Investigations of the Y chromosome, male founder structure and YSTR mutation rates in the Old Order Amish

Mutagenesis of human genomes by endogenous mobile elements on a population scale

Several large-scale Illumina whole-genome sequencing (WGS) and whole-exome sequencing (WES) projects have emerged recently that have provided exceptional opportunities to discover mobile element insertions (MEIs) and study the impact of these MEIs on human genomes. However, these projects also have presented major challenges with respect to the scalability and computational costs associated with performing MEI discovery on tens or even hundreds of thousands of samples. To meet these challenges, we have developed a more efficient and scalable version of our mobile element locator tool (MELT) called CloudMELT. We then used MELT and CloudMELT to perform MEI discovery in 57,919 human genomes and exomes, leading to the discovery of 104,350 nonredundant MEIs. We leveraged this collection (1) to examine potentially active L1 source elements that drive the mobilization of new Alu, L1, and SVA MEIs in humans; (2) to examine the population distributions and subfamilies of these MEIs; and (3) to examine the mutagenesis of GENCODE genes, ENCODE-annotated features, and disease genes by these MEIs. Our study provides new insights on the L1 source elements that drive MEI mutagenesis and brings forth a better understanding of how this mutagenesis impacts human genomes.

Prevalence, control, and treatment of diabetes, hypertension, and high cholesterol in the Amish

BACKGROUND

The burden of diabetes and cardiovascular risk is not uniform across the USA, with much of this disparity tracking differences in socioeconomic status, cultural practices and lifestyle. To further evaluate disparities in these disorders, we assessed the prevalence of diabetes, hypertension, and hypercholesterolemia in an Old Order Amish community that is characterized by distinctive sociocultural practices that include a very cohesive social structure and limited use of modern technologies and medications. We compared prevalence of these conditions with that of the overall US population.

METHOD

We performed a community-wide survey in 5377 Amish individuals aged 18 years and older from the Lancaster County, Pennsylvania, Amish settlement that included a basic physical examination and fasting blood draw during the period 2010-2018. We then compared the prevalence of diabetes, hypertension, and high cholesterol, defined using standard criteria, between the Amish and the European Caucasian subsample of the 2013-2014 US National Health and Nutrition Examination Survey (NHANES).

RESULTS

Prevalence rates for diabetes, hypertension and hypercholesterolemia were 3.3%, 12.7%, and 26.2% in the Amish compared with 13.2%, 37.8% and 35.7% in NHANES (p<0.001 for all). Among individuals with these disorders, Amish were less likely to be aware that they were affected, and among those aware, were less likely to be treated with a medication for their disorder.

CONCLUSION

There is substantially lower prevalence of diabetes, hypertension and hypercholesterolemia in the Amish compared with non-Amish Caucasians in the USA. Possible factors contributing to this disparity include higher physical activity levels in the Amish or other protective sociocultural factors, a greater understanding of which could inform risk reduction interventions for these chronic diseases.

Association of plasma nitrite levels with obesity and metabolic syndrome in the Old Order Amish

OBJECTIVES

Plasma nitrite is a metabolite of nitric oxide and reflects endogenous nitric oxide synthase (NOS) activity. Although plasma nitrites were previously linked with obesity and metabolic syndrome (MetS), the direction of association remains inconsistent, possibly due to sample heterogeneity. In a relatively homogeneous population, we hypothesized that nitrite levels will be positively associated with overweight/obesity and MetS.

METHODS

Fasting nitrite levels were measured in 116 Old Order Amish (78% women). We performed age-and-sex-adjusted ancovas to compare nitrite levels between three groups (a) overweight/obese(-)MetS(-), (b) overweight/obese(+)MetS(-) and (c) overweight/obese(+)MetS)(+). Multivariate linear regressions were conducted on nitrite associations with continuous metabolic variables, with successive adjustments for demographics, body mass index, C-reactive protein and neopterin.

RESULTS

Nitrite levels were higher in the obese/overweight(+)MetS(+) group than in the other two groups (p < 0.001). Nitrites were positively associated with levels of triglycerides (p < 0.0001), total cholesterol (p = 0.048), high-density lipoprotein/cholesterol ratio (p < 0.0001) and fasting glucose (p < 0.0001), and negatively correlated with high-density lipoprotein-cholesterol (p < 0.0001). These associations were robust to adjustments for body mass index and inflammatory markers.

