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Short Tandem Repeat (short + tandem_repeat)
Kinds of Short Tandem Repeat Terms modified by Short Tandem Repeat Selected AbstractsHierarchical modeling of genome-wide Short Tandem Repeat (STR) markers infers native American prehistoryAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 2 2010Cecil M. Lewis Jr. Abstract This study examines a genome-wide dataset of 678 Short Tandem Repeat loci characterized in 444 individuals representing 29 Native American populations as well as the Tundra Netsi and Yakut populations from Siberia. Using these data, the study tests four current hypotheses regarding the hierarchical distribution of neutral genetic variation in native South American populations: (1) the western region of South America harbors more variation than the eastern region of South America, (2) Central American and western South American populations cluster exclusively, (3) populations speaking the Chibchan-Paezan and Equatorial-Tucanoan language stock emerge as a group within an otherwise South American clade, (4) Chibchan-Paezan populations in Central America emerge together at the tips of the Chibchan-Paezan cluster. This study finds that hierarchical models with the best fit place Central American populations, and populations speaking the Chibchan-Paezan language stock, at a basal position or separated from the South American group, which is more consistent with a serial founder effect into South America than that previously described. Western (Andean) South America is found to harbor similar levels of variation as eastern (Equatorial-Tucanoan and Ge-Pano-Carib) South America, which is inconsistent with an initial west coast migration into South America. Moreover, in all relevant models, the estimates of genetic diversity within geographic regions suggest a major bottleneck or founder effect occurring within the North American subcontinent, before the peopling of Central and South America. Am J Phys Anthropol 2010. © 2009 Wiley-Liss, Inc. [source] Allele Frequency Data for 19 Short Tandem Repeats (PowerPlex® 16 and FFFl) in a Belgian Population SampleJOURNAL OF FORENSIC SCIENCES, Issue 2 2006Ronny Decorte Ph.D POPULATION: Belgian Caucasians (Dutch speaking; n=198). [source] Analysis of Short Tandem Repeats by Using SERS Monitoring and Electrochemical Melting,ANGEWANDTE CHEMIE, Issue 34 2010Damion Zum Mitnehmen: Elektrochemisches Schmelzen mit SERS-Detektion an nanostrukturierten Elektroden wurde genutzt, um DNA-Sequenzen mit unterschiedlicher Zahl an kurzen GATA-Tandemwiederholungen zu differenzieren (siehe Diagramm). Die Technik bietet sich für die Konstruktion von transportablen DNA-Analysegeräten an. [source] In this issue: Biotechnology Journal 11/2009BIOTECHNOLOGY JOURNAL, Issue 11 2009Article first published online: 13 NOV 200 Forensic identification on chips Choi and Seo et al., Biotechnol. J. 2009, 4, 1530,1541 Short tandem repeat (STR) analysis can be used for genetic fingerprinting of individuals as it is done for forensic human identification. However, the current state-of-the-art STR genotyping processes and instruments are labor intensive, expensive, time consuming, and lack portability. Micro-total-analysis systems or lab-on-a-chip platforms based on microfabrication technologies have the capability to miniaturize and integrate bioanalysis steps in a single format and have already been successfully applied for forensic STR typing. Researchers from Daejeon, Korea, highlight up-to-date work on advanced microdevices for high-throughput STR genotyping, and a portable integrated microsystem for on-site forensic DNA analysis. Surface plasmon resonance on chips Maynard et al., Biotechnol. J. 2009, 4, 1542,1558 Technologies based on surface plasmon resonance (SPR) have allowed rapid, label-free characterization of protein-protein and protein-small molecule interactions. SPR has become the gold standard in industrial and academic settings, in which the interaction between a pair of soluble binding partners is characterized in detail or a library of molecules is screened for binding against a single soluble protein. In spite of these successes, SPR is only beginning to be adapted to the needs of membrane-bound proteins which are promising targets for drug and biomarker development. This team of authors from Austin, Minneapolis and Rochester (all USA) describe current SPR instrumentation and the potential for SPR nanopore arrays to enable quantitative, high-throughput screening of G-protein coupled receptor ligands and applications in cellular biology. Nucleotide immobilization on chips Sethi et al., Biotechnol. J. 2009, 4, 1513,1529 The development of oligonucleotide-based microarrays (biochips) is of major interest in science and biotechnology industry and has applications in a wide range of research areas including genomics, proteomics, computational biology and pharmaceuticals. Especially microarrays have proven to be a unique method for time and cost efficient analysis of thousands of genes at one. Authors from Delhi and Lucknow, India discuss currently used chemical strategies for immobilization of oligonucleotides and put a special emphasis on post-synthetic immobilization on glass surfaces. Recent advances on these synthesis pathways are presented in detail. [source] An integrated microdevice for high-performance short tandem repeat genotypingBIOTECHNOLOGY JOURNAL, Issue 11 2009Jong Young Choi Abstract Short tandem repeat (STR) analysis provides genetic fingerprinting of individuals, and is considered as a powerful and indispensable technique for