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PubMed1999

Y-chromosome and mitochondrial DNA polymorphisms in Indian populations.

Y-chromosome polymorphism using short tandem repeat (STR) markers on 94 normal males belonging to the Brahmin and Kamma caste populations of Andhra Pradesh, India, and Siddis, a migrant population from Africa, inhabiting Hyderabad, India, revealed heterogeneity as indicated by network analysis. We have observed population-specific haplotypes and alleles. Analysis of Y-Alu polymorphism (YAP) in Siddis showed the presence of Alu insertion in 40% of the individuals. However, YAP insertion was not found in Brahmins and Kammas. The dendrogram based on hypervariable region I (HVR I) of the displacement loop (D-loop) sequence of mitochondrial DNA (mtDNA) of Siddis showed genetic relationships to African populations. YAP and mtDNA analysis of Siddis also confirmed their immigration from Africa.

Alleles↗
PubMed2000

South African G4P[6] asymptomatic and symptomatic neonatal rotavirus strains differ in their NSP4, VP8*, and VP7 genes.

Over the past decade, a G4P[6] strain has been found to be circulating in different neonatal wards in the Pretoria area. This endemic strain was associated with both asymptomatic and symptomatic infection, providing the opportunity to undertake a molecular study of some of the putative "virulence" genes. The genes encoding NSP4, VP8*, and VP7 of two asymptomatic and two Symptomatic strains were sequenced and compared with ST3. Within each of these genes, amino acid substitutions unique to South African strains were recorded. Four conserved amino acid differences between asymptomatic and symptomatic strains at aa 82 (serine to leucine), aa 114 (aspartic acid to glutamic acid), aa 138 (proline to threonine), and aa 169 (leucine to serine) were identified within the NSP4 gene. The hypervariable region of VP8* exhibited 10 specific amino acid differences (at aa 73, 78, 98, 111, 116, 142, 145, 167, 169, and 188) between asymptomatic and symptomatic strains, while three amino acid substitutions within VP7 were noted. These changes to VP7 occurred within the glycosylation site at aa 70 (leucine to serine), at antigenic region A (aa 96, asparagine to threonine), and at aa 318 (aspartic acid to glycine). It may be speculated that these changes are specific to G4P[6] strains. Furthermore, the observed substitutions may also be particular to South African strains. NSP4, VP8*, and VP7 have been associated with virulence and the amino acid substitutions within these genes correlate with both asymptomatic and symptomatic infection observed in neonates.

Amino Acid Sequence↗
PubMed2000

A model for the hepatitis C virus envelope glycoprotein E2.

Several experimental studies on hepatitis C virus (HCV) have suggested the envelope glycoprotein E2 as a key antigen for an effective vaccine against the virus. Knowledge of its structure, therefore, would present a significant step forward in the fight against this disease. This paper reports the application of fold recognition methods in order to produce a model of the HCV E2 protein. Such investigation highlighted the envelope protein E of Tick Borne Encephalitis virus as a possible template for building a model of HCV E2. Mapping of experimental data onto the model allowed the prediction of a composite interaction site between E2 and its proposed cellular receptor CD81, as well as a heparin binding domain. In addition, experimental evidence is provided to show that CD81 recognition by E2 is isolate or strain specific and possibly mediated by the second hypervariable region (HVR2) of E2. Finally, the studies have also allowed a rough model for the quaternary structure of the envelope glycoproteins E1 and E2 complex to be proposed. Proteins 2000;40:355-366.

Amino Acid Sequence↗
PubMed2000

Modeling the HLA component in rheumatoid arthritis: sensitivity to DRB1 allele frequencies.

Rheumatoid arthritis is an inflammatory disease for which positive associations have been described with some HLA-DRB1 alleles. The associated alleles share a similar amino acid sequence in the third hypervariable region, the shared epitope, but differ at position 71 and 86. It has been suggested that HLA susceptibility to rheumatoid arthritis could be due not only to the shared epitope but could also be influenced by specific amino acids at positions 71 and 86. In this study, we investigated the role of these amino acids in rheumatoid arthritis on 203 unrelated patients. An involvement of amino acid 71 was detected but no conclusion was possible regarding amino acid 86. A study of the sensitivity of the conclusions to marker allele frequencies was performed. We showed that the results obtained for amino acid 71 are not very sensitive to allele frequencies but those obtained at position 86 are highly sensitive. This emphasizes the importance of studying the robustness of results to variations in allele frequencies before conclusions are drawn.

Amino Acid Sequence↗
PubMed1997

Use of T cell receptor/HLA-DRB1*04 molecular modeling to predict site-specific interactions for the DR shared epitope associated with rheumatoid arthritis.

