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PubMed2001

Imperfect units of an extended microsatellite structure involving single nucleotide changes.

Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) are widely used as markers in human genome studies. We have characterized a highly polymorphic STR locus (D20S85) with (AAAG)n repeats, by a combination of direct DNA sequencing and single-strand conformation polymorphism (SSCP) analysis. Eight STR alleles were first identified on denaturing gels, and SSCP gels were then used to demonstrate the existence of previously indistinguishable multiple alleles at the locus on the basis of variable allelic flanking sequences. This was confirmed by direct sequencing of the alleles. Four transitions, two G to A and two A to G in the 5'-flanking region of the locus at positions 14, 22, 24, and 26 effectively subdivided the STR alleles into two groups, with frequencies of 0.431 and 0.569, respectively. The mutational processes that generated the polymorphisms involved both simple changes in the number of AAAG repeats and single nucleotide mutations in the region flanking the repeat. The findings have potential application in the avoidance of false linkage and association. A composite locus of this nature, with separate STR and SNP evolutionary histories and resulting from different mutational processes, also could have wide application in studies of selection, drift, migration and inbreeding.

Adult↗
PubMed2001

High-performance genetic analysis using microfabricated capillary array electrophoresis microplates.

This review focuses on some recent advances in realizing microfabricated capillary array electrophoresis (microCAE). In particular, the development of a novel rotary scanning confocal fluorescence detector has facilitated the high-speed collection of sequencing and genotyping data from radially formatted microCAE devices. The concomitant development of a convenient energy-transfer cassette labeling chemistry allows sensitive multicolor labeling of any DNA genotyping or sequencing analyte. High-performance hereditary haemochromatosis and short tandem repeat genotyping assays are demonstrated on these devices along with rapid mitochondrial DNA sequence polymorphism analysis. Progress in supporting technology such as robotic fluid dispensing and batched data analysis is also presented. The ultimate goal is to develop a parallel analysis platform capable of integrated sample preparation and automated electrophoretic analysis with a throughput 10-100 times that of current technology.

Electrophoresis, Capillary↗
PubMed2002

Association of familial and sporadic rheumatoid arthritis with a single corticotropin-releasing hormone genomic region (8q12.3) haplotype.

OBJECTIVE: Rheumatoid arthritis (RA) is a common disabling autoimmune disease with a complex genetic component. We have previously described linkage of a region of chromosome 8q12.3 with RA and association of the microsatellite marker CRHRA1 with RA in 295 affected sibling-pair families. In the current study we aimed to physically link the RA-associated marker with the corticotropin-releasing hormone (CRH) candidate gene, and to examine the genomic region for additional short tandem repeat (STR) genetic markers in order to clarify the association with RA. METHODS: We examined the association of 2 STR markers with disease in the original 295 multicase families and in a cohort of 131 simplex families to refine our understanding of this genetic region in disease susceptibility in sporadic and familial RA. Genomic library screening and sequencing were used to generate physical sequences in the CRH genomic region. Bioinformatic analysis of the sequence flanking the CRH structural gene was used to screen for additional STRs and other genetic features. Genotyping was carried out using a standard fluorescence approach. Estimations of haplotype frequencies were performed to assess linkage disequilibrium. The transmission disequilibrium test was performed using TRANSMIT. RESULTS: Physical cloning and sequencing analyses identified the genomic region linking the CRHRA1 marker and the CRH structural locus. Moreover, we identified a further STR, CRHRA2, which was in strong linkage disequilibrium with CRHRA1 (P = 4.0 x 10(-14)). A haplotype, CRHRA1*10;CRHRA2*14, was preferentially carried by unaffected parents at a frequency of 8.6% compared with the expected frequency of 3.1%. This haplotype was overtransmitted in the multiply affected families (P = 0.0077) and, similarly, in the simplex families (P = 0.024). Combined analysis of both family cohorts confirmed significant evidence for linkage (P = 4.9 x 10(-4)) and association (P = 5.5 x 10(-3)) for this haplotype with RA. CONCLUSION: In demonstrating significant linkage disequilibrium between these 2 markers, we have refined the disease-associated region to a single haplotype and confirmed the significance of this region in our understanding of the genetics of RA.

