Volume measures for linkage disequilibrium

Contribution of Tinnitus and Hearing Loss to Depression: NHANES Population Study

OBJECTIVES

Hearing loss affects the emotional well-being of adults and is sometimes associated with clinical depression. Chronic tinnitus is highly comorbid with hearing loss and separately linked with depression. In this article, the authors investigated the combined effects of hearing loss and tinnitus on depression in the presence of other moderating influences such as demographic, lifestyle, and health factors.

DESIGN

The authors used the National Health and Nutrition Examination Survey data (2011-2012 and 2015-2016) to determine the effects of hearing loss and tinnitus on depression in a population of US adults (20 to 69 years). The dataset included the Patient Health Questionnaire-9 for depression screening, hearing testing using pure-tone audiometry, and information related to multiple demographic, lifestyle, and health factors (n = 5845).

RESULTS

The statistical analysis showed moderate to high associations between depression and hearing loss, tinnitus, and demographic, lifestyle, and health factors, separately. Results of logistic regression analysis revealed that depression was significantly influenced by hearing loss (adjusted odds ratios [OR] = 3.0), the functional impact of tinnitus (adjusted OR = 2.4), and their interaction, both in the absence or presence of the moderating influences. The effect of bothersome tinnitus on depression was amplified in the presence of hearing loss (adjusted OR = 2.4 in the absence of hearing loss to adjusted OR = 14.9 in the presence of hearing loss). Conversely, the effect of hearing loss on depression decreased when bothersome tinnitus was present (adjusted OR = 3.0 when no tinnitus problem was present to adjusted OR = 0.7 in the presence of bothersome tinnitus).

CONCLUSIONS

Together, hearing loss and bothersome tinnitus had a significant effect on self-reported depression symptoms, but their relative effect when comorbid differed. Tinnitus remained more salient than hearing loss and the latter's contribution to depression was reduced in the presence of tinnitus, but the presence of hearing loss significantly increased the effects of tinnitus on depression, even when the effects of the relevant demographic, lifestyle, or health factors were controlled. Treatment strategies that target depression should screen for hearing loss and bothersome tinnitus and provide management options for the conditions.

Genetic insights into crossbred dairy cattle of Pakistan: exploring allele frequency, linkage disequilibrium, and effective population size at a genome-wide scale

Linkage disequilibrium (LD) affects genomic studies accuracy. High-density genotyping platforms identify SNPs across animal genomes, increasing LD evaluation resolution for accurate analysis. This study aimed to evaluate the decay and magnitude of LD in a cohort of 81 crossbred dairy cattle using the GGP_HDv3_C Bead Chip. After quality control, 116,710 Single Nucleotide Polymorphisms (SNPs) across 2520.241 Mb of autosomes were retained. LD extent was assessed between autosomal SNPs within a 10 Mb range using the r2 statistics. LD value declined as inter-marker distance increased. The average r2 value was 0.24 for SNP pairs < 10 kb apart, decreasing to 0.13 for 50-100 kb distances. Minor allele frequency (MAF) and sample size significantly impact LD. Lower MAF thresholds result in smaller r2 values, while higher thresholds show increased r2 values. Additionally, smaller sample sizes exhibit higher average r2 values, especially for larger physical distance intervals (> 50 kb) between SNP pairs. Effective population size and inbreeding coefficient were 150 and 0.028 for the present generation, indicating a decrease in genetic diversity over time. These findings imply that the utilization of high-density SNP panels and customized/breed-specific SNP panels represent a highly favorable approach for conducting genome-wide association studies (GWAS) and implementing genomic selection (GS) in the Bos indicus cattle breeds, whose genomes are still largely unexplored. Furthermore, it is imperative to devise a meticulous breeding strategy tailored to each herd, aiming to enhance desired traits while simultaneously preserving genetic diversity.

Forensic applications and genetic characterization of Liaoning Han population revealed by extended set of autosomal STRs

BACKGROUND

Microsatellites or short tandem repeats (STRs) are considered the gold standard for forensic investigations and autosomal STRs are used for routine forensic personal identification.

