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PubMed2002

Genetic profile of the Madeira Archipelago population using the new PowerPlex16 System kit.

Allele and haplotype frequencies of 17 chromosome STR loci, 15 of them included in the kit PowerPlex 16 System from Promega, were determined in a sample of unrelated males from Madeira and Porto Santo Islands. PowerPlex 16 includes STRs not studied before in the Madeira population. The-kit includes two new allele markers (Penta D and Penta E), which proved to be extremely useful for paternity testing (PD = 0.952 and 0.977, respectively). The study revealed that the Madeira population does not differ from that of the north Portugal. Nevertheless, some loci presented alleles found in sub-Saharan and North European populations which were not reported so far in Portugal.

Alleles↗
PubMed2006

Genetic profile of nine STR loci among Goud and Padmashali populations of Andhra Pradesh, India.

We have analysed nine autosomal STR loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820) in Goud and Padmashali populations belonging to Chittoor and Cuddapah districts of Andhra Pradesh, India, respectively. This data was compared with the available data on Indian populations. Heterozygosity (H), power of discrimination (PD), probability exclusion (PE), typical paternity index (TPI), polymorphism information content (PIC), exact test with Bonferroni corrections and Arlequin analysis were carried out. Average heterozygosity observed in Goud and Padmashali populations were 0.82 and 0.81, respectively. Similarly, PD, PE, TPI and PIC have been found to be almost same between these two populations. Overall data analysis suggests the existence of sub-structuring in Indian populations.

DNA Fingerprinting↗
PubMed2006

Genetic profile of nine autosomal STR loci among Halakki and Kunabhi populations of Karnataka, India.

POPULATION: Blood samples were collected from a total of 84 healthy and unrelated Halakki (44) and Kunabhi (40) populations, with their informed written consent. The geographic location of the sampled area is shown in Fig. 1. Both the populations are endogamous, and they belong to Dravidian linguistic family. Halakki is a tribal group having a population size of approximately 3383. They claim that they originally belong to Gujarat and Rajasthan, and migrated through Andhra Pradesh to Karnataka. Kunabhi is also a tribal population, who are approximately 35,214 in number. The male Kunabhi can be identified by their tattoo marks. A necklace is the symbol of married women. They were hunters and gatherers, but at present they practice agriculture.

DNA Fingerprinting↗
PubMed2002

Genetic profile of the Açores Archipelago population using the new PowerPlex 16 system kit.

Allele and haplotype frequencies of 16 chromosome STR loci, 15 of them included in the Kit PowerPlex16 System from Promega were determined in a sample of unrelated males from the Açores Archipelago. All subjects were subjected to an interview in order to make sure that their ancestors belonged to the same island at least back to three generations. This way we intended to look for possible inter-islands differences. PowerPlex16 includes STRs not studied before in the Açores population. The Kit includes two new allele markers (Penta D and Penta E), which proved to be extremely useful for paternity testing (PD=0.921 and 0.971, respectively). The study revealed that the Açores population is considerable different from the previous studied Madeira population, but does not differ from that of the north Portugal. Nevertheless, some loci presented alleles not previously reported for Portugal.

Alleles↗
PubMed2005

[Genetic profile of Glanzmann's thrombasthenia in south Tunisia. Report of 17 cases (11 families)].

INTRODUCTION: Glanzmann's thrombasthenia (GT) is a rare congenital thrombopathy, with a recessive autosomal transmission. We present here the genealogic study of a series of patients suffering from GT. PATIENTS AND METHODS: This is a retrospective study about all the GT patients treated in Sfax hematology department during 18 years. Final diagnosis was established by agregometry. Genealogic study was based on clinical history. RESULTS: 17 cases of GT from 11 families from the south of Tunisia wen collected. The disease was paricularly frequent in the region of Moulares-Gafsa (7 patients). The percentage of consanguinity was also very high (82%), with a third degree consanguinity of 86%. Family investigation revealed 6 previously unknown cases, and 10 deaths subsequent to hemorrhagic manifestations. CONCLUSION: The high rate of consanguinity, the absence of clinical or biological manifestations in the parents, and the ratio of ill to normal subjects in the same family which was about one to four, are suggestive of an autosomal recessive mode of transmission.

Adolescent↗
PubMed1985

A genetic profile of the South African Ashkenazi Jewish population.