CONCLUSION

Further investigation of the connection between obesity/MetS and plasma nitrite levels may lead to novel dietary and pharmacological approaches that ultimately may contribute to reducing the increasing burden of obesity, MetS and cardiovascular morbidity and mortality.

SOME USES OF MODELS OF QUANTITATIVE GENETIC SELECTION IN SOCIAL SCIENCE

The theory of selection of quantitative traits is widely used in evolutionary biology, agriculture and other related fields. The fundamental model known as the breeder’s equation is simple, robust over short time scales, and it is often possible to estimate plausible parameters. In this paper it is suggested that the results of this model provide useful yardsticks for the description of social traits and the evaluation of transmission models. The differences on a standard personality test between samples of Old Order Amish and Indiana rural young men from the same county and the decline of homicide in Medieval Europe are used as illustrative examples of the overall approach. It is shown that the decline of homicide is unremarkable under a threshold model while the differences between rural Amish and non-Amish young men are too large to be a plausible outcome of simple genetic selection in which assortative mating by affiliation is equivalent to truncation selection.

Three hundred years of low non-paternity in a human population

When cuckoldry is frequent we can expect fathers to withhold investment in offspring that may not be theirs. Human paternal investment can be substantial and is in line with observations from tens of thousands of conceptions that suggest that cuckoldry is rare in humans. The generality of this claim seems to be in question as the rate of cuckoldry varies across populations and studies have mostly been on Western populations. Two additional factors complicate our conclusions, (1) current estimates of the rate of cuckoldry in humans may not reflect our past behaviour as adultery can be concealed by the use of contraceptives; and (2) it is difficult to obtain samples that are random with respect to their paternity certainty. Studies that combine genealogies with Y-chromosome haplotyping are able to circumvent some of these problems by probing into humans' historical behaviour. Here we use this approach to investigate 1273 conceptions over a period of 330 years in 23 families of the Afrikaner population in South Africa. We use haplotype frequency and diversity and coalescent simulations to show that the male population did not undergo a severe bottleneck and that paternity exclusion rates are high for this population. The rate of cuckoldry in this Western population was 0.9% (95% confidence interval 0.4-1.5%), and we argue that given the current data on historical populations we have to conclude that, at least for Western human populations, cuckoldry rate is probably in the range of 1%.

Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome

Obesity has been linked to the human gut microbiota; however, the contribution of gut bacterial species to the obese phenotype remains controversial because of conflicting results from studies in different populations. To explore the possible dysbiosis of gut microbiota in obesity and its metabolic complications, we studied men and women over a range of body mass indices from the Old Order Amish sect, a culturally homogeneous Caucasian population of Central European ancestry. We characterized the gut microbiota in 310 subjects by deep pyrosequencing of bar-coded PCR amplicons from the V1-V3 region of the 16S rRNA gene. Three communities of interacting bacteria were identified in the gut microbiota, analogous to previously identified gut enterotypes. Neither BMI nor any metabolic syndrome trait was associated with a particular gut community. Network analysis identified twenty-two bacterial species and four OTUs that were either positively or inversely correlated with metabolic syndrome traits, suggesting that certain members of the gut microbiota may play a role in these metabolic derangements.

Hypertrophy-associated polymorphisms ascertained in a founder cohort applied to heart failure risk and mortality

A three-stage approach was undertaken using genome-wide, case-control, and case-only association studies to identify genetic variants associated with heart failure mortality. In an Amish founder population (n = 851), cardiac hypertrophy, a trait integral to the adaptive response to failure, was found to be heritable (h² = 0.28, p = 0.0002) and GWAS revealed 21 candidate hypertrophy SNPs. In a case (n = 1,610)-control (n = 463) study in unrelated Caucasians, one of the SNPs associated with hypertrophy (rs2207418, p = 8 × 10⁻⁶), was associated with heart failure, RR = 1.85(1.25-2.73, p = 0.0019). In heart failure cases rs2207418 was associated with increased mortality, HR = 1.51(1.20-1.97, p = 0.0004). There was consistency between studies, with the GG allele being associated with increased ventricular mass (~13 g/m²) in the Amish, heart failure risk, and heart failure mortality. This SNP is in a gene desert of chromosome 20p12. Five genes are within 2.0 mbp of rs2207418 but with low LD between their SNPs and rs2207418. A region near this SNP is highly conserved in multiple vertebrates (lod score = 1,208). This conservation and the internal consistency across studies suggests that this region has biologic importance in heart failure, potentially acting as an enhancer or repressor element. rs2207418 may be useful for predicting a more progressive form of heart failure that may require aggressive therapy.