forensic human identification. However, the current state-of-the-art STR genotyping processes and instruments are labor intensive, expensive, time consuming, and lack portability. Micro-total-analysis systems or lab-on-a-chip platforms based on microfabrication technologies have the capability to miniaturize and integrate bioanalysis steps in a single format. Recent progress in microsystems has demonstrated their successful performance for the forensic STR typing with a reduced cost, high speed, and improved high throughput. The purpose of this review article is to highlight up-to-date work on advanced microdevices for high-throughput STR genotyping, and a portable integrated microsystem for on-site forensic DNA analysis. [source] A systematic approach to molecular quantitative determination of mixed chimaerism following allogeneic bone marrow transplantation: an analysis of its applicability in a group of patients with severe aplastic anaemiaEUROPEAN JOURNAL OF HAEMATOLOGY, Issue 3 2004Rocío Hassan Abstract:, Mixed chimaerism (MC) following allogeneic bone marrow transplantation (allo-BMT) is defined as the persistent cohabitation of haematopoietic cells from recipients and donors. Its kinetics, clinical implications and more efficient laboratory approaches for MC detection are the object of ongoing research in view of the possibility of developing useful markers. Here we describe a sequential analysis of chimaerism using variable number of tandem repeat (VNTR) polymerase chain reaction (PCR) followed by quantitative, fluorescent labelled, short tandem repeat (STR) PCR. A set of four, highly discriminative VNTR and four STR markers was used to assess chimaerism. Sensitivity and regression analysis indicated that this approach was reliable for routine application in a single BMT centre. We studied 12 patients with severe aplastic anaemia (SAA) who had received allo-BMT, and had been conditioned with cyclosphosphamide (Cy) with or without anti-thymocyte globulin (ATG). We found a 50% prevalence of MC in the whole group, with levels between 4% and 37% of recipient cells. A sustained stable MC pattern after BMT was characteristic of the Cy-only conditioned patients but was also recorded in one patient treated with the Cy + ATG regime who showed a sustained MC pattern over a period of 24 months post-BMT. In none of our patients, MC was associated with an increased risk of graft rejection in a median follow-up of 39.5 months. [source] The genetic differences with whole genome linkage disequilibrium mapping between responder and non-responder in interferon-, and ribavirin combined therapy for chronic hepatitis C patientsINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 2 2008P.-J. Chen Summary Interferon-, and ribavirin combined therapy has been a mainstream treatment for hepatitis C infection. The efficacy of this combined treatment is around 30% to 60%, and the factors affecting the responsiveness are still poorly defined. Our study is intended to investigate the genetic differences between responder and non-responder patients. The genome-wide linkage disequilibrium screening for loci associated with genetic difference between two patient groups was conducted by using 382 autosomal short tandem repeat (STR) markers involving 92 patients. We have identified 19 STR markers displaying different allele frequencies between the two patient groups. In addition, based on their genomic location and biological function, we selected the CD81 and IL15 genes to perform single nucleotide polymorphism genotyping. In conclusion, this study may provide a new approach for identifying the associated polymorphisms and the susceptible loci for interferon-, and ribavirin combined therapy in patients with chronic hepatitis C. [source] MICA-STR, HLA-B haplotypic diversity and linkage disequilibrium in the Hunan Han population of southern ChinaINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 4 2006W. Tian Summary Major histocompatibility complex (MHC) class I chain-related gene A (MICA) is located 46 kb centromeric to HLA-B and encodes a stress-inducible protein. MICA allelic variation is thought to be associated with disease susceptibility and immune response to transplants. This study was aimed to investigate the haplotypic diversity and linkage disequilibrium between human leukocyte antigen (HLA)-B and (GCT)n short tandem repeat in exon 5 of MICA gene (MICA-STR) in a southern Chinese Han population. Fifty-eight randomly selected nuclear families with 183 members including 85 unrelated parental samples were collected in Hunan province, southern China. HLA-B generic typing was performed by polymerase chain reaction,sequence-specific priming (PCR,SSP), and samples showing novel HLA-B-MICA-STR linkage were further typed for HLA-B allelic variation by high-resolution PCR,SSP. MICA-STR allelic variation and MICA gene deletion (MICA*Del) were detected by fluorescent PCR,size sequencing and PCR,SSP. Haplotype was determined through family segregation analysis. Statistical analysis was applied to the data of the 85 unrelated parental samples. Nineteen HLA-B specificities and seven MICA-STR allelic variants were observed in 85 unrelated parental samples, the most predominant of which were HLA-B*46, -B60, -B*13, and -B*15, and MICA*A5, MICA*A5.1 and MICA*A4, respectively. Genotype distributions of HLA-B, MICA-STR loci were consistent with Hardy,Weinberg proportions. The HLA-B-MICA-STR haplotypic phases of all 85 unrelated parental samples were unambiguously assigned, which contained 30 kinds of HLA-B, MICA-STR haplotypic combinations, nine of them