Arthritis, Rheumatoid↗
PubMed1996

The phenylalanine hydroxylase locus: a marker for the history of phenylketonuria and human genetic diversity. PAH Mutation Analysis Consortium.

Disease-producing allelic variation describes one aspect of human genetic diversity. Phenylketonuria, the major type of hyperphenylalaninaemia and formerly a functional genetic lethal, has a 2% carrier frequency in temperate-zone populations. Newborn screening for hyperphenylalaninaemia (incidence of 1 in 10000) has made it one of the most widely ascertained human Mendelian traits; 99% of hyperphenylalaninaemia mutations map to the PAH (phenylalanine hydroxylase) gene on 12q24.1, and most cause phenylketonuria. The gene is well characterized. Analysis of 3986 mutant chromosomes by 81 investigators in 26 countries has identified 243 different mutations in 788 different associations (with polymorphic intragenic haplotypes [seven diallelic sites, one short tandem repeat, one variable number of tandem repeats], populations and regions). These data are compiled on a database accessible on the World-Wide Web or as a stand-alone software package. A few phenylketonuria alleles occur at high relative frequencies in particular populations on one or only a few haplotypes, suggesting positive selection in the past. Additional mechanisms (founder effect, drift and recurrent mutation) can explain frequencies and distributions of particular alleles. Allele stratification in Europeans and Orientals implies that mechanism(s) accounting for distribution and high frequencies of PAH alleles were acting before and during demic expansion in Europe and after the European and Oriental radiations.

Genetic Markers↗
PubMed2003

Reduced-intensity bone marrow transplantation from an alternative unrelated donor for myelodysplastic syndrome of first-donor origin.

A male patient had a relapse of myelodysplastic syndrome (MDS) 2 years after BMT from a female matched unrelated donor. Conventional cytogenetics, FISH, and short-tandem repeat chimerism analysis proved a relapse of donor origin. He underwent reduced-intensity BMT after a conditioning with fludarabine and busulfan, since he had impaired renal, liver, and pulmonary functions. Chimerism analysis on day 28 after the second BMT showed mixed chimerism of the first and the second donors, which later turned to full second-donor chimerism on day 60. He developed grade II acute GVHD of the skin and cytomegalovirus reactivation, but both were improved with methylprednisolone and ganciclovir, respectively. He remains in complete remission 6 months after the second BMT. Reduced-intensity second BMT from an alternative donor appeared to be a tolerable treatment option for donor-derived leukemia/MDS after the first conventional transplantation.

Adult↗
PubMed2005

Leukemic relapse in the central nervous system after allogeneic stem cell transplantation with complete remission in the bone marrow and donor-type chimerism: report of two cases.

We studied two cases with leukemia that relapsed in the central nervous system (CNS) after allogeneic stem cell transplantation. One patient underwent peripheral blood stem cell transplantation (SCT) from a related, yet haplotype-mismatched, donor for chronic myelomonocytic leukemia. She was kept in complete remission (CR) in the bone marrow (BM) for 7 months, until relapse in the cerebrospinal fluid (CSF) was evident. In the other patient, with acute lymphoblastic leukemia, systemic relapse occurred when he was still on immunosuppression 6 months after SCT from an unrelated donor. After induction chemotherapy following cessation of immunosuppression, the BM examination proved CR. During consolidation chemotherapy, however, he developed leukemic dissemination in the CSF, despite the fact that the BM was in CR. Chimerism status in the BM mononuclear cells and fractionated peripheral blood (PB) cells (granulocytes, T-lymphocytes, and the others) was assessed by short tandem repeat analysis. In both patients, the BM cells and all the fractions of the PB cells proved donor-type chimeras. These results seem to suggest that the graft-versus-leukemia effects might not be as effective in the CNS as in the BM, even when complete T-lymphoid chimerism is achieved.

Adult↗
PubMed2005

Donor cell derived acute myeloid leukemia after allogeneic cord blood transplantation in a patient with adult T-cell lymphoma.

