Consanguinity around the world: what do the genomic data of the HGDP-CEPH diversity panel tell us?

Epidemiological characterization of rare diseases in Brazil: A retrospective study of the Brazilian Rare Diseases Network

BACKGROUND

The Brazilian Policy for Comprehensive Care for People with Rare Diseases was implemented in 2014; however, national epidemiological data on rare diseases (RDs) are scarce and mainly focused on specific disorders. To address this gap, University Hospitals, Reference Services for Neonatal Screening, and Reference Services for Rare Diseases, all of which are public health institutions, established the Brazilian Rare Diseases Network (RARAS) in 2020. The objective of this study was to perform a comprehensive nationwide epidemiological investigation of individuals with RDs in Brazil. This retrospective survey collected data from patients receiving care in 34 healthcare facilities affiliated with RARAS in 2018 and 2019.

RESULTS

The survey included 12,530 participants with a median age of 15.0 years, with women representing 50.5% of the cohort. Classification according to skin color demonstrated that 5044 (47.4%) participants were admixed. Most had a confirmed diagnosis (63.2%), with a predominance of phenylketonuria (PKU), cystic fibrosis (CF), and acromegaly. Common clinical manifestations included global developmental delay and seizures. The average duration of the diagnostic odyssey was 5.4 years (± 7.9 years). Among the confirmed diagnoses, 52.2% were etiological (biochemical: 42.5%; molecular: 30.9%), while 47.8% were clinical. Prenatal diagnoses accounted for 1.2%. Familial recurrence and consanguinity rates were 21.6% and 6.4%, respectively. Mainstay treatments included drug therapy (55.0%) and rehabilitation (15.6%). The Public Health System funded most diagnoses (84.2%) and treatments (86.7%). Hospitalizations were reported in 44.5% of cases, and the mortality rate was 1.5%, primarily due to motor neuron disease and CF.

CONCLUSION

This study marks a pioneering national-level data collection effort for rare diseases in Brazil, offering novel insights to advance the understanding, management, and resource allocation for RDs. It unveils an average diagnostic odyssey of 5.4 years and a higher prevalence of PKU and CF, possibly associated with the specialized services network, which included newborn screening services.

Measuring the Efficiency of Purging by non-random Mating in Human Populations

Human populations harbor a high concentration of deleterious genetic variants. Here, we tested the hypothesis that non-random mating practices affect the distribution of these variants, through exposure in the homozygous state, leading to their purging from the population gene pool. To do so, we produced whole-genome sequencing data for two pairs of Asian populations exhibiting different alliance rules and rates of inbreeding, but with similar effective population sizes. The results show that populations with higher rates of inbred matings do not purge deleterious variants more efficiently. Purging therefore has a low efficiency in human populations, and different mating practices lead to a similar mutational load.

Guidelines for genetic ancestry inference created through roundtable discussions

The use of genetic and genomic technology to infer ancestry is commonplace in a variety of contexts, particularly in biomedical research and for direct-to-consumer genetic testing. In 2013 and 2015, two roundtables engaged a diverse group of stakeholders toward the development of guidelines for inferring genetic ancestry in academia and industry. This report shares the stakeholder groups' work and provides an analysis of, commentary on, and views from the groundbreaking and sustained dialogue. We describe the engagement processes and the stakeholder groups' resulting statements and proposed guidelines. The guidelines focus on five key areas: application of genetic ancestry inference, assumptions and confidence/laboratory and statistical methods, terminology and population identifiers, impact on individuals and groups, and communication or translation of genetic ancestry inferences. We delineate the terms and limitations of the guidelines and discuss their critical role in advancing the development and implementation of best practices for inferring genetic ancestry and reporting the results. These efforts should inform both governmental regulation and self-regulation.

Population-based change-point detection for the identification of homozygosity islands

MOTIVATION

This work is motivated by the problem of identifying homozygosity islands on the genome of individuals in a population. Our method directly tackles the issue of identification of the homozygosity islands at the population level, without the need of analysing single individuals and then combine the results, as is made nowadays in state-of-the-art approaches.

RESULTS

We propose regularized offline change-point methods to detect changes in the parameters of a multidimensional distribution when we have several aligned, independent samples of fixed resolution. We present a penalized maximum likelihood approach that can be efficiently computed by a dynamic programming algorithm or approximated by a fast binary segmentation algorithm. Both estimators are shown to converge almost surely to the set of change-points without the need of specifying a priori the number of change-points. In simulation, we observed similar performances from the exact and greedy estimators. Moreover, we provide a new methodology for the selection of the regularization constant which has the advantage of being automatic, consistent, and less prone to subjective analysis.

AVAILABILITY AND IMPLEMENTATION

The data used in the application are from the Human Genome Diversity Project (HGDP) and is publicly available. Algorithms were implemented using the R software R Core Team (R: A Language and Environment for Statistical Computing. Vienna (Austria): R Foundation for Statistical Computing, 2020.) in the R package blockcpd, found at https://github.com/Lucas-Prates/blockcpd.

The Global, Regional, and National Burden of Psoriasis: Results and Insights From the Global Burden of Disease 2019 Study

Background: Psoriasis is a common, chronic, inflammatory, debilitating, systemic disease with a great impact on healthcare systems worldwide. As targeted therapies have transformed the therapeutic landscape, updated estimates of the Global Burden of Disease (GBD) imposed by psoriasis are necessary in order to evaluate the effects of past health care policies and to orient and inform new national and international healthcare strategies. Methods: Data were extracted from the GBD 2019 study, which collates a systematic review of relevant scientific literature, national surveys, claims data, and primary care sources on the prevalence of psoriasis. Prevalence data were combined with disability weight (DW) to yield years lived with disability (YLDs). Measures of burden at global, regional, and national levels were generated for incidence, prevalence, and YLDs, due to psoriatic disease. All measures were reported as absolute numbers, percentages, and crude and age-adjusted rates per 100,000 persons. In addition, psoriasis burden was assessed by socio-demographic index (SDI). Findings: According to the GBD 2019 methodology, there were 4,622,594 (95% uncertainty interval or UI 4,458,904-4,780,771) incident cases of psoriasis worldwide in 2019. The age-standardized incidence rate in 2019 was 57.8 (95% UI 55.8-59.7) per 100,000 people. With respect to 1990, this corresponded to a decrease of 20.0% (95% UI -20.2 to -19.8). By sex, the age-standardized incidence rate was similar between men [57.8 (95% UI 55.8-59.8) per 100,000 people] and women [(57.8 (95% UI 55.8-59.7) per 100,000 people]. With respect to 1990, this corresponded to a decrease by 19.5% (95% UI -19.8 to -19.2) and by 20.4% (95% UI -20.7 to -20.2) for men and women, respectively. The age-standardized incidence rate per 100,000 persons was found to vary widely across geographic locations. Regionally, high-income countries and territories had the highest age-standardized incidence rate of psoriasis [112.6 (95% UI 108.9-116.1)], followed by high-middle SDI countries [69.4 (95% UI 67.1-71.9)], while low SDI countries reported the lowest rate [38.1 (95% UI 36.8-39.5)]. Similar trends were detected for prevalence and YLDs. Conclusion: In general, psoriasis burden is greatest in the age group of 60-69 years, with a relatively similar burden among men and women. The burden is disproportionately greater in high-income and high SDI index countries of North America and Europe. With advances in psoriasis therapeutics, objective evaluation of psoriasis disease burden is critical to track the progress at the population level.

