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PubMed2006

Primary transcripts and expressions of mammal intergenic microRNAs detected by mapping ESTs to their flanking sequences.

MicroRNAs (miRNAs) are a class of approximately 22-nt small RNAs that regulate posttranscriptional gene expression. Thousands of expressed sequence tags (ESTs) have been identified by using upstream 2500-nt and downstream 4000-nt flanking sequences to BLAST in the dbEST database. The cotranscription of the miRNAs and their flanking sequences covered by the matched ESTs is verified by RT-PCR. It directly reveals that a large portion of mammalian intergenic miRNAs are first transcribed as long primary transcripts (pri-miRNAs). Also, the transcripts' ranges of tens of pri-miRNAs are predicted by the EST-extension method. We then extracted the tissue-specific expression information from the annotations of the matched ESTs and established the expression profile of the studied miRNAs for tens of tissues. This provided a new way to establish the expression profiles of miRNAs. Results show that the human brain, lung, liver, and eye and the mouse brain, eye, and mammary gland are tissues in which enriched numbers of miRNAs are expressed.

3' Flanking Region↗
PubMed2002

Mutational and expression analysis of the reelin pathway components CDK5 and doublecortin in gangliogliomas.

Gangliogliomas represent highly differentiated glioneuronal tumors frequently occurring in young patients with focal epilepsies. Dysplastic neurons are a neuropathological hallmark of this neoplasm. Here, we have analyzed two major components of the reelin pathway associated with neuronal migration and cortical cytoarchitecture in gangliogliomas, i.e., cyclin-dependent kinase 5 (CDK5) and doublecortin (DCX). The genomic structure of human CDK5 was identified by an " in silico" cloning approach using the "high throughput genomic sequencing" (htgs) databank, NCBI BLAST 2.1. DNA sequence analysis of CDK5 and DCX was carried out in tissue samples obtained from 23 patients and compared with control DNA from non-affected individuals ( n=100). For gene expression analysis of CDK5 and DCX, a quantitative real time reverse transcription-PCR TaqMan assay was used with mRNA from gangliogliomas ( n=22) and non-lesional central nervous tissue control tissue ( n=7). The human CDK5 gene is located on chromosome 7q36 and contains 12 exons. Its coding sequence reveals 90.1% homology to the mouse counterpart. A novel pseudogene of CDK5 was found on chromosome 8. While the mutational analysis of CDK5 and DCX did not reveal any sequence alterations in gangliogliomas, a lower expression was observed for both genes in tumor compared to control tissue samples. The present data indicate that mutations of CDK5 and DCX genes are not involved in the development of gangliogliomas. A novel pseudogene on chromosome 8 has to be taken into account for future studies on CDK5.

Animals↗
PubMed2002

Continental and subcontinental distributions of mtDNA control region types.

When the mtDNA profile of a crime scene matches that of a suspect, it is necessary to determine the probability of a chance match by consulting the frequencies of the identified allele in a "reference population". The ceiling principle suggests that that population should be chosen in which the allele of the suspect is found at the highest frequency, in order to give the suspect the maximum benefit of doubt. Recently, we advocated the use of a worldwide mitochondrial database combined with a geographical information system to identify the regions of the world with the highest frequencies of matching mtDNA types. Here, we demonstrate that the alternative approach of defining a ceiling reference population on the basis of continent or phenotype (race) is too coarse for a non-negligible percentage of mtDNA control region types.

DNA, Mitochondrial↗
PubMed2002

Rare failures in the amelogenin sex test.

Determination of sex using the amelogenin sex test is well established in the forensic field especially for casework and DNA databasing purposes. The sex test is part of commercially available PCR kits. Among 29,432 phenotypic male individuals stored in the Austrian National DNA database, 6 individuals were found to lack the amelogenin Y-specific PCR product which was confirmed using alternative amelogenin primers. The amplification of eight Y-chromosomal STR markers resulted in full profiles in five out of the six samples, one sample failed to amplify Y-STRs at all. The amplification of a fragment of the SRY gene gave positive results in all six samples, confirming the male phenotype of the individuals. The observed failure rate of the amelogenin sex test was 0.018% in this study.

Amelogenin↗
PubMed2002

Sequence variations in the primer binding regions of the highly polymorphic STR system SE33.