We report a patient with adult T-cell lymphoma who developed acute myeloid leukemia (AML) after allogeneic cord blood transplantation (CBT). Fluorescence in situ hybridization (FISH) studies and molecular analysis using short tandem repeat (STR) sequences proved the AML to be of donor origin. Although 25 cases of donor cell leukemia (DCL) occurring after allogeneic bone marrow transplantation have previously been reported, there have been no reports of DCL after CBT. This case is the first-reported DCL patient after CBT.

Acute Disease↗
PubMed2006

Acute myeloid leukemia of donor origin after allogeneic bone marrow transplantation for precursor T-cell acute lymphoblastic leukemia: case report and review of the literature.

We report a case of donor-derived acute myeloid leukemia (AML) occurring in a 33-year-old man after allogeneic bone marrow transplantation (BMT) for precursor T-cell acute lymphoblastic -leukemia (T-ALL). The cells for BMT were from his human leukocyte antigen (HLA)-matched sister. Fluorescence in-situ hybridization (FISH) analysis showed the AML to be of donor origin (i.e., karyotypically female) with an 11q23 (mixed lineage leukemia (MLL) gene) translocation, while the original T-ALL exhibited a male karyotype with abnormalities of chromosomes 6, 8, and a t(10;14)(q24;q11.2). Subsequent molecular short tandem repeat studies confirmed the AML to be of donor origin. Donor-cell leukemia (DCL) after allogeneic BMT is a rare, yet well-documented, event. Our report presents clinicopathologic information about a case of DCL and a review of the recent literature.

Adult↗
PubMed2006

Hemoglobin Loves Park [beta68 (E12) Leu-->Phe]: report of five cases including one originating from a de novo mutation.

Hemoglobin (Hb) Loves Park [beta68 (E12) Leu-->Phe] was identified in a 2-year-old Portuguese boy with anemia, microcytosis, and hypochromia. This Hb variant was detected by isoelectric focusing and quantified by reverse-phase high-performance liquid chromatography (HPLC) (48.4%), and the DNA mutation was identified by HBB (beta-globin gene) sequencing. Hematological and biochemical analyses performed on his parents revealed normal hematological parameters and normal hemoglobin and globin chain profiles. DNA sequence analysis of the HBB gene of both parents showed the absence of the Hb Loves Park mutation. Study of the haplotypes in the beta-globin gene cluster confirmed parenthood. Moreover, paternity was confirmed by the study of nine short tandem repeats (STRs) and four variable-number tandem repeat (VNTRs) loci. The most likely explanation for these results is that the Hb Loves Park mutation has occurred de novo in this family. The original American cases of Hb Loves Park, from a family of Italian origin, which were never published, as well as two additional cases, are also included in this report. Functional studies revealed that Hb Loves Park is stable and has a decreased oxygen affinity.

Amino Acid Substitution↗
PubMedDate not supplied

Behavior of loci D1S1656 and D12S391 in a sample from Maracaibo, Venezuela.

Two recently reported short tandem repeat polymorphisms characterized by PCR, D1S1656 and D12S391, were investigated in a sample from Maracaibo, an admixed population of Venezuela, in order to evaluate their application in forensic and population genetics studies. The unbiased heterozygosities were 0.9011 and 0.8444 for locus D1S1656 and D12S391, respectively. The joint discrimination power and joint probability of exclusion were 0.99972 and 0.93287. When allele frequencies of locus D1S1656 from Maracaibo were compared with eight other populations, our group clustered with the European or European-derived samples, mainly from Spain. In the comparison of locus D12S391 with 16 populations, Maracaibo clustered with 3 Asian samples. The high heterozygosity and discrimination power make these two loci important candidates to be considered for STR packages for forensic and population genetic purposes.

Alleles↗
PubMedDate not supplied

Historical genetics: spatiotemporal analysis of the formation of the Brazilian population.

A total of 1037 individuals living in five different sociogeographic regions of Brazil were studied in relation to 12 short tandem repeat polymorphisms. The objective was to assess the degree of European, African, and Amerindian contributions to their gene pools. Although most of the genetic variability was found within regions, significant differences were also observed between regions. The estimated relative proportions of the above-indicated continental contributions showed intermediate values between those obtained with uniparental (mtDNA, Y-chromosome) data, and a higher percentage of European heritage as compared to previous autosome results. A north-south trend of increasing European contribution was also found, in agreement with the history of the Brazilian population.

