European population substructure: clustering of northern and southern populations

Regional European genetic ancestry predicts type I interferon level and risk of severe viral infection

BACKGROUND

Viral infection outcomes vary widely between individuals, ranging from mild symptoms to severe organ failure and death, and it is clear that host genetic factors play a role in this variability. Type I interferon (IFN) is a critical anti-viral cytokine, and we have previously noted differences in type I IFN levels between world populations.

METHODS

In this study, we investigate the interrelationship between regional European genetic ancestry, type I IFN levels and severe viral infection outcomes.

RESULTS

In cohorts of European ancestry lupus patients living in Europe, we noted higher IFN in the Northwestern populations as compared to Southeastern populations. In an independent cohort of European ancestry lupus patients from the USA with varying proportional regional European genetic admixture, we observed the same Northwest vs. Southeast European ancestry IFN gradient. We developed a model to predict type I IFN level based on regional European ancestry (Area under the curve (AUC) = 0.73, P = 6.1e-6). Examining large databases containing serious viral outcomes data, we found that lower predicted IFN in the corresponding European country was significantly correlated with increased viral infection fatality rate, including Coronavirus Disease 2019 (COVID-19), viral hepatitis and HIV [correlation coefficients: -0.79 (P = 4e-2), -0.94 (P = 6e-3) and -0.96 (P = 8e-2), respectively].

CONCLUSIONS

This association between predicted type I IFN level and viral outcome severity suggests a potential causal relationship, as greater intrinsic type I IFN is beneficial in host defense against viruses. Genetic testing could provide insight into individual and population level risk of fatality due to viruses prior to infection, across a wide range of viral pathogens.

KRAS and BRAF Mutation Rates and Survival Outcomes in Colorectal Cancer in an Ethnically Diverse Patient Cohort

KRAS and BRAF mutation rates in colorectal cancer (CRC) reported from various mono-ethnic studies vary amongst different ethnic groups. However, these differences in mutation rates may not be statistically significant or may be due to differences in environmental and/or laboratory factors across countries rather than racial genetic differences. Here, we compare the KRAS/BRAF mutation rates and survival outcomes in CRC between ethnic groups at a single institution. We also investigate the contributions of genetic, environmental, and laboratory factors to the variations in KRAS/BRAF mutation rates reported from different countries. Clinicopathological data from 453 ethnically diverse patients with CRC were retrospectively analyzed at Liverpool Hospital, NSW Australia (2014-2016). KRAS/BRAF mutations were detected using real-time PCR (Therascreen kits from Qiagen). Mismatch repair (MMR) status was determined using immunohistochemical staining. Four ethnic groups were analyzed: Caucasian, Middle Eastern, Asian, and South American. Overall survival data were available for 406 patients. There was no significant difference in KRAS mutation rates between Caucasians (41.1%), Middle Easterners (47.9%), Asians (44.8%), and South Americans (25%) (p = 0.34). BRAF mutation rates differed significantly between races (p = 0.025), with Caucasians having the highest rates (13.5%) and Middle Easterners the lowest (0%). A secondary analysis in which Caucasians were divided into three subgroups showed that ethnic grouping correlated significantly with KRAS mutation rate (p = 0.009), with central and eastern Europeans having the highest rates (58.3%). There were no significant differences in overall survival (OS) or disease-free survival (DFS) between the four races. The similarity in KRAS mutation rates across races raises the possibility that the differences in KRAS mutation rates reported from various countries may either not be statistically significant or may be due to environmental and/or laboratory factors rather than underlying racial genetic differences. In contrast, we verified that BRAF mutation rates differ significantly between races, suggesting racial genetic differences may be responsible for the discrepant BRAF mutation rates reported from different countries.

Unappreciated subcontinental admixture in Europeans and European Americans and implications for genetic epidemiology studies

European-ancestry populations are recognized as stratified but not as admixed, implying that residual confounding by locus-specific ancestry can affect studies of association, polygenic adaptation, and polygenic risk scores. We integrate individual-level genome-wide data from ~19,000 European-ancestry individuals across 79 European populations and five European American cohorts. We generate a new reference panel that captures ancestral diversity missed by both the 1000 Genomes and Human Genome Diversity Projects. Both Europeans and European Americans are admixed at the subcontinental level, with admixture dates differing among subgroups of European Americans. After adjustment for both genome-wide and locus-specific ancestry, associations between a highly differentiated variant in LCT (rs4988235) and height or LDL-cholesterol were confirmed to be false positives whereas the association between LCT and body mass index was genuine. We provide formal evidence of subcontinental admixture in individuals with European ancestry, which, if not properly accounted for, can produce spurious results in genetic epidemiology studies.

Developing CIRdb as a catalog of natural genetic variation in the Canary Islanders

The current inhabitants of the Canary Islands have a unique genetic makeup in the European diversity landscape due to the existence of African footprints from recent admixture events, especially of North African components (> 20%). The underrepresentation of non-Europeans in genetic studies and the sizable North African ancestry, which is nearly absent from all existing catalogs of worldwide genetic diversity, justify the need to develop CIRdb, a population-specific reference catalog of natural genetic variation in the Canary Islanders. Based on array genotyping of the selected unrelated donors and comparisons against available datasets from European, sub-Saharan, and North African populations, we illustrate the intermediate genetic differentiation of Canary Islanders between Europeans and North Africans and the existence of within-population differences that are likely driven by genetic isolation. Here we describe the overall design and the methods that are being implemented to further develop CIRdb. This resource will help to strengthen the implementation of Precision Medicine in this population by contributing to increase the diversity in genetic studies. Among others, this will translate into improved ability to fine map disease genes and simplify the identification of causal variants and estimate the prevalence of unattended Mendelian diseases.

The Pioneer Advantage: Filling the blank spots on the map of genome diversity in Europe

Documenting genome diversity is important for the local biomedical communities and instrumental in developing precision and personalized medicine. Currently, tens of thousands of whole-genome sequences from Europe are publicly available, but most of these represent populations of developed countries of Europe. The uneven distribution of the available data is further impaired by the lack of data sharing. Recent whole-genome studies in Eastern Europe, one in Ukraine and one in Russia, demonstrated that local genome diversity and population structure from Eastern Europe historically had not been fully represented. An unexpected wealth of genomic variation uncovered in these studies was not so much a consequence of high variation within their population, but rather due to the "pioneer advantage." We discovered more variants because we were the first to prospect in the Eastern European genome pool. This simple comparison underscores the importance of removing the remaining geographic genome deserts from the rest of the world map of the human genome diversity.

