The Fate of 12 Recessive Mutations in A Single Village

The landscape of autosomal recessive variants in an isolated community: Implications for population screening for reproductive purposes

As a result of the preference for consanguineous/endogamous marriages, the Israeli Arab population is composed of isolated communities with relatively frequent autosomal recessive (AR) conditions in each community. Clinical diagnosis of affected individuals has uncovered the pathogenic variants throughout the years. We investigated the diversity of pathogenic AR variants in a single village in northern Israel by exome analysis of 50 random, healthy adults descendants of the founders. Only likely pathogenic and pathogenic variants in known AR genes were selected. In this study 48 AR variants were found, of which 12 had been previously diagnosed in patients from this village, and for 11 with a frequency compatible with the frequency already known. Among the other 36 variants, 12 had been previously diagnosed in affected individuals in other Arab communities in Israel and 24 variants had not been previously characterized in this population. Of the 35 variants associated with conditions of moderate-severe medical consequences, only eight were known previously in this village. These findings emphasize the importance to better delineate the conditions at risk in a defined community, in particular for the development of preventive measures such as screening tests for reproductive couples, and for genetic counseling.

Genetic counseling of high-risk isolated populations: A worldwide challenge

BACKGROUND

Isolated populations with high rates of consanguinity and genetic disorders can be found in most parts of the world. The aim of our paper was to highlight the unique challenges faced in genetic counseling for such patients and to discuss the ways to facilitate the difficulties, with an emphasis on the crucial role of electronic medical records (EMR).

CASE

We report a couple presenting with elevated maternal alpha-fetoprotein in three pregnancies, in which an erroneous diagnosis of epidermolysis bullosa was established in the past and carried along through several years. The live born proband had no evidence of skin disease; however, soon after birth she was diagnosed with congenital nephrotic syndrome. Sequencing of NPHS1 gene yielded a homozygous likely pathogenic genetic variant c.2104G > A (p.Gly702Arg). Population screening performed in the village of residence revealed a carrier frequency of 1-47. This high frequency justified including testing for the founder genetic variant in the national program for population screening.

CONCLUSIONS

Our report highlights the caution, suspicion and time investment which should be practiced and addressed in genetic counseling of high-risk isolated populations. Using EMR may facilitate reaching the correct diagnosis, enable accurate genetic counseling and provide information for decision-making to the couples, as well as "save" a large community from devastating diseases.

Report of a Second Lebanese Family with Basel-Vanagaite-Smirin-Yosef Syndrome: Possible Founder Mutation

Basel-Vanagaite-Smirin-Yosef syndrome (OMIM 616449) is a rare autosomal recessive genetic disorder characterized by severe developmental delay and variable craniofacial, neurological, cardiac, and ocular anomalies in the presence of variants in the MED25 gene. So far, only a handful of patients have been reported with this condition globally. Here, we report an additional Lebanese family with 2 affected siblings presenting with severely delayed psychomotor and language development as well as craniofacial anomalies. By whole-exome sequencing (WES), a homozygous variant was found in the MED25 gene, c.518T>C, predicted to result in a p.Ile173Thr change in the MED25 protein. This change has recently been reported in another Lebanese family. Review of the literature, the importance of this mutation in the Lebanese population, and the possibility that this condition may be underdiagnosed and only effectively detected using molecular techniques such as WES are discussed.

Effects of mating patterns on genealogical trees: Assessment of the high carrier rate of Familial Mediterranean Fever in rural Israeli districts

We investigate the spread from ancestors to descendants, under a model of sexual reproduction, of hereditary elements distinguishing individuals from their fellow human beings. These hereditary elements, termed labels, are either symbolic, implying a socio-cultural or ethnic self-determined category, or biological, i.e. a DNA sequence (for example founder mutations). The impact of various modes of preferential (assortative) mating on the dissemination of a known ancestral label was studied for both kinds of labels, the symbolic and the biological. For the socio-cultural based labeling, both mathematical modeling and simulation studies were carried out, and disclosed a marked delay in the spread of the labels in future generations, compared to the case where mating was random. The transmission of biological labels (founder mutations) from an ancestor to descendants under various modes and degrees of assortative mating was investigated by simulations and supplemented by an in-depth analysis of allele frequencies of Familial Mediterranean Fever (FMF) in an Israeli Muslim Arab village. The high carrier frequency of FMF in this village was satisfactorily explained solely by the presence of a founder effect and a pronounced high factor of selective mating, causing segregation and consanguinity among its inhabitants. Contribution of further evolutionary mechanisms such as heterozygote advantage, drift, differential reproductive success or selection pressure was not essential to explain these results.