Fine-scale population structure and demographic history of British Pakistanis

Previous genetic and public health research in the Pakistani population has focused on the role of consanguinity in increasing recessive disease risk, but little is known about its recent population history or the effects of endogamy. Here, we investigate fine-scale population structure, history and consanguinity patterns using genotype chip data from 2,200 British Pakistanis. We reveal strong recent population structure driven by the biraderi social stratification system. We find that all subgroups have had low recent effective population sizes (Ne), with some showing a decrease 15‒20 generations ago that has resulted in extensive identity-by-descent sharing and homozygosity, increasing the risk of recessive disorders. Our results from two orthogonal methods (one using machine learning and the other coalescent-based) suggest that the detailed reporting of parental relatedness for mothers in the cohort under-represents the true levels of consanguinity. These results demonstrate the impact of cultural practices on population structure and genomic diversity in Pakistanis, and have important implications for medical genetic studies.

The structure of first-cousin marriages in Brazil

This paper deals with the frequency and structure of first-cousin marriages, by far the most important and frequent type of consanguineous mating in human populations. Based on the analysis of large amounts of data from the world literature and from large Brazilian samples recently collected, we suggest some explanations for the asymmetry of sexes among the parental sibs of first-cousin marriages. We suggest also a simple manner to correct the method that uses population surnames to assess the different Wright fixation indexes FIS, FST and FIT taking into account not only alternative methods of surname transmission, but also the asymmetries that are almost always observed in the distribution of sexes among the parental sibs of first-cousins.

A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences

The number of national reference populations that are whole-genome sequenced are rapidly increasing. Partly driving this development is the fact that genetic disease studies benefit from knowing the genetic variation typical for the geographical area of interest. A whole-genome sequenced Swedish national reference population (n = 1000) has been recently published but with few samples from northern Sweden. In the present study we have whole-genome sequenced a control population (n = 300) (ACpop) from Västerbotten County, a sparsely populated region in northern Sweden previously shown to be genetically different from southern Sweden. The aggregated variant frequencies within ACpop are publicly available (DOI 10.17044/NBIS/G000005) to function as a basic resource in clinical genetics and for genetic studies. Our analysis of ACpop, representing approximately 0.11% of the population in Västerbotten, indicates the presence of a genetic substructure within the county. Furthermore, a demographic analysis showed that the population from which samples were drawn was to a large extent geographically stationary, a finding that was corroborated in the genetic analysis down to the level of municipalities. Including ACpop in the reference population when imputing unknown variants in a Västerbotten cohort resulted in a strong increase in the number of high-confidence imputed variants (up to 81% for variants with minor allele frequency < 5%). ACpop was initially designed for cancer disease studies, but the genetic structure within the cohort will be of general interest for all genetic disease studies in northern Sweden.

Relatedness coefficients in pedigrees with inbred founders

We study an extension of the standard framework for pedigree analysis, in which we allow pedigree founders to be inbred. This solves a number of practical challenges in calculating coefficients of relatedness, including condensed identity coefficients. As a consequence we expand considerably the class of pedigrees for which such coefficients may be efficiently computed. An application of this is the modelling of background inbreeding as a continuous effect. We also use inbred founders to shed new light on constructibility of relatedness coefficients, i.e., the problem of finding a genealogy yielding a given set of coefficients. In particular, we show that any theoretically admissible coefficients for a pair of noninbred individuals can be produced by a finite pedigree with inbred founders. Coupled with our computational methods, implemented in the R package ribd, this allows for the first time computer analysis of general constructibility solutions, thus making them accessible for practical use.

Genomic evidence for MHC disassortative mating in humans

Although pervasive in many animal species, the evidence for major histocompatibility complex (MHC) disassortative mating in humans remains inconsistent across studies. Here, to revisit this issue, we analyse dense genotype data for 883 European and Middle Eastern couples. To distinguish MHC-specific effects from socio-cultural confounders, the pattern of relatedness between spouses in the MHC region is compared to the rest of the genome. Couples from Israel exhibit no significant pattern of relatedness across the MHC region, whereas across the genome, they are more similar than random pairs of individuals, which may reflect social homogamy and/or cousin marriages. On the other hand, couples from The Netherlands and more generally from Northern Europe are significantly more MHC-dissimilar than random pairs of individuals, and this pattern of dissimilarity is extreme when compared with the rest of the genome. Our findings support the hypothesis that the MHC influences mate choice in humans in a context-dependent way: MHC-driven preferences may exist in all populations but, in some populations, social constraints over mate choice may reduce the ability of individuals to rely on such biological cues when choosing their mates.