AIM

To provide a precise population database on an extended set of STRs which has never been done before and explore the forensic characteristics of 20 autosomal STRs.

SUBJECTS AND METHODS

In the current study, we explored the genetic characteristics of 20 STRs loci in 1138 unrelated Han individuals using Goldeneye® 20A multiplex amplification system kit in the Liaoning Han population. Additionally, phylogenetic analysis based on the Nei's standard genetic distance was performed between the Han population and other relevant populations.

RESULTS

A total of 253 alleles were observed while allelic frequencies ranged from 0.00043 to 0.5369. The combined discrimination power was 99.99999999999999999999789% and the combined exclusion power was 99.999998231%. Most of the loci were in HWE while only five pairs were out of LE. Population genetic analysis showed that the Han population has similarities with other East Asian populations.

CONCLUSION

GoldenEyeTM 20A kit detects high diversity in the Liaoning Han population. These STRs which are part of this kit can be used for forensic investigations. Population genetic analysis showed that the Han population is different from the minority populations of Xinjiang.

Genetic Loci Controlling Carotenoid Biosynthesis in Diverse Tropical Maize Lines

The discovery and use of genetic markers associated with carotenoid levels can help to exploit the genetic potential of maize for provitamin A accumulation more effectively. Provitamin A carotenoids are classes of carotenoids that are precursors of vitamin A, an essential micronutrient in humans. Vitamin A deficiency is a global public health problem affecting millions of people, especially in developing countries. Maize is one of the most important staple crops targeted for provitamin A biofortification to help alleviate vitamin A deficiency in developing countries. A genome-wide association study (GWAS) of maize endosperm carotenoids was conducted using a panel of 130 diverse yellow maize tropical inbred lines genotyped with Genotyping by Sequencing (GBS) SNP markers. Numerous significant association signals co-localizing with the known carotenoid biosynthesis genes crtRB1, lcyE and ZEP1 were identified. The GWAS confirmed previously reported large effects of the two major carotenoid biosynthesis genes lcyE and crtRB1 In addition, significant novel associations were detected for several transcription factors (e.g., RING zinc finger domain and HLH DNA-binding domain super family proteins) that may be involved in regulation of carotenoid biosynthesis in maize. When the GWAS was re-conducted by including the major effects of lcyE and crtRB1 genes as covariates, a SNP in a gene coding for an auxin response factor 20 transcription factor was identified which displayed an association with β-carotene and provitamin A levels. Our study provides a foundation for design and implementation of genomics-assisted selection strategies for provitamin A maize breeding in tropical regions, and advances efforts toward identification of additional genes (and allelic variants) involved in the regulation of carotenoid biosynthesis in plants.

Estimating Disequilibrium Coefficients

Gametic phase disequilibrium is the nonrandom association of alleles within gametes. Linkage disequilibrium (LD) describes the special case of deviation from independence between alleles at two linked genetic loci. Estimation of allelic LD requires knowledge of haplotypes. Genotype-based LD measures dispense with the haplotype estimation step and avoid bias in LD estimation. In this chapter, the most important measures for allelic and genotypic LD are introduced. The use of software packages for LD estimation is illustrated.

Effective Population Size and Signatures of Selection Using Bovine 50K SNP Chips in Korean Native Cattle (Hanwoo)

Inferring the effective population size and the pattern of selection signatures is of interest both from an evolutionary perspective and to improve models for mapping of quantitative trait genes. We used DNA samples of 61 sires and 486 progeny of the Hanwoo, genotyped by the Illumina Bovine SNP50 BeadChip, to analyze the genetic structure. Our study showed a persistent decline in effective population size throughout the period considered, but suggested a marked decline at one distinctive time point (100th generation) and two sharp decline intervals (50th-25th generation and 25th-10th generation). This pattern can be explained by Hanwoo formation and the modern breeding program. Our results revealed 95 regions exhibiting the footprint of recent positive selection at a threshold level of 0.01. We found an overlap of the 11 core regions presenting top P-values and those that had previously been identified as harboring quantitative trait loci from other breeds. The information generated from this study can be used to better understand the mechanism of selection in Hanwoo breeding, and provide important implications for the design and application of association studies in the Hanwoo population.