State of the Art for Microhaplotypes

In recent years, the number of publications on microhaplotypes has averaged more than a dozen papers annually. Many have contributed to a significant increase in the number of highly polymorphic microhaplotype loci. This increase allows microhaplotypes to be very informative in four main areas of forensic uses of DNA: individualization, ancestry inference, kinship analysis, and mixture deconvolution. The random match Probability (RMP) can be as small as 10−100 for a large panel of microhaplotypes. It is possible to measure the heterozygosity of an MH as the effective number of alleles (Ae). Ae > 7.5 exists for African populations and >4.5 exists for Native American populations for a smaller panel of two dozen selected microhaplotypes. Using STRUCTURE, at least 10 different ancestral clusters can be defined by microhaplotypes. The Ae for a locus is also identical to the Paternity Index (PI), the measure of how informative a locus will be in parentage testing. High Ae loci can also be useful in missing persons cases. Finally, high Ae microhaplotypes allow the near certainty of seeing multiple additional alleles in a mixture of two or more individuals in a DNA sample. In summary, a panel of higher Ae microhaplotypes can outperform the standard CODIS markers.

Admixture Mapping of Sepsis in European Individuals With African Ancestries

Sepsis is a severe systemic inflammatory response to infections that is accompanied by organ dysfunction. Although the ancestral genetic background is a relevant factor for sepsis susceptibility, there is a lack of studies using the genetic singularities of a recently admixed population to identify loci involved in sepsis susceptibility. Here we aimed to discover new sepsis loci by completing the first admixture mapping study of sepsis in Canary Islanders, leveraging their distinctive genetic makeup as a mixture of Europeans and African ancestries. We used a case-control approach and inferred local ancestry blocks from genome-wide data from 113,414 polymorphisms genotyped in 343 patients with sepsis and 410 unrelated controls, all ascertained for grandparental origin in the Canary Islands (Spain). Deviations in local ancestries between cases and controls were tested using logistic regressions, followed by fine-mapping analyses based on imputed genotypes, in silico functional assessments, and gene expression analysis centered on the region of interest. The admixture mapping analysis detected that local European ancestry in a locus spanning 1.2 megabases of chromosome 8p23.1 was associated with sepsis (lowest p = 1.37 × 10⁻⁴; Odds Ratio [OR] = 0.51; 95%CI = 0.40–0.66). Fine-mapping studies prioritized the variant rs13249564 within intron 1 of MFHAS1 gene associated with sepsis (p = 9.94 × 10⁻⁴; OR = 0.65; 95%CI = 0.50–0.84). Functional and gene expression analyses focused on 8p23.1 allowed us to identify alternative genes with possible biological plausibility such as defensins, which are well-known effector molecules of innate immunity. By completing the first admixture mapping study of sepsis, our results revealed a new genetic locus (8p23.1) harboring a number of genes with plausible implications in sepsis susceptibility.

Ethnic-specific associations between dietary consumption and gestational diabetes mellitus incidence: A meta-analysis

Globally, one in seven pregnant women are diagnosed with gestational diabetes mellitus (GDM), conferring short- and long-term health risks to both mother and child. While dietary prevention strategies are common in clinical practice, their effectiveness in different ethnicities is uncertain. To better inform prevention strategies, here the effects of unhealthy and healthy diets on GDM risk within distinct ethnic or cultural populations and geographic regions were evaluated and summarised. Pubmed, Scopus, Cochrane and OVID were systematically searched to identify randomised controlled trials (RCTs) and observational studies that investigated diet and GDM. A grouped analysis of common 'healthy' and 'unhealthy' diets was performed first, before analysing individual dietary patterns (e.g., prudent, Mediterranean). Random effect models and dose response analyses were performed where possible. PROSPERO (CRD42019140873). Thirty-eight publications provided information on 5 population groups: white European (WE), Asian, Iranian, Mediterranean and Australian. No associations were identified between healthy diets and GDM incidence in RCTs in any population. However, when synthesizing observational studies, healthy diets reduced odds of GDM by 23% (95% CI: 0.70-0.89, p<0.001, I2 = 75%), while unhealthy diets increased odds of GDM by 61% (95% CI: 1.41-1.81, p<0.0001, I2 = 0%) in WE women. No evidence of consistent effects in other populations were observed, even when adequately powered. Diet consistently associated with GDM risk in WEs but not in other populations. Heterogenous use and reporting of ethnically and culturally appropriate diets and dietary assessment tools, particularly in RCTs, raises uncertainty regarding the lack of association found in non-WE populations. Future studies require the use of culturally appropriate tools to confidently evaluate dietary and metabolic mediators of GDM and inform culturally-specific dietary prevention strategies.

Quantifying simultaneous innovations in evolutionary medicine

To what extent do simultaneous innovations occur and are independently from each other? In this paper we use a novel persistent keyword framework to systematically identify innovations in a large corpus containing academic papers in evolutionary medicine between 2007 and 2011. We examine whether innovative papers occurring simultaneously are independent from each other by evaluating the citation and co-authorship information gathered from the corpus metadata. We find that 19 out of 22 simultaneous innovative papers do, in fact, occur independently from each other. In particular, co-authors of simultaneous innovative papers are no more geographically concentrated than the co-authors of similar non-innovative papers in the field. Our result suggests producing innovative work draws from a collective knowledge pool, rather than from knowledge circulating in distinct localized collaboration networks. Therefore, new ideas can appear at multiple locations and with geographically dispersed co-authorship networks. Our findings support the perspective that simultaneous innovations are the outcome of collective behavior.

Admixture mapping of asthma in southwestern Europeans with North African ancestry influences

The prevalence of asthma symptoms in Canary Islanders, a southwestern European population from Spain, is almost three times higher than the country average. Because the genetic risks identified so far explain <5% of asthma heritability, here we aimed to discover new asthma loci by completing the first admixture mapping study in Canary Islanders leveraging their distinctive genetic makeup, where significant northwest African influences coexist in the European genetic diversity landscape. A 2-stage study was conducted in 1,491 unrelated individuals self-declaring having a Canary Islands origin for the 4 grandparents. Local ancestry estimates were obtained for the shared positions with reference data from putative ancestral populations from Europe, North Africa, and sub-Saharan Africa. Case-control deviations in local ancestry were tested for each ancestry separately using logistic regressions adjusted for principal components, followed by fine-mapping analyses based on imputed genotypes and analyses of the likely deleterious exonic variants. The admixture mapping analysis of asthma detected that local North African ancestry in a locus spanning 365 kb of chromosome 16q23.3 was associated with asthma risk at study-wide significance [lowest P = 1.12 × 10^-4; odds ratio (OR) = 2.05; 95% confidence interval (CI) = 1.41-3.00]. Fine-mapping studies identified a variant associated with asthma, and results were replicated in independent samples (rs3852738, OR = 1.34; 95% CI = 1.13-1.59, P = 7.58 × 10^-4). Whole exome sequencing data from a subset of individuals revealed an enrichment of likely deleterious variants among asthma cases in 16q23.3, particularly in the phospholipase Cγ2 (PLCG2) gene (P = 3.67 × 10^-4). By completing the first mapping study of asthma in admixed populations from Europe, our results revealed a new plausible asthma locus.