Jeanne Calment's Unique 122-Year Life Span: Facts and Factors; Longevity History in Her Genealogical Tree

Jeanne Calment's (JC) still unmatched validated human life span of 122 years and 164 days, over 3 years longer than any other, surprises many. While her case is broadly accepted as a golden standard of validation, her record age still raises skepticism among some. The probability of such a record to be achieved by someone born in the second half of the 19th century, in the world population documentarily eligible to age validation, and also in the G7 countries, can be calculated by applying some logistic and Gompertz mortality models to these populations, taken, respectively, from the age of 117 and of 100. This probability appears substantial, respectively, 7.1% and 4.7%, when using a four-parameter logistic model, which I validated on the observed survivals of centenarians until the age of 118. A 3-year interval with the second oldest is then expected. The known facts and documents constitute consistent evidence that JC died at 122: regular official records during her life, her verified memories from her 19th century life, her usage of specialized terms and of an abbreviation system specific to this period of time, photographs, her signature and handwriting, testimonies from numerous witnesses of her life, plus the expertise of gerontologists. Meanwhile, nothing contradicts her record: the daughter/mother identity swap hypothesis appears unrealistic and not supported by any evidence; especially no plausible motive can be found, on the contrary. The latest article, which defends this hypothesis, "Bayesian assessment of the longevity of JC," contains major errors, making its result subjective and invalid. The study of JC's genealogical tree on six generations, using longevity performance and total immediate ancestor longevity indicators, shows how, in two centuries, her ancestors have been living 10% longer on average at each generation, increasingly overperforming their French 25-year-old contemporaries, from around 7% in the early 18th century to 43% for her parents, and up to 56% for her older brother and 80% for herself, which suggests a progressive concentration of longevity factors. In addition to the hereditary factors, JC's personal overperformance suggests also some environmental factors, and indeed many are known. Further knowledge could be obtained by studying JC's existing blood and DNA samples: those could not only provide an additional proof of her authenticity, but more importantly could be of immense contribution for understanding deeper the factors and patterns of her longevity, and more generally the longevity and aging processes in humans in general as well.

Massively parallel sequencing of autosomal STRs and identity-informative SNPs highlights consanguinity in Saudi Arabia

While many studies have been undertaken of Middle Eastern populations using autosomal STR profiling by capillary electrophoresis, little has so far been published from this region on the forensic use of massively parallel sequencing (MPS). Here, we carried out MPS of 27 autosomal STRs and 91 identity-informative SNPs (iiSNPs) with the Verogen ForenSeq™ DNA Signature Prep Kit on a representative sample of 89 Saudi Arabian males, and analysed the resulting sequence data using Verogen's ForenSeq Universal Analysis Software (UAS) v1.3 and STRait Razor v3.0. This revealed sequence variation in the composition of complex STR arrays, and SNPs in their flanking regions, which raised the number of STR alleles from 238 distinct length variants to 357 sequence sub-variants. Similarly, between one and three additional polymorphic sites were observed within the amplicons of 37 of the 91 iiSNPs, forming up to six microhaplotypes per locus. These further enhance discrimination compared to the biallelic target SNP data presented by the primary UAS interface. In total, we observed twenty-two STR alleles previously unrecognised in the STRait Razor v3.0 default allele list, along with nine SNPs flanking target iiSNPs that were not highlighted by the UAS. Sequencing reduced the STR-based random match probability (RMP) from 2.62E-30 to 3.49E-34, and analysis of the iiSNP microhaplotypes reduced RMP from 9.97E-37 to 6.83E-40. The lack of significant linkage disequilibrium between STRs and target iiSNPs allowed the two marker types to be combined using the product rule, yielding a RMP of 2.39E-73. Evidence of consanguinity was apparent from both marker types. While TPOX was the only locus displaying a significant deviation from Hardy-Weinberg equilibrium, 23 out of 27 STRs and 63 out of 91 iiSNPs showed fewer than expected heterozygotes, demonstrating an overall homozygote excess probably reflecting the high frequency of first-cousin marriages in Saudi Arabia. We placed our data in a global context by considering the same markers in the Human Genome Diversity Panel (HGDP), revealing that the Saudi sample was typical of Middle Eastern populations, with a higher level of inbreeding than is seen in most European, African and Central/South Asian populations, correlating with known patterns of endogamy. Given reduced levels of diversity within endogamous groups, the ability to combine the discrimination power of both STRs and SNPs offers significant benefits in the analysis of forensic evidence in Saudi Arabia and the Middle East region more generally.

From matrimonial practices to genetic diversity in Southeast Asian populations: the signature of the matrilineal puzzle

In matrilineal populations, the descent group affiliation is transmitted by women whereas the socio-political power frequently remains in the hands of men. This situation, named the 'matrilineal puzzle', is expected to promote local endogamy as a coping mechanism allowing men to maintain their decision-making power over their natal descent group. In this paper, we revisit this 'matrilineal puzzle' from a population genetics' point of view. Indeed, such tendency for local endogamy in matrilineal populations is expected to increase their genetic inbreeding and generate isolation-by-distance patterns between villages. To test this hypothesis, we collected ethno-demographic data for 3261 couples and high-density genetic data for 675 individuals from 11 Southeast Asian populations with a wide range of social organizations: matrilineal and matrilocal populations (M), patrilineal and patrilocal populations (P) or cognatic populations with predominant matrilocal residence (C). We observed that M and C populations have higher levels of village endogamy than P populations, and that such higher village endogamy leads to higher genetic inbreeding. M populations also exhibit isolation-by-distance patterns between villages. We interpret such genetic patterns as the signature of the 'matrilineal puzzle'. Notably, our results suggest that any form of matrilocal marriage (whatever the descent rule is) increases village endogamy. These findings suggest that male dominance, when combined with matrilocality, constrains inter-village migrations, and constitutes an underexplored cultural process shaping genetic patterns in human populations. This article is part of the theme issue 'The evolution of female-biased kinship in humans and other mammals'.

Congenital heart defects in children with cleft lips and/or palates at an academic hospital in central South Africa

Background: Globally, cleft deformities are the most common craniofacial anomalies and show an association with congenital heart defects. Little research on cleft lips and/or palates (CL/P) and congenital heart defects has been reported from Africa, and none from South Africa. In 2001, it was proposed that CL/P be listed as one of six priority conditions for monitoring and notification to South African health authorities. This goal of creating a national registry has not been achieved. A near-fatal anaesthetic incident following a missed cardiac lesion in a child with a cleft lip and palate prompted this study. Objectives: To describe the prevalence of congenital heart defects diagnosed in children with CL/P presenting for corrective surgery during the Smile Week over three consecutive years (2013–2015) at an academic hospital in South Africa. Methods: A retrospective, descriptive file review of 62 patients with CL/P was performed. Since 2013, echocardiography has been performed on all patients with CL/P. Results: Twenty-three, 21 and 18 patients were operated in 2013, 2014 and 2015, respectively. Of these patients, 85.5% (n = 53) had no clinical evidence of a cardiac defect, of which eight did have clinically significant cardiac defects on echocardiography. Sixteen patients (25.8%) in total (n = 16/62) with a cleft deformity had a clinically significant congenital heart lesion. Of the 16 patients with a cardiac defect on transthoracic echocardiography, only four had clinical evidence of cardiac defect. Therefore, sensitivity of clinical examination was 25%, whereas the specificity was 89.1%. Three of the four patients with a syndrome had a clinically significant echocardiographic finding. Conclusion: A national guideline for the preoperative care of patients with CL/P, including routine echocardiography, is needed. Furthermore, a national registry is required for patients with CL/P with associated congenital anomalies.

Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy

When closely related individuals mate, they produce inbred offspring, which often have lower fitness than outbred ones. Geographical exogamy, by favouring matings between distant individuals, is thought to be an inbreeding avoidance mechanism; however, no data has clearly tested this prediction. Here, we took advantage of the diversity of matrimonial systems in humans to explore the impact of geographical exogamy on genetic diversity and inbreeding. We collected ethno-demographic data for 1,344 individuals in 16 populations from two Inner Asian cultural groups with contrasting dispersal behaviours (Turko-Mongols and Indo-Iranians) and genotyped genome-wide single nucleotide polymorphisms in 503 individuals. We estimated the population exogamy rate and confirmed the expected dispersal differences: Turko-Mongols are geographically more exogamous than Indo-Iranians. Unexpectedly, across populations, exogamy patterns correlated neither with the proportion of inbred individuals nor with their genetic diversity. Even more surprisingly, among Turko-Mongols, descendants from exogamous couples were significantly more inbred than descendants from endogamous couples, except for large distances (>40 km). Overall, 37% of the descendants from exogamous couples were closely inbred. This suggests that in Inner Asia, geographical exogamy is neither efficient in increasing genetic diversity nor in avoiding inbreeding, which might be due to kinship endogamy despite the occurrence of dispersal.

Inbreeding estimates in human populations: Applying new approaches to an admixed Brazilian isolate

The analysis of genomic data (~400,000 autosomal SNPs) enabled the reliable estimation of inbreeding levels in a sample of 541 individuals sampled from a highly admixed Brazilian population isolate (an African-derived quilombo in the State of São Paulo). To achieve this, different methods were applied to the joint information of two sets of markers (one complete and another excluding loci in patent linkage disequilibrium). This strategy allowed the detection and exclusion of markers that biased the estimation of the average population inbreeding coefficient (Wright's fixation index FIS), which value was eventually estimated as around 1% using any of the methods we applied. Quilombo demographic inferences were made by analyzing the structure of runs of homozygosity (ROH), which were adapted to cope with a highly admixed population with a complex foundation history. Our results suggest that the amount of ROH <2Mb of admixed populations should be somehow proportional to the genetic contribution from each parental population.

Runs of homozygosity: windows into population history and trait architecture

Long runs of homozygosity (ROH) arise when identical haplotypes are inherited from each parent and thus a long tract of genotypes is homozygous. Cousin marriage or inbreeding gives rise to such autozygosity; however, genome-wide data reveal that ROH are universally common in human genomes even among outbred individuals. The number and length of ROH reflect individual demographic history, while the homozygosity burden can be used to investigate the genetic architecture of complex disease. We discuss how to identify ROH in genome-wide microarray and sequence data, their distribution in human populations and their application to the understanding of inbreeding depression and disease risk.

A model-based approach to characterize individual inbreeding at both global and local genomic scales

Inbreeding results from the mating of related individuals and may be associated with reduced fitness because it brings together deleterious variants in one individual. In general, inbreeding is estimated with respect to an arbitrary base population consisting of ancestors that are assumed unrelated. We herein propose a model-based approach to estimate and characterize individual inbreeding at both global and local genomic scales by assuming the individual genome is a mosaic of homozygous-by-descent (HBD) and non-HBD segments. The HBD segments may originate from ancestors tracing back to different periods in the past defining distinct age-related classes. The lengths of the HBD segments are exponentially distributed with class-specific parameters reflecting that inbreeding of older origin generates on average shorter stretches of observed homozygous markers. The model is implemented in a hidden Markov model framework that uses marker allele frequencies, genetic distances, genotyping error rates and the sequences of observed genotypes. Note that genotyping errors, low-fold sequencing or genotype-by-sequencing data are easily accommodated under this framework. Based on simulations under the inference model, we show that the genomewide inbreeding coefficients and the parameters of the model are accurately estimated. In addition, when several inbreeding classes are simulated, the model captures them if their ages are sufficiently different. Complementary analyses, either on data sets simulated under more realistic models or on human, dog and sheep real data, illustrate the range of applications of the approach and how it can reveal recent demographic histories among populations (e.g., very recent bottlenecks or founder effects). The method also allows to clearly identify individuals resulting from extreme consanguineous matings.

Composite likelihood method for inferring local pedigrees

Pedigrees contain information about the genealogical relationships among individuals and are of fundamental importance in many areas of genetic studies. However, pedigrees are often unknown and must be inferred from genetic data. Despite the importance of pedigree inference, existing methods are limited to inferring only close relationships or analyzing a small number of individuals or loci. We present a simulated annealing method for estimating pedigrees in large samples of otherwise seemingly unrelated individuals using genome-wide SNP data. The method supports complex pedigree structures such as polygamous families, multi-generational families, and pedigrees in which many of the member individuals are missing. Computational speed is greatly enhanced by the use of a composite likelihood function which approximates the full likelihood. We validate our method on simulated data and show that it can infer distant relatives more accurately than existing methods. Furthermore, we illustrate the utility of the method on a sample of Greenlandic Inuit.

Pedigrees contain information about the genealogical relationships among individuals. This information can be used in many areas of genetic studies such as disease association studies, conservation efforts, and for inferences about the demographic history and social structure of a population. Despite their importance, pedigrees are often unknown and must be estimated from genetic information. However, pedigree inference remains a difficult problem due to the high cost of likelihood computation and the enormous number of possible pedigrees that must be considered. These difficulties limit existing methods in their ability to infer pedigrees when the sample size or the number of markers is large, or when the sample contains only distant relatives. In this report, we present a method that circumvents these computational challenges in order to infer pedigrees of complex structure for a large number of individuals. Using simulations, we find that the method can infer distant relatives much more accurately than existing methods. Furthermore, we show that even pairwise inferences of relatedness can be improved substantially by consideration of the pedigree structure with other related individuals in the sample.

