H, Albert M, Janssen K, Gill P, Bleka Ø. An overview of autosomal STRs and identity SNPs in a Norwegian population using massively parallel sequencing. Forensic Sci Int Genet 2024; 71:103057. [PMID: 38733649 DOI: 10.1016/j.fsigen.2024.103057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 02/27/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024]
Abstract
In recent years, probabilistic genotyping software has been adapted for the analysis of massively parallel sequencing (MPS) forensic data. Likelihood ratios (LR) are based on allele frequencies selected from populations of interest. This study provides an outline of sequence-based (SB) allele frequencies for autosomal short tandem repeats (aSTRs) and identity single nucleotide polymorphisms (iSNPs) in 371 individuals from Southern Norway. 27 aSTRs and 94 iSNPs were previously analysed with the ForenSeq™ DNA Signature Prep Kit (Verogen). The number of alleles with frequencies less than 0.05 for sequenced-based alleles was 4.6 times higher than for length-based alleles. Consistent with previous studies, it was observed that sequence-based data (both with and without flanks) exhibited higher allele diversity compared to length-based (LB) data; random match probabilities were lower for SB alleles confirming their advantage to discriminate between individuals. Two alleles in markers D22S1045 and Penta D were observed with SNPs in the 3´ flanking region, which have not been reported before. Also, a novel SNP with a minor allele frequency (MAF) of 0.001, was found in marker TH01. The impact of the sample size on minor allele frequency (MAF) values was studied in 88 iSNPs from Southern Norway (n = 371). The findings were then compared to a larger Norwegian population dataset (n = 15,769). The results showed that the smaller Southern Norway dataset provided similar results, and it was a representative sample. Population structure was analyzed for regions within Southern Norway; FST estimates for aSTR and iSNPs did not indicate any genetic structure. Finally, we investigated the genetic differences between Southern Norway and two other populations: Northern Norway and Denmark. Allele frequencies between these populations were compared, and we found no significant frequency differences (p-values > 0.0001). We also calculated the pairwise FST values per marker and comparisons between Southern and Northern Norway showed small differences. In contrast, the comparisons between Southern Norway and Denmark showed higher FST values for some markers, possibly driven by distinct alleles that were present in only one of the populations. In summary, we propose that allele frequencies from each population considered in this study could be used interchangeably to calculate genotype probabilities.
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Affiliation(s)
- Maria Martin Agudo
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway; Department of Forensic Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Håvard Aanes
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway
| | - Michel Albert
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway
| | - Kirstin Janssen
- Centre for Forensic Genetics, UiT The Arctic University of Norway, Norway
| | - Peter Gill
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway; Department of Forensic Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Øyvind Bleka
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway.
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2
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Gerard D. Double reduction estimation and equilibrium tests in natural autopolyploid populations. Biometrics 2023; 79:2143-2156. [PMID: 35848417 DOI: 10.1111/biom.13722] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 07/11/2022] [Indexed: 11/27/2022]
Abstract
Many bioinformatics pipelines include tests for equilibrium. Tests for diploids are well studied and widely available, but extending these approaches to autopolyploids is hampered by the presence of double reduction, the comigration of sister chromatid segments into the same gamete during meiosis. Though a hindrance for equilibrium tests, double reduction rates are quantities of interest in their own right, as they provide insights about the meiotic behavior of autopolyploid organisms. Here, we develop procedures to (i) test for equilibrium while accounting for double reduction, and (ii) estimate the double reduction rate given equilibrium. To do so, we take two approaches: a likelihood approach, and a novel U-statistic minimization approach that we show generalizes the classical equilibrium χ2 test in diploids. For small sample sizes and uncertain genotypes, we further develop a bootstrap procedure based on our U-statistic to test for equilibrium. We validate our methods on both simulated and real data.