High-resolution inference of genetic relationships among Jewish populations

Recent studies have used genome-wide single-nucleotide polymorphisms (SNPs) to investigate relationships among various Jewish populations and their non-Jewish historical neighbors, often focusing on small subsets of populations from a limited geographic range or relatively small samples within populations. Here, building on the significant progress that has emerged from genomic SNP studies in the placement of Jewish populations in relation to non-Jewish populations, we focus on population structure among Jewish populations. In particular, we examine Jewish population-genetic structure in samples that span much of the historical range of Jewish populations in Europe, the Middle East, North Africa, and South Asia. Combining 429 newly genotyped samples from 29 Jewish and 3 non-Jewish populations with previously reported genotypes on Jewish and non-Jewish populations, we investigate variation in 2789 individuals from 114 populations at 486,592 genome-wide autosomal SNPs. Using multidimensional scaling analysis, unsupervised model-based clustering, and population trees, we find that, genetically, most Jewish samples fall into four major clusters that largely represent four culturally defined groupings, namely the Ashkenazi, Mizrahi, North African, and Sephardi subdivisions of the Jewish population. We detect high-resolution population structure, including separation of the Ashkenazi and Sephardi groups and distinctions among populations within the Mizrahi and North African groups. Our results refine knowledge of Jewish population-genetic structure and contribute to a growing understanding of the distinctive genetic ancestry evident in closely related but historically separate Jewish communities.

Genomic Analyses of Human European Diversity at the Southwestern Edge: Isolation, African Influence and Disease Associations in the Canary Islands

Despite the genetic resemblance of Canary Islanders to other southern European populations, their geographical isolation and the historical admixture of aborigines (from North Africa) with sub-Saharan Africans and Europeans have shaped a distinctive genetic makeup that likely affects disease susceptibility and health disparities. Based on single nucleotide polymorphism array data and whole genome sequencing (30×), we inferred that the last African admixture took place ∼14 generations ago and estimated that up to 34% of the Canary Islander genome is of recent African descent. The length of regions in homozygosis and the ancestry-related mosaic organization of the Canary Islander genome support the view that isolation has been strongest on the two smallest islands. Furthermore, several genomic regions showed significant and large deviations in African or European ancestry and were significantly enriched in genes involved in prevalent diseases in this community, such as diabetes, asthma, and allergy. The most prominent of these regions were located near LCT and the HLA, two well-known targets of selection, at which 40‒50% of the Canarian genome is of recent African descent according to our estimates. Putative selective signals were also identified in these regions near the SLC6A11-SLC6A1, KCNMB2, and PCDH20-PCDH9 genes. Taken together, our findings provide solid evidence of a significant recent African admixture, population isolation, and adaptation in this part of Europe, with the favoring of African alleles in some chromosome regions. These findings may have medical implications for populations of recent African ancestry.

Genetic history of the population of Crete

The medieval history of several populations often suffers from scarcity of contemporary records resulting in contradictory and sometimes biased interpretations by historians. This is the situation with the population of the island of Crete, which remained relatively undisturbed until the Middle Ages when multiple wars, invasions, and occupations by foreigners took place. Historians have considered the effects of the occupation of Crete by the Arabs (in the 9th and 10th centuries C.E.) and the Venetians (in the 13th to the 17th centuries C.E.) to the local population. To obtain insights on such effects from a genetic perspective, we studied representative samples from 17 Cretan districts using the Illumina 1 million or 2.5 million arrays and compared the Cretans to the populations of origin of the medieval conquerors and settlers. Highlights of our findings include (1) small genetic contributions from the Arab occupation to the extant Cretan population, (2) low genetic contribution of the Venetians to the extant Cretan population, and (3) evidence of a genetic relationship among the Cretans and Central, Northern, and Eastern Europeans, which could be explained by the settlement in the island of northern origin tribes during the medieval period. Our results show how the interaction between genetics and the historical record can help shed light on the historical record.

Human ancestry indentification under resource constraints -- what can one chromosome tell us about human biogeographical ancestry?

BACKGROUND

While continental level ancestry is relatively simple using genomic information, distinguishing between individuals from closely associated sub-populations (e.g., from the same continent) is still a difficult challenge.

METHODS

We study the problem of predicting human biogeographical ancestry from genomic data under resource constraints. In particular, we focus on the case where the analysis is constrained to using single nucleotide polymorphisms (SNPs) from just one chromosome. We propose methods to construct such ancestry informative SNP panels using correlation-based and outlier-based methods.

RESULTS

We accessed the performance of the proposed SNP panels derived from just one chromosome, using data from the 1000 Genome Project, Phase 3. For continental-level ancestry classification, we achieved an overall classification rate of 96.75% using 206 single nucleotide polymorphisms (SNPs). For sub-population level ancestry prediction, we achieved an average pairwise binary classification rates as follows: subpopulations in Europe: 76.6% (58 SNPs); Africa: 87.02% (87 SNPs); East Asia: 73.30% (68 SNPs); South Asia: 81.14% (75 SNPs); America: 85.85% (68 SNPs).

CONCLUSION

Our results demonstrate that one single chromosome (in particular, Chromosome 1), if carefully analyzed, could hold enough information for accurate prediction of human biogeographical ancestry. This has significant implications in terms of the computational resources required for analysis of ancestry, and in the applications of such analyses, such as in studies of genetic diseases, forensics, and soft biometrics.

Pancreatic adenocarcinoma, chronic pancreatitis, and MODY-8 diabetes: is bile salt-dependent lipase (or carboxyl ester lipase) at the crossroads of pancreatic pathologies?

Pancreatic adenocarcinomas and diabetes mellitus are responsible for the deaths of around two million people each year worldwide. Patients with chronic pancreatitis do not die directly of this disease, except where the pathology is hereditary. Much current literature supports the involvement of bile salt-dependent lipase (BSDL), also known as carboxyl ester lipase (CEL), in the pathophysiology of these pancreatic diseases. The purpose of this review is to shed light on connections between chronic pancreatitis, diabetes, and pancreatic adenocarcinomas by gaining an insight into BSDL and its variants. This enzyme is normally secreted by the exocrine pancreas, and is diverted within the intestinal lumen to participate in the hydrolysis of dietary lipids. However, BSDL is also expressed by other cells and tissues, where it participates in lipid homeostasis. Variants of BSDL resulting from germline and/or somatic mutations (nucleotide insertion/deletion or nonallelic homologous recombination) are expressed in the pancreas of patients with pancreatic pathologies such as chronic pancreatitis, MODY-8, and pancreatic adenocarcinomas. We discuss the possible link between the expression of BSDL variants and these dramatic pancreatic pathologies, putting forward the suggestion that BSDL and its variants are implicated in the cell lipid metabolism/reprogramming that leads to the dyslipidemia observed in chronic pancreatitis, MODY-8, and pancreatic adenocarcinomas. We also propose potential strategies for translation to therapeutic applications.

Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe

BACKGROUND

The history of human populations occupying the plains and mountain ridges separating Europe from Asia has been eventful, as these natural obstacles were crossed westward by multiple waves of Turkic and Uralic-speaking migrants as well as eastward by Europeans. Unfortunately, the material records of history of this region are not dense enough to reconstruct details of population history. These considerations stimulate growing interest to obtain a genetic picture of the demographic history of migrations and admixture in Northern Eurasia.