Genetic Structure of and Evidence for Admixture between Western and Korean Native Pig Breeds Revealed by Single Nucleotide Polymorphisms

Comprehensive information on genetic diversity and introgression is desirable for the design of rational breed improvement and conservation programs. Despite the concerns regarding the genetic introgression of Western pig breeds into the gene pool of the Korean native pig (KNP), the level of this admixture has not yet been quantified. In the present study, we genotyped 93 animals, representing four Western pig breeds and KNP, using the porcine SNP 60K BeadChip to assess their genetic diversity and to estimate the level of admixture among the breeds. Expected heterozygosity was the lowest in Berkshire (0.31) and highest in Landrace (0.42). Population differentiation (F_ST) estimates were significantly different (p<0.000), accounting for 27% of the variability among the breeds. The evidence of inbreeding observed in KNP (0.029) and Yorkshire (0.031) may result in deficient heterozygosity. Principal components one (PC1) and two (PC2) explained approximately 35.06% and 25.20% of the variation, respectively, and placed KNP somewhat proximal to the Western pig breeds (Berkshire and Landrace). When K = 2, KNP shared a substantial proportion of ancestry with Western breeds. Similarly, when K = 3, over 86% of the KNP individuals were in the same cluster with Berkshire and Landrace. The linkage disquilbrium (LD) values at r²_0.3, the physical distance at which LD decays below a threshold of 0.3, ranged from 72.40 kb in Landrace to 85.86 kb in Yorkshire. Based on our structure analysis, a substantial level of admixture between Western and Korean native pig breeds was observed.

Linkage Disequilibrium Estimation of Chinese Beef Simmental Cattle Using High-density SNP Panels

Linkage disequilibrium (LD) plays an important role in genomic selection and mapping quantitative trait loci (QTL). In this study, the pattern of LD and effective population size (N_e) were investigated in Chinese beef Simmental cattle. A total of 640 bulls were genotyped with IlluminaBovinSNP50BeadChip and IlluminaBovinHDBeadChip. We estimated LD for each autosomal chromosome at the distance between two random SNPs of <0 to 25 kb, 25 to 50 kb, 50 to 100 kb, 100 to 500 kb, 0.5 to 1 Mb, 1 to 5 Mb and 5 to 10 Mb. The mean values of r² were 0.30, 0.16 and 0.08, when the separation between SNPs ranged from 0 to 25 kb to 50 to 100 kb and then to 0.5 to 1 Mb, respectively. The LD estimates decreased as the distance increased in SNP pairs, and increased with the increase of minor allelic frequency (MAF) and with the decrease of sample sizes. Estimates of effective population size for Chinese beef Simmental cattle decreased in the past generations and N_e was 73 at five generations ago.

Estimating disequilibrium coefficients

Gametic phase disequilibrium (GPD) is the nonrandom association of alleles within gametes. Linkage disequilibrium (LD) describes the special case of deviation from independence between alleles at two linked genetic loci. Estimation of allelic LD requires knowledge of haplotypes. Genotype-based LD measures dispense with the haplotype estimation step and avoid bias in LD estimation. In this chapter, the most important measures for allelic and genotypic LD are introduced. The use of software packages for LD estimation is illustrated.

Population-genetic comparison of the Sorbian isolate population in Germany with the German KORA population using genome-wide SNP arrays

Background

The Sorbs are an ethnic minority in Germany with putative genetic isolation, making the population interesting for disease mapping. A sample of N = 977 Sorbs is currently analysed in several genome-wide meta-analyses. Since genetic differences between populations are a major confounding factor in genetic meta-analyses, we compare the Sorbs with the German outbred population of the KORA F3 study (N = 1644) and other publically available European HapMap populations by population genetic means. We also aim to separate effects of over-sampling of families in the Sorbs sample from effects of genetic isolation and compare the power of genetic association studies between the samples.

