Genetic Structure of Duplicated Sequences Revealed by Genotyping Single Sperm
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE11957 | GEO | 2008/07/25
SECONDARY ACCESSION(S): PRJNA105821
REPOSITORIES: GEO
Similar Datasets
Project description:Three different experimental approaches were evaluated for discrimination of genomic variance in and between duplicated sequences using 48 markers in duplicon regions and 17 SNPs in unique sequences previously characterized in another study. We found only the method high-throughput single sperm typing could conclusively resolve the alleles of all markers. Resulting data from single sperm analysis were also used to examine the genetic structure of duplicon markers in the human population. Single sperm typing can be a rapid, efficient and accurate method for initial screening and assessment of genetic variation and for detailed genetic analysis of duplicon markers. Keywords: Genotyping Sixty-five markers including 17 MSVs, 12 PSVs, 19 SIDs and 17 SNPs in unique sequences described in Fredman et al. were selected for study. The samples include 40 genomic DNA samples from four ethnic groups, semen samples from 11 donors, and 10 to 20 sperm from each donor except one, AB012, for whom 65 sperm were analyzed. Both genomic and sperm DNA samples were subject to multiplex amplification followed by microarray analysis. Genotypes were determined by using the Accutyping software. Semen samples were genotyped on both strands. Allele status in these samples were compared and analyzed. The single sperm typing method allowed us to identify markers residing in non-unique sequence, to analyze the detailed genetic structure of the duplicons and to learn whether different alleles are present for the duplicon sequences in the human population.
2008-07-25 | E-GEOD-11957 | biostudies-arrayexpress
Project description:Genetic Structure of Duplicated Sequences Revealed by Genotyping Single Sperm
| PRJNA105821 | ENA
Project description:Replicates of strains used in comparison of microarray to RAPD analysis for the publication. Findings from use of an open-reading frame-specific Campylobacter jejuni DNA microarray to investigate genetic diversity among clinical isolates associated with 5 independent clusters of infection were compared with data from random amplified polymeric DNA (RAPD) and Penner serotyping analyses. The DNA microarray provides a highly specific epidemiological typing tool for analysis of C. jejuni isolates and reveals both divergent and highly conserved gene classes among isolates Set of arrays that are part of repeated experiments Keywords: Biological Replicate
2005-11-16 | GSE3610 | GEO
Project description:Single-cell transcriptomics has become the definitive method for classifying cell types and states, and can be augmented with genotype information to improve cell lineage identification. Due to constraints of short-read sequencing, current methods to detect natural genetic barcodes often require cumbersome primer panels and early commitment to targets. Here we devise a flexible long-read sequencing workflow and analysis pipeline, termed nanoranger, that starts from intermediate single-cell cDNA libraries to detect cell lineage-defining features, including single-nucleotide variants, fusion genes, isoforms, sequences of chimeric antigen and TCRs. Through systematic analysis of these classes of natural ‘barcodes’, we define the optimal targets for nanoranger, namely those loci close to the 5’ end of highly expressed genes with transcript lengths shorter than 4 kB. As proof-of-concept, we apply nanoranger to longitudinal tracking of subclones of acute myeloid leukemia (AML) and describe the heterogeneous isoform landscape of thousands of marrow-infiltrating immune cells. We propose that enhanced cellular genotyping using nanoranger can improve the tracking of single-cell tumor and immune cell co-evolution.
2023-10-31 | GSE243227 | GEO
Project description:Replicates of strains used in comparison of microarray to RAPD analysis for the publication. Findings from use of an open-reading frame-specific Campylobacter jejuni DNA microarray to investigate genetic diversity among clinical isolates associated with 5 independent clusters of infection were compared with data from random amplified polymeric DNA (RAPD) and Penner serotyping analyses. The DNA microarray provides a highly specific epidemiological typing tool for analysis of C. jejuni isolates and reveals both divergent and highly conserved gene classes among isolates Set of arrays that are part of repeated experiments Biological Replicate Computed
2005-11-15 | E-GEOD-3610 | biostudies-arrayexpress
Project description:Copy number variations (CNVs) constitute the largest portion of the human genome variation. We determined a genome-wide high resolution SNP/CNV haplotype structure of Asians, by analyzing a collection of complete hydatidiform moles (CHMs) of Japanese, using high-density DNA arrays. CHMs are tissues carrying duplicated haploid genomes derived from single sperms, and are suitable material for the detection of CNVs, because they are expected to reveal greater signal to noise ratio in hybridization experiments. Also, the absence of heterozygosity ensures straightforward CNV interpretation without being bothered by overlapping CNV segments. We genotyped 100 CHM genomes using Affymetrix SNP 6.0 and Illumina 1M-duo, created a definitive haplotype map including 1.7 million SNPs and 2339 CNV region (CNVR) that is presented as D-HaploDB Phase 4.1.