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Affiliation(s)
- David Gerard
- Department of Mathematics and Statistics, American University, Washington, District of Columbia, USA
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3
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Cui W, Chen M, Yang Y, Cai M, Lan Q, Xie T, Zhu B. Applications of 1993 single nucleotide polymorphism loci in forensic pairwise kinship identifications and inferences. Forensic Sci Int Genet 2023; 65:102889. [PMID: 37247510 DOI: 10.1016/j.fsigen.2023.102889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/19/2023] [Accepted: 05/11/2023] [Indexed: 05/31/2023]
Abstract
Kinship testing plays critical roles in criminal investigations, missing person searches, civil disputes, as well as identifying disaster victims. The existing commonly used short tandem repeat (STR) loci have limited effectiveness in the identification of second-degree and more distant kinships. In this study, a total of 1993 SNP loci of 119 Chinese Han individuals from eight families were sequenced on the MGISEQ-2000RS platform. The system powers of this panel for kinship identifications were evaluated based on both the likelihood ratio (LR) and identical by state (IBS) methods. The results indicated that this panel could be used as an effective tool to kinship analyses including paternity testing, full sibling testing, second-degree kinships, and first cousin kinship analyses. Both the LR and IBS methods could be applied in distinguishing first-degree and second-degree pairs from unrelated individuals. Based on the 1993 SNP loci, LR>1000 and LR<0.001 are recommended as the thresholds of identifying first-cousin kinships from unrelated individuals, and the system power of such thresholds was 0.9470. Besides, kinship coefficients for different kinship pairs were estimated and then were used to predict the kinships for pairwise individuals. This panel performs an effective kinship inference power for the predictions of first-degree, second-degree kinships and unrelated individual pairs, while presenting low sensitivity in the prediction of first-cousin kinships.
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Affiliation(s)
- Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Man Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Yan Yang
- Golden Bridge Big Data Technology Co., LTD, Beijing, China
| | - Meiming Cai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Tong Xie
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China.
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
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4
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Graffelman J, Weir BS. The transitivity of the Hardy-Weinberg law. Forensic Sci Int Genet 2022; 58:102680. [PMID: 35313226 PMCID: PMC10693928 DOI: 10.1016/j.fsigen.2022.102680] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 02/12/2022] [Accepted: 02/20/2022] [Indexed: 11/27/2022]
Abstract
The Hardy-Weinberg law is shown to be transitive in the sense that a multi-allelic polymorphism that is in equilibrium will retain its equilibrium status if any allele together with its corresponding genotypes is deleted from the population. Similarly, the transitivity principle also applies if alleles are joined, which leads to the summation of allele frequencies and their corresponding genotype frequencies. These basic polymorphism properties are intuitive, but they have apparently not been formalized or investigated. This article provides a straightforward proof of the transitivity principle, and its usefulness in genetic data analysis is explored, using high-quality autosomal microsatellite databases from the US National Institute of Standards and Technology. We address the reduction of multi-allelic polymorphisms to variants with fewer alleles, two in the limit. Equilibrium test results obtained with the original and reduced polymorphisms are generally observed to be coherent, in particular when results obtained with length-based and sequence-based microsatellites are compared. We exploit the transitivity principle in order to identify disequilibrium-related alleles, and show its usefulness for detecting population substructure and genotyping problems that relate to null alleles and allele imbalance.
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Affiliation(s)
- Jan Graffelman
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Carrer Jordi Girona, 1-3, 08034, Barcelona, Spain; Department of Biostatistics, University of Washington, University Tower, 15th Floor, 4333 Brooklyn Avenue, Seattle, WA 98105-9461, United States of America.
| | - Bruce S Weir
- Department of Biostatistics, University of Washington, University Tower, 15th Floor, 4333 Brooklyn Avenue, Seattle, WA 98105-9461, United States of America
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5
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Recursive Test of Hardy-Weinberg Equilibrium in Tetraploids. Trends Genet 2021; 37:504-513. [DOI: 10.1016/j.tig.2020.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 02/08/2023]
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6
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Graffelman J, Ortoleva L. A network algorithm for the X chromosomal exact test for Hardy-Weinberg equilibrium with multiple alleles. Mol Ecol Resour 2021; 21:1547-1557. [PMID: 33687797 PMCID: PMC8251783 DOI: 10.1111/1755-0998.13373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/24/2021] [Accepted: 03/01/2021] [Indexed: 11/27/2022]
Abstract
Statistical methodology for testing the Hardy–Weinberg equilibrium at X chromosomal variants has recently experienced considerable development. Up to a few years ago, testing X chromosomal variants for equilibrium was basically done by applying autosomal test procedures to females only. At present, male alleles can be taken into account in asymptotic and exact test procedures for both the bi‐ and multiallelic case. However, current X chromosomal exact procedures for multiple alleles rely on a classical full enumeration algorithm and are computationally expensive, and in practice not feasible for more than three alleles. In this article, we extend the autosomal network algorithm for exact Hardy–Weinberg testing with multiple alleles to the X chromosome, achieving considerable reduction in computation times for multiallelic variants with up to five alleles. The performance of the X chromosomal network algorithm is assessed in a simulation study. Beyond four alleles, a permutation test is, in general, the more feasible approach. A detailed description of the algorithm is given, and examples of X chromosomal indels and microsatellites are discussed.
