Dvora Filon

The Y Chromosome Pool of Jews as Part of the Genetic Landscape of the Middle East

A sample of 526 Y chromosomes representing six Middle Eastern populations (Ashkenazi, Sephardic, and Kurdish Jews from Israel; Muslim Kurds; Muslim Arabs from Israel and the Palestinian Authority Area; and Bedouin from the Negev) was analyzed for 13 binary polymorphisms and six microsatellite loci. The investigation of the genetic relationship among three Jewish communities revealed that Kurdish and Sephardic Jews were indistinguishable from one another, whereas both differed slightly, yet significantly, from Ashkenazi Jews. The differences among Ashkenazim may be a result of low-level gene flow from European populations and/or genetic drift during isolation. Admixture between Kurdish Jews and their former Muslim host population in Kurdistan appeared to be negligible. In comparison with data available from other relevant populations in the region, Jews were found to be more closely related to groups in the north of the Fertile Crescent (Kurds, Turks, and Armenians) than to their Arab neighbors. The two haplogroups Eu 9 and Eu 10 constitute a major part of the Y chromosome pool in the analyzed sample. Our data suggest that Eu 9 originated in the northern part, and Eu 10 in the southern part of the Fertile Crescent. Genetic dating yielded estimates of the expansion of both haplogroups that cover the Neolithic period in the region. Palestinian Arabs and Bedouin differed from the other Middle Eastern populations studied here, mainly in specific high-frequency Eu 10 haplotypes not found in the non-Arab groups. These chromosomes might have been introduced through migrations from the Arabian Peninsula during the last two millennia. The present study contributes to the elucidation of the complex demographic history that shaped the present-day genetic landscape in the region.

Sex identification of archaeological human remains based on amplification of the X and Y amelogenin alleles

Sex identification of archaeological human remains is essential for the exploration of gender differences in past populations. Traditional morphometric analyses fail to identify the gender of incomplete skeletal remains and that of immature individuals. In the present work, we have established a sensitive and reliable method, based on amplification of the single-copy amelogenin-encoding gene (AMG). The Y allele carries a small deletion in the first intron, facilitating the design of distinct X- and Y-specific polymerase chain reactions. Amplification with three primers, two of which are allele-specific, allows unambiguous identification of both X and Y chromosome signals in a single reaction, providing an internal control. For added confidence, the reaction may be performed in separate tubes for each allele. Using this method, the sex was determined from the skeletal remains of 18 individuals, including young children, out of 22 examined from periods ranging from 200 to around 8000 years ago. The state of skeletal preservation ranged from poor to good. Cortical and cranial bones, as well as teeth, were found to provide sufficiently preserved DNA. The success of retrieval of amplifiable DNA was not related either to the period or to the burial site. On the other hand, the method of DNA purification was critical. In our hands, direct DNA purification by Chelex from minute samples of bone/tooth powder gave the best results. This study demonstrates the applicability of the method for gender determination in skeletal remains from different periods.

High-resolution Y chromosome haplotypes of Israeli and Palestinian Arabs reveal geographic substructure and substantial overlap with haplotypes of Jews

High-resolution Y chromosome haplotype analysis was performed in 143 paternally unrelated Israeli and Palestinian Moslem Arabs (I&P Arabs) by screening for 11 binary polymorphisms and six microsatellite loci. Two frequent haplotypes were found among the 83 detected: the modal haplotype of the I&P Arabs (∼14%) was spread throughout the region, while its one-step microsatellite neighbor, the modal haplotype of the Galilee sample (∼8%), was mainly restricted to the north. Geographic substructuring within the Arabs was observed in the highlands of Samaria and Judea. Y chromosome variation in the I&P Arabs was compared to that of Ashkenazi and Sephardic Jews, and to that of North Welsh individuals. At the haplogroup level, defined by the binary polymorphisms only, the Y chromosome distribution in Arabs and Jews was similar but not identical. At the haplotype level, determined by both binary and microsatellite markers, a more detailed pattern was observed. Single-step microsatellite networks of Arab and Jewish haplotypes revealed a common pool for a large portion of Y chromosomes, suggesting a relatively recent common ancestry. The two modal haplotypes in the I&P Arabs were closely related to the most frequent haplotype of Jews (the Cohen modal haplotype). However, the I&P Arab clade that includes the two Arab modal haplotypes (and makes up 32% of Arab chromosomes) is found at only very low frequency among Jews, reflecting divergence and/or admixture from other populations.