Brazil↗
PubMedDate not supplied

Genomic ancestry of a sample population from the state of São Paulo, Brazil.

Allelic frequencies of eight autosomal short-tandem repeat (STR) loci (TH01, TPOx, CSF1PO, vWA, FES/FPS, F13A1, F13B, and CD4) were determined in 400 individuals born in the State of São Paulo. No significant deviations from Hardy-Weinberg equilibrium were found in any loci analyzed. The Unweighted Pair-Group Method with Arithmetic Mean (UPGMA) tree constructed based on genetic distances revealed that the present population was grouped with Europeans, and separated from African and Amerindian populations. Estimates of admixture components based on the gene identity method revealed 79% European, 14% African, and 7% Amerindian contributions to this Brazilian population sample.

Brazil↗
PubMedDate not supplied

Gene flow in the Iberian Peninsula determined from Y-chromosome STR loci.

In this work, seven multiallelic short-tandem repeat (STR) loci from the nonrecombining region of the human Y-chromosome (DYS19, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, and DYS393) were typed in a sample of residents in the Basque Country (RBAS). In all, 40 different Y-STR haplotypic combinations were identified, resulting in a value of haplotypic diversity of 0.979. Y-STR data compiled from previous works were used for studying Y-chromosome diversity in the Iberian Peninsula and for assessing the effects of migratory movements on the genetic background of the population living currently in territories traditionally occupied by native (autochthonous) Basques. An analysis of the spatial distribution of allelic frequencies of the Y-STRs revealed a geographic pattern characterized by variation gradients (frequency clines) oriented for the most part in the direction southwest-northeast. Accordingly, a neighbor-joining analysis showed a relative polarization between populations located in the northeast and center of the Iberian Peninsula, and the rest of the samples considered. The study sample (RBAS) occupied an intermediate position in the population tree between the autochthonous Basques (BASQ) and the remaining samples. Interestingly, the RBAS collection only showed genetic heterogeneity with that of native Basques (PhiST = 0.013, P < 0.05). Estimates of admixture proportions in the gene pool of RBAS indicated a high level of hybridization with Basque (56%) and non-Basque (44%) genes, which could explain the genetic differentiation observed between BASQ and RBAS.

Chromosomes, Human, Y↗
PubMedDate not supplied

Ethnogenomic diversity of Caucasus, Daghestan.

Autosomal short-tandem repeats (STRs) were typed in ethnic populations of Kubachians, Dargins, Avars, Lezgins, Kumiks, and Nogais of the Caucasus (Daghestan, Russia) at the University of Utah. Daghestan ethnic populations demonstrated differences in STR allele frequency distributions, but these differences were much lower among these ethnic groups compared to worldwide ethnic groups. The observed genetic diversity was low while F(ST) values were high, both of which provided supporting evidence for small population sizes and high levels of isolation among the ethnic groups. An analysis of genetic distance from the three major continents, encompassing Daghestan populations and groups, reveals three distinct clusters: all populations of African affiliation, European and Daghestan populations except the Nogais, and Asian populations with ethnic Nogais.

Dagestan↗
PubMed2002

Association of tetralogy of Fallot with a distinct region of del22q11.2.

Congenital heart defects (CHDs) appear in greater frequency among relatives of patients and in individuals with DiGeorge syndrome (DGS) or velo-cardio-facial syndrome (VCFS). A majority of these patients and part of the apparently nonsyndromic CHD patients with conotruncal defects manifest hemizygous deletions within chromosome 22q11.2 (del22q11). We tested myocardial tissues of 31 CHD patients, 21 with tetralogy of Fallot (TOF) and 10 with a double-chamber right ventricle (DCRV). DNA isolated from tissues removed at corrective surgery was analyzed for homo- or heterozygosity of nine polymorphic short tandem repeat (STR) markers along the 22q11.2 region. DNA from the blood of 45 healthy individuals represented the general population. Ten of the 21 TOF patients (48%) showed homozygosity for three or more consecutive markers, indicating deletions of various sizes. No such indication was found for DCRV patients. Heterozygosity for markers D22S1648, D22S941, and D22S944 was lower in the TOF group than in normal controls, defining a minimal critical region (MCR) for the deletion. Our findings support an association between TOF and hemizygosity in 22q11.2, suggesting a distinct region, between markers D22S1638 and COMT, that may harbor TOF susceptibility genes.

