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At least 73 records · Page 4Linked to original sources
PubMed2026

ECHO: a nanopore sequencing-based workflow for (epi)genetic profiling of the human repeatome.

SUMMARY: The human genome is dominated by repetitive DNA, whose genetic and epigenetic variation plays a key role in gene regulation, genome stability, and disease. Recent advances in long-read sequencing now enable large-scale, haplotype-resolved, and DNA methylation-informative analysis of the human genome, including on previously inaccessible complex and repetitive regions. However, the comprehensive, simultaneous characterisation of the "human repeatome" remains challenging, largely due to the lack of comprehensive tools integrated in a single pipeline that can capture the full spectrum of variation across diverse types of DNA repeats. Here, we present ECHO, a user-friendly, Snakemake-based pipeline for the "(Epi)genomic Characterisation of Human Repetitive Elements using Oxford Nanopore Sequencing." ECHO provides a reproducible and scalable framework for end-to-end analysis of whole-genome nanopore sequencing data, enabling integrative but also tailored (epi)genetic analyses of the human repeatome. AVAILABILITY AND IMPLEMENTATION: ECHO is freely available at Github: https://github.com/leenput/ECHO-pipeline, with the archived version at Zenodo: https://zenodo.org/records/19068468.

Humans↗
PubMed2003

Autosomal recessive polycystic kidney disease. Clinical and genetic profile. (Review and a case report).

BACKGROUND: Autosomal recessive polycystic kidney disease (ARPKD) is a genetic disorder inherited in a recessive manner. The ARPKD gene is located on chromosome 6. The disease is characterised by specific changes in the kidney and liver. AIM: To make a review of modern achievements in studying the clinical, genetic and diagnostic problems concerning ARPKD and contribute an illustrative case. RESULTS: We reviewed modern research on the molecular genetics of autosomal recessive polycystic kidney disease related to PKHD1 gene located on chromosome 6p21-cen, as well as on the role of fibrocystin in the terminal differentiation of the collecting and biliary ductules. The clinical manifestations of the disease in infancy and in early childhood are analysed. A diagnostic algorithm is proposed incorporating both clinical and genetic methods. The illustrative case we reported of a 22-year-old patient with ARPKD supports the view that the disease occurs, though rarely, later than in childhood. CONCLUSION: The authors recommend that in cases with late manifestation of the disease in adolescence with chronic renal failure, possibilities be searched for extracorporeal replacement (renal transplantation) when this is allowed by the complications associated with the congenital liver fibrosis.

Adult↗
PubMed2005

Genetic profile and serosurvey for virus infections of Japanese wild boars in Shikoku Island.

To estimate the genetic background of Japanese wild boars inhibiting the 4 prefectures of Shikoku Island (Kagawa, Tokushima, Kouchi and Ehime), we examined haplotypes of mitochondrial DNA (mtDNA) and genotypes of the nuclear glucosephosphate isomerase-processed pseudogene (GPIP) in 189 wild boars. Of the 8 different mtDNA haplotypes (J5, J10, J12, J13, J15, J19, J20 and E33) detected in Shikoku Island, the first to be identified were J19 and J20 (of Japanese wild boar lineage) and E33 (of European domestic pig lineage). The presence of haplotype E33 indicates local crossbreeding between wild boar and escaped domestic pigs and/or crossbred Inobuta. Four kinds of the GPIP genotypes were detected from 189 wild baors in Shikoku Island, but no European GPIP alleles were found. In 113 wild boars, no antibodies against Classical Swine Fever or Aujeszky's disease were detected, suggesting that they had not been exposed to those pathogens.

Animals↗
PubMed2003

Genetic profiling of colorectal cancer liver metastases by combined comparative genomic hybridization and G-banding analysis.