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Affiliation(s)
- Jan Graffelman
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain.,Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Leonardo Ortoleva
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain.,Department of Control and Computer Engineering, Politecnico di Torino, Torino, Italy
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7
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Bolat H, Ercan ES, Ünsel-Bolat G, Tahillioğlu A, Yazici KU, Bacanli A, Pariltay E, Aygüneş Jafari D, Kosova B, Özgül S, Rohde LA, Akin H. DRD4 genotyping may differentiate symptoms of attention-deficit/hyperactivity disorder and sluggish cognitive tempo. ACTA ACUST UNITED AC 2020; 42:630-637. [PMID: 32491038 PMCID: PMC7678899 DOI: 10.1590/1516-4446-2019-0630] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 01/17/2020] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Studies to reduce the heterogeneity of attention-deficit/hyperactivity disorder (ADHD) have increased interest in the concept of sluggish cognitive tempo (SCT). The aim of this study was to investigate if the prevalence of two variable-number tandem repeats (VNTRs) located within the 3'-untranslated region of the DAT1 gene and in exon 3 of the dopamine D4 receptor (DRD4) gene differ among four groups (31 subjects with SCT but no ADHD, 146 individuals with ADHD but no SCT, 67 subjects with SCT + ADHD, and 92 healthy controls). METHODS We compared the sociodemographic profiles, neurocognitive domains, and prevalence of two VNTRs in SCT and ADHD subjects versus typically developing (TD) controls. RESULTS The SCT without ADHD group had a higher proportion of females and lower parental educational attainment. Subjects in this group performed worse on neuropsychological tests, except for psychomotor speed and commission errors, compared to controls. However, the ADHD without SCT group performed significantly worse on all neuropsychological domains than controls. We found that 4R homozygosity for the DRD4 gene was most prevalent in the ADHD without SCT group. The SCT without ADHD group had the highest 7R allele frequency, differing significantly from the ADHD without SCT group. CONCLUSION The 7R allele of DRD4 gene was found to be significantly more prevalent in SCT cases than in ADHD cases. No substantial neuropsychological differences were found between SCT and ADHD subjects.
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Affiliation(s)
- Hilmi Bolat
- Department of Medical Genetics, Balikesir Atatürk City Hospital, Balikesir, Turkey
| | - Eyüp S Ercan
- Department of Child and Adolescent Psychiatry, Ege University, Izmir, Turkey
| | - Gül Ünsel-Bolat
- Department of Child and Adolescent Psychiatry, Balikesir University Faculty of Medicine, Balikesir, Turkey
| | - Akin Tahillioğlu
- Department of Child and Adolescent Psychiatry, Ege University, Izmir, Turkey
| | - Kemal U Yazici
- Department of Child and Adolescent Psychiatry, Firat University, Izmir, Turkey
| | - Ali Bacanli
- Department of Child and Adolescent Psychiatry, Baskent University, Izmir, Turkey
| | - Erhan Pariltay
- Department of Medical Genetics, Ege University, Izmir, Turkey
| | | | - Buket Kosova
- Department of Medical Biology, Ege University, Izmir, Turkey
| | - Semiha Özgül
- Department of Bioistatistics and Medical Informatics, Ege University, Izmir, Turkey
| | - Luis A Rohde
- Programa de Transtornos de Déficit de Atenção/Hiperatividade (ProDAH), Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Instituto Nacional de Psiquiatria do Desenvolvimento para Crianças e Adolescentes, São Paulo, SP, Brazil
| | - Haluk Akin
- Department of Medical Genetics, Ege University, Izmir, Turkey
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8
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Leukel C, Schümann D, Kalisch R, Sommer T, Bunzeck N. Dopamine Related Genes Differentially Affect Declarative Long-Term Memory in Healthy Humans. Front Behav Neurosci 2020; 14:539725. [PMID: 33328916 PMCID: PMC7673390 DOI: 10.3389/fnbeh.2020.539725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/04/2020] [Indexed: 11/22/2022] Open
Abstract