Characteristics of genetic diseases in consanguineous populations in the genomic era: Lessons from Arab communities in North Israel

The health outcome of consanguineous/endogamous unions is an increased risk of autosomal recessive disorders in their progeny. This manuscript is focused on consanguineous/endogamous populations living in North Israel. Molecular tools show that spouses' relatedness and hence their risks for congenital diseases among offspring are often greater than the risk calculated on the basis of reported pedigrees. Revealing founder mutations allow for effective genetic counseling, but also induce genetic screening of the whole community in case the mutations are found to be frequent. More complex genetic mechanisms, such as co-inheritance of more than one condition, allelic and even locus heterogeneity, have been identified. These mechanisms make genetic counseling more challenging but with the advancement of molecular techniques, diseases can be better deciphered. Yet, the presence of multiple mutations responsible for genetic diseases in isolated populations, and occasionally locus heterogeneity of diseases, is an unexpected phenomenon that still needs mechanistic clarification. It seems probably that addressing genetic counseling challenges and estimations of risks for genetic morbidity in consanguineous/endogamous couples will be achieved by introducing high-throughput genetic technologies into daily practice. The genomic era has expanded dramatically the translation of research products to genetic counseling tools, and this tendency is expected to yield a stronger impact in a near future.

Evitação e proibição do incesto: fatores psicobiológicos e culturais

Resumo Embora historicamente a regulação proibitiva do incesto seja considerada um fenômeno cultural quase universal que não é influenciado por fatores psicobiológicos relativos à história evolutiva da espécie humana, evidências recentes têm questionado essa visão tradicional e defendido que a evitação e a proibição do incesto são influenciadas biológica e cognitivamente com a cultura. Este artigo objetiva desenvolver uma discussão teórica acerca da inibição e proibição do incesto, enfatizando os mecanismos evolutivos subjacentes a esses fenômenos. Argumenta-se a existência de mecanismos endógenos que evoluíram porque inibem a atividade sexual entre parentes próximos e que formam a base para regular socialmente a proibição do incesto (mecanismo exógeno). Destaca-se o efeito Westermarck, no qual a proximidade de pessoas que vivem juntas desde a infância provoca uma aversão ao intercurso sexual entre elas. A ausência de propensão ao incesto e sua proibição institucional constituem uma complexa integração entre fatores psicobiológicos e culturais.

A founder mutation underlies a severe form of phosphoglutamase 3 (PGM3) deficiency in Tunisian patients

Phosphoglucomutase 3 (PGM3) protein catalyzes the conversion of N-acetyl-d-glucosamine-6-phosphate (GlcNAc-6-P) to N-acetyl-d-glucosamine-1-phosphate (GlcNAc-1-P), which is required for the synthesis of uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) an important precursor for protein glycosylation. Mutations in PGM3 gene have been recently shown to underlie a new congenital disorder of glycosylation often associated to elevated IgE. Herein, we report twelve PGM3 deficient patients. They belong to three highly consanguineous families, originating from a rural district in the west central Tunisia. The patient's clinical phenotype is characterized by severe respiratory and cutaneous infections as well as developmental delay and severe mental retardation. Fourteen patients died in early infancy before diagnosis supporting the severity of the clinical phenotype. Laboratory findings revealed elevated IgE, CD4 lymphopenia and impaired T cell proliferation in most patients. Genetic analysis showed the presence, of a unique homozygous mutation (p.Glu340del) in PGM3 gene leading to reduced PGM3 abundance. Segregating analysis using fifteen polymorphic markers overlapping PGM3 gene showed that all patients inherited a common homozygous haplotype encompassing 10-Mb on chromosome 6. The founder mutational event was estimated to have occurred approximately 100 years ago. To date, (p.Glu340del) mutation represents the first founder mutation identified in PGM3 gene. These findings will facilitate the development of preventive approaches through genetic counselling and prenatal diagnosis in the affected families.

The Israeli National Genetic database: a 10-year experience

Background

The Israeli National and Ethnic Mutation database (http://server.goldenhelix.org/israeli) was launched in September 2006 on the ETHNOS software to include clinically relevant genomic variants reported among Jewish and Arab Israeli patients. In 2016, the database was reviewed and corrected according to ClinVar (https://www.ncbi.nlm.nih.gov/clinvar) and ExAC (http://exac.broadinstitute.org) database entries. The present article summarizes some key aspects from the development and continuous update of the database over a 10-year period, which could serve as a paradigm of successful database curation for other similar resources.

Results

In September 2016, there were 2444 entries in the database, 890 among Jews, 1376 among Israeli Arabs, and 178 entries among Palestinian Arabs, corresponding to an ~4× data content increase compared to when originally launched. While the Israeli Arab population is much smaller than the Jewish population, the number of pathogenic variants causing recessive disorders reported in the database is higher among Arabs (934) than among Jews (648). Nevertheless, the number of pathogenic variants classified as founder mutations in the database is smaller among Arabs (175) than among Jews (192). In 2016, the entire database content was compared to that of other databases such as ClinVar and ExAC. We show that a significant difference in the percentage of pathogenic variants from the Israeli genetic database that were present in ExAC was observed between the Jewish population (31.8%) and the Israeli Arab population (20.6%).