The majority of genetic studies of colorectal carcinogenesis have focused on changes found in primary tumors. Despite the fact that liver metastases are a leading cause of colorectal cancer deaths, the molecular genetic basis of the advanced disease stages remains poorly understood. We performed comparative genomic hybridization (CGH) on 17 liver metastases from colorectal carcinomas and compared the quantitative profile with the qualitative profile previously obtained with chromosome banding. An average of 12.6 aberrations per tumor was found by CGH. Chromosome 18 and chromosome arms 4q, 8p, and 17p were most frequently lost, whereas chromosomes 7 and 20 and chromosome arms 6p, 8q, and 13q were most frequently gained. We compared the chromosome banding and CGH data after converting the karyotypes into net copy number gains and losses. Ten tumors showed agreement between the findings of the two techniques, whereas five tumors did not (in two cases, no mitotic cells were obtained for banding analysis). All five discordant cases had a "simple" abnormal or normal karyotype, but revealed multiple changes by CGH. A likely explanation for this discrepancy is that in vitro growth before G-banding selected against the cancer cells. Interestingly, by comparing the CGH profiles of the "complex" vs. the "simple"/normal karyotype groups, deletion of 8p and gain of 16q were seen more frequently in the former group. The liver metastases had the same aberrations as seen in primary colorectal carcinomas, summarized in a literature survey. However, these aberrations were seen more frequently in liver metastases, which may be attributable to increased genetic instability.

Chromosome Aberrations↗
PubMed2002

Prevalence and comparison of genetic profiles of Campylobacter strains isolated from poultry and sporadic cases of campylobacteriosis in humans.

Between July 1998 and June 1999, 93 lots of broiler chickens distributed on 57 farms were sampled in two abattoirs of the province of Quebec (Canada). A total of 2,325 samples of cecal material were analyzed to determine the prevalence of campylobacters. Biotyping and pulsed-field gel electrophoresis (PFGE) were done on 20% of the Campylobacter isolates to study the distribution within poultry production. Macrorestriction profiles were compared with profiles of 24 Campylobacter strains isolated from sporadic cases of human diarrheic patients in order to evaluate genetic relationships. Approximately 40% of the broiler chickens in 60% of the lots and 67% of the farms were colonized. Biotypes I and II of Campylobacter jejuni were the most prevalent biotypes in poultry and human isolates. The PFGE dendograms revealed a high genetic diversity among poultry isolates, with 49 different genotypes from the 56 positive lots. More than 75% of these lots were colonized by a unique genotype. All positive lots raised simultaneously on the same farm had common genotype(s). Different genotypes were isolated from lots raised at different grow-out periods on a farm. In some cases, identical genotypes were found at different grow-out periods on a farm and also from different farms. Macrorestriction profiles showed that approximately 20% of human Campylobacter isolates were genetically related to genotypes found in poultry. This genetic relationship and the high prevalence of C. jejuni biotypes I and II in poultry indicated that Campylobacter in broiler production of the province of Quebec could be a potential source of hazard for public health.

Animals↗
PubMed2001

A genetic profile of contemporary Jewish populations.

The Jews are an ancient people with a history spanning several millennia. Genetic studies over the past 50 years have shed light on Jewish origins, the relatedness of Jewish communities and the genetic basis of Mendelian disorders among Jewish peoples. In turn, these observations have been used to develop genetic testing programmes and, more recently, to attempt to discover new genes for susceptibility to common diseases.

Genetic Diseases, Inborn↗
PubMed2004

Genetic profile of bone metastases in renal cell carcinoma.