Persistent Staphylococcus aureus colonization is not a strongly heritable trait in Amish families

About 20% of adults are persistently colonized with S. aureus in the anterior nares. Host genetic factors could contribute susceptibility to this phenotype. The objective of this study was to determine whether the phenotype of persistent S. aureus colonization aggregates in family members who live in different households. Healthy adults and their eligible same sex siblings who lived in different households were recruited from the Old Order Amish of Lancaster, Pennsylvania. All participants had two cultures of the anterior nares to determine if they were persistently colonized with S. aureus. Three hundred and ninety eight participants finished the study, of whom 166 were index cases and 232 were siblings of index cases. Eighteen per cent (71/398) of all participants and 17% (29/166) of index cases were persistently colonized with S. aureus. Twenty two per cent (8/36) of siblings of persistently colonized index cases were persistently colonized with S. aureus compared to 17% (34/196) of siblings of non-persistently colonized index cases, yielding a prevalence rate ratio of 1.28 (95% CI: 0.65–2.54, p = 0.64) and sibling relative risk of 1.25 (95% CI: 0.65–2.38, p = 0.51). The heritability of persistent colonization was 0.19±0.21 (p = 0.31). Persistent S. aureus colonization does not strongly aggregate in Amish family members in different households and heritability is low, suggesting that environmental factors or acquired host factors are more important than host genetic factors in determining persistent S. aureus colonization in this community.

Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications

Nonrecombining Y-chromosomal microsatellites (Y-STRs) are widely used to infer population histories, discover genealogical relationships, and identify males for criminal justice purposes. Although a key requirement for their application is reliable mutability knowledge, empirical data are only available for a small number of Y-STRs thus far. To rectify this, we analyzed a large number of 186 Y-STR markers in nearly 2000 DNA-confirmed father-son pairs, covering an overall number of 352,999 meiotic transfers. Following confirmation by DNA sequence analysis, the retrieved mutation data were modeled via a Bayesian approach, resulting in mutation rates from 3.78 × 10(-4) (95% credible interval [CI], 1.38 × 10(-5) - 2.02 × 10(-3)) to 7.44 × 10(-2) (95% CI, 6.51 × 10(-2) - 9.09 × 10(-2)) per marker per generation. With the 924 mutations at 120 Y-STR markers, a nonsignificant excess of repeat losses versus gains (1.16:1), as well as a strong and significant excess of single-repeat versus multirepeat changes (25.23:1), was observed. Although the total repeat number influenced Y-STR locus mutability most strongly, repeat complexity, the length in base pairs of the repeated motif, and the father's age also contributed to Y-STR mutability. To exemplify how to practically utilize this knowledge, we analyzed the 13 most mutable Y-STRs in an independent sample set and empirically proved their suitability for distinguishing close and distantly related males. This finding is expected to revolutionize Y-chromosomal applications in forensic biology, from previous male lineage differentiation toward future male individual identification.

Extent and distribution of linkage disequilibrium in the Old Order Amish

Knowledge of the extent and distribution of linkage disequilibrium (LD) is critical to the design and interpretation of gene mapping studies. Because the demographic history of each population varies and is often not accurately known, it is necessary to empirically evaluate LD on a population-specific basis. Here we present the first genome-wide survey of LD in the Old Order Amish (OOA) of Lancaster County Pennsylvania, a closed population derived from a modest number of founders. Specifically, we present a comparison of LD between OOA individuals and US Utah participants in the International HapMap project (abbreviated CEU) using a high-density single nucleotide polymorphism (SNP) map. Overall, the allele (and haplotype) frequency distributions and LD profiles were remarkably similar between these two populations. For example, the median absolute allele frequency difference for autosomal SNPs was 0.05, with an inter-quartile range of 0.02–0.09, and for autosomal SNPs 10–20 kb apart with common alleles (minor allele frequency≥0.05), the LD measure r² was at least 0.8 for 15 and 14% of SNP pairs in the OOA and CEU, respectively. Moreover, tag SNPs selected from the HapMap CEU sample captured a substantial portion of the common variation in the OOA (∼88%) at r²≥0.8. These results suggest that the OOA and CEU may share similar LD profiles for other common but untyped SNPs. Thus, in the context of the common variant-common disease hypothesis, genetic variants discovered in gene mapping studies in the OOA may generalize to other populations.