have not been reported in the literature. Significant positive linkage disequilibria between certain HLA-B and MICA-STR alleles, including HLA-B*13 and MICA*A4, HLA-B*38 and MICA*A9, HLA-B*58 and MICA*A9, HLA-B*46 and MICA*A5, HLA-B*51 and MICA*A6, HLA-B*52 and MICA*A6, and HLA-B60 and MICA*A5.1, were observed. HLA-B*48 was linked to MICA*A5, MICA*A5.1 and MICA*Del. HLA-B*5801-MICA*A10 linkage was found in a family. Our data indicated a high degree of haplotypic diversity and strong linkage disequilibrium between MICA-STR and HLA-B in a southern Chinese Han population, the data will inform future studies on anthropology, donor,recipient HLA matching in clinical transplantation and HLA-linked disease association. [source] Direct STR Amplification from Whole Blood and Blood- or Saliva-Spotted FTA® without DNA Purification,JOURNAL OF FORENSIC SCIENCES, Issue 2 2008Su Jeong Park Ph.D. Abstract:, The DNA purification step has been thought to be essential for typing of STR DNA. However, this process is time-consuming, and there is a risk of unexpected cross-contamination during purification. We report a new method for direct short tandem repeat (STR) amplification using a newly developed direct PCR buffer, AnyDirectÔ, which can amplify STR loci from whole blood and blood- or saliva-spotted FTA® cards without DNA purification. The autosomal and Y chromosomal STR loci were analyzed for whole blood and blood or saliva spots of random individuals, followed by comparison of the results with those of corresponding purified DNA. The results from whole blood and blood spots showed perfect concordance with those from purified DNA without allele or locus drop-out. However, in the case of saliva spots, no amplification or locus drop-out was observed in some of the samples, which offers a topic for further study. Additionally, some commercial hot-start DNA polymerases other than AmpliTaq Gold® DNA polymerase were also found to be compatible with this buffer system. Therefore, this direct PCR buffer was demonstrated to be useful for fast forensic DNA analysis or criminal DNA databases for which there is no need to store DNA samples. [source] The Application of Miniplex Primer Sets in the Analysis of Degraded DNA from Human Skeletal Remains§JOURNAL OF FORENSIC SCIENCES, Issue 2 2006Kerry L. Opel M.A. ABSTRACT: A new set of multiplexed PCR primers has been applied to the analysis of human skeletal remains to determine their efficacy in analyzing degraded DNA. These primer sets, known as Miniplexes, produce shorter amplicons (50,280 base pairs (bp)) than standard short tandem repeat (STR) kits, but still utilize the 13 CODIS STR loci, providing results that are searchable on national DNA databases. In this study, a set of 31 different human remains were exposed to a variety of environmental conditions, extracted, and amplified with commercial and Miniplex DNA typing kits. The amplification efficiency of the Miniplex sets was then compared with the Promega PowerPlex® 16 system. Sixty-four percent of the samples generated full profiles when amplified with the Miniplexes, while only 16% of the samples generated full profiles with the Powerplex® 16 kit. Complete profiles were obtained for 11 of the 12 Miniplex loci with amplicon sizes less than 200 bp. These data suggest smaller PCR amplicons may provide a useful alternative to mitochondrial DNA for anthropological and forensic analysis of degraded DNA from human skeletal remains. [source] Application of short tandem repeat of genomic DNA and mitochondrial DNA for identification of mixed-up tissue specimensPATHOLOGY INTERNATIONAL, Issue 1 2000Kenji Sano Deoxyribonucleic acid (DNA) typing methods, short tandem repeat of genomic DNA and mitochondrial DNA with the use of polymerase chain reaction amplification, were applied to formalin-fixed, paraffin-embedded tissues submitted for diagnosis, to identify and sort out mixed-up tissue specimens. These techniques were found to be reliable, reproducible and specific for personal identification, and thus to eliminate the need for further examinations and to prevent unnecessary surgery. [source] Autosomal microsatellite variability of the Arrernte people of AustraliaAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 1 2008M. A. Alfonso-Sánchez The genomic diversity of the Arrernte people of Australia or caterpillar people was investigated utilizing 13 autosomal short tandem repeat (STR) markers. Significant departures from Hardy,Weinberg equilibrium were detected at the D18S51, TPOX and CSF1PO loci, which persisted after applying the Bonferroni correction. Gene diversity values oscillate between 0.6302 (CSF1PO) and 0.8731 (D21S11). Observed heterozygosity (Ho) ranges from 0.2632 (D18S51) to 0.8333 (vWA) and is lower than the expected heterozygosity (He) for 12 of the 13 loci analyzed. The genetic relationships of the Arrernte with Middle Eastern, East Asian, South Asian and Indian populations were analyzed by distance-based methods, including Neighbor-Joining trees and nonmetric multidimensional scaling. In addition, the genetic contribution of the populations included in the analysis to the Arrernte gene pool was estimated utilizing weighted least square coefficients. Although the Arrernte population exhibits a remarkable level of genetic differentiation, results of the phylogeographic analyses based on autosomal microsatellite data suggest a certain degree of genetic relatedness between the Arrernte tribe of Australia and populations from the Indian subcontinent. In contrast, the STR diversity analyses failed to detect substantial East Asian contribution