OBJECTIVE: To use molecular modeling tools to analyze the potential structural basis for the genetic association of rheumatoid arthritis (RA) with the major histocompatibility complex (MHC) "shared epitope," a set of conserved amino acid residues in the third hypervariable region of the DRbeta chain. METHODS: Homology model building techniques were used to construct molecular models of the arthritis-associated DRB1*0404 molecule and a T cell receptor (TCR) from T cell clone EM025, which is specific for DR4 molecules containing the shared epitope sequence. Interactive graphics techniques were used to orient the TCR on the DR molecule, guided by surface complementarity analysis. RESULTS: The predicted TCR-MHC-peptide complex involved multiple interactions and specificity for the shared epitope. TCR residues CDR1beta D30, CDR2beta N51, and CDR3beta Q97 were positioned to potentially participate in hydrogen bond interactions with the shared epitope DRbeta residues Q70 and R71. CONCLUSION: These results suggest a structural mechanism in which specific TCR recognition and possibly Vbeta selection are directly influenced by the disease-associated MHC polymorphisms.

Amino Acid Sequence↗
PubMed1998

Polymorphisms of HLA class II genes and autoimmune responses to Ro/SS-A-La/SS-B among Japanese subjects.

OBJECTIVE: To investigate HLA class II allele associations with autoantibody responses to Ro/SS-A and La/SS-B among Japanese subjects. METHODS: Haplotype and allele distributions, along with molecular polymorphisms, of HLA class II genes were analyzed by polymerase chain reaction-restriction fragment length polymorphism in 41 Japanese women with precipitating autoantibodies to Ro/SS-A and/or La/SS-B. RESULTS: Among women with both Ro/SS-A and La/SS-B antibodies, the HLA class II haplotype DRB1*08032/DQA1*0103/DQB1*0601 and DRB1*08032 allele showed significantly increased frequencies compared with patients with anti-Ro/SS-A alone or with normal controls. All women with both anti-Ro/SS-A and anti-La/SS-B, but not those with anti-Ro/SS-A alone, carried DRB1 alleles that shared the same amino acid residues at positions 14-31 and 71 of the hypervariable regions of the DRB1 chain. All anti-Ro/SS-A positive women carried 1 or 2 alleles of DQB1*06 and DQB1*03 subtypes that shared the same amino acid residues at positions 71-77 of the DQB1 chain. HLA class II allele distributions did not differ among 3 anti-Ro/SS-A positive groups with different disease expressions, i.e., patients with systemic lupus erythematosus, patients with primary Sjögren's syndrome, and women with no apparent symptoms of rheumatic disease. CONCLUSION: HLA class II allele distributions differ among anti-Ro/SS-A positive subjects according to the presence or absence of coexisting anti-La/SS-B antibodies, but not according to disease expression. Our findings suggest that different HLA class II molecules might control the development of anti-Ro/SS-A and/or anti-La/SS-B antibodies in the autoimmune response to the Ro/SS-A-La/SS-B complex.

Adolescent↗
PubMed1999

Genetic risk and protective factors for idiopathic inflammatory myopathy in Koreans and American whites: a tale of two loci.

OBJECTIVE: To better understand genetic contributions to autoimmunity, immunogenetic markers were studied in two racially discrete and geographically isolated populations of patients with idiopathic inflammatory myopathy (IIM). METHODS: Clinical characteristics, as well as clinical and autoantibody subsets, were defined in 151 American white patients and 50 Korean patients with IIM. HLA-DRB1 and DQA1 genotyping was performed on patients and racially matched controls by standard molecular techniques. Gm allotypes and phenotypes were determined by the hemagglutination-inhibition method. RESULTS: HLA-DRB1*0301, the linked allele DQA1*0501, and DRB1 alleles sharing the first hypervariable region motif 9EYSTS13 were major genetic risk factors for the development of myositis in whites (corrected P [Pcorr] < 0.0004, odds ratio [OR] 11.2, 4.5, and 3.1, respectively, for each factor versus controls). Although both the white and Korean patients had a similar distribution of clinical characteristics, autoantibody profiles, and clinical groups, no HLA-DRB1 nor DQA1 allele or motif was found to be a risk factor for IIM in the Korean patients. However, DRB1*14 was a protective factor in Korean patients without myositis-specific autoantibodies (Pcorr = 0.004, OR 0.046). In addition, although no Gm phenotype or allotype was identified as a risk factor in whites, Gm 21 was a protective factor for the development of IIM in Koreans (Pcorr = 0.024, OR 0.3). CONCLUSION: Although myositis patients in the US and Korea share similar clinical and serologic features, the immune response genes predisposing to and protecting from myositis in each of these ethnic groups differ at two chromosomal loci. These data suggest that multiple genetic loci should be studied to identify risk and protective factors for some autoimmune diseases in various ethnic populations.