Results

The degree of relatedness was significantly higher in the Sorbs. Principal components analysis revealed a west to east clustering of KORA individuals born in Germany, KORA individuals born in Poland or Czech Republic, Half-Sorbs (less than four Sorbian grandparents) and Full-Sorbs. The Sorbs cluster is nearest to the cluster of KORA individuals born in Poland. The number of rare SNPs is significantly higher in the Sorbs sample. FST between KORA and Sorbs is an order of magnitude higher than between different regions in Germany. Compared to the other populations, Sorbs show a higher proportion of individuals with runs of homozygosity between 2.5 Mb and 5 Mb. Linkage disequilibrium (LD) at longer range is also slightly increased but this has no effect on the power of association studies.

Oversampling of families in the Sorbs sample causes detectable bias regarding higher FST values and higher LD but the effect is an order of magnitude smaller than the observed differences between KORA and Sorbs. Relatedness in the Sorbs also influenced the power of uncorrected association analyses.

Conclusions

Sorbs show signs of genetic isolation which cannot be explained by over-sampling of relatives, but the effects are moderate in size. The Slavonic origin of the Sorbs is still genetically detectable.

Regarding LD structure, a clear advantage for genome-wide association studies cannot be deduced. The significant amount of cryptic relatedness in the Sorbs sample results in inflated variances of Beta-estimators which should be considered in genetic association analyses.

Single nucleotide polymorphism selection using independent component analysis

Bioinformatics research in genome wide association studies necessitates the development of algorithms capable of manipulating very-large datasets of Single Nucleotide Polymorphisms (SNP). To facilitate such association studies, we propose a novel framework for SNP selection using Independent Component Analysis (ICA). Compared to previous ICA-based methods, our framework works as a filtering technique to reduce the number of SNPs in a dataset, without the need for any class labels. We evaluate the proposed method by applying it on three published SNP datasets, and comparing the results to SNP selection methods based on Principal Component Analysis (PCA). Our results show the capability of ICA to capture an increased or matching amount of information from the datasets.

Extensive linkage disequilibrium in a wild bird population

Knowledge about the extent and patterns of linkage disequilibrium (LD) can provide important insights into demographic processes and strategies to identify the genetic basis of complex phenotypes in wild populations. However, data on the extent and patterns of LD from non-model vertebrate species from the wild are still scarce. We conducted so far the most extensive and detailed examination of LD in a pedigreed wild bird population using genotypes from 97 autosomal and 6 gonosomal microsatellites and a recently established linkage map of Siberian jays (Perisoreus infaustus). Analysis of syntenic marker pairs showed high levels of LD that extended over tens of centimorgans or several megabases and generally decayed as an increasing function of intermarker distance. In addition, significant LD was also very common between nonsyntenic markers. Patterns of LD varied across different linkage groups possibly because of the differences in chromosomal structure (macro-, micro-, and Z-chromosome). In particular, the level of LD was significantly lower on the Z-chromosome than on the autosomes at comparable genetic distances. In general, the high levels and extent of LD in this population are likely owing to its relatively small size, significant intrapopulation genetic structure, and occurrence of inbreeding. Whatever the cause, the long-range LD between syntenic loci suggests that LD mapping of phenotypic traits in this population using low-density markers maps is feasible. However, the frequent occurrence of LD between nonsyntenic markers suggests that the combined use of linkage and LD methods is needed to reduce the likelihood of false-positive associations between marker loci and traits of ecological and evolutionary interest.

Haplotype block partitioning as a tool for dimensionality reduction in SNP association studies

BACKGROUND

Identification of disease-related genes in association studies is challenged by the large number of SNPs typed. To address the dilution of power caused by high dimensionality, and to generate results that are biologically interpretable, it is critical to take into consideration spatial correlation of SNPs along the genome. With the goal of identifying true genetic associations, partitioning the genome according to spatial correlation can be a powerful and meaningful way to address this dimensionality problem.