Reconstructing Druze population history

The Druze are an aggregate of communities in the Levant and Near East living almost exclusively in the mountains of Syria, Lebanon and Israel whose ~1000 year old religion formally opposes mixed marriages and conversions. Despite increasing interest in genetics of the population structure of the Druze, their population history remains unknown. We investigated the genetic relationships between Israeli Druze and both modern and ancient populations. We evaluated our findings in light of three hypotheses purporting to explain Druze history that posit Arabian, Persian or mixed Near Eastern-Levantine roots. The biogeographical analysis localised proto-Druze to the mountainous regions of southeastern Turkey, northern Iraq and southeast Syria and their descendants clustered along a trajectory between these two regions. The mixed Near Eastern–Middle Eastern localisation of the Druze, shown using both modern and ancient DNA data, is distinct from that of neighbouring Syrians, Palestinians and most of the Lebanese, who exhibit a high affinity to the Levant. Druze biogeographic affinity, migration patterns, time of emergence and genetic similarity to Near Eastern populations are highly suggestive of Armenian-Turkish ancestries for the proto-Druze.

Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery

The Greater Middle East (GME) has been a central hub of human migration and population admixture. The tradition of consanguinity, variably practiced in the Persian Gulf region, North Africa, and Central Asia, has resulted in an elevated burden of recessive disease. Here we generated a whole-exome GME variome from 1,111 unrelated subjects. We detected substantial diversity and admixture in continental and subregional populations, corresponding to several ancient founder populations with little evidence of bottlenecks. Measured consanguinity rates were an order of magnitude above those in other sampled populations, and the GME population exhibited an increased burden of runs of homozygosity (ROHs) but showed no evidence for reduced burden of deleterious variation due to classically theorized 'genetic purging'. Applying this database to unsolved recessive conditions in the GME population reduced the number of potential disease-causing variants by four- to sevenfold. These results show variegated genetic architecture in GME populations and support future human genetic discoveries in Mendelian and population genetics.

Evolution of GOUNDRY, a cryptic subgroup of Anopheles gambiae s.l., and its impact on susceptibility to Plasmodium infection

The recent discovery of a previously unknown genetic subgroup of Anopheles gambiae sensu lato underscores our incomplete understanding of complexities of vector population demographics in Anopheles. This subgroup, named GOUNDRY, does not rest indoors as adults and is highly susceptible to Plasmodium infection in the laboratory. Initial description of GOUNDRY suggested it differed from other known Anopheles taxa in surprising and sometimes contradictory ways, raising a number of questions about its age, population size and relationship to known subgroups. To address these questions, we sequenced the complete genomes of 12 wild-caught GOUNDRY specimens and compared these genomes to a panel of Anopheles genomes. We show that GOUNDRY is most closely related to Anopheles coluzzii, and the timing of cladogenesis is not recent, substantially predating the advent of agriculture. We find a large region of the X chromosome that has swept to fixation in GOUNDRY within the last 100 years, which may be an inversion that serves as a partial barrier to contemporary gene flow. Interestingly, we show that GOUNDRY has a history of inbreeding that is significantly associated with susceptibility to Plasmodium infection in the laboratory. Our results illuminate the genomic evolution of one of probably several cryptic, ecologically specialized subgroups of Anopheles and provide a potent example of how vector population dynamics may complicate efforts to control or eradicate malaria.

Six Novel Loci Associated with Circulating VEGF Levels Identified by a Meta-analysis of Genome-Wide Association Studies

Vascular endothelial growth factor (VEGF) is an angiogenic and neurotrophic factor, secreted by endothelial cells, known to impact various physiological and disease processes from cancer to cardiovascular disease and to be pharmacologically modifiable. We sought to identify novel loci associated with circulating VEGF levels through a genome-wide association meta-analysis combining data from European-ancestry individuals and using a dense variant map from 1000 genomes imputation panel. Six discovery cohorts including 13,312 samples were analyzed, followed by in-silico and de-novo replication studies including an additional 2,800 individuals. A total of 10 genome-wide significant variants were identified at 7 loci. Four were novel loci (5q14.3, 10q21.3, 16q24.2 and 18q22.3) and the leading variants at these loci were rs114694170 (MEF2C, P = 6.79x10^-13), rs74506613 (JMJD1C, P = 1.17x10^-19), rs4782371 (ZFPM1, P = 1.59x10^-9) and rs2639990 (ZADH2, P = 1.72x10^-8), respectively. We also identified two new independent variants (rs34528081, VEGFA, P = 1.52x10^-18; rs7043199, VLDLR-AS1, P = 5.12x10^-14) at the 3 previously identified loci and strengthened the evidence for the four previously identified SNPs (rs6921438, LOC100132354, P = 7.39x10^-1467; rs1740073, C6orf223, P = 2.34x10^-17; rs6993770, ZFPM2, P = 2.44x10^-60; rs2375981, KCNV2, P = 1.48x10^-100). These variants collectively explained up to 52% of the VEGF phenotypic variance. We explored biological links between genes in the associated loci using Ingenuity Pathway Analysis that emphasized their roles in embryonic development and function. Gene set enrichment analysis identified the ERK5 pathway as enriched in genes containing VEGF associated variants. eQTL analysis showed, in three of the identified regions, variants acting as both cis and trans eQTLs for multiple genes. Most of these genes, as well as some of those in the associated loci, were involved in platelet biogenesis and functionality, suggesting the importance of this process in regulation of VEGF levels. This work also provided new insights into the involvement of genes implicated in various angiogenesis related pathologies in determining circulating VEGF levels. The understanding of the molecular mechanisms by which the identified genes affect circulating VEGF levels could be important in the development of novel VEGF-related therapies for such diseases.

Vascular Endothelial Growth Factor (VEGF) is a protein with a fundamental role in development of vascular system. The protein, produced by many types of cells, is released in the blood. High levels of VEGF have been observed in different pathological conditions especially in cancer, cardiovascular, and inflammatory diseases. Therefore, identifying the genetic factors influencing VEGF levels is important for predicting and treating such pathologies. The number of genetic variants associated with VEGF levels has been limited. To identify new loci, we have performed a Genome Wide Association Study meta-analysis on a sample of more than 16,000 individuals from 10 cohorts, using a high-density genetic map. This analysis revealed 10 variants associated with VEGF circulating levels, 6 of these being novel associations. The 10 variants cumulatively explain more than 50% of the variability of VEGF serum levels. Our analyses have identified genes known to be involved in angiogenesis related diseases and genes implicated in platelet metabolism, suggesting the importance of links between this process and VEGF regulation. Overall, these data have improved our understanding of the genetic variation underlying circulating VEGF levels. This in turn could guide our response to the challenge posed by various VEGF-related pathologies.