2014-02-13 | GSE54948 | GEO
Project description:Chagas disease is one of the most important neglected diseases with an estimated number of 12 million infected individuals, the majority living in Central and South America. The Trypanosoma cruzi (T.cruzi) protozoan parasite is the etiological agent of Chagas disease. T.cruzi is highly genetically diverse and a new nomenclature assigned each strain to seven genetic groups (TcI-TcVI and Tcbat), named Discrete Typing Units (DTUs), based on their biochemical, immunological and phenotypical characteristics. T.cruzi DTUs have been correlated to diverse clinical outcomes highlighting the importance of molecular epidemiological screens. Despite the development of T.cruzi typing methods based on genetic signatures, each method presenting its own advantages and challenges. The work presented here shows the application of mass spectrometry for Trypanosoma cruzi Strain Typing Assay using MS2 peptide spectral libraries (Tc-STAMS2). The novelty of the method is based on the use of peptide fragmentation spectra as strain-specific fingerprints to classify and identify DTUs. Initially, a spectra library is generated from characterized T.cruzi strains. The library is subsequently inspected using MS/MS spectra from unknown strains and confidently assigned to a specific strain in an automated and computationally-driven approach. The Tc-STAMS2 method was challenged to test several variables such as sample type and preparation, instrument setup and identification platform. Tc-STAMS2 provided high confidence and robustness in T.cruzi strain typing. The Tc-STAMS2 method represents a proof-of-concept of a complementary strategy to the current DNA-based T. cruzi genotyping methods. Moreover, the method allows the identification of strain-specific features that could be related to the biology of T.cruzi strains and their clinical outcomes.
2018-03-19 | PXD008088 | Pride
Project description:Genotype of 480 EM93 segregants using 2965 genetic markers to study the genomic structure and recombination in EM93
2011-09-01 | E-TABM-1174 | biostudies-arrayexpress
Project description:The human hair proteome offers new insight in the field of human identification. Hair often contains DNA that has been degraded due to the process of cornification. The smaller fragments of DNA present a challenge for obtaining useful information concerning the identity of the donor. Proteomic genotyping offers an alternative approach which starts with protein, a biomolecule abundant in the hair shaft. Nonsynonymous single nucleotide polymorphisms may be detected in the sequence of these proteins, allowing the inference of SNP genotypes. Population genetics-based information from these genotypes may be used to calculate random match probability or even infer ancestry. The current challenge of this research is to optimize processing chemistry in order to maximize genetic information from a single human hair shaft. Results indicate that optimal conditions for proteomic analysis of a single human hair include 6 hrs of reduction with 100 mM dithiothreitol at room temperature, alkylation with 200 mM iodoacetamide for 45 min, and 6 hrs of digestion with two 1:50 (enzyme:protein) additions of stabilized trypsin at room temperature, with stirring incorporated into all three steps. Our final conditions using optimized temperatures and incubation times for disulfide reduction and protein digestion produced random match probabilities of up to 1 in 624 million from a single hair with a median value of 1 in 1.1 million, compared to a maximum random match probability of 1 in 1380 and a median value of 1 in 24 for the original processing method.
2020-06-10 | PXD016155 | Pride
Project description:Genotyping arrays are tools for high throughput genotyping, which is required in genome-wide association studies (GWAS). Since the first cucumber genome draft was reported, genetic maps were constructed mainly based on simple-sequence repeats (SSRs) or on combinations of SSRs and other sequence-related amplified polymorphism (SRAP). In this study we developed the first cucumber genotyping array which consisted of 32,864 single nucleotide polymorphisms (SNPs). These markers cover the cucumber genome every 2.1Kb and have parents/F1 hybridizations as a training set. The training set was validated with Fludigm technology and had 98% concordance. The application of the genotyping array was illustrated by constructed a genetic map of 600 cM in length based on recombinant inbred lines (RIL) population of a 9930XGy14 cross of which compromise of 11564 SNPs. The markers collinearity between the genetic map and genome references of the two parents estimated as R2=0.97. Moreover, this comparison supports a translocation in the beginning of chromosome 5 that occurred in the lineage of 9930 and Gy14 as well as local variation in the recombination rate. We also used the array to investigate the local allele frequencies along the cucumber genome and found specific region with segregation distortions. We believe that the genotyping array together with the training set would be a powerful tool in applications such as quantitative-trait loci (QTL) analysis and GWAS.
2015-05-01 | GSE57294 | GEO