The South African Ashkenazi Jewish population is described in terms of the prevailing frequencies of the genes at 25 red cell enzyme and serum protein loci and 4 placental enzyme loci. Variation was encountered in 23 of these systems. The Tay-Sachs allele which occurs at polymorphic frequencies in Ashkenazi populations was found at a frequency of 0.022, which suggests that approximately 1 baby with Tay-Sachs disease could be expected out of every 2,000 born in this community should preventive measures not be taken. The atypical serum pseudocholinesterase cholinesterase allele was encountered at a relatively low frequency and instances of scoline apnoea would be expected to occur only during approximately 1 out of every 10,000 surgical operations performed. A single case of glucose-6-phosphate dehydrogenase deficiency was discovered during the survey. In general, the allele frequencies in the systems studied do not differ radically from those of Ashkenazi populations living in other parts of the world. In accordance with other Ashkenazi populations, the frequencies of certain alleles in our samples provide support for the belief that the Ashkenazim have their origin in the Middle East.

Alleles↗
PubMed1990

The NXSM recombinant inbred strains of mice: genetic profile for 58 loci including the Mtv proviral loci.

We report the construction of 17 recombinant inbred (RI) strains of mice derived from the progenitor strains NZB/BINRe and SM/J and the typing of this RI strain set, designated NXSM, for 58 loci distributed on 16 autosomes and the X chromosome. Two backcrosses involving NZB/BINJ and SM/J were constructed to confirm chromosomal assignments and determine gene orders suggested from NXSM RI strain data. From these results we recommend that chromosomal assignments and gene orders suggested from analyses of RI strain sets be confirmed using data obtained by other means. We also typed NZB/BINJ and SM/J for mammary tumor proviral (Mtv) loci. Both strains share three previously described Mtv loci: Mtv-7, Mtv-14 and Mtv-17. In addition, NZB/BINJ contains the previously described Mtv-3 and Mtv-9 loci and two new Mtv proviral loci: Mtv-27 located on chromosome (Chr) 1 and Mtv-28 located on the X chromosome. SM/J contains the previously described loci Mtv-6 and Mtv-8. Four LTR, mink cell focus-forming murine leukemia viral loci were identified and mapped: Ltrm-1 on Chr 12, Ltrm-2 on Chr 16, Ltrm-3 on Chr 5, and Ltrm-4 on Chr 13. The Tgn locus was positioned proximal to the Ly-6 locus on Chr 15.

Animals↗
PubMed2001

Genetic profile of 81 retinoblastoma patients from a referral hospital in southern India.

PURPOSE: To determine chromosomal abnormalities and inheritance pattern in patients with retinoblastoma from a referral hospital in southern India. MATERIALS AND METHODS: Eighty-one retinoblastoma patients from 78 families were included in this study. Peripheral venous blood was taken for chromosomal analysis and pedigree was ascertained for segregation analysis. RESULTS: Male to female ratio was 1.7:1, 55.56% were bilateral retinoblastoma, the mean age of onset was 12.37 months in bilateral and 33.07 months in unilateral cases (p=0.048). Majority (90.12%) had sporadic inheritance and 6.17% had autosomal dominant inheritance. In chromosomal abnormalities, 8.33% had 13q14 deletion, three cases had de novo balanced translocations. CONCLUSION: The age of onset of the disease was much earlier in the bilateral cases compared to unilateral cases. Sporadic inheritance was predominant while only a small percentage of patients had autosomal dominant inheritance. The percentage of patients with 13q14 deletion was higher than reported in the literature and three novel chromosomal translocations were observed. This is one of the largest series of cases reported from India.

Adolescent↗
PubMed2007

Mesenteric desmoid tumors in Singapore familial adenomatous polyposis patients: clinical course and genetic profile in a predominantly Chinese population.