OBJECTIVE: The aim of this study was to define specific genetic alterations which are common in bone metastases in renal cancer patients. METHODS: Tumor DNA from 31 metastases and 13 related primary tumors was extracted from paraffin embedded tissue sections. DOP-PCR was performed to amplify the whole DNA. After labelling by PCR, CGH was performed according to standard protocols. RESULTS: The mean number of aberrations per metastasis was 6.3 (1-13). Losses of chromosomes 3p (76%), 6 (20%), 8p (20%), 9 (34%), 14q (27%) and 18 (20%) as well as gains of chromosomes 5 (45%), 8q (34%) and 17 (27%) were detected frequently. Thirteen related primary tumors were also investigated. In 7 cases, at least one identical alteration was found in both primary tumor and metastases. In these cases, the number of alterations was mostly higher in primary tumors than in metastases without statistical significance. However, in general, the frequency of alterations was higher in metastases. CONCLUSIONS: Bone metastases from renal cell carcinoma are characterized by typical genetic alterations. Changes leading to metastasizing happen early in tumor pathogenesis. However, further accumulation of genetic changes occurs in metastases leading to a more complex genetic pattern which might be necessary for progression to clinically relevant metastases.

Bone Neoplasms↗
PubMed2004

Lessons from genetic profiling in soft tissue sarcomas.

Soft tissue sarcomas represent a heterogeneous group of tumors and include over 50 histotypes. Some of these tumor types are characterized by specific chromosomal translocations, whereas other types show complex genetic aberrations. The recent developments within gene expression technologies have now been applied to studies of soft tissue sarcomas (STS) and the first results indicate that genetic signatures are useful for classification and diagnosis. Distinctive expression profiles have been found in e.g. gastrointestinal stromal tumors (GISTs), synovial sarcomas, malignant peripheral nerve sheath tumors (MPNSTs), and in subsets of liposarcomas. The more pleomorphic tumor types, such as high-grade variants of leiomyosarcomas, malignant fibrous histiocytomas (MFHs), fibrosarcomas, and subtypes of liposarcomas, show a greater variability among the expression profiles, but interestingly subsets with distinctive expression profiles can be identified also among these tumors. The data available place many of the genes hypothesized to be involved in the development of a certain type of STS, such as the KIT gene in GIST development, among the top discriminating genes. Thereby expression profiling provides novel insights into the pathogenesis of STS. Although much work remains to be done to validate the data and to define optimal discriminating gene lists, the current lessons from gene expression studies in STS are encouraging and imply that genetic signatures may serve as diagnostic and prognostic markers and may help identify novel therapeutic strategies.

Chromosome Aberrations↗
PubMed2000

Distinct genetic profiles in colorectal tumors with or without the CpG island methylator phenotype.

Colorectal cancers (CRCs) are characterized by multiple genetic (mutations) and epigenetic (CpG island methylation) alterations, but it is not known whether these evolve independently through stochastic processes. We have recently described a novel pathway termed CpG island methylator phenotype (CIMP) in CRC, which is characterized by the simultaneous methylation of multiple CpG islands, including several known genes, such as p16, hMLH1, and THBS1. We have now studied mutations in K-RAS, p53, DPC4, and TGFbetaRII in a panel of colorectal tumors with or without CIMP. We find that CIMP defines two groups of tumors with significantly different genetic lesions: frequent K-RAS mutations were found in CIMP(+) CRCs (28/41, 68%) compared with CIMP(-) cases (14/47, 30%, P = 0.0005). By contrast, p53 mutations were found in 24% (10/41) of CIMP(+) CRCs vs. 60% (30/46) of CIMP(-) cases (P = 0.002). Both of these differences were independent of microsatellite instability. These interactions between CIMP, K-RAS mutations, and p53 mutations were preserved in colorectal adenomas, suggesting that they occur early in carcinogenesis. The distinct combinations of epigenetic and genetic alterations in each group suggest that activation of oncogenes and inactivation of tumor suppressor genes is related to the underlying mechanism of generating molecular diversity in cancer, rather than simply accumulate stochastically during cancer development.

Adenoma↗
PubMed2004

Genetic profile of cumulative mutational damage associated with early pulmonary adenocarcinoma: bronchioloalveolar carcinoma vs. stage I invasive adenocarcinoma.