Five cases were found with sequence variation in the primer binding region of the highly polymorphic STR system SE33 used in the German genetic database. This variation can produce homozygote mistyping because of failed primer binding. We calculated a variation rate of 0.0022 (0.0006-0.0056) that could lead to complications in database matching. To avoid errors in individual genetic characterisation for SE33 as described here, it is suggested that two different primer pairs should be used.

Base Sequence↗
PubMed2004

Allele frequencies of the 15 AmpF lSTR Identifiler loci in the population of Vojvodina Province, Serbia and Montenegro.

The 15 AmpF lSTR Identifiler loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818 and FGA) were analyzed in the sample of 100 unrelated, autochthonous healthy adult Serbians from Novi Sad (Vojvodina Province, Serbia and Montenegro). The agreement with HWE was confirmed for all loci with the exception of D7S820 (based on the chi2-test only). The combined power of discrimination (PD) and the combined power of exclusion (PE) for the 15 tested STR loci were 0.99999999999999995 and 0.9999990, respectively. According to the presented data, D2S1338 and D18S51 are the most informative markers. Based on allelic frequencies and statistical parameters for forensic testing, it may be suggested that the AmpF lSTR Identifiler detection system represents a powerful strategy for individual identification and parentage analysis in the Serbian population.

Adult↗
PubMed2004

Population genetics of the 15 AmpF lSTR Identifiler loci in Kosovo Albanians.

The 15 AmpF lSTR Identifiler loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, THO1, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818 and FGA) were analyzed in a sample of 136 unrelated Albanian adults from Kosovo. The agreement with HWE was confirmed for all loci with the exception of TPOX (based on the exact test only). The combined power of discrimination (PD) and the combined power of exclusion (PE) for the 15 studied loci were 0.99999999999999997 and 0.9999995, respectively. According to the presented data, FGA proved to be the most informative marker. An interpopulation comparison between Kosovo Albanians and Croatians (as an example of a population from the Balkans) revealed significant differences in four out of nine loci.

Adult↗
PubMed2004

Bosnian population data for the 15 STR loci in the Power Plex 16 kit.

The PowerPlex 16 amplification kit was used for the analysis of allele frequencies for the 15 STR loci (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, VWA, D8S1179, TPOX and FGA) in unrelated, autochthonous healthy adults from Bosnia ( n=123 for TH01, Penta E, D16S539, CSF1PO, Penta D and TPOX, n=210 for D3S1358, D21S11, D18S51, D5S818, D13S317, D7S820, VWA, D8S1179 and FGA). The agreement with HWE was confirmed for all loci with the exception of Penta D (based on the chi(2)-test only). The combined power of discrimination (PD) and the combined power of exclusion (PE) for the 15 studied loci were 0.999999999999999997 and 0.999999, respectively.

Adult↗
PubMed2004

Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database.

Large forensic mtDNA databases which adhere to strict guidelines for generation and maintenance, are not available for many populations outside of the United States and western Europe. We have established a high quality mtDNA control region sequence database for urban Nairobi as both a reference database for forensic investigations, and as a tool to examine the genetic variation of Kenyan sequences in the context of known African variation. The Nairobi sequences exhibited high variation and a low random match probability, indicating utility for forensic testing. Haplogroup identification and frequencies were compared with those reported from other published studies on African, or African-origin populations from Mozambique, Sierra Leone, and the United States, and suggest significant differences in the mtDNA compositions of the various populations. The quality of the sequence data in our study was investigated and supported using phylogenetic measures. Our data demonstrate the diversity and distinctiveness of African populations, and underline the importance of establishing additional forensic mtDNA databases of indigenous African populations.

Black People↗
PubMed2001

Identification and characterization of two novel human polymorphic STRs on the Y chromosome.

From sequence database information, we have identified two male-specific and polymorphic tetranucleotide STRs, DYS 441 (GDB:10013873) and DYS 442 (GDB: 10030304), on the Y chromosome. Analysis of 184 males allowed 7 and 5 alleles to be distinguished in the DYS 441 and DYS 442 systems, respectively, yielding 21 haplotypes. The gene diversities were 0.72 and 0.51, respectively and the haplotype diversity was 0.85.

Base Sequence↗
PubMed2002

A new database of mitochondrial DNA hypervariable regions I and II sequences from 162 Japanese individuals.