In humans, monetary reward can promote behavioral performance including response times, accuracy, and subsequent recognition memory. Recent studies have shown that the dopaminergic system plays an essential role here, but the link to interindividual differences remains unclear. To further investigate this issue, we focused on previously described polymorphisms of genes affecting dopaminergic neurotransmission: DAT1 40 base pair (bp), DAT1 30 bp, DRD4 48 bp, and cannabinoid receptor type 1 (CNR1). Specifically, 669 healthy humans participated in a delayed recognition memory paradigm on two consecutive days. On the first day, male vs. female faces served as cues predicting an immediate monetary reward upon correct button presses. Subsequently, participants performed a remember/know recognition memory task on the same day and 1 day later. As predicted, reward increased accuracy and accelerated response times, which were modulated by DAT 30 bp. However, reward did not promote subsequent recognition memory performance and there was no interaction with any genotype tested here. Importantly, there were differential effects of genotype on declarative long-term memory independent of reward: (a) DAT1 40 bp was linked to the quality of memory with a more pronounced difference between recollection and familiarity in the heterozygous and homozygous 10-R as compared to homozygous 9-R; (b) DAT1 30 bp was linked to memory decay, which was most pronounced in homozygous 4-R; (c) DRD4 48 bp was linked to overall recognition memory with higher performance in the short allele group; and (d) CNR1 was linked to overall memory with reduced performance in the homozygous short group. These findings give new insights into how polymorphisms, which are related to dopaminergic neuromodulation, differentially affect long-term recognition memory performance.
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Affiliation(s)
- Carla Leukel
- Department of Psychology, University of Lübeck, Lübeck, Germany
| | - Dirk Schümann
- Department of Systems Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Raffael Kalisch
- Department of Systems Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Neuroimaging Center (NIC), Focus Program Translational Neuroscience, Johannes Gutenberg University Medical Center, Mainz, Germany.,Leibniz Institute for Resilience Research (LIR), Mainz, Germany
| | - Tobias Sommer
- Department of Systems Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nico Bunzeck
- Department of Psychology, University of Lübeck, Lübeck, Germany.,Department of Systems Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Center of Brain, Behavior and Metabolism (CBBM), University of Lübeck, Lübeck, Germany
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9
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Hague MTJ, Stokes AN, Feldman CR, Brodie ED, Brodie ED. The geographic mosaic of arms race coevolution is closely matched to prey population structure. Evol Lett 2020; 4:317-332. [PMID: 32774881 PMCID: PMC7403720 DOI: 10.1002/evl3.184] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/11/2020] [Accepted: 05/22/2020] [Indexed: 01/09/2023] Open
Abstract
Reciprocal adaptation is the hallmark of arms race coevolution. Local coadaptation between natural enemies should generate a geographic mosaic pattern where both species have roughly matched abilities across their shared range. However, mosaic variation in ecologically relevant traits can also arise from processes unrelated to reciprocal selection, such as population structure or local environmental conditions. We tested whether these alternative processes can account for trait variation in the geographic mosaic of arms race coevolution between resistant garter snakes (Thamnophis sirtalis) and toxic newts (Taricha granulosa). We found that predator resistance and prey toxin levels are functionally matched in co-occurring populations, suggesting that mosaic variation in the armaments of both species results from the local pressures of reciprocal selection. By the same token, phenotypic and genetic variation in snake resistance deviates from neutral expectations of population genetic differentiation, showing a clear signature of adaptation to local toxin levels in newts. Contrastingly, newt toxin levels are best predicted by genetic differentiation among newt populations, and to a lesser extent, by the local environment and snake resistance. Exaggerated armaments suggest that coevolution occurs in certain hotspots, but prey population structure seems to be of particular influence on local phenotypic variation in both species throughout the geographic mosaic. Our results imply that processes other than reciprocal selection, like historical biogeography and environmental pressures, represent an important source of variation in the geographic mosaic of coevolution. Such a pattern supports the role of "trait remixing" in the geographic mosaic theory, the process by which non-adaptive forces dictate spatial variation in the interactions among species.