Observed and expected frequencies of structural hemoglobin variants in newborn screening surveys in Africa and the Middle East: deviations from Hardy-Weinberg equilibrium

PURPOSE

Our objective was to compare observed and expected genotype proportions from newborn screening surveys of structural hemoglobin variants.

METHODS

We conducted a systematic review of newborn screening surveys of hemoglobins S and C in Africa and the Middle East. We compared observed frequencies to those expected assuming Hardy-Weinberg equilibrium (HWE). Significant deviations were identified by an exact test. The fixation index FIS was calculated to assess excess homozygosity. We compared newborn estimates corrected and uncorrected for HWE deviations using demographic data.

RESULTS

Sixty samples reported genotype counts for hemoglobin variants in Africa and the Middle East. Observed and expected counts matched in 27%. The observed number of sickle cell anemia (SCA) individuals was higher than expected in 42 samples, reaching significance (P < 0.05) in 24. High FIS values were common across the study regions. The estimated total number of newborns with SCA, corrected based on FIS, was 33,261 annual births instead of 24,958 for the 38 samples across sub-Saharan Africa and 1,109 annual births instead of 578 for 12 samples from the Middle East.

CONCLUSION

Differences between observed and expected genotype frequencies are common in surveys of hemoglobin variants in the study regions. Further research is required to identify and quantify factors responsible for such deviations. Estimates based on HWE might substantially underestimate the annual number of SCA-affected newborns (up to one-third in sub-Saharan Africa and one-half in the Middle East).

High level of inbreeding in final phase of 1000 Genomes Project

The 1000 Genomes Project provides a unique source of whole genome sequencing data for studies of human population genetics and human diseases. The last release of this project includes more than 2,500 sequenced individuals from 26 populations. Although relationships among individuals have been investigated in some of the populations, inbreeding has never been studied. In this article, we estimated the genomic inbreeding coefficient of each individual and found an unexpected high level of inbreeding in 1000 Genomes data: nearly a quarter of the individuals were inbred and around 4% of them had inbreeding coefficients similar or greater than the ones expected for first-cousin offspring. Inbred individuals were found in each of the 26 populations, with some populations showing proportions of inbred individuals above 50%. We also detected 227 previously unreported pairs of close relatives (up to and including first-cousins). Thus, we propose subsets of unrelated and outbred individuals, for use by the scientific community. In addition, because admixed populations are present in the 1000 Genomes Project, we performed simulations to study the robustness of inbreeding coefficient estimates in the presence of admixture. We found that our multi-point approach (FSuite) was quite robust to admixture, unlike single-point methods (PLINK).

Relationship inference from the genetic data on parents or offspring: A comparative study

Relationship inference in a population is of interest for many areas of research from anthropology to genetics. It is possible to directly infer the relationship between the two individuals in a couple from their genetic data or to indirectly infer it from the genetic data of one of their offspring. For this reason, one can wonder if it is more advantageous to sample couples or single individuals to study relationships of couples in a population. Indeed, sampling two individuals is more informative than sampling one as we are looking at four haplotypes instead of two, but it also doubles the cost of the study and is a more complex sampling scheme. To answer this question, we performed simulations of 1000 trios from 10 different relationships using real human haplotypes to have realistic genome-wide genetic data. Then, we compared the genome sharing coefficients and the relationship inference obtained from either a pair of individuals or one of their offspring using both single-point and multi-point approaches. We observed that for relationships closer than 1st cousin, pairs of individuals were more informative than one of their offspring for relationship inference, and kinship coefficients obtained from single-point methods gave more accurate or equivalent genome sharing estimations. For more remote relationships, offspring were more informative for relationship inference, and inbreeding coefficients obtained from multi-point methods gave more accurate genome sharing estimations. In conclusion, relationship inference on a parental pair or on one of their offspring provides complementary information. When possible, sampling trios should be encouraged as it could allow spanning a wider range of potential relationships.

Extensive genome-wide autozygosity in the population isolates of Daghestan

Isolated populations are valuable resources for mapping disease genes, as inbreeding increases genome-wide homozygosity and enhances the ability to map disease alleles on a genetically uniform background within a relatively homogenous environment. The populations of Daghestan are thought to have resided in the Caucasus Mountains for hundreds of generations and are characterized by a high prevalence of certain complex diseases. To explore the extent to which their unique population history led to increased levels of inbreeding, we genotyped >550 000 autosomal single-nucleotide polymorphisms (SNPs) in a set of 14 population isolates speaking Nakh-Daghestanian (ND) languages. The ND-speaking populations showed greatly elevated coefficients of inbreeding, very high numbers and long lengths of Runs of Homozygosity, and elevated linkage disequilibrium compared with surrounding groups from the Caucasus, the Near East, Europe, Central and South Asia. These results are consistent with the hypothesis that most ND-speaking groups descend from a common ancestral population that fragmented into a series of genetic isolates in the Daghestanian highlands. They have subsequently maintained a long-term small effective population size as a result of constant inbreeding and very low levels of gene flow. Given these findings, Daghestanian population isolates are likely to be useful for mapping genes associated with complex diseases.

Genome-wide inbreeding estimation within Lebanese communities using SNP arrays

Consanguineous marriages have been widely practiced in several global communities with varying rates depending on religion, culture, and geography. In consanguineous marriages, parents pass to their children autozygous segments known as homozygous by descent segments. In this study, single-nucleotide polymorphisms were analyzed in 165 unrelated Lebanese people from Greek Orthodox, Maronite, Shiite and Sunni communities. Runs of homozygosity, total inbreeding levels, remote consanguinity, and population admixture and structure were estimated. The inbreeding coefficient value was estimated to be 1.61% in offspring of unrelated parents over three generations and 8.33% in offspring of first cousins. From these values, remote consanguinity values, resulting from genetic drift or recurrent consanguineous unions, were estimated in offspring of unrelated and first-cousin parents to be 0.61 and 1.2%, respectively. This remote consanguinity value suggests that for any unrelated marriages in Lebanon, the mates could be related as third cousins or as second cousins once removed. Under the assumption that 25% of marriages occur between first cousins, the mean inbreeding value of 2.3% may explain the increased incidence of recessive disease in offspring. Our analysis reveals a common ancestral population in the four Lebanese communities we studied.