RESULTS

We genotyped and analyzed 1076 individuals from 30 populations with geographical coverage spanning from Baltic Sea to Baikal Lake. Our dense sampling allowed us to describe in detail the population structure, provide insight into genomic history of numerous European and Asian populations, and significantly increase quantity of genetic data available for modern populations in region of North Eurasia. Our study doubles the amount of genome-wide profiles available for this region. We detected unusually high amount of shared identical-by-descent (IBD) genomic segments between several Siberian populations, such as Khanty and Ket, providing evidence of genetic relatedness across vast geographic distances and between speakers of different language families. Additionally, we observed excessive IBD sharing between Khanty and Bashkir, a group of Turkic speakers from Southern Urals region. While adding some weight to the "Finno-Ugric" origin of Bashkir, our studies highlighted that the Bashkir genepool lacks the main "core", being a multi-layered amalgamation of Turkic, Ugric, Finnish and Indo-European contributions, which points at intricacy of genetic interface between Turkic and Uralic populations. Comparison of the genetic structure of Siberian ethnicities and the geography of the region they inhabit point at existence of the "Great Siberian Vortex" directing genetic exchanges in populations across the Siberian part of Asia. Slavic speakers of Eastern Europe are, in general, very similar in their genetic composition. Ukrainians, Belarusians and Russians have almost identical proportions of Caucasus and Northern European components and have virtually no Asian influence. We capitalized on wide geographic span of our sampling to address intriguing question about the place of origin of Russian Starovers, an enigmatic Eastern Orthodox Old Believers religious group relocated to Siberia in seventeenth century. A comparative reAdmix analysis, complemented by IBD sharing, placed their roots in the region of the Northern European Plain, occupied by North Russians and Finno-Ugric Komi and Karelian people. Russians from Novosibirsk and Russian Starover exhibit ancestral proportions close to that of European Eastern Slavs, however, they also include between five to 10 % of Central Siberian ancestry, not present at this level in their European counterparts.

CONCLUSIONS

Our project has patched the hole in the genetic map of Eurasia: we demonstrated complexity of genetic structure of Northern Eurasians, existence of East-West and North-South genetic gradients, and assessed different inputs of ancient populations into modern populations.

Effect of Exceptional Parental Longevity and Lifestyle Factors on Prevalence of Cardiovascular Disease in Offspring

Offspring of parents with exceptional longevity (OPEL) manifest lower prevalence of cardiovascular disease (CVD), but the role of lifestyle factors in this unique cohort is not known. Our study tested whether OPEL have lesser prevalence of CVD independent of lifestyle factors. Prevalence of CVD and CVD risk factors was assessed in a population of community-dwelling Ashkenazi Jewish adults aged 65 to 94 years. Participants included OPEL (n = 395), defined as having at least 1 parent living past the age of 95 years, and offspring of parents with usual survival (OPUS, n = 450), defined as having neither parent survive to 95 years. Medical and lifestyle information was obtained using standardized questionnaires. Socioeconomic status was defined based on validated classification scores. Dietary intake was evaluated with the Block Brief Food Frequency Questionnaire (2000) in a subgroup of the study population (n = 234). Our study found no significant differences in the prevalence of obesity, smoking, alcohol use, physical activity, social strata scores, and dietary intake between the 2 groups. After adjustment for age and gender, the OPEL demonstrated 29% lower odds of having hypertension (95% confidence interval [CI] 0.53 to 0.95), 65% lower odds of having had a stroke (95% CI 0.14 to 0.88), and 35% lower odds of having CVD (95% CI 0.43 to 0.98), compared with OPUS. In conclusion, exceptional parental longevity is associated with lower prevalence of CVD independent of lifestyle, socioeconomic status, and nutrition, thus highlighting the potential role of genetics in disease-free survival among individuals with exceptional parental longevity.

The role of dietary patterns and exceptional parental longevity in healthy aging

BACKGROUND

Individuals with exceptional longevity and their offspring manifest a lower prevalence of age-related diseases than families without longevity. However, the contribution of dietary habits to protection from disease has not been systematically assessed in families with exceptional longevity.

OBJECTIVE

The aim of this study is to compare dietary patterns between individuals with parental longevity and individals without parental longevity.

METHODS

Dietary intake was evaluated using the Block Brief Food Frequency Questionnaire in 234 community dwelling Ashkenazi Jewish adults aged 65 years and older who were participants of the LonGenity study, which enrolls the offspring of parents with exceptional longevity (OPEL) and offspring of parents with usual survival (OPUS).

RESULTS

OPEL constituted 38% of the subjects. The two groups had similar daily intake of total calories (1119 vs. 1218 kcal, p = 0.83), grams of cholesterol (141 g vs. 143 g, p = 0.19), and grams of sodium (1324 g vs.1475 g, p = 0.45), in OPEL vs. OPUS respectively. There were also no significant differences in the intake of other macronutrients, micronutrients, nutritional supplements and consumption of various food groups between OPEL and OPUS after adjustment for age and sex.

DISCUSSION

A healthy diet is associated with a lower risk of several chronic diseases. Our study revealed that dietary intake did not differ between OPEL and OPUS; thus, pointing to the role of longevity genes in protecting from disease among individuals with familial longevity.

CONCLUSION

The offspring of long-lived parents do not differ in their dietary patterns compared to individuals without parental longevity.

What Ancestry Can Tell Us About the Genetic Origins of Inter-Ethnic Differences in Asthma Expression

Differences in asthma prevalence have been described across different populations, suggesting that genetic ancestry can play an important role in this disease. In fact, several studies have demonstrated an association between African ancestry with increased asthma susceptibility and severity, higher immunoglobulin E levels, and lower lung function. In contrast, Native American ancestry has been shown to have a protective role for this disease. Genome-wide association studies have allowed the identification of population-specific genetic variants with varying allele frequency among populations. Additionally, the correlation of genetic ancestry at the chromosomal level with asthma and related traits by means of admixture mapping has revealed regions of the genome where ancestry is correlated with the disease. In this review, we discuss the evidence supporting the association of genetic ancestry with asthma susceptibility and asthma-related traits, and highlight the regions of the genome harboring ancestry-specific genetic risk factors.

Bosnian study of APOE distribution (BOSAD): a comparison with other European populations

BACKGROUND

The ε2, ε3 and ε4 alleles of APOE gene have been associated with several diseases in different populations. Data on the frequency of alleles are used in both a clinical and evolutionary context. Although the data on frequency of these alleles are numerous, there are no reports for the population of Bosnia and Herzegovina.

AIM

To estimate the frequency of APOE alleles in a healthy Bosnian population and compare it to data for other European populations.

SUBJECTS AND METHODS

Overall, 170 unrelated Bosnian subjects (108 female and 62 male), aged 53.0 (±5.0) years were included in this study. Genotypes were determined by real-time PCR.