Conclusions

The Israeli genetic database was launched in 2006 on the ETHNOS software and is available online ever since. It allows querying the database according to the disorder and the ethnicity; however, many other features are not available, in particular the possibility to search according to the name of the gene. In addition, due to the technical limitations of the previous ETHNOS software, new features and data are not included in the present online version of the database and upgrade is currently ongoing.

Consanguinity and rare neurological disease. A five year experience from the Korle Bu Teaching Hospital, Accra, Ghana

Introduction

Marriage between close biological kin is not regarded as advantageous in the western world but in other parts of the world, consanguineous unions persist. Consanguineous marriage increases the birth prevalence of individuals with recessive disorders. In Accra, Ghana, consanguinity is beginning to emerge as a significant cause of rare neurological disease at the central referral hospital at Korle Bu in Ghana.

Method

Documentation of rare neurological and genetic diseases over a five year period resulting from consanguinity (2010-2015) presenting to the Department of Child Health, Korle Bu Teaching Hospital, Accra.

Results

One of the three siblings with zeroderma pigmentosum was identified as the rare De Sanctis Cacchione syndrome which has not been previously reported from West Africa. Five cases of spinal muscular atrophy including three consecutive siblings with the disease, MCAD deficiency (1), inborn errors of metabolism (1), ceroid lipoid fuscinosis (6), a case of Meckel Gruber syndrome.

Conclusion

Rare neurological disease occurs in West African communities as a result of consanguinity.

Characterising the spectrum of autosomal recessive hereditary hearing loss in Iran

BACKGROUND

Countries with culturally accepted consanguinity provide a unique resource for the study of rare recessively inherited genetic diseases. Although hereditary hearing loss (HHL) is not uncommon, it is genetically heterogeneous, with over 85 genes causally implicated in non-syndromic hearing loss (NSHL). This heterogeneity makes many gene-specific types of NSHL exceedingly rare. We sought to define the spectrum of autosomal recessive HHL in Iran by investigating both common and rarely diagnosed deafness-causing genes.

DESIGN

Using a custom targeted genomic enrichment (TGE) panel, we simultaneously interrogated all known genetic causes of NSHL in a cohort of 302 GJB2-negative Iranian families.

RESULTS

We established a genetic diagnosis for 67% of probands and their families, with over half of all diagnoses attributable to variants in five genes: SLC26A4, MYO15A, MYO7A, CDH23 and PCDH15. As a reflection of the power of consanguinity mapping, 26 genes were identified as causative for NSHL in the Iranian population for the first time. In total, 179 deafness-causing variants were identified in 40 genes in 201 probands, including 110 novel single nucleotide or small insertion-deletion variants and three novel CNV. Several variants represent founder mutations.

CONCLUSION

This study attests to the power of TGE and massively parallel sequencing as a diagnostic tool for the evaluation of hearing loss in Iran, and expands on our understanding of the genetics of HHL in this country. Families negative for variants in the genes represented on this panel represent an excellent cohort for novel gene discovery.

Controversies and considerations regarding the termination of pregnancy for foetal anomalies in Islam

Background

Approximately one-fourth of all the inhabitants on earth are Muslims. Due to unprecedented migration, physicians are often confronted with cultures other than their own that adhere to different pdigms.

Discussion

In Islam, and most religions, abortion is forbidden. Islam is considerably liberal concerning abortion, which is dependent on (i) the threat of harm to mothers, (ii) the status of the pregnancy before or after ensoulment (on the 120^th day of gestation), and (iii) the presence of foetal anomalies that are incompatible with life. Considerable variation in religious edicts exists, but most Islamic scholars agree that the termination of a pregnancy for foetal anomalies is allowed before ensoulment, after which abortion becomes totally forbidden, even in the presence of foetal abnormalities; the exception being a risk to the mother’s life or confirmed intrauterine death.

Summary

The authors urge Muslim law makers to also consider abortion post ensoulment if it is certain that the malformed foetus will decease soon after birth or will be severely malformed and physically and mentally incapacitated after birth to avoid substantial hardship that may continue for years for mothers and family members. The authors recommend that an institutional committee governed and monitored by a national committee make decisions pertaining to abortion to ensure that ethics are preserved and mistakes are prevented. Anomalous foetuses must be detected at the earliest possible time to enable an appropriate medical intervention prior to the 120^th day.