PURPOSE: This study examined the mutational profile of the adenomatous polyposis coli gene in relation to the development of desmoid tumors in familial adenomatous polyposis patients from a predominantly Chinese population. METHODS: This is a retrospective review of all patients with familial adenomatous polyposis coli from the Singapore Polyposis Registry. Identification of specific adenomatous polyposis coli gene mutation was performed and clinical course of associated desmoid disease obtained from case records and a computerized database. RESULTS: Two hundred five patients from 75 families afflicted with familial adenomatous polyposis coli were reviewed, with gene mutations identified in 107 patients. Of these, 23 (11.2 percent) developed desmoids. The male-to-female ratio was 1:1.3 and the ethnic distribution was Chinese (n=17) and Malay (n=6). Of the 92 patients with mutations 5' to codon 1444, 11 patients (12 percent) developed desmoids compared with 6 of 15 (40 percent) patients with adenomatous polyposis coli gene mutations 3' to codon 1444 (P<0.01). The clinical course of desmoid tumors can be divided into stable (n=11), variable (n=3), progressive (n=6), and aggressive growth (n=3). Only 3 (13 percent) patients with aggressive tumor growth required chemotherapy. There was no correlation between the site of mutation and the clinical progression of the desmoids. Seventy-four percent of these desmoids (17/23) developed at a mean interval of 2.98 years after restorative proctocolectomy, while only 30 percent (7/23) were diagnosed preoperatively or discovered during the initial surgery. The most common complications related to the mesenteric desmoids were intestinal obstruction (21.7 percent), ureteric obstruction (17.4 percent), and encasement of superior mesenteric vessels (13 percent). CONCLUSION: The clinical course of desmoids in an individual familial adenomatous polyposis patient remains unpredictable and no reliable genetic marker is available for prognostication in desmoid disease.

Adenomatous Polyposis Coli↗
PubMed2002

Prevalence and genetic profiling of virulence determinants of non-O157 Shiga toxin-producing Escherichia coli isolated from cattle, beef, and humans, Calcutta, India.

We investigated the prevalence of Shiga toxin-producing Escherichia coli (STEC) in hospitalized diarrhea patients in Calcutta, India, as well as in healthy domestic cattle and raw beef samples collected from the city's abattoir. Multiplex polymerase chain reaction using primers specific for stx1 and stx2 detected STEC in 18% of cow stool samples, 50% of raw beef samples, and 1.4% and 0.6% of bloody and watery stool samples, respectively, from hospitalized diarrhea patients. Various virulence genes in the STEC isolates indicated that stx1 allele predominated. Plasmid-borne markers, namely, hlyA, katP, espP, and etpD, were also identified. Bead enzyme-linked immunosorbent assay and Vero cell assay were performed to detect and evaluate the cytotoxic effect of the Shiga toxins produced by the strains. STEC is not an important cause of diarrhea in India; however, its presence in domestic cattle and beef samples suggests that this enteropathogen may become a major public health problem in the future.

Adolescent↗
PubMed2004

Genetic profile of an Oka varicella vaccine virus variant isolated from an infant with zoster.

Varicella virus vaccine strain Oka (V-Oka) has in rare cases caused zoster in vaccinated people. Despite broad usage of V-Oka, little is known about varicella-zoster virus genomic sequence variation of strains in vaccine and isolates from patients with vaccine adverse events. Direct sequencing of 20 regions of V-Oka-GSK was compared to the sequences of the original V-Oka-Biken, GlaxoSmithKline Oka vaccine (V-Oka-GSK), and Oka-parental (P-Oka) strains. We analyzed single nucleotide polymorphisms (SNP) differentiating the Oka parental and Oka vaccine strains identified in open reading frames (ORFs) 6, 9A, 10, 21, 31, 39, 50, 51, 52, 54, 55, and 59 and eight base substitutions within ORF 62. Sixteen of these SNP impose an amino acid change in the corresponding gene product. The genotypic analysis revealed that (i) both V-Oka-GSK and V-Oka-Biken comprise mixtures of strains represented in variable proportion from lot to lot; (ii) V-Oka-GSK/zoster isolated from the zoster patient had six wild-type SNP in ORF 9A, 10, 21, 52, 55, and 62 (mutation 108838); (iii) none of the six revertant SNP would reliably discriminate Oka vaccine from the wild type; and (iv) the genomic variation found in V-Oka/zoster might be associated with changes in the biological behavior of the virus. Further studies will be needed to identify potential virulence factors in variant vaccine strains.

Amino Acid Substitution↗
PubMed1998

Genetic profile of pNOB8 from Sulfolobus: the first conjugative plasmid from an archaeon.