RESULTS

In our group the prevalence of heterozygotes E2/E3, E2/E4 and E3/E4 was 20.6%, 3.5% and 12.9%, respectively, while the prevalence of homozygotes E2/E2, E3/E3, E4/E4 was 0.6%, 61.2% and 1.2%, respectively, with a mean frequency of ε2, ε3 and ε4 alleles of 12.6%, 78.0% and 9.4%, respectively.

CONCLUSIONS

In studied European populations we observed a linear, gradually increasing trend in the frequency of ε4 allele from South to North (Pearson's test 0,7656, p value <0.00001), and the Bosnian population fits into this pattern perfectly.

The distribution of mitochondrial DNA haplogroup H in southern Iberia indicates ancient human genetic exchanges along the western edge of the Mediterranean

BACKGROUND

The structure of haplogroup H reveals significant differences between the western and eastern edges of the Mediterranean, as well as between the northern and southern regions. Human populations along the westernmost Mediterranean coasts, which were settled by individuals from two continents separated by a relatively narrow body of water, show the highest frequencies of mitochondrial haplogroup H. These characteristics permit the analysis of ancient migrations between both shores, which may have occurred via primitive sea crafts and early seafaring. We collected a sample of 750 autochthonous people from the southern Iberian Peninsula (Andalusians from Huelva and Granada provinces). We performed a high-resolution analysis of haplogroup H by control region sequencing and coding SNP screening of the 337 individuals harboring this maternal marker. Our results were compared with those of a wide panel of populations, including individuals from Iberia, the Maghreb, and other regions around the Mediterranean, collected from the literature.

RESULTS

Both Andalusian subpopulations showed a typical western European profile for the internal composition of clade H, but eastern Andalusians from Granada also revealed interesting traces from the eastern Mediterranean. The basal nodes of the most frequent H sub-haplogroups, H1 and H3, harbored many individuals of Iberian and Maghrebian origins. Derived haplotypes were found in both regions; haplotypes were shared far more frequently between Andalusia and Morocco than between Andalusia and the rest of the Maghreb. These and previous results indicate intense, ancient and sustained contact among populations on both sides of the Mediterranean.

CONCLUSIONS

Our genetic data on mtDNA diversity, combined with corresponding archaeological similarities, provide support for arguments favoring prehistoric bonds with a genetic legacy traceable in extant populations. Furthermore, the results presented here indicate that the Strait of Gibraltar and the adjacent Alboran Sea, which have often been assumed to be an insurmountable geographic barrier in prehistory, served as a frequently traveled route between continents.

Expression of truncated bile salt-dependent lipase variant in pancreatic pre-neoplastic lesions

Pancreatic adenocarcinoma (PDAC) is a dismal disease. The lack of specific symptoms still leads to a delay in diagnosis followed by death within months for most patients. Exon 11 of the bile salt-dependent lipase (BSDL) gene encoding variable number of tandem repeated (VNTR) sequences has been involved in pancreatic pathologies. We hypothesized that BSDL VNTR sequences may be mutated in PDAC. The amplification of BSDL VNTR from RNA extracted from pancreatic SOJ-6 cells allowed us to identify a BSDL amplicon in which a cytosine residue is inserted in a VNTR sequence. This insertion gives rise to a premature stop codon, resulting in a truncated protein and to a modification of the C-terminal amino-acid sequence; that is PRAAHG instead of PAVIRF. We produced antibodies directed against these sequences and examined pancreatic tissues from patients with PDAC and PanIN. Albeit all tissues were positive to anti-PAVIRF antibodies, 72.2% of patient tissues gave positive reaction with anti-PRAAHG antibodies, particularly in dysplastic areas of the tumor. Neoplastic cells with ductal differentiation were not reactive to anti-PRAAHG antibodies. Some 70% of PanIN tissues were also reactive to anti-PRAAHG antibodies, suggesting that the C insertion occurs early during pancreatic carcinogenesis. Data suggest that anti-PRAAHG antibodies were uniquely reactive with a short isoform of BSDL specifically expressed in pre-neoplastic lesions of the pancreas. The detection of truncated BSDL reactive to antibodies against the PRAAHG C-terminal sequence in pancreatic juice or in pancreatic biopsies may be a new tool in the early diagnosis of PDAC.

Efficient and Accurate Multiple-Phenotype Regression Method for High Dimensional Data Considering Population Structure

A typical genome-wide association study tests correlation between a single phenotype and each genotype one at a time. However, single-phenotype analysis might miss unmeasured aspects of complex biological networks. Analyzing many phenotypes simultaneously may increase the power to capture these unmeasured aspects and detect more variants. Several multivariate approaches aim to detect variants related to more than one phenotype, but these current approaches do not consider the effects of population structure. As a result, these approaches may result in a significant amount of false positive identifications. Here, we introduce a new methodology, referred to as GAMMA for generalized analysis of molecular variance for mixed-model analysis, which is capable of simultaneously analyzing many phenotypes and correcting for population structure. In a simulated study using data implanted with true genetic effects, GAMMA accurately identifies these true effects without producing false positives induced by population structure. In simulations with this data, GAMMA is an improvement over other methods which either fail to detect true effects or produce many false positive identifications. We further apply our method to genetic studies of yeast and gut microbiome from mice and show that GAMMA identifies several variants that are likely to have true biological mechanisms.

Secular change of sexually dimorphic cranial variables in Euro-Americans and Germans

Crania are a reliable source for sex estimation in Euro-Americans, Europeans, and most other populations. Besides morphological assessments, the application of Fordisc® has become a useful tool within the last two decades, creating discriminant functions from morphometric data. Unfortunately, until now, white populations are mostly represented by measurements of American individuals. Therefore, classification rates are lower for European skulls than for Euro-Americans. The aim of this study was to show differences in sexual dimorphism between German and Euro-American crania. Furthermore, their secular change from the nineteenth to the twentieth century has been investigated. Analyses have been performed on glabella subtense (GLS), mastoid height (MDH), and bizygomatic breadth (ZYB). Fordisc® 3.1 was used to study sexual dimorphism and secular change, whereas SAS® was used to perform a two-level ANOVA to test for variation in sex dimorphism. Euro-Americans show greater dimorphism than Germans in all three measurements tested. This larger difference is even increasing from the late nineteenth through the late twentieth century in terms of GLS and MDH, while it stays almost the same in the present Europeans. These results explain the unsatisfying classification rates of German and other European crania on Fordisc®. Data collection for European Fordisc® samples is in progress and should improve the current situation.