Adult↗
PubMed1999

Antibodies to type II collagen and HLA disease susceptibility markers in rheumatoid arthritis.

OBJECTIVE: To seek associations between antibodies to native and denatured type II collagen (NCII and DCII) and HLA in rheumatoid arthritis (RA). METHODS: One hundred fourteen patients with clinically well-defined RA were HLA-DR and DQ typed. Those who were DR4 positive were subtyped for DRB1*0401-*0408 alleles by polymerase chain reaction using allele-specific oligonucleotide probes. Antibodies to human NCII and DCII (heat-denatured) were measured by enzyme-linked immunosorbent assay. The frequency of HLA alleles was compared in patients grouped according to the presence and absence of antibodies to NCII and DCII. RESULTS: Twenty-seven patients (24%) were positive for antibodies to NCII. There was a significant increase in the frequency of HLA-DR7 in anti-NCII-positive patients compared with anti-NCII-negative patients (30% versus 9%; P = 0.019) and a significant decrease in HLA-DR3 (7% versus 28%; P = 0.044). Repeating the analyses after excluding the 16 patients who were DR7 positive revealed a significant increase in the frequency of HLA-DR1 in anti-NCII-positive patients compared with anti-NCII-negative patients (63% versus 27%; P = 0.045). Moreover, antibodies to NCII were associated with the third hypervariability region susceptibility sequence QRRAA that is present in DRB1*0101, *0404, *0405, and *0408 (84% versus 47%; P = 0.0085); 24 of 27 anti-NCII-positive patients were positive for either DR7, DR1, or DRB1*0404 or *0408. Thirty patients (26%) were positive for antibodies to DCII. There was a significant increase in the frequency of HLA-DR3 in anti-DCII-positive patients compared with anti-DCII-negative patients (40% versus 18%; P = 0.028). CONCLUSION: The genetic associations between HLA-DR alleles and antibodies to CII in RA patients is in keeping with the collagen-induced arthritis model and implicates autoimmunity to CII as a major component in the multifactorial pathogenesis of RA.

Alleles↗
PubMed1987

Dysfunctional alpha-globin genes in hemoglobin H disease in blacks: variation in restriction fragment size permits the detection of the -alpha/-alpha T genotype.

Hemoglobin H (HbH) disease is most often due to deletion of three of the four alpha-globin genes (genotype --/--alpha). In black subjects although the -alpha/chromosome is common, the --/haplotype is very rare and few examples of HbH disease have been detected. We have studied three black siblings with HbH by restriction endonuclease mapping of the alpha-like gene complex (5'-zeta-psi zeta-psi alpha 2-psi alpha 1-alpha 2-alpha 1-3') using zeta- and alpha- specific probes. The presence of size differences in the previously described hypervariable region between the zeta and psi zeta genes results in a restriction fragment length polymorphism which permitted the detection of single alpha genes on both number 16 chromosomes in these subjects. Quantitative DNA hybridization by a slot-blot technique confirmed that their genomes contained two alpha-globin genes. The results establish that in these black subjects HbH disease is associated with dysfunctional alpha-globin genes (genotype: -alpha/-alpha T).

Black People↗
PubMed1993

A new alpha-thalassemia-2 deletion resulting in microcytosis and hypochromia and in vitro chain imbalance in the heterozygote.

We have detected a novel alpha-thalassemia-2 with a large (18+ kb) deletion involving the alpha 1- and theta 1-globin genes and the 3' hypervariable region sequence. Unexpectedly, the heterozygote had a mild anemia with a marked microcytosis and hypochromia, and an in vitro alpha/beta chain synthesis ratio of 0.62-0.66. It is suggested that the deletion includes a sequence that is involved in the in cis regulation of the alpha 2-globin gene.

Adult↗
PubMed1994

A new deletional alpha-thalassemia detected in Yemenites with hemoglobin H disease.

A new large deletion from the human alpha-globin gene cluster is characterized. It involves at least 39 kb and includes the two alpha-globin genes, the theta 1-gene, all the pseudogenes, and the two hypervariable regions (HVRs), interzeta-HVR and alpha-globin 3'HVR. The conserved zeta-globin gene has been identified in various restriction fragments of abnormal size. The new deletion was found in four unrelated Israeli patients with Hb H disease, all originating in Yemen, and has been designated--YEM. It is the only two-gene deletion identified in this ethnic group.