PedHunter 2.0 and its usage to characterize the founder structure of the Old Order Amish of Lancaster County

BACKGROUND

Because they are a closed founder population, the Old Order Amish (OOA) of Lancaster County have been the subject of many medical genetics studies. We constructed four versions of Anabaptist Genealogy Database (AGDB) using three sources of genealogies and multiple updates. In addition, we developed PedHunter, a suite of query software that can solve pedigree-related problems automatically and systematically.

METHODS

We report on how we have used new features in PedHunter to quantify the number and expected genetic contribution of founders to the OOA. The queries and utility of PedHunter programs are illustrated by examples using AGDB in this paper. For example, we calculated the number of founders expected to be contributing genetic material to the present-day living OOA and estimated the mean relative founder representation for each founder. New features in PedHunter also include pedigree trimming and pedigree renumbering, which should prove useful for studying large pedigrees.

RESULTS

With PedHunter version 2.0 querying AGDB version 4.0, we identified 34,160 presumed living OOA individuals and connected them into a 14-generation pedigree descending from 554 founders (332 females and 222 males) after trimming. From the analysis of cumulative mean relative founder representation, 128 founders (78 females and 50 males) accounted for over 95% of the mean relative founder contribution among living OOA descendants.

DISCUSSION/CONCLUSIONS

The OOA are a closed founder population in which a modest number of founders account for the genetic variation present in the current OOA population. Improvements to the PedHunter software will be useful in future studies of both the OOA and other populations with large and computerized genealogies.

Aspirin Resistance in healthy drug-naive men versus women (from the Heredity and Phenotype Intervention Heart Study)

This study was designed to determine the factors that contribute to interindividual variation in the antiplatelet effects of aspirin. We measured platelet response to aspirin in 745 (400 men and 345 women) drug-naive asymptomatic subjects of the Heredity and Phenotype Intervention (HAPI) Heart Study. Whole blood platelet aggregometry was performed to assess response to arachidonic acid, adenosine diphosphate, and collagen at baseline and after 14 days of aspirin 81 mg/day. There was wide interindividual variation in platelet aggregation in response to aspirin, with no clear biological threshold to define aspirin resistance. Variation in platelet function before and after aspirin was heritable. Women exhibited greater platelet aggregability in response to adenosine diphosphate and collagen at baseline and after aspirin administration. The degree to which aspirin inhibited collagen-induced platelet aggregation was also significantly less in women compared with men (mean +/- SD percent inhibition of collagen-induced [1 microg/ml] platelet aggregation 49.9 +/- 30.9 vs 57.5 +/- 42.5 in women and men, respectively, p = 0.005). Using a cutoff <70% inhibition of collagen-induced platelet aggregation, 21% of the total population demonstrated aspirin resistance, which occurred in 30% of women and 16% of men (p = 0.0002). Aspirin-resistant subjects were older, had significantly higher total cholesterol and low-density lipoprotein cholesterol levels, lower hematocrit, and higher platelet count compared with aspirin-sensitive subjects. In conclusion, in this study group, platelet function is heritable. There is wide interindividual variation in platelet response to aspirin as defined by whole blood platelet aggregometry, with women having lower mean percent inhibition of platelet aggregation and greater prevalence of aspirin resistance than men.

A genome-wide scan in an Amish pedigree with parkinsonism

The identification of familial Parkinson Disease (PD) genes is yielding important molecular pathogenetic insights. In an effort to identify additional PD genes, we studied an eight generation Amish pedigree with apparent autosomal dominant parkinsonism with incomplete penetrance. Phenotypic variability ranged from idiopathic PD to progressive supranuclear palsy (PSP), with the average age at onset 53 years (range of 39 to 74 years). We identified markers on chromosome 3 and 7 that were significant at a genome-wide level by parametric and nonparametric criteria, lod > 3 and non-parametric P-value < 0.10, respectively. We also identified markers on chromosomes 10 and 22 with lod > 3. These data suggest that parkinsonism in this pedigree is genetically complex, with contributions from several loci.