Localizing Ashkenazic Jews to Primeval Villages in the Ancient Iranian Lands of Ashkenaz

The Yiddish language is over 1,000 years old and incorporates German, Slavic, and Hebrew elements. The prevalent view claims Yiddish has a German origin, whereas the opposing view posits a Slavic origin with strong Iranian and weak Turkic substrata. One of the major difficulties in deciding between these hypotheses is the unknown geographical origin of Yiddish speaking Ashkenazic Jews (AJs). An analysis of 393 Ashkenazic, Iranian, and mountain Jews and over 600 non-Jewish genomes demonstrated that Greeks, Romans, Iranians, and Turks exhibit the highest genetic similarity with AJs. The Geographic Population Structure analysis localized most AJs along major primeval trade routes in northeastern Turkey adjacent to primeval villages with names that may be derived from "Ashkenaz." Iranian and mountain Jews were localized along trade routes on the Turkey's eastern border. Loss of maternal haplogroups was evident in non-Yiddish speaking AJs. Our results suggest that AJs originated from a Slavo-Iranian confederation, which the Jews call "Ashkenazic" (i.e., "Scythian"), though these Jews probably spoke Persian and/or Ossete. This is compatible with linguistic evidence suggesting that Yiddish is a Slavic language created by Irano-Turko-Slavic Jewish merchants along the Silk Roads as a cryptic trade language, spoken only by its originators to gain an advantage in trade. Later, in the 9th century, Yiddish underwent relexification by adopting a new vocabulary that consists of a minority of German and Hebrew and a majority of newly coined Germanoid and Hebroid elements that replaced most of the original Eastern Slavic and Sorbian vocabularies, while keeping the original grammars intact.

Genome-wide association study of colorectal cancer in Hispanics

This manuscript describes the first large-scale genome-wide association study of colorectal cancer in Hispanics and Latinos. Our results demonstrate the broad replication of known susceptibility regions and the importance of fine-mapping in ethnic minority populations.

Genome-wide association studies (GWAS) have identified 58 susceptibility alleles across 37 regions associated with the risk of colorectal cancer (CRC) with P < 5×10⁻⁸. Most studies have been conducted in non-Hispanic whites and East Asians; however, the generalizability of these findings and the potential for ethnic-specific risk variation in Hispanic and Latino (HL) individuals have been largely understudied. We describe the first GWAS of common genetic variation contributing to CRC risk in HL (1611 CRC cases and 4330 controls). We also examine known susceptibility alleles and implement imputation-based fine-mapping to identify potential ethnicity-specific association signals in known risk regions. We discovered 17 variants across 4 independent regions that merit further investigation due to suggestive CRC associations (P < 1×10⁻⁶) at 1p34.3 (rs7528276; Odds Ratio (OR) = 1.86 [95% confidence interval (CI): 1.47–2.36); P = 2.5×10⁻⁷], 2q23.3 (rs1367374; OR = 1.37 (95% CI: 1.21–1.55); P = 4.0×10⁻⁷), 14q24.2 (rs143046984; OR = 1.65 (95% CI: 1.36–2.01); P = 4.1×10⁻⁷) and 16q12.2 [rs142319636; OR = 1.69 (95% CI: 1.37–2.08); P=7.8×10⁻⁷]. Among the 57 previously published CRC susceptibility alleles with minor allele frequency ≥1%, 76.5% of SNPs had a consistent direction of effect and 19 (33.3%) were nominally statistically significant (P < 0.05). Further, rs185423955 and rs60892987 were identified as novel secondary susceptibility variants at 3q26.2 (P = 5.3×10^–5) and 11q12.2 (P = 6.8×10⁻⁵), respectively. Our findings demonstrate the importance of fine mapping in HL. These results are informative for variant prioritization in functional studies and future risk prediction modeling in minority populations.

No evidence from genome-wide data of a Khazar origin for the Ashkenazi Jews

The origin and history of the Ashkenazi Jewish population have long been of great interest, and advances in high-throughput genetic analysis have recently provided a new approach for investigating these topics. We and others have argued on the basis of genome-wide data that the Ashkenazi Jewish population derives its ancestry from a combination of sources tracing to both Europe and the Middle East. It has been claimed, however, through a reanalysis of some of our data, that a large part of the ancestry of the Ashkenazi population originates with the Khazars, a Turkic-speaking group that lived to the north of the Caucasus region ~1,000 years ago. Because the Khazar population has left no obvious modern descendants that could enable a clear test for a contribution to Ashkenazi Jewish ancestry, the Khazar hypothesis has been difficult to examine using genetics. Furthermore, because only limited genetic data have been available from the Caucasus region, and because these data have been concentrated in populations that are genetically close to populations from the Middle East, the attribution of any signal of Ashkenazi-Caucasus genetic similarity to Khazar ancestry rather than shared ancestral Middle Eastern ancestry has been problematic. Here, through integration of genotypes from newly collected samples with data from several of our past studies, we have assembled the largest data set available to date for assessment of Ashkenazi Jewish genetic origins. This data set contains genome-wide single-nucleotide polymorphisms in 1,774 samples from 106 Jewish and non-Jewish populations that span the possible regions of potential Ashkenazi ancestry: Europe, the Middle East, and the region historically associated with the Khazar Khaganate. The data set includes 261 samples from 15 populations from the Caucasus region and the region directly to its north, samples that have not previously been included alongside Ashkenazi Jewish samples in genomic studies. Employing a variety of standard techniques for the analysis of population-genetic structure, we found that Ashkenazi Jews share the greatest genetic ancestry with other Jewish populations and, among non-Jewish populations, with groups from Europe and the Middle East. No particular similarity of Ashkenazi Jews to populations from the Caucasus is evident, particularly populations that most closely represent the Khazar region. Thus, analysis of Ashkenazi Jews together with a large sample from the region of the Khazar Khaganate corroborates the earlier results that Ashkenazi Jews derive their ancestry primarily from populations of the Middle East and Europe, that they possess considerable shared ancestry with other Jewish populations, and that there is no indication of a significant genetic contribution either from within or from north of the Caucasus region.

Pharmacogenomics of estrogens on changes in carotid artery intima-medial thickness and coronary arterial calcification: Kronos Early Estrogen Prevention Study

Prior to the initiation of menopausal hormone treatment (MHT), genetic variations in the innate immunity pathway were found to be associated with carotid artery intima-medial thickness (CIMT) and coronary arterial calcification (CAC) in women (n = 606) enrolled in the Kronos Early Estrogen Prevention Study (KEEPS). Whether MHT might affect these associations is unknown. The association of treatment outcomes with variation in the same 764 candidate genes was evaluated in the same KEEPS participants 4 yr after randomization to either oral conjugated equine estrogens (0.45 mg/day), transdermal 17β-estradiol (50 μg/day), each with progesterone (200 mg/day) for 12 days each month, or placebo pills and patch. Twenty SNPs within the innate immunity pathway most related with CIMT after 4 yr were not among those associated with CIMT prior to MHT. In 403 women who completed the study in their assigned treatment group, single nucleotide polymorphisms (SNPs) within the innate immunity pathway were found to alter the treatment effect on 4 yr change in CIMT (i.e., significant interaction between treatment and genetic variation in the innate immunity pathway; P < 0.001). No SNPs by treatment effects were observed with changes of CAC >5 Agatston units after 4 yr. Results of this study suggest that hormonal status may interact with genetic variants to influence cardiovascular phenotypes, specifically, the pharmacogenomic effects within the innate immunity pathway for CIMT.