Adult↗
PubMed2002

Clinical, cytogenetic, and molecular findings in 45,X/47,XX,+18 mosaicism: clinical report and review of the literature.

We report cytogenetic and molecular findings performed in a patient with double mosaic aneuploidy. Chromosome analysis of amniotic fluid cells from a 17-week-old fetus was performed because of advanced maternal age. Two karyotypes were detected: 45,X and 47,XX,+18 (50:50%). The same cell lines were determined in uncultured and cultured amniocytes of a second amniotic fluid sample, in fetal lymphocytes, and in uncultured and cultured cells of achilles tendon by conventional cytogenetics and fluorescence in situ hybridization (FISH). In the different investigated tissues, the percentage of cells with 45,X karyotype ranged from 20-99% and the percentage of cells with 47,XX,+18 ranged from 1-80%. The pregnancy was terminated at 22 + 0 weeks because of a severe cardiac malformation. Pathologic examination showed a fetus with aspects typical for manifestation of trisomy 18 and monosomy X, especially in the internal organs. The parent and cell stage of origin was determined by short tandem repeat typing and revealed a maternal meiotic division error that led to trisomy 18, as well as a somatic loss of a paternal sex chromosome. Only two other patients with the same mosaicism have been reported so far. Genetic counseling and prognosis remains challenging.

Adult↗
PubMed2002

Genome-wide scan for linkage to schizophrenia in a Spanish-origin cohort from Costa Rica.

Genetic isolates have been useful cohorts in which to search for genes underlying disorders of unknown pathology. One such cohort is thought to exist in the Central Valley of Costa Rica surrounding the city of San Jose. Previous investigators identified a rare dominant gene for hereditary deafness in this population, and a suggestive linkage of severe bipolar psychosis has been reported in another study. Ninety-nine families with at least one pair of siblings affected with schizophrenia or a schizophrenia-spectrum diagnosis had clinical evaluations and DNA collected for genotyping. The Marshfield Medical Research Foundation (NHLBI) Mammalian Genotyping Service performed all genotyping using 404 short-tandem repeat polymorphic markers (STRPs) spaced on average 10 cM apart. Data were analyzed using the nonparametric program, GeneHunterPlus. The population structure was investigated using the STRUCT program. No region was found with genome-wide significance for linkage. Using a phenotype of schizophrenia plus schizoaffective disorder, the highest maximum likelihood score (MLS) observed was 1.78 (P < 0.004) at 176.6 cM from pter on chromosome 5q, an area previously implicated by some other groups. In addition, five regions on chromosomes 1p, 2p, 2q, 14p, and 8p had MLSs above 1.0. All other regions produced scores below 1.0. Population genetic analysis reveals no evidence for population substructure, for admixture with other populations, such as Amerindians, or for inbreeding in the parental generation. The latter casts some doubt on this population being an isolate, although there was evidence of inbreeding among the offspring.

Chromosome Mapping↗
PubMed1994

Progress in a genome scan for linkage in schizophrenia in a large Swedish kindred.

Genetic linkage studies of a kindred from Sweden segregating for schizophrenia have been performed using a genetic model (autosomal dominant, f = 0.72, q = 0.02, phenocopies = 0.001) as described in Kennedy et al., 1988. Analyses of the restriction fragment length polymorphism (RFLP), allele-specific oligonucleotides (ASO), and short tandem repeat (STR also called microsatellite) data for 180 polymorphisms (individual probe-enzyme, ASO, or STR systems) at 155 loci have been completed using the MLINK and LIPED programs. Linkage to schizophrenia was excluded, under the given model, at 47 loci; indeterminate lod scores occurred at 108 loci. The total exclusion region across 20 chromosomes is estimated at 330 cM; 211 cM excluded by pairwise analyses and 119 cM previously excluded by multipoint analyses (Kennedy et al., 1989: Schizophr Bull 15:383-391; Moises et al. 1991: Genet Epidemiol 2:99-110; Hallmayer et al., 1992: Arch Gen Psychiatry 49:216-219).

Alleles↗