To detect the possible genetic alterations characteristic of bronchioloalveolar carcinoma (BAC) and to study molecular genetic factors responsible for determining the biologic aggressiveness of pulmonary adenocarcinoma, comparative analysis of loss of heterozygosity (LOH) on 9 chromosomal regions was performed in 14 BACs and in 20 stage I adenocarcinomas (AD). The most frequently affected chromosome regions in BAC were 8q and 17p. In stage I AD, more than 60% of the cases showed LOH of 1p, 3p, 5q, 7q, 17p, and 18q loci, and LOH of 1p, 3p, 7q, and 18q was observed with greater frequency than in BAC (P < 0.05). Fractional allele loss (FAL) was significantly greater in stage I AD than in BAC (P < 0.001). In cases with microdissection of multiple sites, intratumoral heterogeneity of LOH status was observed in 73% of BAC and 94% of stage I AD, and homogeneous distribution of LOH of 9p was unique to BAC. The high FAL value was associated with a poor prognosis of BAC, but this trend did not reach statistical significance (P = 0.098). In stage I AD, no correlation was found between LOH of particular chromosomal region or FAL and clinical outcome. LOH of 1p, 3p, 7q, and 18q was associated with invasive properties of pulmonary AD and may be useful in identifying invasive adenocarcinoma when conventional histomorphological tools are not helpful.

Adenocarcinoma, Bronchiolo-Alveolar↗
PubMed1994

A genetic profile of Romany (Gypsy) subethnic group from a single region in Slovakia.

The data presented here are on population structure and genetic markers (ABO, RH, MN, HP) in two series of so-called Slovak Romany subethnic groups from a single region (Gemer) in the Southeastern part of Slovakia. The results demonstrate that favourable conditions have existed for population genetic mechanisms operating in isolated populations, namely genetic drift and inbreeding. In addition, an attempt was made to compare the observed data with those available for other Romany populations and for Slovaks.

Blood Group Antigens↗
PubMed2005

Genetic profiling of central giant cell granuloma of the jaws.

Central giant cell granuloma (CGCG) of the jaws is a central osteolytic lesion characterized histologically by multinucleated giant cells in a background of ovoid to spindle-shaped mesenchymal cells. Whether CGCG is a reactive lesion or a truly benign neoplasm remains undetermined, and the mechanism determining the onset of the disease remains unknown. To have more information regarding the genetic events involved in CGCG, the authors decided to perform an expression profile. Samples were derived from two surgically resected CGCG of the mandible. RNA extracted from a pool of three normal bone tissues was used as control. By using DNA microarrays containing 19,200 genes, the authors identified several genes whose expression was significantly up- or down-regulated. The differentially expressed genes cover a broad range of functional activities: cell cycle regulation; signal transduction; and vesicular transport. It was also possible to detect some genes whose function is unknown. The authors believe the data reported to be the first genetic portrait of CGCG of the jaws. Several markers have been identified that can potentially help in identifying some biological behavior (ie, quiescent versus aggressive lesions), as well as genes whose products could be potentially disease-specific targets for therapy. However, the authors think that more cases are needed, especially those comparing quiescent and aggressive lesions, before the exact profile of CGCG is known.

Gene Expression↗
PubMed2004

Genetic profiling of Hypericum (St. John's Wort) species by nuclear ribosomal ITS sequence analysis.

A PCR-based DNA amplification method was applied to genetically distinguish the popular dietary supplement Hypericum perforatum L. (common St. John's Wort) from other related Hypericum species. Nuclear ribosomal gene sequences of the internal transcribed spacer (ITS) region were analyzed for 50 Hypericum taxa native to the Old and New Worlds, representing 11 of the 36 currently accepted taxonomic sections. This study provides a genetic method for authentication of commercial H. perforatum preparations. In addition, these data allow a preliminary assessment of phylogenetic relationships within the genus, revealing three strongly supported monophyletic clades, plus several secondary monophyletic groupings. Using ITS gene sequences, we were able to distinguish H. perforatum from all other species of Hypericum included in this study.

DNA, Plant↗