Dormant phages of Helicobacter pylori reveal distinct populations in Europe

Prophages of Helicobacter pylori, a bacterium known to co-evolve in the stomach of its human host, were recently identified. However, their role in the diversity of H. pylori strains is unknown. We demonstrate here and for the first time that the diversity of the prophage genes offers the ability to distinguish between European populations, and that H. pylori prophages and their host bacteria share a complex evolutionary history. By comparing the phylogenetic trees of two prophage genes (integrase and holin) and the multilocus sequence typing (MLST)-based data obtained for seven housekeeping genes, we observed that the majority of the strains belong to the same phylogeographic group in both trees. Furthermore, we found that the Bayesian analysis of the population structure of the prophage genes identified two H. pylori European populations, hpNEurope and hpSWEurope, while the MLST sequences identified one European population, hpEurope. The population structure analysis of H. pylori prophages was even more discriminative than the traditional MLST-based method for the European population. Prophages are new players to be considered not only to show the diversity of H. pylori strains but also to more sharply define human populations.

Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort

Using genome-wide genotypes, we characterized the genetic structure of 103,006 participants in the Kaiser Permanente Northern California multi-ethnic Genetic Epidemiology Research on Adult Health and Aging Cohort and analyzed the relationship to self-reported race/ethnicity. Participants endorsed any of 23 race/ethnicity/nationality categories, which were collapsed into seven major race/ethnicity groups. By self-report the cohort is 80.8% white and 19.2% minority; 93.8% endorsed a single race/ethnicity group, while 6.2% endorsed two or more. Principal component (PC) and admixture analyses were generally consistent with prior studies. Approximately 17% of subjects had genetic ancestry from more than one continent, and 12% were genetically admixed, considering only nonadjacent geographical origins. Self-reported whites were spread on a continuum along the first two PCs, indicating extensive mixing among European nationalities. Self-identified East Asian nationalities correlated with genetic clustering, consistent with extensive endogamy. Individuals of mixed East Asian-European genetic ancestry were easily identified; we also observed a modest amount of European genetic ancestry in individuals self-identified as Filipinos. Self-reported African Americans and Latinos showed extensive European and African genetic ancestry, and Native American genetic ancestry for the latter. Among 3741 genetically identified parent-child pairs, 93% were concordant for self-reported race/ethnicity; among 2018 genetically identified full-sib pairs, 96% were concordant; the lower rate for parent-child pairs was largely due to intermarriage. The parent-child pairs revealed a trend toward increasing exogamy over time; the presence in the cohort of individuals endorsing multiple race/ethnicity categories creates interesting challenges and future opportunities for genetic epidemiologic studies.

Ancestry informative markers for distinguishing between Thai populations based on genome-wide association datasets

The main purpose of this work was to identify a set of AIMs that stratify the genetic structure and diversity of the Thai population from a high-throughput autosomal genome-wide association study. In this study, more than one million SNPs from the international HapMap database and the Thai depression genome-wide association study have been examined to identify ancestry informative markers (AIMs) that distinguish between Thai populations. An efficient strategy is proposed to identify and characterize such SNPs and to test high-resolution SNP data from international HapMap populations. The best AIMs are identified to stratify the population and to infer genetic ancestry structure. A total of 124 AIMs were clearly clustered geographically across the continent, whereas only 89 AIMs stratified the Thai population from East Asian populations. Finally, a set of 273 AIMs was able to distinguish northern from southern Thai subpopulations. These markers will be of particular value in identifying the ethnic origins in regions where matching by self-reports is unavailable or unreliable, which usually occurs in real forensic cases.

Portuguese crypto-Jews: the genetic heritage of a complex history

The first documents mentioning Jewish people in Iberia are from the Visigothic period. It was also in this period that the first documented anti-Judaic persecution took place. Other episodes of persecution would happen again and again during the long troubled history of the Jewish people in Iberia and culminated with the Decrees of Expulsion and the establishment of the Inquisition: some Jews converted to Catholicism while others resisted and were forcedly baptized, becoming the first Iberian Crypto-Jews. In the 18th century the official discrimination and persecution carried out by the Inquisition ended and several Jewish communities emerged in Portugal. From a populational genetics point of view, the worldwide Diaspora of contemporary Jewish communities has been intensely studied. Nevertheless, very little information is available concerning Sephardic and Iberian Crypto-Jewish descendants. Data from the Iberian Peninsula, the original geographic source of Sephardic Jews, is limited to two populations in Portugal, Belmonte, and Bragança district, and the Chueta community from Mallorca. Belmonte was the first Jewish community studied for uniparental markers. The construction of a reference model for the history of the Portuguese Jewish communities, in which the genetic and classical historical data interplay dynamically, is still ongoing. Recently an enlarged sample covering a wide region in the Northeast Portugal was undertaken, allowing the genetic profiling of male and female lineages. A Jewish specific shared female lineage (HV0b) was detected between the community of Belmonte and Bragança. In contrast to what was previously described as a hallmark of the Portuguese Jews, an unexpectedly high polymorphism of lineages was found in Bragança, showing a surprising resistance to the erosion of genetic diversity typical of small-sized isolate populations, as well as signs of admixture with the Portuguese host population.

Secular trends in the relationship between surnames in a population: Study of a border town

The study of surnames in a territory over time is an opportunity to obtain knowledge of the evolution of allelic frequencies. Geographic and cultural factors influence the renovation of surnames and reflect accelerations or delays in the gene flow. Political borders may also condition the genetic structure of a population. Using isonymy, this paper studies the evolution (from 1750 to 2006) of the frequencies of surnames and the components of inbreeding in Olivenza, a border town whose sovereignty was transferred from Portugal to Spain in 1801. After the change in dominion the number of Portuguese surnames fell sharply and the expected values for a population so close to Portugal recovered only after a long period of time. The results indicate that although the border has made population movement more difficult, and has therefore had an impact on the rate of gene exchange, a certain gene flow with Portugal persisted.

Self-reported race/ethnicity in the age of genomic research: its potential impact on understanding health disparities

This review explores the limitations of self-reported race, ethnicity, and genetic ancestry in biomedical research. Various terminologies are used to classify human differences in genomic research including race, ethnicity, and ancestry. Although race and ethnicity are related, race refers to a person's physical appearance, such as skin color and eye color. Ethnicity, on the other hand, refers to communality in cultural heritage, language, social practice, traditions, and geopolitical factors. Genetic ancestry inferred using ancestry informative markers (AIMs) is based on genetic/genomic data. Phenotype-based race/ethnicity information and data computed using AIMs often disagree. For example, self-reporting African Americans can have drastically different levels of African or European ancestry. Genetic analysis of individual ancestry shows that some self-identified African Americans have up to 99% of European ancestry, whereas some self-identified European Americans have substantial admixture from African ancestry. Similarly, African ancestry in the Latino population varies between 3% in Mexican Americans to 16% in Puerto Ricans. The implication of this is that, in African American or Latino populations, self-reported ancestry may not be as accurate as direct assessment of individual genomic information in predicting treatment outcomes. To better understand human genetic variation in the context of health disparities, we suggest using "ancestry" (or biogeographical ancestry) to describe actual genetic variation, "race" to describe health disparity in societies characterized by racial categories, and "ethnicity" to describe traditions, lifestyle, diet, and values. We also suggest using ancestry informative markers for precise characterization of individuals' biological ancestry. Understanding the sources of human genetic variation and the causes of health disparities could lead to interventions that would improve the health of all individuals.