Consanguineous Marriage and Human Evolution

Mate choice among early human groups and in many historical populations was subject to both demographic and social constraints, ensuring that most unions were between couples who had coinherited substantial proportions of their genomes from common ancestors. Even in populations in which close consanguineous marriage was proscribed, community endogamy would have been sufficient to ensure high levels of homozygosity. Consanguineous marriage remains the choice of an estimated 10.4% of the global population, although there has been an overall decline in its popularity, especially in developed countries. Recent studies have indicated that the shift from consanguineous marriage to panmixia has been accompanied by a reduction in homozygosity. The concomitant predicted decrease in incidence of both recessive single-gene disorders and more common adult-onset diseases will have a significant impact on the health of future generations.

The molecular basis of autosomal recessive diseases among the Arabs and Druze in Israel

The Israeli population mainly includes Jews, Muslim and Christian Arabs, and Druze In the last decade, data on genetic diseases present in the population have been systematically collected and are available online in the Israeli national genetic database ( http://www.goldenhelix.org/server/israeli ). In the non-Jewish population, up to 1 July 2010, the database included molecular data on six diseases relatively frequent in the whole population: thalassemia, familial Mediterranean fever (FMF), cystic fibrosis, deafness, phenylketonuria and congenital adrenal hyperplasia, as well as data on 195 autosomal recessive diseases among Muslim Israeli Arabs, 11 among the Christian Arabs and 31 among Druze. A single mutation was characterized in 149 out of the 238 rare disorders for which the molecular basis was known. In many diseases, mutation had never been observed in any other population and was present in one family only suggesting that it occurred as a de novo event. In other diseases, the mutation was present in more than one community or even in other populations such as Bedouins from the Arab peninsula or Christians from Lebanon. In the 89 other disorders, more than one mutation was characterized either in the same gene or in more than one gene. While it is probable that most of these cases represent random events in some cases such as Bardet Biedl among the Bedouins, the reason may be a selective advantage to the heterozygotes.

Evolution in health and medicine Sackler colloquium: Consanguinity, human evolution, and complex diseases

There is little information on inbreeding during the critical early years of human existence. However, given the small founding group sizes and restricted mate choices it seems inevitable that intrafamilial reproduction occurred and the resultant levels of inbreeding would have been substantial. Currently, couples related as second cousins or closer (F >or= 0.0156) and their progeny account for an estimated 10.4% of the global population. The highest rates of consanguineous marriage occur in north and sub-Saharan Africa, the Middle East, and west, central, and south Asia. In these regions even couples who regard themselves as unrelated may exhibit high levels of homozygosity, because marriage within clan, tribe, caste, or biraderi boundaries has been a long-established tradition. Mortality in first-cousin progeny is approximately 3.5% higher than in nonconsanguineous offspring, although demographic, social, and economic factors can significantly influence the outcome. Improving socioeconomic conditions and better access to health care will impact the effects of consanguinity, with a shift from infant and childhood mortality to extended morbidity. At the same time, a range of primarily social factors, including urbanization, improved female education, and smaller family sizes indicate that the global prevalence of consanguineous unions will decline. This shift in marriage patterns will initially result in decreased homozygosity, accompanied by a reduction in the expression of recessive single-gene disorders. Although the roles of common and rare gene variants in the etiology of complex disease remain contentious, it would be expected that declining consanguinity would also be reflected in reduced prevalence of complex diseases, especially in population isolates.

Genetic isolates in ophthalmic diseases

In recent years, noteworthy gains have been made in unravelling the genetic contribution to some complex ocular diseases, principally age-related macular degeneration. Yet, a relatively poor understanding of the genetic aetiology for many other heritable blinding diseases, such as glaucoma, keratoconus and myopia, remains. Genetic isolates, populations with varying degrees of geographical or cultural seclusion, provide an effective means for investigating the molecular mechanisms involved in human diseases. This is particularly true for rare diseases in which founded alleles can be rapidly driven to a high frequency due to restriction of gene flow in the population. Recent success in complex gene mapping has resulted from the widened linkage disequilibrium (LD) in the genome of genetically isolated populations. An improved understanding of the predisposing genetic risk factors allows for enhanced screening modalities and paves the foundations for the translation of genomic technology into the clinic. This review focuses on the role population isolates have had in the investigation of genes underlying complex eye diseases and discusses their likely usefulness given the expansion of large-scale case-control association studies.

Compound heterozygosity for three common MEFV mutations in a highly consanguineous family with familial Mediterranean fever

Consanguinity is not the only factor influencing the occurrence of autosomal recessive disorders such as familial Mediterranean fever (FMF). The extended, multiple consanguineous Turkish pedigree presented here demonstrates that the population frequency of certain mutations (so-called "ancient" mutations) can be at least equally important. In high-risk populations different combinations of mutations can occur within the same family, increasing not only the intrafamilial clinical variability, but also causing considerable recurrence risks even in marriages with unrelated spouses.