to the genetic background of the Arrernte group. Am. J. Hum. Biol., 2008. © 2007 Wiley-Liss, Inc. [source] Maximum likelihood estimates of admixture in northeastern Mexico using 13 short tandem repeat lociAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 4 2002Ricardo M. Cerda-Flores Tetrameric short tandem repeat (STR) polymorphisms are widely used in population genetics, molecular evolution, gene mapping and linkage analysis, paternity tests, forensic analysis, and medical applications. This article provides allelic distributions of the STR loci D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, CSF1PO, TPOX, TH01, and D16S539 in 143 Mestizos from Northeastern Mexico, estimates of contributions of genes of European (Spanish), American Indian and African origin in the gene pool of this admixed Mestizo population (using 10 of these loci); and a comparison of the genetic admixture of this population with the previously reported two polymorphic molecular markers, D1S80 and HLA-DQA1 (n = 103). Genotype distributions were in agreement with Hardy-Weinberg expectations (HWE) for almost all 13 STR markers. Maximum likelihood estimates of admixture components yield a trihybrid model with Spanish, Amerindian, and African ancestry with the admixture proportions: 54.99% ± 3.44, 39.99% ± 2.57, and 5.02% ± 2.82, respectively. These estimates were not significantly different from those obtained using D1S80 and HLA-DQA1 loci (59.99% ± 5.94, 36.99% ± 5.04, and 3.02% ± 2.76). In conclusion, Mestizos of Northeastern Mexico showed a similar ancestral contribution independent of the markers used for evolutionary purposes. Further validation of this database supports the use of the 13 STR loci along with D1S80 and HLA-DQA1 as a battery of efficient DNA forensic markers in Northeastern Mestizo populations of Mexico. Am. J. Hum. Biol. 14:429,439, 2002. © 2002 Wiley-Liss, Inc. [source] The utility of an erythroblast scoring system and gender-independent short tandem repeat (STR) analysis for the detection of aneuploid fetal cells in maternal bloodPRENATAL DIAGNOSIS, Issue 7 2005Dong Hyun Cha Abstract Objective The aim of this study was to determine whether fetal nucleated red blood cells (NRBCs) could be distinguished from maternal cells in peripheral blood using an erythroblast scoring system based on the unique morphological and hemoglobin staining characteristics of this cell type. Presumptive fetal NRBCs were further analyzed for the presence of paternally inherited DNA polymorphisms to prove fetal origin. Methods NRBCs were isolated by density gradient separation, CD15/45 depletion, and gamma hemoglobin positive selection from peripheral blood of nine women following termination of pregnancy for trisomy 21 (n = 4), 18 (n = 1), 13 (n = 2), and other genetic abnormalities (n = 2). Candidate fetal NRBCs, based on four discrete morphological and hemoglobin staining criteria, were then subjected to fluorescent PCR (polymerase chain reaction) amplification of chromosome 21 (D21S1411, D21S11) and chromosome 18 (D18S535) short tandem repeat (STR) DNA polymorphisms. Results In all cases, candidate fetal NRBCs were accurately identified on the basis of morphologic and hemoglobin staining characteristics and confirmed to be fetal in origin based on the presence of shared and nonshared polymorphic DNA alleles when compared to DNA isolated from maternal cells. Conclusions Using the erythroblast scoring system and subsequent analysis of inherited DNA polymorphisms, we were able to distinguish fetal NRBCs from maternal cells and prove fetal origin independent of gender. These results suggest that this novel combined approach to fetal cell isolation and genetic analysis is a promising method for noninvasive prenatal diagnostic applications. Copyright © 2005 John Wiley & Sons, Ltd. [source] QF-PCR-based prenatal detection of aneuploidy in a southeast Asian populationPRENATAL DIAGNOSIS, Issue 6 2004R. Quaife Abstract Objectives We have investigated the efficacy of using quantitative fluorescent polymerase chain reaction (QF-PCR) for the prenatal recognition of aneuploidy in chromosomes 13, 18, 21, X and Y. A total of 1115 samples, from mainly southeast Asian patients, were analysed and compared in a blind trial to the results previously obtained cytogenetically. Methods A multiplex PCR involving 15 short tandem repeat (STR) sequences was used. The probability of two or more of these markers being informative was calculated, and this required the multiplex PCR to be modified. Results The QF-PCR and previous cytogenetic results concurred, except for two products of conception (POC). One of these may be a case of complete uniparental disomy that was not recognized cytogenetically. The other was tetraploid, and as such appeared normal using QF-PCR. A mosaic trisomy 18 was correctly identified. The population sample was of a mainly Chinese, ethnic origin, and the allele frequency, size and heterozygosity appeared more restricted than the population groups analysed hitherto. Conclusion The QF-PCR methodology is an efficient cost-effective method of screening for major chromosome aneuploidy, and, for certain referral categories, could be used alone. It also appears to be applicable to patients of different ethnic origins. Copyright © 2004 John Wiley & Sons, Ltd. [source] Genetic evidence for the Mongolian ancestry of KalmyksAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 4 2005Ivan Nasidze Abstract The Kalmyks are an ethnic group along the lower Volga River in Russia who are thought to have migrated there from Mongolia about 300 years ago. To