The influence of admixture and consanguinity on population genetic diversity in Middle East

The Middle East (ME) is an important crossroad where modern humans migrated 'out of Africa' and spread into Europe and Asia. After the initial peopling and long-term isolation leading to well-differentiated populations, the ME also had a crucial role in subsequent human migrations among Africa, Europe and Asia; thus, recent population admixture has been common in the ME. On the other hand, consanguinity, a well-known practice in the ME, often reduces genetic diversity and works in opposition to admixture. Here, we explored the degree to which admixture and consanguinity jointly affected genetic diversity in ME populations. Genome-wide single-nucleotide polymorphism data were generated in two representative ME populations (Arabian and Iranian), with comparisons made with populations worldwide. Our results revealed an overall higher genetic diversity in both ME populations relative to other non-African populations. We identified a much larger number of long runs of homozygosity in ME populations than in any other populations, which was most likely attributed to high levels of consanguineous marriages that significantly decreased both individual and population heterozygosity. Additionally, we were able to distinguish African, European and Asian ancestries in ME populations and quantify the impact of admixture and consanguinity with statistical approaches. Interestingly, genomic regions with significantly excessive ancestry from individual source populations are functionally enriched in olfactory pathways, which were suspected to be under natural selection. Our findings suggest that genetic admixture, consanguinity and natural selection have collectively shaped the genetic diversity of ME populations, which has important implications in both evolutionary studies and medical practices.

Population-genetic influences on genomic estimates of the inbreeding coefficient: a global perspective

BACKGROUND/AIMS

Culturally driven marital practices provide a key instance of an interaction between social and genetic processes in shaping patterns of human genetic variation, producing, for example, increased identity by descent through consanguineous marriage. A commonly used measure to quantify identity by descent in an individual is the inbreeding coefficient, a quantity that reflects not only consanguinity, but also other aspects of kinship in the population to which the individual belongs. Here, in populations worldwide, we examine the relationship between genomic estimates of the inbreeding coefficient and population patterns in genetic variation.

METHODS

Using genotypes at 645 microsatellites, we compare inbreeding coefficients from 5,043 individuals representing 237 populations worldwide to demographic consanguinity frequency estimates available for 26 populations as well as to other quantities that can illuminate population-genetic influences on inbreeding coefficients.

RESULTS

We observe higher inbreeding coefficient estimates in populations and geographic regions with known high levels of consanguinity or genetic isolation and in populations with an increased effect of genetic drift and decreased genetic diversity with increasing distance from Africa. For the small number of populations with specific consanguinity estimates, we find a correlation between inbreeding coefficients and consanguinity frequency (r = 0.349, p = 0.040).

CONCLUSIONS

The results emphasize the importance of both consanguinity and population-genetic factors in influencing variation in inbreeding coefficients, and they provide insight into factors useful for assessing the effect of consanguinity on genomic patterns in different populations.

Random inbreeding, isonymy, and population isolates in Argentina

Population isolates are an important tool in identifying and mapping genes of Mendelian diseases and complex traits. The geographical identification of isolates represents a priority from a genetic and health care standpoint. The purpose of this study is to analyze the spatial distribution of consanguinity by random isonymy (F ST) in Argentina and its relationship with the isolates previously identified in the country. F ST was estimated from the surname distribution of 22.6 million electors registered for the year 2001 in the 24 provinces, 5 geographical regions, and 510 departments of the country. Statistically significant spatial clustering of F ST was determined using the SaTScan V5.1 software. F ST exhibited a marked regional and departamental variation, showing the highest values towards the North and West of Argentina. The clusters of high consanguinity by random isonymy followed the same distribution. Recognized Argentinean genetic isolates are mainly localized at the north of the country, in clusters of high inbreeding. Given the availability of listings of surnames in high-capacity storage devices for different countries, estimating F ST from them can provide information on inbreeding for all levels of administrative subdivisions, to be used as a demographic variable for the identification of isolates within the country for public health purposes.

Population and genomic lessons from genetic analysis of two Indian populations

Indian demographic history includes special features such as founder effects, interpopulation segregation, complex social structure with a caste system and elevated frequency of consanguineous marriages. It also presents a higher frequency for some rare mendelian disorders and in the last two decades increased prevalence of some complex disorders. Despite the fact that India represents about one-sixth of the human population, deep genetic studies from this terrain have been scarce. In this study, we analyzed high-density genotyping and whole-exome sequencing data of a North and a South Indian population. Indian populations show higher differentiation levels than those reported between populations of other continents. In this work, we have analyzed its consequences, by specifically assessing the transferability of genetic markers from or to Indian populations. We show that there is limited genetic marker portability from available genetic resources such as HapMap or the 1,000 Genomes Project to Indian populations, which also present an excess of private rare variants. Conversely, tagSNPs show a high level of portability between the two Indian populations, in contrast to the common belief that North and South Indian populations are genetically very different. By estimating kinship from mates and consanguinity in our data from trios, we also describe different patterns of assortative mating and inbreeding in the two populations, in agreement with distinct mating preferences and social structures. In addition, this analysis has allowed us to describe genomic regions under recent adaptive selection, indicating differential adaptive histories for North and South Indian populations. Our findings highlight the importance of considering demography for design and analysis of genetic studies, as well as the need for extending human genetic variation catalogs to new populations and particularly to those with particular demographic histories.

FSuite: exploiting inbreeding in dense SNP chip and exome data

FSuite is a user-friendly pipeline developed for exploiting inbreeding information derived from human genomic data. It can make use of single nucleotide polymorphism chip or exome data. Compared with other software, the advantage of FSuite is that it provides a complete suite of scripts to describe and use the inbreeding information. It includes a module to detect inbred individuals and estimate their inbreeding coefficient, a module to describe the proportion of different mating types in the population and the individual probability to be offspring of different mating types that can be useful for population genetic studies. It also allows the identification of shared regions of homozygosity between affected individuals (homozygosity mapping) that can be used to identify rare recessive mutations involved in monogenic or multifactorial diseases.

AVAILABILITY AND IMPLEMENTATION

FSuite is developed in Perl and uses R functions to generate graphical outputs. This pipeline is freely available under GNU GPL license at: http://genestat.cephb.fr/software/index.php/FSuite.