RESULTS

We developed and validated an MCMC Algorithm To Identify blocks of Linkage DisEquilibrium (MATILDE) for clustering contiguous SNPs, and a statistical testing framework to detect association using partitions as units of analysis. We compared its ability to detect true SNP associations to that of the most commonly used algorithm for block partitioning, as implemented in the Haploview and HapBlock software. Simulations were based on artificially assigning phenotypes to individuals with SNPs corresponding to region 14q11 of the HapMap database. When block partitioning is performed using MATILDE, the ability to correctly identify a disease SNP is higher, especially for small effects, than it is with the alternatives considered. Advantages can be both in terms of true positive findings and limiting the number of false discoveries. Finer partitions provided by LD-based methods or by marker-by-marker analysis are efficient only for detecting big effects, or in presence of large sample sizes. The probabilistic approach we propose offers several additional advantages, including: a) adapting the estimation of blocks to the population, technology, and sample size of the study; b) probabilistic assessment of uncertainty about block boundaries and about whether any two SNPs are in the same block; c) user selection of the probability threshold for assigning SNPs to the same block.

CONCLUSION

We demonstrate that, in realistic scenarios, our adaptive, study-specific block partitioning approach is as or more efficient than currently available LD-based approaches in guiding the search for disease loci.

Virus population dynamics and acquired virus resistance in natural microbial communities

Viruses shape microbial community structure and function by altering the fitness of their hosts and by promoting genetic exchange. The complexity of most natural ecosystems has precluded detailed studies of virus-host interactions. We reconstructed virus and host bacterial and archaeal genome sequences from community genomic data from two natural acidophilic biofilms. Viruses were matched to their hosts by analyzing spacer sequences that occur among clustered regularly interspaced short palindromic repeats (CRISPRs) that are a hallmark of virus resistance. Virus population genomic analyses provided evidence that extensive recombination shuffles sequence motifs sufficiently to evade CRISPR spacers. Only the most recently acquired spacers match coexisting viruses, which suggests that community stability is achieved by rapid but compensatory shifts in host resistance levels and virus population structure.

Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel

BACKGROUND

The extent of linkage disequilibrium (LD) within a population determines the number of markers that will be required for successful association mapping and marker-assisted selection. Most studies on LD in cattle reported to date are based on microsatellite markers or small numbers of single nucleotide polymorphisms (SNPs) covering one or only a few chromosomes. This is the first comprehensive study on the extent of LD in cattle by analyzing data on 1,546 Holstein-Friesian bulls genotyped for 15,036 SNP markers covering all regions of all autosomes. Furthermore, most studies in cattle have used relatively small sample sizes and, consequently, may have had biased estimates of measures commonly used to describe LD. We examine minimum sample sizes required to estimate LD without bias and loss in accuracy. Finally, relatively little information is available on comparative LD structures including other mammalian species such as human and mouse, and we compare LD structure in cattle with public-domain data from both human and mouse.

RESULTS

We computed three LD estimates, D', Dvol and r2, for 1,566,890 syntenic SNP pairs and a sample of 365,400 non-syntenic pairs. Mean D' is 0.189 among syntenic SNPs, and 0.105 among non-syntenic SNPs; mean r2 is 0.024 among syntenic SNPs and 0.0032 among non-syntenic SNPs. All three measures of LD for syntenic pairs decline with distance; the decline is much steeper for r2 than for D' and Dvol. The value of D' and Dvol are quite similar. Significant LD in cattle extends to 40 kb (when estimated as r2) and 8.2 Mb (when estimated as D'). The mean values for LD at large physical distances are close to those for non-syntenic SNPs. Minor allelic frequency threshold affects the distribution and extent of LD. For unbiased and accurate estimates of LD across marker intervals spanning < 1 kb to > 50 Mb, minimum sample sizes of 400 (for D') and 75 (for r2) are required. The bias due to small samples sizes increases with inter-marker interval. LD in cattle is much less extensive than in a mouse population created from crossing inbred lines, and more extensive than in humans.

CONCLUSION

For association mapping in Holstein-Friesian cattle, for a given design, at least one SNP is required for each 40 kb, giving a total requirement of at least 75,000 SNPs for a low power whole-genome scan (median r2 > 0.19) and up to 300,000 markers at 10 kb intervals for a high power genome scan (median r2 > 0.62). For estimation of LD by D' and Dvol with sufficient precision, a sample size of at least 400 is required, whereas for r2 a minimum sample of 75 is adequate.