investigate their origins, we studied mtDNA and Y-chromosome variation in 99 Kalmyks. Both mtDNA HV1 sequences and Y-chromosome SNP haplogroups indicate a close relationship of Kalmyks with Mongolians. In addition, genetic diversity for both mtDNA and the Y chromosome are comparable in Kalmyks, Mongolians, and other Central Asian groups, indicating that the Kalmyk migration was not associated with a substantial bottleneck. The so-called "Genghis Khan" Y-chromosome short tandem repeat (STR) haplotype was found in high frequency (31.3%) among Kalmyks, further supporting a strong genetic connection between Kalmyks and Mongolians. Genetic analyses of even recent, relatively well-documented migrations such as of the Kalmyks can therefore lead to new insights concerning such migrations. Am J Phys Anthropol 126:, 2005. © 2005 Wiley-Liss, Inc. [source] Genetic characterization of rhesus macaques (Macaca mulatta) in NepalAMERICAN JOURNAL OF PRIMATOLOGY, Issue 5 2006Randall C. Kyes Abstract Indian-origin rhesus macaques (Macaca mulatta) have long served as an animal model for the study of human disease and behavior. Given the current shortage of Indian-origin rhesus, many researchers have turned to rhesus macaques from China as a substitute. However, a number of studies have identified marked genetic differences between the Chinese and Indian animals. We investigated the genetic characteristics of a third rhesus population, the rhesus macaques of Nepal. Twenty-one rhesus macaques at the Swoyambhu Temple in Kathmandu, Nepal, were compared with more than 300 Indian- and Chinese-origin rhesus macaques. The sequence analyses of two mitochondrial DNA (mtDNA) loci, from the HVS I and 12,S rRNA regions, showed that the Nepali animals were more similar to Indian-origin than to Chinese-origin animals. The distribution of alleles at 24 short tandem repeat (STR) loci distributed across 17 chromosomes also showed greater similarity between the Nepali and Indian-origin animals. Finally, an analysis of seven major histocompatibility complex (MHC) alleles showed that the Nepali animals expressed Class I alleles that are common to Indian-origin animals, including Mamu-A*01. All of these analyses also revealed a low level of genetic diversity within this Nepali rhesus sample. We conclude that the rhesus macaques of Nepal more closely resemble rhesus macaques of Indian origin than those of Chinese origin. As such, the Nepali rhesus may offer an additional resource option for researchers who wish to maintain research protocols with animals that possess key genetic features characteristic of Indian-origin rhesus macaques. Am. J. Primatol. 68:1,11, 2006. © 2005 Wiley-Liss, Inc. [source] Mutations in the first MyTH4 domain of MYO15A are a common cause of DFNB3 hearing lossTHE LARYNGOSCOPE, Issue 4 2009A. Eliot Shearer BSc Abstract Objectives. To use clinical and genetic analyses to determine the mutation causing autosomal recessive nonsyndromic hearing loss (ARNSHL) segregating in two consanguineous Iranian families. Study Design. Family study. Methods. Members of each family received otologic and audiometric examination for the type and extent of hearing loss. Linkage mapping using Affymetrix 50K GeneChips and short tandem repeat (STRP) analysis localized the hearing loss in both families to the DFNB3 locus. Direct sequencing of the MYO15A gene was completed on affected members of both families. Results. Family L-3165 segregated a novel homozygous missense mutation (c.6371G>A) that results in a p.R2124Q amino acid substitution in the myosin XVa protein, while family L-896 segregated a novel homozygous missense (c.6555C>T) mutation resulting in a p.P2073S amino acid change. Conclusions. These are the first MYO15A mutations reported to cause DFNB3 sensorineural hearing loss in the Iranian population. Like other mutations located in the myosin tail homology 4 (MyTH4) domain, the p.R2124Q and p.P2073S mutations are predicted to disrupt the function of the myosin XVa protein, which is integral to the mechanosensory activity of hair cells in the inner ear. Laryngoscope, 2009 [source] Monozygotic Transplantation: Concerns and OpportunitiesAMERICAN JOURNAL OF TRANSPLANTATION, Issue 11 2008N. Krishnan We describe the case of a 24-year-old female with end-stage renal disease from focal segmental glomerulosclerosis (FSGS) diagnosed at age 16, who underwent monozygotic triplet transplantation at age 21 from her sister. Monozygosity was established by buccal smear DNA PCR amplification using short tandem repeat (1) profiling for 16 genetic alleles. All immunosuppression was discontinued by 1 month posttransplant. To evaluate the use of immunosuppression in HLA identical monozygotic transplantation, we interrogated the OPTN (Organ Procurement Transplant Network) database for all transplants conducted from 1987 to 2006. We identified 194 probable identical twin transplantations based on age, gender, race, ethnic category, blood type and HLA match. We evaluated the use of various immunosuppressive agents at discharge, 6 months and 1, 2 and 3 years after transplantation. Seventy-one percent of these patients at discharge and 34% at the end of 1 year were on immunosuppression. At discharge 61% received steroids and 30% received calcineurin inhibitors and 66% of these remained on calcineurin inhibitors at 1 year. Renal function was superior among those not maintained on immunosuppression. Thus, monozygotic transplantation confers an immunologic advantage that allows immunosuppression elimination despite a risk of recurrent glomerular disease such as FSGS with appropriate