A database of mitochondrial DNA (mtDNA) hypervariable region 1 (HV1) and region 2 (HV2) sequences of the mtDNA control region was established from 162 unrelated Japanese individuals. The random match probability and the genetic diversity for this database were 0.96% and 0.997, respectively. Length heteroplasmy in the C-stretch regions located around position 16189 in HVI and 310 in HV2 was observed in 37% and 38% of the samples, respectively. A strategy using internal sequencing primers was devised to obtain confirmed sequences in these length heteroplasmic individuals. This database, combined with other mtDNA sequence databases from the Japanese population, will permit the significance of mtDNA match results to be properly reported in mtDNA typing casework in Japan.

Base Sequence↗
PubMed2001

An annotated mtDNA database.

We have compiled a database of mitochondrial DNA (mtDNA) control region, hypervariable regions 1 (HVR1) and 2 (HVR2) sequences of a total of 14,138 individuals compiled from 103 mtDNA publications before 1 January 2000, 13 data sets published in 2000 and 2001 and 2 unpublished data sets of Iraqi Kurds and Indians from Kerala. By contacting the authors and by other means, we have confirmed and corrected sequence errors, eliminated duplications and harmonised the sequence format. These changes affected all but 26 of the 116 publications. Furthermore, we have implemented a geographic information system ("mtradius") which searches for closest matches to a given mtDNA control region sequence and displays them on a geographic map. A potential application is to estimate a chance matching probability when a forensic stain and a suspect have an identical mtDNA sequence: we suggest that the geographic area with the highest frequency of closely related mtDNA sequence types may be used to define a reference population to give the suspect the maximum benefit of doubt in accordance with the ceiling principle.

DNA Fingerprinting↗
PubMed2003

Analysis of the gene expression profile of Schistosoma japonicum cercariae by a strategy based on expressed sequence tags.

We present an analysis of the expression profile of Schistosoma japonicum cercariae by a strategy based on expressed sequence tags (ESTs). A cDNA library from S. japoniucm cercariae was constructed and was used to generate ESTs. In total, 201 clones randomly selected from the library were sequenced; 136 ESTs were successfully obtained and sent to the BLAST server for homology searching. Among the 136 ESTs, 85 (62.50%) did not match any protein or gene sequence published in the BLAST databases; these comprised 75 (55.15%) ESTs matched (or partly matched) S. japonicum and Schistosoma mansoni ESTs, 4 (2.94%) matched human ESTs and 6 (4.41%) that did not match any sequence. Fifty-one (37.50%) ESTs were identified by the BLAST server; these consisted of 8 (5.88%), 9 (6.62%) and 34 (25.00%) that showed high homology with genes or proteins reported from S. japonicum, S. mansoni and other organisms, respectively. These identified ESTs can be grouped into nine categories: transporters (1.96%), secretory proteins (1.96%), kinases (3.92%), proteases (5.88%), structural and cytoskeletal proteins (13.73%), metabolism-related proteins (9.80%), regulatory and signaling proteins (11.76%), transcription and translation machinery (25.50%), and others (25.50%). Several interesting new genes cloned from this cDNA library are discussed here. These findings will be valuable for the understanding of the biology of this parasite.

Animals↗
PubMed2001

Transposition of IS10 from the host Escherichia coli genome to a plasmid may lead to cloning artefacts.

During recloning of Nicotiana tabacum L. repetitive sequence R8.3 in Escherichia coli, a modified clone that differed from the original by the insertion of an IS10 sequence was unintentionally produced. The insert was flanked by a 9-bp direct repeat derived from the R8.3 sequence, the 9-bp duplication of acceptor DNA in the site of insertion being a characteristic of IS10 transposition events. A database search using the FASTA program showed IS10 and other prokaryotic IS elements inserted into numerous eukaryotic clones. Unexpectedly, the IS10, which is not a natural component of the E. coli genome, appeared to be by far the most frequent contaminant of DNA databases among several IS sequences tested. In the GenEMBL database, the IS10 query sequence yielded positive scores with more than 500 eukaryotic clones. Insertions of shortened IS10 sequences having only one intact terminal inverted repeat were commonly found. Most full-length IS10 insertions (32 out of 40 analyzed) were flanked by 9-bp direct repeats having the consensus 5'-NPuCNN-NGPyN-3' with a strong preference for 5'-TGCTNA-GNN-3'. One insertion was flanked by an inverted repeat of more than 400 bp in length. PCR amplification and Southern analysis revealed the presence of IS10 sequences in E. coli strains commonly used for DNA cloning, including some reported to be Tn10-free. No IS10-specific PCR product was obtained with N. tabacum or human DNA. Our data suggest that transposition of IS10 elements may accompany cloning steps, particularly into large BAC vectors. This might lead to the relatively frequent contamination of DNA databases by this bacterial sequence. It is estimated that one in approximately every thousand eukaryotic clone in the databases is contaminated by IS-derived sequences. We recommend checking submitted sequences for the presence of IS10 and other IS elements. In addition, DNA databases should be corrected by removing contaminating IS sequences.