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Affiliation(s)
- Michael T J Hague
- Division of Biological Sciences University of Montana Missoula Montana 59812.,Department of Biology University of Virginia Charlottesville Virginia 22904
| | - Amber N Stokes
- Department of Biology California State University Bakersfield California 93311
| | - Chris R Feldman
- Department of Biology University of Nevada Reno Nevada 89557
| | - Edmund D Brodie
- Department of Biology Utah State University Logan Utah 84322
| | - Edmund D Brodie
- Department of Biology University of Virginia Charlottesville Virginia 22904
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10
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Sex linkage of the skeletal muscle sodium channel gene (SCN4A) explains apparent deviations from Hardy-Weinberg equilibrium of tetrodotoxin-resistance alleles in garter snakes (Thamnophis sirtalis). Heredity (Edinb) 2020; 124:647-657. [PMID: 32111979 DOI: 10.1038/s41437-020-0300-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/13/2020] [Accepted: 02/13/2020] [Indexed: 01/01/2023] Open
Abstract
The arms race between tetrodotoxin-bearing Pacific newts (Taricha) and their garter snake predators (Thamnophis) in western North America has become a classic example of coevolution, shedding light on predator-prey dynamics, the molecular basis of adaptation, and patterns of convergent evolution. Newts are defended by tetrodotoxin (TTX), a neurotoxin that binds to voltage-gated sodium channels (Nav proteins), arresting electrical activity in nerves and muscles and paralyzing would-be predators. However, populations of the common garter snake (T. sirtalis) have overcome this defense, largely through polymorphism at the locus SCN4A, which renders the encoded protein (Nav1.4) less vulnerable to TTX. Previous work suggests that SCN4A commonly shows extreme deviations from Hardy-Weinberg equilibrium (HWE) in these populations, which has been interpreted as the result of intense selection imposed by newts. Here we show that much of this apparent deviation can be attributed to sex linkage of SCN4A. Using genomic data and quantitative PCR, we show that SCN4A is on the Z chromosome in Thamnophis and other advanced snakes. Taking Z-linkage into account, we find that most apparent deviations from HWE can be explained by female hemizygosity rather than low heterozygosity. Sex linkage can affect mutation rates, selection, and drift, and our results suggest that Z-linkage of SCN4A may make significant contributions to the overall dynamics of the coevolutionary arms race between newts and snakes.
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11
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Stanković B, Kotur N, Gašić V, Klaassen K, Ristivojević B, Stojiljković M, Pavlović S, Zukić B. Pharmacogenomics landscape of COVID-19 therapy response in Serbian population and comparison with worldwide populations. J Med Biochem 2020; 39:488-499. [PMID: 33312066 DOI: 10.5937/jomb0-26725] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022] Open
Abstract
Background Since there are no certified therapeutics to treat COVID-19 patients, drug repurposing became important. With lack of time to test individual pharmacogenomics markers, population pharmacogenomics could be helpful in predicting a higher risk of developing adverse reactions and treatment failure in COVID-19 patients. Aim of our study was to identify pharmacogenes and pharmacogenomics markers associated with drugs recommended for COVID-19 treatment, chloroquine/hydroxychloroquine, azithromycin, lopinavir and ritonavir, in population of Serbia and other world populations. Methods Genotype information of 143 individuals of Serbian origin was extracted from database previously obtained using TruSight One Gene Panel (Illumina). Genotype data of individuals from different world populations were extracted from the 1000 Genome Project. Fisher's exact test was used for comparison of allele frequencies. Results We have identified 11 potential pharmacogenomics markers in 7 pharmacogenes relevant for COVID-19 treatment. Based on high alternative allele frequencies in population and the functional effect of the variants, ABCB1 rs1045642 and rs2032582 could be relevant for reduced clearance of azithromycin, lopinavir and ritonavir drugs and UGT1A7 rs17868323 for hyperbilirubinemia in ritonavir treated COVID-19 patients in Serbian population. SLCO1B1 rs4149056 is a potential marker of lopinavir response, especially in Italian population. Our results confirmed that pharmacogenomics profile of African population is different from the rest of the world. Conclusions Considering population specific pharmacogenomics landscape, preemptive testing for pharmacogenes relevant for drugs used in COVID-19 treatment could contribute to better understanding of the inconsistency in therapy response and could be applied to improve the outcome of the COVID-19 patients.