evaluation and management. [source] A proposal for standardization in forensic bovine DNA typing: allele nomenclature of 16 cattle-specific short tandem repeat lociANIMAL GENETICS, Issue 5 2009L. H. P. Van De Goor Summary In this study, a proposal is presented for the allele nomenclature of 16 polymorphic short tandem repeat (STR) loci (BM1824, BM2113, ETH10, ETH225, INRA023, SPS115, TGLA122, TGLA126, TGLA227, ETH3, TGLA53, BM1818, CSRM60, CSSM66, HAUT27 and ILSTS006) for bovine genotyping (Bos taurus). The nomenclature is based on sequence data of the polymorphic region(s) of the STR loci as recommended by the DNA commission of the International Society of Forensic Genetics for human DNA typing. To cover commonly and rarely occurring alleles, a selection of animals homozygous for the alleles at these STR loci were analysed and subjected to sequence studies. The alleles of the STR loci consisted either of simple or compound dinucleotide repeat patterns. Only a limited number of alleles with the same fragment size showed different repeat structures. The allele designation described here was based on the number of repeats including all variable regions within the amplified fragment. The set of 16 STR markers should be propagated for the use in all bovine applications including forensic analysis. [source] MHC microsatellites in a Southern Brazilian populationINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 5 2009C. Sens-Abuázar Summary Microsatellites are short tandem repeats of 1,6 bp DNA fragments, which are found throughout the genome. Due to their high levels of polymorphism, many of them are used as markers for population studies. Here we report an investigation on four microsatellites (D6S273, D6S2792, STR_MICA and D6S2810) located within the major histocompatibility complex in a sample of 281 Southern Brazilians of European ancestry. Allelic and haplotypic frequencies are described, as well as linkage disequilibrium (LD) between alleles of these microsatellites and alleles of three HLA genes: HLA-B, HLA-DRB1 and HLA-DQB1. The most polymorphic microsatellite was D6S2810, located close to the HLA-B locus. Strong LD was observed between alleles of microsatellites and HLA genes. The strongest associations occurred among STR_MICA*A5.1,HLA-B*13, STR_MICA*A6,HLA-B*49, STR_MICA*A9,HLA-B*39, STR_MICA*A9,HLAB*57, D6S2810*334,HLA-B*14, D6S2810*334,HLA-B*38, STR_MICA*A5.1,HLA-DRB1*1501,HLA-DQB1*0602 and D6S2810*344,HLA-DRB1*0411,HLA-DQB1*0302. This study contributes with important information on HLA haplotypes, and is potentially useful in resolving cases of low resolution HLA genotyping ambiguities. [source] Analysis of chimerism during the early period after allogeneic peripheral stem cell transplantationINTERNATIONAL JOURNAL OF LABORATORY HEMATOLOGY, Issue 6 2001B. Gleissner As there are few reports on early evaluation of chimerism, we assessed fluorescence short tandem repeats (STR) by polymerase chain reaction (PCR) assays to analyse donor and recipient characteristics at early time points after peripheral stem cell transplantation (PBSCT). Peripheral blood of 13 patients was analysed in 1- to 2-day intervals starting from the day of PBSCT. Donor and recipient allelic patterns were determined by a commercially available multiplex STR assay that simultaneously evaluates four or five gene loci. Mixed chimerism appeared in all patients during days 1,9 after transplantation and preceded haematologic engraftment for 3,12 days. Even patients without myeloablative conditioning therapy (n=4) revealed donor allelic patterns within 1,5 days. Nine patients changed during the following days to a complete donor allelic pattern and had an uncomplicated post-transplant disease course. Four patients did not consistently retain complete donor chimerism; two of them relapsed within the next 3 months, one died from septicemia within 7 days, and the fourth, transplanted for aplastic anaemia, is still in complete remission. Overall, STR analysis using a simple and comparatively cheap multiplex system permits the detection of chimerism very early after transplantation and may provide relevant information that correlates with the clinical follow-up. [source] Resolving Paternity Relationships Using X-Chromosome STRs and Bayesian NetworksJOURNAL OF FORENSIC SCIENCES, Issue 4 2007Didier Hatsch Ph.D. Abstract:, X-chromosomal short tandem repeats (X-STRs) are very useful in complex paternity cases because they are inherited by male and female offspring in different ways. They complement autosomal STRs (as-STRs) allowing higher paternity probabilities to be attained. These probabilities are expressed in a likelihood ratio (LR). The formulae needed to calculate LR depend on the genotype combinations of suspected pedigrees. LR can also be obtained by the use of Bayesian networks (BNs). These are graphical representations of real situations that can be used to easily calculate complex probabilities. In the present work, two BNs are presented, which are designed to derive LRs for half-sisters/half-sisters and mother/daughter/paternal grandmother relationships. These networks were validated against known formulae and show themselves to be useful in other suspect pedigree situations than those for which they were developed. The BNs were applied in two paternity cases. The application of the mother/daughter/paternal grandmother BN highlighted the complementary value of X-STRs to as-STRs. The same case evaluated without the mother underlined that missing information tends to be conservative if the alleged father is the biological father and otherwise