Genetic analysis of β-thalassemia intermedia in Israel : Diversity of mechanisms and unpredictability of phenotype

Molecular analysis was performed on 95 Israeli patients with thalassemia intermedia, representing 60 families of Arab (Moslem and Christian), Jewish, Druze, and Samaritan origin. There was a wide range of phenotypic severity, with baseline hemoglobin levels ranging from 5.5 to 10.7. Eighteen thalassemia mutations were found (29 genotypes), which were subdivided into groups, according to the severity of mutations. A consistently mild phenotype (10 families) was caused by compound heterozygosity for a silent mutation, such as −101 C‐T or by coexistence of triplicated α‐globin genes with thalassemia trait. In 39 thalassemia intermedia families, the genotype which was found was one which led to severe thalassemia intermedia, or, in other families, was associated with thalassemia major. Elevated hemoglobin F ameliorated the disease in some patients with a severe genotype. We did not find a beneficial effect of concurrent α‐thalassemia in any of the families studied. In 11 families, only one β‐thalassemia allele was identified. One was a dominant thalassemia intermedia allele. Three additional families with heterozygous β‐thalassemia had excess α‐globin genes (5 or 6 total). In 7 of these heterozygotes, no explanation was found for the thalassemia intermedia phenotype. Our results suggest a substantial influence of as yet unknown genetic modifiers. These findings have important implications for prenatal diagnosis and for the genetic counseling of families with thalassemia intermedia. Am. J. Hematol. 54:16–22, 1997

Rapid detection of the common Mediterranean α-globin deletions/rearrangements using PCR

The most frequent molecular lesions causing α‐thalassemia are deletions of one or more α‐globin genes. Detection of these deletions generally requires genomic Southern analysis, which is cumbersome and time consuming. We have designed new sets of primers for PCR identification of the common Mediterranean α‐globin gene rearrangements, including the ‐α3.7 deletion and the αααanti3.7 triplication, the ‐α4.2 deletion, and the ‐‐Med allele. We have established reaction conditions that provide easily interpretable, unambiguous diagnoses. Some of the PCR reactions are multiplex, simultaneously identifying several genotypes, thus reducing the time and cost of screening and prenatal testing. The use of these methods should facilitate carrier screening and identification of couples at risk for α‐thalassemia. Am. J. Hematol. 58:306–310, 1998.

Diversity of α‐globin mutations and clinical presentation of α‐thalassemia in Israel

α‐Thalassemia is among the worlds most common single gene disorders, caused primarily by gene deletions. In Israel, where αo‐trait thalassemia is uncommon, it is of particular importance because of its phenotypic interactions with β‐thalassemia in hetero‐ and homozygotes. In a study of 232 individuals referred for molecular evaluation of anemia, 303 chromosomes carried α‐globin gene abnormalities; 6 gene rearrangements and 11 point mutations were identified. This unexpected heterogeneity is in part due to the many ethnic subgroups represented by these patients. Our findings include nine unique Israeli alleles, 3 of which are described here for the first time. An equal number of point mutations was found in the α2‐globin gene as compared to α1. A threonine deletion in codon 39 of the α1‐globin gene, found frequently in Arabs, is unique to Israel and probably represents one of several indigenous alleles. Among Arabs, point mutations were more frequent than large deletions. Surprisingly, in Ashkenazi Jews, who resided for many centuries in a nonmalarial environment, a single α‐globin gene deletion −α3.7 was found in many cases. The clinical presentation of individuals carrying two or more α‐globin lesions was highly variable. In general, the severity correlated inversely with the number of functional α‐globin genes. In some cases, impairment of two α‐globin genes by point mutations led to a thalassemia‐intermedia‐like picture which could be misdiagnosed as β‐thalassemia. We conclude that α‐thalassemia is phenotypically and genotypically more heterogeneous than previously recognized. DNA analysis is invaluable as it provides a specific diagnosis and enables reliable genetic counseling. Am. J. Hematol. 65:196–203, 2000.© 2000 Wiley‐Liss, Inc.