Could inbred cases identified in GWAS data succeed in detecting rare recessive variants where affected sib-pairs have failed?

To detect fully penetrant rare recessive variants that could constitute Mendelian subentities of complex diseases, we propose a novel strategy, the HBD-GWAS strategy, which can be applied to genome-wide association study (GWAS) data. This strategy first involves the identification of inbred individuals among cases using the genome-wide SNP data and then focuses on these inbred affected individuals and searches for genomic regions of shared homozygosity by descent that could harbor rare recessive disease-causing variants. In this second step, analogous to homozygosity mapping, a heterogeneity lod-score, HFLOD, is computed to quantify the evidence of linkage provided by the data. In this paper, we evaluate this strategy theoretically under different scenarios and compare its performances with those of linkage analysis using affected sib-pair (ASP) data. If cases affected by these Mendelian subentities are not enriched in the sample of cases, the HBD-GWAS strategy has almost no power to detect them, unless they explain an important part of the disease prevalence. The HBD-GWAS strategy outperforms the ASP linkage strategy only in a very limited number of situations where there exists a strong allelic heterogeneity. When several rare recessive variants within the same gene are involved, the ASP design indeed often fails to detect the gene, whereas, by focusing on inbred individuals using the HBD-GWAS strategy, the gene might be detected provided very large samples of cases are available.

Unexpected relationships and inbreeding in HapMap phase III populations

Correct annotation of the genetic relationships between samples is essential for population genomic studies, which could be biased by errors or omissions. To this end, we used identity-by-state (IBS) and identity-by-descent (IBD) methods to assess genetic relatedness of individuals within HapMap phase III data. We analyzed data from 1,397 individuals across 11 ethnic populations. Our results support previous studies (Pemberton et al., 2010; Kyriazopoulou-Panagiotopoulou et al., 2011) assessing unknown relatedness present within this population. Additionally, we present evidence for 1,657 novel pairwise relationships across 9 populations. Surprisingly, significant Cotterman's coefficients of relatedness K1 (IBD1) values were detected between pairs of known parents. Furthermore, significant K2 (IBD2) values were detected in 32 previously annotated parent-child relationships. Consistent with a hypothesis of inbreeding, regions of homozygosity (ROH) were identified in the offspring of related parents, of which a subset overlapped those reported in previous studies (Gibson et al. 2010; Johnson et al. 2011). In total, we inferred 28 inbred individuals with ROH that overlapped areas of relatedness between the parents and/or IBD2 sharing at a different genomic locus between a child and a parent. Finally, 8 previously annotated parent-child relationships had unexpected K0 (IBD0) values (resulting from a chromosomal abnormality or genotype error), and 10 previously annotated second-degree relationships along with 38 other novel pairwise relationships had unexpected IBD2 (indicating two separate paths of recent ancestry). These newly described types of relatedness may impact the outcome of previous studies and should inform the design of future studies relying on the HapMap Phase III resource.

Genomic patterns of homozygosity in worldwide human populations

Genome-wide patterns of homozygosity runs and their variation across individuals provide a valuable and often untapped resource for studying human genetic diversity and evolutionary history. Using genotype data at 577,489 autosomal SNPs, we employed a likelihood-based approach to identify runs of homozygosity (ROH) in 1,839 individuals representing 64 worldwide populations, classifying them by length into three classes-short, intermediate, and long-with a model-based clustering algorithm. For each class, the number and total length of ROH per individual show considerable variation across individuals and populations. The total lengths of short and intermediate ROH per individual increase with the distance of a population from East Africa, in agreement with similar patterns previously observed for locus-wise homozygosity and linkage disequilibrium. By contrast, total lengths of long ROH show large interindividual variations that probably reflect recent inbreeding patterns, with higher values occurring more often in populations with known high frequencies of consanguineous unions. Across the genome, distributions of ROH are not uniform, and they have distinctive continental patterns. ROH frequencies across the genome are correlated with local genomic variables such as recombination rate, as well as with signals of recent positive selection. In addition, long ROH are more frequent in genomic regions harboring genes associated with autosomal-dominant diseases than in regions not implicated in Mendelian diseases. These results provide insight into the way in which homozygosity patterns are produced, and they generate baseline homozygosity patterns that can be used to aid homozygosity mapping of genes associated with recessive diseases.

Consanguinity in Centre d'Étude du Polymorphisme Humain (CEPH) pedigrees

A set of Centre d'Étude du Polymorphisme Humain (CEPH) cell lines serves as a large reference collection that has been widely used as a benchmark for allele frequencies in the analysis of genetic variants, to create linkage maps of the human genome, to study the genetics of gene expression, to provide samples to the HapMap and 1000 Genomes projects, and for a variety of other applications. An explicit feature of the CEPH collection is that these multigenerational families represent reference panels of known relatedness, consisting mostly of three-generation pedigrees with large sibships, two parents, and grandparents. We applied identity-by-state (IBS) and identity-by-descent (IBD) methods to high-density genotype data from 186 CEPH individuals in 13 families. We identified unexpected relatedness between nominally unrelated grandparents both within and between pedigrees. For one pair, the estimated Cotterman coefficient of relatedness k1 exceeded 0.2, consistent with one-eighth sharing (eg, first-cousins). Unexpectedly, significant IBD2 values were discovered in both second-degree and parent-child relationships. These were accompanied by regions of homozygosity in the offspring, which corresponded to blocks lacking IBS0 in purportedly unrelated parents, consistent with inbreeding. Our findings support and extend a 1999 report, based on the use of short tandem-repeat polymorphisms, that several CEPH families had regions of homozygosity consistent with autozygosity. We benchmarked our IBD approach (called kcoeff) against both RELPAIR and PREST software packages. Our findings may affect the interpretation of previous studies and the design of future studies that rely on the CEPH resource.

Assessing the influence of consanguinity on congenital heart disease

Numerous articles have been published linking consanguineous marriage to an elevated prevalence of congenital heart disease, with ventricular septal defects and atrial septal defects the most commonly cited disorders. While initially persuasive, on closer examination many of these studies have fundamental shortcomings in their design and in the recruitment of study subjects and controls. Improved matching of cases and controls, to include recognition of the long-established community boundaries within which most marriages are contracted, and the assessment of consanguinity within specific levels and types of marital union would improve and help to focus the study outcomes. At the same time, major discrepancies between studies in their reported prevalence and types of congenital heart disease suggest an urgent need for greater standardization in the classification and reporting of these disorders.