nonconservative. The half-sisters case shows a limitation of statistical interpretations in regard to high allelic frequencies. [source] The Garífuna (Black Carib) people of the Atlantic coasts of Honduras: Population dynamics, structure, and phylogenetic relations inferred from genetic data, migration matrices, and isonymyAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 1 2010Edwin-Francisco Herrera-Paz The aim of this study is to assess population dynamics, structure, and phylogenetic relations of the populations that inhabit the Caribbean coasts of Honduras: the Garífuna (or Black Carib) people, an admixture of Black Africans and Red Carib Native Amerindians. Thirteen autosomal tetranucleotide microsatellite markers of the DNA (namely short tandem repeats) were genotyped in samples from the Garifuna communities of Bajamar, in the Department of Cortés; Corozal, in the Department of Atlántida; and Iriona, in the Department of Gracias a Dios. Each subject in the study filled a questionnaire with the following information: complete name and surname of participant, and places of birth of the participant, his/her parents, and grandparents. We performed analyses that included determination of migration rates and residence patterns from information of places of birth, fixation indices from genetic data, and analysis of surnames of the sampled subjects (isonymy). Migration matrices showed a migration wave from east to west in the parents and grandparents of the subjects. A raise in migration rates and a shift in predominating residence pattern from neolocality to matrilocality from grandparents to parents were observed. Analysis of isonymy conjunctly with values for FIS in each community showed high endogamy in Bajamar, and recent, high immigration in Iriona. A dendrogram constructed with allele frequencies of the Garifuna and other populations from the Americas, Africa, and Europe revealed the close relationships of this ethnic group with Afro-Caribbean and African Populations. Am. J. Hum. Biol. 2010. © 2009 Wiley-Liss, Inc. [source] Y-chromosome variation in South Iberia: Insights into the North African contributionAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 3 2009Luis Alvarez Population of Pedroches Valley, a hypothetical Berber settlement, located in the northwest portion of Córdoba province (Andalusia, Spain), had been analyzed for its Y-chromosome diversity. Moreover, to contextualize this population, 127 Y-chromosomes from a general Andalusia sample and a North African Berber community (Marrakech, Morocco) were also typed. For all samples, 24 single nucleotide polymorphisms of the non-recombining portion of the Y-chromosome (NRY) were analyzed and those samples described as belonging to E3b1b-M81 haplogroup were also typed for 16 Y-chromosome short tandem repeats. Our Analysis showed low levels of North African E3b1b-M81 haplogroup in the Pedroches Valley population (1.5%), which is a lower contribution than would be expected. This result rejects the hypothesis of a gradual genetic assimilation of Berber settlers during the Islamic period. Am. J. Hum. Biol., 2009. © 2009 Wiley-Liss, Inc. [source] The consanguinity effect on QF-PCR diagnosis of autosomal anomaliesPRENATAL DIAGNOSIS, Issue 5 2006Michel B. Choueiri Abstract Objectives Quantitative Fluorescent PCR (QF-PCR) is a simpler and faster method of detecting common chromosomal abnormalities when compared to cytogenetic analysis. The aim of our study is to investigate the applicability of this methodology in a population where consanguineous marriages are common and to estimate the heterozygous frequency of the PCR markers used. Methods Four hundred and twenty-three DNA samples were extracted from uncultured amniocytes and amplified with 18 short tandem repeats (STR) markers specific to chromosomes 13, 18 and 21. Amplification products were analyzed using the GeneScan software. Results QF-PCR correctly identified all the numerical abnormalities related to chromosomes 13, 18 and 21. A total of 24 autosomal trisomies (5.7%) were detected. The markers D21S1432 and D21S11 were the most consistent in providing unequivocal positive results for chromosome 21 and the heterozygosity percentages of the markers used were lower than the values reported in Western populations. Conclusion QF-PCR is reliable for the prenatal diagnosis of numerical anomalies of the chromosomes 13, 18 and 21 in our study population. The absence of STR heterozygosity data from Lebanon and surrounding countries makes our study very useful for the development of a reliable QF-PCR trisomy detection test. Copyright © 2006 John Wiley & Sons, Ltd. [source] Rapid prenatal diagnosis of aneuploidies and zygosity in multiple pregnancies by amniocentesis with single insertion of the needle and quantitative fluorescent PCRPRENATAL DIAGNOSIS, Issue 8 2003Vincenzo Cirigliano Abstract Objective To investigate amniotic fluid (AF) samples retrieved in multiple pregnancies by single insertion of the needle, for rapid assessment of chromosome copy number, zygosity, and cross-contamination between fetuses, using Quantitative Fluorescent Polymerase Chain Reaction (QF-PCR) amplification of highly polymorphic microsatellite markers. Methods Fifty-two multiple pregnancies were selected (47 twins, 5 triplets) and 108 samples of amniotic fluid were sampled between 12 to 20 weeks of gestation (mean 15.5) using the single-needle technique. Aneuploidy screening by QF-PCR amplification of short tandem repeats (STRs) on chromosomes X, Y, 21, 13, and 18 was carried out within 24 h of collection. Owing to the sampling