Spatial localization of recent ancestors for admixed individuals

Ancestry analysis from genetic data plays a critical role in studies of human disease and evolution. Recent work has introduced explicit models for the geographic distribution of genetic variation and has shown that such explicit models yield superior accuracy in ancestry inference over nonmodel-based methods. Here we extend such work to introduce a method that models admixture between ancestors from multiple sources across a geographic continuum. We devise efficient algorithms based on hidden Markov models to localize on a map the recent ancestors (e.g., grandparents) of admixed individuals, joint with assigning ancestry at each locus in the genome. We validate our methods by using empirical data from individuals with mixed European ancestry from the Population Reference Sample study and show that our approach is able to localize their recent ancestors within an average of 470 km of the reported locations of their grandparents. Furthermore, simulations from real Population Reference Sample genotype data show that our method attains high accuracy in localizing recent ancestors of admixed individuals in Europe (an average of 550 km from their true location for localization of two ancestries in Europe, four generations ago). We explore the limits of ancestry localization under our approach and find that performance decreases as the number of distinct ancestries and generations since admixture increases. Finally, we build a map of expected localization accuracy across admixed individuals according to the location of origin within Europe of their ancestors.

Echoes from Sepharad: signatures on the maternal gene pool of crypto-Jewish descendants

The majority of genetic studies on Jewish populations have been focused on Ashkenazim, and genetic data from the Sephardic original source, the Iberian Peninsula, are particularly scarce. Regarding the mitochondrial genome, the available information is limited to a single Portuguese village, Belmonte, where just two different lineages (a single one corresponding to 93.3%) were found in 30 individuals. Aiming at disclosing the ancestral maternal background of the Portuguese Jewry, we enlarged the sampling to other crypto-Jewish descendants in the Bragança district (NE Portugal). Fifty-seven complete mtDNA genomes were newly sequenced and - in contrast with Belmonte - a high level of diversity was found, with five haplogroups (HV0b, N1, T2b11, T2e and U2e) being putatively identified as Sephardic founding lineages. Therefore - in sharp contrast with Belmonte - these communities have managed to escape the expected inbreeding effects caused by centuries of religious repression and have kept a significant proportion of the Sephardic founder gene pool. This deeper analysis of the surviving Sephardic maternal lineages allowed a much more comprehensive and detailed perspective on the origins and survival of the Sephardic genetic heritage. In line with previously published results on Sephardic paternal lineages, our findings also show a surprising resistance to the erosion of genetic diversity in the maternal lineages.

The FGA Thr312Ala polymorphism and risk of intracerebral haemorrhage in Polish and Greek populations

BACKGROUND AND PURPOSE

Spontaneous intracerebral haemorrhage (ICH) is the most fatal form of stroke with the highest morbidity and disability rate of all stroke types. Recent data suggest that the genetic background has a sizeable and mostly undiscovered effect on the brain haemorrhage risk. Since the coagulation system is crucial to ICH pathology, we studied the significance of the FGA Thr312Ala polymorphism in two European populations.

MATERIALS AND METHODS

We genotyped 550 and 224 controls as well as 261 and 242 stroke patients in Polish and Greek populations, respectively. The ICH diagnosis was confirmed by computed tomography. The FGA Thr312Ala polymorphism was analysed using real-time polymorphism chain reaction.

RESULTS

Both crude and multivariable regression analyses showed that the studied polymorphism is a protective factor in the Polish population under the dominant and additive models of inheritance. Those results did not replicate in the Greek population. The meta-analysis of results from the Polish and the Greek populations proved that FGA Thr312Ala polymorphism affects the risk of ICH in the dominant model of inheritance.

CONCLUSIONS

The FGA Thr312Ala polymorphism affects a risk for ICH in the Polish but not in the Greek population. An advanced meta-analysis of well-designed studies with a significant number of cases might provide useful information of novel polymorphisms, including the FGA Thr312Ala polymorphism, and their role in ICH pathology.

Association of exceptional parental longevity and physical function in aging

Offspring of parents with exceptional longevity (OPEL), who are more likely to carry longevity-associated genotypes, may age more successfully than offspring of parents with usual survival (OPUS). Maintenance of physical function is a key attribute of successful aging. While many genetic and non-genetic factors interact to determine physical phenotype in aging, examination of the contribution of exceptional parental longevity to physical function in aging is limited. The LonGenity study recruited a relatively genetically homogenous cohort of Ashkenazi Jewish (AJ) adults age 65 and older, who were defined as either OPEL (having at least one parent who lived to age 95 or older) or OPUS (neither parent survived to age 95). Subjective and objective measures of physical function were compared between the two groups, accounting for potential confounders. Of the 893 LonGenity subjects, 365 were OPEL and 528 were OPUS. OPEL had better objective and subjective measures of physical function than OPUS, especially on unipedal stance (p = 0.009) and gait speed (p = 0.002). Results support the protective role of exceptional parental longevity in preventing decline in physical function, possibly via genetic mechanisms that should be further explored.

Association mapping of the PARK10 region for Parkinson's disease susceptibility genes

BACKGROUND

Previous studies indicate that as many as six genes within the PARK10 region (RNF11, UQCRH, HIVEP3, EIF2B3, USP24, ELAVL4) might modify susceptibility or age at onset in Parkinson's disease (PD).

METHODS

We sought to identify new PD susceptibility genes and to validate previously nominated candidate genes within the PARK10 region using a two-stage design. We used data from a large, publicly-available genome-wide association study (GWAS) in the discovery stage (n = 2000 cases and 1986 controls) and data from three independent studies for the replication stage (total n = 2113 cases and 2095 controls). Marker density was increased by imputation using HapMap 3 and 1000 Genomes reference panels, and over 40,000 single nucleotide polymorphisms (SNPs) were used in the final analysis. The association between each SNP and PD was modeled using logistic regression with an additive allele dosage effect and adjusted for sex, age, and axes of geographical variation.

RESULTS

Although the discovery stage yielded promising findings for SNPs in several novel genes, including DAB1, none of the results were validated in the replication stage. Furthermore, in meta-analyses across all datasets no genes within PARK10 reached significance after accounting for multiple testing.

CONCLUSION

Our results suggest that common variation in the PARK10 region is not associated with PD risk. However, additional studies are needed to assess the role of PARK10 in modifying age at onset and to determine whether rare variants in this region might affect PD susceptibility.