Autoradiography↗
PubMed1994

Prenatal diagnosis of unusual hemoglobinopathies.

While analyzing 280 hemoglobinopathy kindreds with prescribed molecular tests, 3 unusual mutations were observed that required additional characterization. In the first case, the hypervariable region flanking the alpha-globin genes generated an intermediate length 8.2 kb psi zeta-globin gene fragment on a Southeast Asian chromosome with two deleted alpha-globin genes. Rehybridization of the Southern blot with alpha-globin probe distinguished the mutation unambiguously. In the second case, restriction enzyme analysis of a PCR amplified black beta-globin gene detected a novel beta-83 point mutation adjacent to a promoter element. In the third case, which was uninformative with available allele specific oligonucleotides (ASOs), total genomic PCR amplification and sequencing identified a single basepair insertion in codon 36/37 of an Iranian beta-globin gene that shifted the reading frame and obliterated gene activity. Developing additional region-specific ASOs will further diminish the number of cases that must be characterized by genomic PCR sequencing.

Anemia, Sickle Cell↗
PubMed2005

Subspecies composition and founder contribution of the captive U.S. chimpanzee (Pan troglodytes) population.

Chimpanzees are presently classified into three subspecies: Pan troglodytes verus from west Africa, P.t. troglodytes from central Africa, and P.t. schweinfurthii from east Africa. A fourth subspecies (P.t. vellerosus), from Cameroon and northern Nigeria, has been proposed. These taxonomic designations are based on geographical origins and are reflected in sequence variation in the first hypervariable region (HVR-I) of the mtDNA D-loop. Although advances have been made in our understanding of chimpanzee phylogenetics, little has been known regarding the subspecies composition of captive chimpanzees. We sequenced part of the mtDNA HVR-I region in 218 African-born population founders and performed a phylogenetic analysis with previously characterized African sequences of known provenance to infer subspecies affiliations. Most founders were P.t. verus (95.0%), distantly followed by the troglodytes schweinfurthii clade (4.6%), and a single P.t. vellerosus (0.4%). Pedigree-based estimates of genomic representation in the descendant population revealed that troglodytes schweinfurthii founder representation was reduced in captivity, vellerosus representation increased due to prolific breeding by a single male, and reproductive variance resulted in uneven representation among male P.t.verus founders. No increase in mortality was evident from between-subspecies interbreeding, indicating a lack of outbreeding depression. Knowledge of subspecies and their genomic representation can form the basis for phylogenetically informed genetic management of extant chimpanzees to preserve rare genetic variation for research, conservation, or possible future breeding.

Africa↗
PubMed2002

Mitochondrial DNA variability of West New Guinea populations.

This paper reports human mitochondrial DNA variability in West New Guinea (the least known, western side of the island of New Guinea), not yet described from a molecular perspective. The study was carried out on 202 subjects from 12 ethnic groups, belonging to six different Papuan language families, representative of both mountain and coastal plain areas. Mitochondrial DNA hypervariable region 1 (HVS 1) and the presence of the 9-bp deletion (intergenic region COII-tRNA(Lys)) were investigated. HVS 1 sequencing identified 73 polymorphic sites defining 89 haplotypes; the 9-bp deletion, which is considered a marker of Austronesian migration in the Pacific, was found to be absent in the whole West New Guinea study sample. Statistical analysis applied to the resulting haplotypes reveal high heterogeneity and an intersecting distribution of genetic variability in these populations, despite their cultural and geographic diversity. The results of subsequent phylogenetic approaches subdivide mtDNA diversity in West New Guinea into three main clusters (groups I-III), defined by sets of polymorphisms which are also shared by some individuals from Papua New Guinea. Comparisons with worldwide HVS 1 sequences stored in the MitBASE database show the absence of these patterns outside Oceania and a few Indonesian subjects, who also lack the 9-bp deletion. This finding, which is consistent with the effects of genetic drift and prolonged isolation of West New Guinea populations, lead us to regard these patterns as New Guinea population markers, which may harbor the genetic memory of the earliest human migrations to the island.

Base Sequence↗
PubMed2003

Mitochondrial DNA from pre-Columbian Ciboneys from Cuba and the prehistoric colonization of the Caribbean.