procedure, the eventual presence of contamination between fetuses was also evaluated in every case. Results Normal and aneuploid fetuses were readily identified by QF-PCR. Fetal reduction was made available, for trisomic fetuses, without further waiting for completion of fetal karyotyping. In twin gestations, the ultrasound examination of chorionicity was always in agreement with the molecular assessment of zygosity. Contamination between fetuses due to the sampling procedure with a single puncture was never observed. Conclusion Rapid prenatal diagnosis of aneuploidies by QF-PCR is a sensitive, efficient, and reliable assay. When applied in multiple pregnancies, it has the added value of allowing the assessment of zygosity in all cases, independently of chorionicity and fetal sex. Copyright © 2003 John Wiley & Sons, Ltd. [source] Genetic structure of native circumpolar populations based on autosomal, mitochondrial, and Y chromosome DNA markersAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 1 2010Rohina Rubicz Abstract This study investigates the genetic structure of the present-day inhabitants of Beringia in order to answer questions concerning their origins and evolution. According to recent studies, the ancestors of Native Americans paused for a time in Beringia, during which they differentiated genetically from other Asians before peopling the New World. Furthermore, the Koryaks of Kamchatka share a "ubiquitous" allele (D9S1120) with Native Americans, indicating they may have descended from the same ancestral Beringian population that gave rise to the New World founders. Our results show that a genetic barrier exists between Kamchatkans (Koryaks and Even) and Bering Island inhabitants (Aleuts, mixed Aleuts, and Russians), based on Analysis of Molecular Variance (AMOVA) and structure analysis of nine autosomal short tandem repeats (STRs). This is supported by mitochondrial DNA evidence, but not by analysis of Y chromosome markers, as recent non-native male admixture into the region appears to have partially obscured ancient population relationships. Our study indicates that while Aleuts are descended from the original New World founders, the Koryaks are unlikely to represent a Beringian remnant of the ancestral population that gave rise to Native Americans. They are instead, like the Even, more recent arrivals to Kamchatka from interior Siberia, and the "ubiquitous" allele in Koryaks may result from recent gene flow from Chukotka. Genbank accession numbers for mtDNA sequences: GQ922935-GQ922973. Am J Phys Anthropol 143:62,74, 2010. © 2010 Wiley-Liss, Inc. [source] Human Y-chromosome short tandem repeats: A tale of acculturation and migrations as mechanisms for the diffusion of agriculture in the Balkan PeninsulaAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2010Sheyla Mirabal Abstract Southeastern Europe and, particularly, the Balkan Peninsula are especially useful when studying the mechanisms responsible for generating the current distribution of Paleolithic and Neolithic genetic signals observed throughout Europe. In this study, 404 individuals from Montenegro and 179 individuals from Serbia were typed for 17 Y-STR loci and compared across 9 Y-STR loci to geographically targeted previously published collections to ascertain the phylogenetic relationships of populations within the Balkan Peninsula and beyond. We aim to provide information on whether groups in the region represent an amalgamation of Paleolithic and Neolithic genetic substrata, or whether acculturation has played a critical role in the spread of agriculture. We have found genetic markers of Middle Eastern, south Asian and European descent in the area, however, admixture analyses indicate that over 80% of the Balkan gene pool is of European descent. Altogether, our data support the view that the diffusion of agriculture into the Balkan region was mostly a cultural phenomenon although some genetic infiltration from Africa, the Levant, the Caucasus, and the Near East has occurred. Am J Phys Anthropol, 2010. © 2010 Wiley-Liss, Inc. [source] A western Eurasian male is found in 2000-year-old elite Xiongnu cemetery in Northeast MongoliaAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2010Kijeong Kim Abstract We analyzed mitochondrial DNA (mtDNA), Y-chromosome single nucleotide polymorphisms (Y-SNP), and autosomal short tandem repeats (STR) of three skeletons found in a 2,000-year-old Xiongnu elite cemetery in Duurlig Nars of Northeast Mongolia. This study is one of the first reports of the detailed genetic analysis of ancient human remains using the three types of genetic markers. The DNA analyses revealed that one subject was an ancient male skeleton with maternal U2e1 and paternal R1a1 haplogroups. This is the first genetic evidence that a male of distinctive Indo-European lineages (R1a1) was present in the Xiongnu of Mongolia. This might indicate an Indo-European migration into Northeast Asia 2,000 years ago. Other specimens are a female with mtDNA haplogroup D4 and a male with Y-SNP haplogroup C3 and mtDNA haplogroup D4. Those haplogroups are common in Northeast Asia. There was no close kinship among them. The genetic evidence of U2e1 and R1a1 may help to clarify the migration patterns of Indo-Europeans and ancient East-West contacts of the Xiongnu Empire. Artifacts in the tombs suggested that the Xiongnu had a system of the social stratification. The West Eurasian male might show the racial tolerance of the Xiongnu Empire and some insight into the Xiongnu society. Am J Phys Anthropol, 2010. © 2010 Wiley-Liss, Inc. [source] | ||||||||||||||||