The complete nucleotide sequence of the archaeal conjugative plasmid, pNOB8, from the Sulfolobus isolate NOB8-H2, was determined. The plasmid is 41,229 bp in size and contains about 50 ORFs. Several direct sequence repeats are present, the largest of which is a perfect 85-bp repeat and a site of intraplasmid recombination in foreign Sulfolobus hosts. This recombination event produces a major deletion variant, pNOB8-33, which is not stably maintained. Less than 20% of the ORFs could be assigned putative functions after extensive database searches. Tandem ORFs 315 and 470, within the deleted 8-kb region, show significant sequence similarity to the protein superfamilies of ParA (whole protein) and ParB (N-terminal half), respectively, that are important for plasmid and chromosome partitioning in bacteria. A putative cis-acting element is also present that exhibits six 24-mer repeats containing palindromic sequences which are separated by 39 or 42 bp. By analogy with bacterial systems, this element may confer plasmid incompatibility and define a group of incompatible plasmids in Archaea. Although several ORFs can form putative trans-membrane or membrane-binding segments, only two ORFs show significant sequence similarity to bacterial conjugative proteins. ORF630b aligns with the TrbE protein superfamily, which contributes to mating pair formation in Bacteria, while ORF1025 aligns with the TraG protein superfamily. We infer that the conjugative mechanism for Sulfolobus differs considerably from known bacterial mechanisms. Finally, two transposases were detected; ORF413 is flanked by an imperfect 32-bp inverted repeat with a 5-bp direct repeat at the ends, and ORF406 is very similar in sequence to an insertion element identified in the Sulfolobus solfataricus P2 genome.

Amino Acid Sequence↗
PubMed2006

Progressive low-grade oligodendrogliomas: response to temozolomide and correlation between genetic profile and O6-methylguanine DNA methyltransferase protein expression.

BACKGROUND: Loss of heterozygosity (LOH) on chromosomes 1p and 19q has been associated with chemosensitivity and improved prognosis in patients with oligodendrogliomas. The DNA repair enzyme O6-methylguanine DNA methyltransferase (MGMT) may induce resistance to DNA-alkylating agents. Recent studies demonstrated that temozolomide (TMZ), an oral alkylating agent, has efficacy in the treatment of patients with progressive, low-grade oligodendroglioma (LGO). However, to the authors' knowledge, limited data are available regarding the 1p/19q profile and its correlation with MGMT protein expression and response to treatment with DNA-alkylating drugs. METHODS: Adult patients with magnetic resonance imaging (MRI) findings and/or clinical deterioration compatible with progressive LGO were eligible for the study if they were radiotherapy-naive. TMZ cycles were repeated every 28 days at a dose of 200 mg/m2 daily for 5 consecutive days. Clinical and MRI data were used to evaluate outcomes, and Kaplan-Meier estimates were used to assess the median time to tumor progression (TTP). The 1p/19q status was analyzed from paired tumor-blood DNA samples using polymerase chain reaction-based microsatellite analysis. MGMT protein expression was estimated semiquantitatively by immunohistochemistry using paraffin embedded tumor sections. RESULTS: There were 28 patients who received treatment, and the median time from diagnosis to tumor progression was 33.5 months. The median number of TMZ cycles per patient was 12.5. Marked clinical improvements were recorded in 15 patients (54%), and objective responses were recorded in 17 patients (61%). The median TTP was 31 months, and the progression-free survival rate was 70% at 24 months. Loss of chromosome 1p and low MGMT protein expression were associated with objective response (P < .003 and P < .04, respectively). CONCLUSIONS: TMZ was active in patients with progressive LGO, and their response to treatment was associated with 1p deletion and low MGMT protein expression. The authors suggest the possible use of MGMT immunostaining as a surrogate marker for predicting tumor chemosensitivity.

Adolescent↗
PubMed2004

Muscle satellite cell-specific genes identified by genetic profiling of MyoD-deficient myogenic cell.

Satellite cells are committed myogenic progenitors that give rise to proliferating myoblasts during postnatal growth and repair of skeletal muscle. To identify genes expressed at different developmental stages in the satellite cell myogenic program, representational difference analysis of cDNAs was employed to identify more than 50 unique mRNAs expressed in wild-type myoblasts and MyoD-/- myogenic cells. Novel expression patterns for several genes, such as Pax7, Asb5, IgSF4, and Hoxc10, were identified that were expressed in both quiescent and activated satellite cells. Several previously uncharacterized genes that represent putative MyoD target genes were also identified, including Pw1, Dapk2, Sytl2, and NLRR1. Importantly, many genes such as IgSF4, Neuritin, and Klra18 that were expressed exclusively in MyoD-/- myoblasts were also expressed by satellite cells in undamaged muscle in vivo but were not expressed by primary myoblasts. These data are consistent with a biological role for activated satellite cells that induce Myf5 but not MyoD. Lastly, additional endothelial and hematopoietic markers were identified supporting a nonsomitic developmental origin of the satellite cell myogenic lineage.

Animals↗