To assess the genetic affinities of extinct Ciboneys (also called Guanajuatabeys) from Cuba, 47 pre-Columbian skeletal samples belonging to this group were analyzed using ancient DNA techniques. At the time of European contact, the center and east of Cuba were occupied by agriculturalist Taino groups, while the west was mainly inhabited by Ciboneys, hunter-gatherers who have traditionally been considered a relic population descending from the initial colonization of the Caribbean. The mtDNA hypervariable region I (HVR-I) and haplogroup-specific markers were amplified and sequenced in 15 specimens using overlapping fragments; amplification from second extractions from the same sample, independent replication in different laboratories, and cloning of some PCR products support the authenticity of the sequences. Three of the five major mtDNA Amerindian lineages (A, C, and D) are present in the sample analyzed, in frequencies of 0.07, 0.60, and 0.33, respectively. Different phylogenetic analyses seem to suggest that the Caribbean most likely was populated from South America, although the data are still inconclusive, and Central American influences cannot be discarded. Our hypothesis is that the colonization of the Caribbean mainly took place in successive migration movements that emanated from the same area in South America, around the Lower Orinoco Valley: the first wave consisted of hunter-gatherer groups (ancestors of the Ciboneys), a subsequent wave of agriculturalists (ancestors of the Tainos), and a latter one of nomadic Carib warriors. However, further genetic studies are needed to confirm this scenario.

Bone and Bones↗
PubMed2004

Genetic analysis and ethnic affinities from two Scytho-Siberian skeletons.

We extracted DNA from two skeletons belonging to the Sytho-Siberian population, which were excavated from the Sebÿstei site (dating back 2,500 years) in the Altai Republic (Central Asia). Ancient DNA was analyzed by autosomal short tandem repeats (STRs) and by the sequencing of the hypervariable region 1 (HV1) of the mitochondrial DNA (mtDNA) control region. The results showed that these two skeletons were not close relatives. Moreover, their haplogroups were characteristic of Asian populations. Comparison with the haplogroup of 3,523 Asian and American individuals linked one skeleton with a putative ancestral paleo-Asiatic population and the other with Chinese populations. It appears that the genetic study of ancient populations of Central Asia brings important elements to the understanding of human population movements in Asia.

Adult↗
PubMed2001

DNA diversity and population admixture in Anatolia.

The Turkic language was introduced in Anatolia at the start of this millennium, by nomadic Turkmen groups from Central Asia. Whether that cultural transition also had significant population-genetics consequences is not fully understood. Three nuclear microsatellite loci, the hypervariable region I of the mitochondrial genome, six microsatellite loci of the Y chromosome, and one Alu insertion (YAP) were amplified and typed in 118 individuals from four populations of Anatolia. For each locus, the number of chromosomes considered varied between 51-200. Genetic variation was large within samples, and much less so between them. The contribution of Central Asian genes to the current Anatolian gene pool was quantified using three different methods, considering for comparison populations of Mediterranean Europe, and Turkic-speaking populations of Central Asia. The most reliable estimates suggest roughly 30% Central Asian admixture for both mitochondrial and Y-chromosome loci. That (admittedly approximate) figure is compatible both with a substantial immigration accompanying the arrival of the Turkmen armies (which is not historically documented), and with continuous gene flow from Asia into Anatolia, at a rate of 1% for 40 generations. Because a military invasion is expected to more deeply affect the male gene pool, similar estimates of admixture for female- and male-transmitted traits are easier to reconcile with continuous migratory contacts between Anatolia and its Asian neighbors, perhaps facilitated by the disappearance of a linguistic barrier between them.

Adult↗
PubMed2005

Brief communication: mtDNA variation in North Cameroon: lack of Asian lineages and implications for back migration from Asia to sub-Saharan Africa.

The hypervariable region-1 and four nucleotide positions (10400, 10873, 12308, and 12705) of the coding region of mitochondrial DNA (mtDNA) were analyzed in 441 individuals belonging to eight populations (Daba, Fali, Fulbe, Mandara, Uldeme, Podokwo, Tali, and Tupuri) from North Cameroon and four populations (Bakaka, Bassa, Bamileke, and Ewondo) from South Cameroon. All mtDNAs were assigned to five haplogroups: three sub-Saharan (L1, L2, and L3), one northern African (U6), and one European (U5). Our results contrast with the observed high frequencies of a Y-chromosome haplogroup of probable Asian origin (R1*-M173) in North Cameroon. As a first step toward a better understanding of the evident discrepancy between mtDNA and Y-chromosome data, we propose two contrasting scenarios. The first one, here termed "migration and asymmetric admixture," implies a back migration from Asia to North Cameroon of a population group carrying the haplotype R1*-M173 at high frequency, and an admixture process restricted to migrant males. The second scenario, on the other hand, temed "divergent drift," implies that modern populations of North Cameroon originated from a small population group which migrated from Asia to Africa and in which, through genetic drift, Y-chromosome haplotype R1*-M173 became predominant, whereas the Asian mtDNA haplogroups were lost.

Africa South of the Sahara↗