Severe thalassaemia intermedia caused by interaction of homozygosity for α-globin gene triplication with heterozygosity for β thalassaemia

Summary A 3‐year‐old child was evaluated for β‐thalassaemia intermedia. Molecular characterization including β‐globin gene sequence analysis revealed heterozygosity for a single β‐thalassaemia mutation, IVSI nt1 (GA). In addition the patient was found to be homozygous for α‐globin gene triplication (αααanti3,7/αααanti3,7). The propositus has a significantly more severe phenotype than has been previously reported with this combination of genetic defects. In contrast, four individuals heterozygous for both triplicated α and for β‐thalassaemia had a phenotype of thalassaemia minor, and a fifth had very mild thalassaemia intermedia.

THE β+-IVS-I-6 (T → C) MUTATION ACCOUNTS FOR HALF OF THE THALASSEMIA CHROMOSOMES IN THE PALESTINIAN POPULATIONS OF THE MOUNTAIN REGIONS

A study of the spectrum of β-thalassemia mutations in the southern part of the West Bank of the Palestinian Authority revealed the presence of 10 different β-globin mutations. The study included 41 patients and 54 carriers of β-thalassemia and sickle cell anemia. The spectrum of mutations observed was typically Mediterranean. However, their relative frequencies was unique. The predominant allele was IVS-I-6 (T → C), with an exceptionally high frequency of 48.5% for this mutation. The homozygous IVS-I-6 patients had widely variable clinical presentations, from typical transfusion-dependent thalassemia major to non-transfusion-dependent thalassemia intermedia phenotype. Since it is so widespread in these West Bank populations, the IVS-I-6 mutation may date back to ancient times. The nonsense mutation at codon 37 (G → A) was found at a relatively high frequency of 11.3%, supporting the hypothesis that it originated in this region. The other mutations, at decreasing frequencies ranging from 9.5–1.5%, were: IVS-I-110 (G → A), frameshift codon 5 (−CT), IVS-I-1 (G → A), IVS-II-1 (G → A), Hb S [β6(A3)Glu → Val], frameshift codons 8/9 (+G), codon 39 (C → T), and −30 (T → A). Our findings will improve health care for the Palestinian population, and also has implications for the study of the origin and spread of thalassemia in the Middle East.

Y chromosome evidence for a founder effect in Ashkenazi Jews

Recent genetic studies, based on Y chromosome polymorphic markers, showed that Ashkenazi Jews are more closely related to other Jewish and Middle Eastern groups than to their host populations in Europe. However, Ashkenazim have an elevated frequency of R-M17, the dominant Y chromosome haplogroup in Eastern Europeans, suggesting possible gene flow. In the present study of 495 Y chromosomes of Ashkenazim, 57 (11.5%) were found to belong to R-M17. Detailed analyses of haplotype structure, diversity and geographic distribution suggest a founder effect for this haplogroup, introduced at an early stage into the evolving Ashkenazi community in Europe. R-M17 chromosomes in Ashkenazim may represent vestiges of the mysterious Khazars.

Molecular analysis of beta-thalassemia in Vietnam.

The molecular basis of the thalassemias has been studied in many of the worlds populations. Here we report the results of the first screening for mutations in Vietnam. Twenty-three unrelated patients, of which 17 have Hb E/β-thalassemia, were diagnosed and β-globin mutations were detected in all 46 chromosomes. Four previously reported South Asian mutations were found. The most common mutations were the nonsense in codon 17 (A→T) and the frameshift at codons 41/42 (-TTCT) (30 and 22%, respectively). The rare frameshift mutation at codon 95 (+A) was present in 9% of the 46 chromosomes studied, suggesting that it is indigenous to Vietnam. These results will serve as an initial database for DNA-based prenatal diagnosis of thalassemia in Vietnam.