Animals↗
PubMed2002

Homogeneity and distinctiveness of Polish paternal lineages revealed by Y chromosome microsatellite haplotype analysis.

Different regional populations from Poland were studied in order to assess the genetic heterogeneity within Poland, investigate the genetic relationships with other European populations and provide a population-specific reference database for anthropological and forensic studies. Nine Y-chromosomal microsatellites were analysed in a total of 919 unrelated males from six regions of Poland and in 1,273 male individuals from nine other European populations. AMOVA revealed that all of the molecular variation in the Polish dataset is due to variation within populations, and no variation was detected among populations of different regions of Poland. However, in the non-Polish European dataset 9.3% ( P<0.0001) of the total variation was due to differences among populations. Consequently, differences in R(ST)-values between all possible pairs of Polish populations were not statistically significant, whereas significant differences were observed in nearly all comparisons of Polish and non-Polish European populations. Phylogenetic analyses demonstrated tight clustering of Polish populations separated from non-Polish groups. Population clustering based on Y-STR haplotypes generally correlates well with the geography and history of the region. Thus, our data are consistent with the assumption of homogeneity of present-day paternal lineages within Poland and their distinctiveness from other parts of Europe, at least in respect to their Y-STR haplotypes. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00439-002-0728-0.

Alleles↗
PubMed2004

Fine mapping a gene for pediatric gastroesophageal reflux on human chromosome 13q14.

We previously mapped a gene for severe pediatric gastroesophageal reflux disease ( GERD1) to a 9-cM interval on chromosome 13q14. In this report, we present the results of DNA sequencing and allelic association analyses that were done in an attempt to clone the GERD1 gene. Using a candidate transcript approach, we screened affected individuals for mutations in all transcribed regions of all genes, putative genes, and ESTs identified within the 6.2-Mb GERD1 locus based on alignments with the GenBank cDNA databases. From a total of 50 identifiable genes and 99 EST clusters in the GERD1 locus, we identified 163 polymorphisms (143 SNPs and 20 INDELs) in 21 genes and 37 ESTs. The patterns of inheritance and/or the high population frequencies of all polymorphic alleles identified in this study argued against causative relationships between any of the alleles and the GERD phenotype. Using a subset of 51 SNPs distributed throughout the GERD1 locus, we performed case-control and family (TDT) allelic association analyses on two sets of samples. The case-control study was performed with 73 GERD cases and 93 controls, and the family study was performed using 22 small families. SNP 160 (position 38,925,329 Mb, UCSChg15 map) gave a significant P value prior to multiple test correction in both the case control and family studies, while SNP168 (at 40,442,903 Mb) showed significant association after multiple test correction in the case-control sample, but was uninformative in the family sample. The results suggest that the GERD1 gene might be located near SNP160 or SNP168.

Adult↗
PubMed2001

Identification of 96 single nucleotide polymorphisms in eight genes involved in iron metabolism: efficiency of bioinformatic extraction compared with a systematic sequencing approach.

Single nucleotide polymorphisms (SNPs) can significantly contribute to the characterization of the genes predisposing to iron overloads or deficiencies. We report an SNP survey of coding and non-coding regions of eight genes involved in iron metabolism, by two successive methods. First, we made use of the public domain sequence data, by using assembled expressed sequence tags, non-redundant sequences, and SNP database screening. We extracted 77 potential SNPs of which only 31 could be further validated by sequencing DNA from 44 unrelated multi-ethnic individuals. Our results indicate that a bioinformatic approach may be effective only in those cases where candidate SNPs are extracted from two different data sources or in cases of experimentally confirmed SNPs. Second, additional systematic sequencing of DNA from 24 unrelated Breton subjects increased the number of SNPs over a total length of 86 kb to 96. The average distance between the SNPs and minor allele frequencies were higher than reported by others authors; this discrepancy may reflect the nature of the genes studied and the ethnic homogeneity of our test population.

Cation Transport Proteins↗