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Affiliation(s)
- Biljana Stanković
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Nikola Kotur
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Vladimir Gašić
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Kristel Klaassen
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Bojan Ristivojević
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Maja Stojiljković
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Sonja Pavlović
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
| | - Branka Zukić
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Biomedicine, Belgrade
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12
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Backenroth D, Carmi S. A test for deviations from expected genotype frequencies on the X chromosome for sex-biased admixed populations. Heredity (Edinb) 2019; 123:470-478. [PMID: 31101879 DOI: 10.1038/s41437-019-0233-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/19/2019] [Accepted: 04/29/2019] [Indexed: 11/09/2022] Open
Abstract
Genome-wide scans for deviations from expected genotype frequencies, as determined by the Hardy-Weinberg equilibrium (HWE), are commonly applied to detect genotyping errors and deviations from random mating. In contrast to the autosomes, genotype frequencies on the X chromosome do not reach HWE within a single generation. Instead, if allele frequencies in males and females initially differ, they oscillate for a few generations toward equilibrium. Allele frequency differences between the sexes are expected in populations that have experienced recent sex-biased admixture, namely, their male and female founders differed in ancestry. Sex-biased admixture does not allow testing for HWE on X, because deviations are naturally expected, even under random mating (post admixture) and error-free genotyping. In this paper, we develop a likelihood ratio test and a χ2 test to detect deviations from expected genotype frequencies on X, beyond natural deviations due to sex-biased admixture. We demonstrate by simulations that our tests are powerful for detecting deviations due to non-random mating, while at the same time they do not reject the null under historical sex-biased admixture and random mating thereafter. We also demonstrate that when applied to 1000 Genomes project populations, our likelihood ratio test rejects fewer SNPs than other tests, but we describe limitations in the interpretation of the results.
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Affiliation(s)
- Daniel Backenroth
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
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13
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Wellek S, Ziegler A. Testing for goodness rather than lack of fit of an X-chromosomal SNP to the Hardy-Weinberg model. PLoS One 2019; 14:e0212344. [PMID: 30789927 PMCID: PMC6383894 DOI: 10.1371/journal.pone.0212344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/31/2019] [Indexed: 02/01/2023] Open
Abstract
The problem of checking the genotype distribution obtained for some diallelic marker for compatibility with the Hardy-Weinberg equilibrium (HWE) condition arises also for loci on the X chromosome. The possible genotypes depend on the sex of the individual in this case: for females, the genotype distribution is trinomial, as in the case of an autosomal locus, whereas a binomial proportion is observed for males. Like in genetic association studies with autosomal SNPs, interest is typically in establishing approximate compatibility of the observed genotype frequencies with HWE. This requires to replace traditional methods tailored for detecting lack of fit to the model with an equivalence testing procedure to be derived by treating approximate compatibility with the model as the alternative hypothesis. The test constructed here is based on an upper confidence bound and a simple to interpret combined measure of distance between true and HWE conforming genotype distributions in female and male subjects. A particular focus of the paper is on the derivation of the asymptotic distribution of the test statistic under null alternatives which is not of the usual Gaussian form. A closed sample size formula is also provided and shown to behave satisfactorily in terms of the approximation error.
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Affiliation(s)
- Stefan Wellek
- Department of Biostatistics, CIMH Mannheim, Mannheim Medical School of the University of Heidelberg, Mannheim, Germany
- Department of Medical Biostatistics, Epidemiology & Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Andreas Ziegler
- Institute of Medical Biometry and Statistics, University of Lübeck, Lübeck, Germany
- StatSol, Moenring 2, Lübeck, Germany
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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Graffelman J, Weir BS. Multi-allelic exact tests for Hardy-Weinberg equilibrium that account for gender. Mol Ecol Resour 2018; 18:461-473. [PMID: 29288525 PMCID: PMC5969302 DOI: 10.1111/1755-0998.12748] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/15/2017] [Accepted: 12/19/2017] [Indexed: 11/29/2022]
Abstract
Statistical tests for Hardy–Weinberg equilibrium are important elementary tools in genetic data analysis. X‐chromosomal variants have long been tested by applying autosomal test procedures to females only, and gender is usually not considered when testing autosomal variants for equilibrium. Recently, we proposed specific X‐chromosomal exact test procedures for bi‐allelic variants that include the hemizygous males, as well as autosomal tests that consider gender. In this study, we present the extension of the previous work for variants with multiple alleles. A full enumeration algorithm is used for the exact calculations of tri‐allelic variants. For variants with many alternate alleles, we use a permutation test. Some empirical examples with data from the 1,000 genomes project are discussed.
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Affiliation(s)
- Jan Graffelman
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain.,Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Bruce S Weir
- Department of Biostatistics, University of Washington, Seattle, WA, USA
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