*  "High-Resolution Maps of Mouse Reference Populations." by Petr Simecek, Jiri Forejt et al.
Genetic reference panels are widely used to map complex, quantitative traits in model organisms. We have generated new high-resolution genetic maps of 259 mouse inbred strains from recombinant inbred strain panels (C57BL/6J x DBA/2J, ILS/IbgTejJ x ISS/IbgTejJ, C57BL/6J x A/J) and chromosome substitution strain panels (C57BL/6J-Chr#, C57BL/6J-Chr#, C57BL/6J-Chr#). We genotyped all samples using the Affymetrix Mouse Diversity Array with an average inter-marker spacing of 4.3kb. The new genetic maps provide increased precision in the localization of recombination breakpoints compared to the previous maps. Although the strains were presumed to be fully inbred, we found residual heterozygosity in 40% of individual mice from five of the six panels. We also identified de novo deletions and duplications, in homozygous or heterozygous state, ranging in size from 21kb to 8.4Mb. Almost two-thirds (46 out of 76) of these deletions overlap exons of protein coding genes and may have phenotypic ...
  http://mouseion.jax.org/stfbaop/17/
*  A genetic map of mouse chromosome 12 composed of polymorphic DNA fragments. | JEM
Mouse chromosome 12 encodes the heavy chains of immunoglobulins (Igh), a family of T cell surface molecules, and a tumor antigen that may be homologous to immunoglobulins. To refine and extend the genetic map of this chromosome, a procedure has been developed to isolate chromosome 12-specific DNA fragments from a somatic cell hybrid carrying the chromosome on a Chinese hamster background. Five fragments have been isolated and characterized in detail. All are polymorphic, defining loci D12-1, 2, 3, 4, and 5. Using recombinant inbred mouse strains, a tentative linkage map of chromosome 12 has been worked out that incorporates these markers, the c-fos oncogene, Igh, and Pre-1/alpha 1 antitrypsin. This strategy should be applicable to any mouse chromosome or chromosomal region that can be isolated in a somatic cell hybrid. ...
  http://jem.rupress.org/content/160/3/827
*  Interpreting Experimental Mapping Data Records
MGI contains genetic mapping and linkage data, including haplotype data for linkage crosses, recombinant inbred (RI) strain distribution patterns, in-situ hybridization data, deletion mapping information, translocation breakpoint mapping, somatic cell hybrids, concordance tables, congenic strain information, and physical mapping information. Depending upon the experiment type, Mapping Data records may have the following fields: ...
  http://www.informatics.jax.org/userhelp/mapping_experimental_data_help.shtml
*  Fun with GEDMatch Chromosome Mapping - GenealogyResearchJournal
Have you uploaded your raw DNA files to GEDMatch.com? If not, you should consider it. Not only is there the possibility of connecting with new cousins who tested with different DNA companies, there are some nifty tools not available anywhere else. There are a variety of chromosome mapping tools that allow you to analyze your DNA in a variety of ways.. My Ancestry is Split. Just a brief note about my ancestry before we get started so you'll have something to compare the charts to.. My dad's side is 100% French…Southern France, Basque region…most of my ancestors well into the 1700s came from the same towns.. My mom's side is more complication. Her makeup is Portuguese/Azorean (her father's side), Irish (her maternal maternal grandparents), British (maternal grandfather), and Welsh (maternal paternal grandparents). This pie chart represents how the Eurogenes K36 utility sees my genetic makeup.. ...
  http://www.researchjournal.yourislandroutes.com/2017/05/fun-with-gedmatch-chromosome-mapping/
*  Not Much on Chromosome 21 | healthPlexus.net
Last month, a multinational consortium reported the completion of the sequencing of chromosome 21, the smallest human chromosome. A description of the sequence soon followed. Chromosome 21 represents approximately 1 to 1.5% of the total human genome. It was expected to be relatively gene-poor based on the fact that trisomy 21 is one of the only viable human trisomies. Surprisingly, researchers found that it contained even fewer genes than they had expected; only 225 genes were identified, compared with the 545 found on chromosome 22. The total length of the sequence is 33.8 million base pairs (or megabases, Mb).. Chromosome 21 has been of particular interest since it was discovered in 1959 that Down's syndrome occurs when there are three copies of the chromosome. The complete sequence analysis is expected to have profound implications for research in this ...
  http://healthplexus.net/article/not-much-chromosome-21
*  Detailed mapping of the ERG-ETS2 interval of human chromosome 21 and comparison with the region of conserved synteny on mouse...
Owczarek C.M., Portbury K.J., Hardy M.P., O'Leary D.A., Kudoh J., Shibuya K., Shimizu N., Kola I., Hertzog P.J.. We have carried out a detailed annotation of 550 kb of genomic DNA on human chromosome 21 containing the ERG and ETS2 genes. Comparative genomic analysis between this region and the interval of conserved synteny on mouse chromosome 16 indicated that the order and orientation of the ERG and ETS2 genes were conserved and revealed several regions containing potential conserved noncoding sequences. Four pseudogenes including those for small protein G, laminin receptor, human transposase protein and meningioma-expressed antigen were identified. A potentially novel gene (C21orf24) with alternative mRNA transcripts, consensus splice donor and acceptor sites, but no coding potential nor murine orthologue, was identified and found to be expressed in a range of human cell lines. We have identified four novel splice variants ...
  http://www.uniprot.org/citations/14693372
*  Linkage study - Conservapedia
A linkage study aims at establishing linkage between genes. Linkage is the tendency for genes and other genetic markers to be inherited together because of their location near one another on the same chromosome. A genetic marker is simply a segment of DNA with an identifiable physical location on a chromosome whose inheritance can be followed. A genetic marker can have a function and thus be a gene. Or a marker can be a section of DNA with no known function. Because DNA segments that lie near each other on a chromosome tend to be inherited together, markers are often used as tools for tracking the inheritance pattern of a gene that has not yet been identified but whose approximate location is known. The statistical estimate of whether two loci are likely to lie near each other on a chromosome and are therefore likely to be inherited together is called a LOD score. A LOD score of 3 or more is generally taken to indicate that the two loci are ...
  http://www.conservapedia.com/Linkage_study
*  Endotoxin-tolerant Mice Have Mutations in Toll-like Receptor 4 (Tlr4) | JEM
Using high-resolution genetic mapping techniques, we have restricted the position of the Lps gene to a 0.9-cM region of chromosome 4, flanked proximally by D4Nds9 and distally by D4Mit178. A 1.7-Mb cloned DNA contig spanning this interval was sequentially assembled using YAC, BAC, and P1 clones. Our data differ significantly from another recently published physical map encompassing the Lps locus ((37)). In this contig, a gap (estimated at 100 kb by fluorescence in situ hybridization) exists in the BAC contig between D4Nds9 and D4Mit178. Comparison of BAC clone addresses common to both maps suggests that this gap corresponds to the center of our contig, and is ∼950 kb in size. Finally, through cDNA selection and nucleotide sequencing of randomly cloned sheared BACs from our contig, we have identified three transcription units within the Lps candidate region, including Tlr4, and two novel genes.. We provide evidence that implicates mouse Tlr4 as a critical regulator of the innate host response ...
  http://jem.rupress.org/content/189/4/615
*  First version of Chromosome Mapping Tool | Kitty Cooper's Blog
32-63. your great-great-great grandparents. If you leave the numbers in for parents, you can then use your chromosome mapper to map starting with your children.. In terms of colors, you would need four palettes instead of two. In my Excel spreadsheet I used shades of pink for my mother's maternal line and shades of orange for her paternal line; and shades of blue for my father's paternal line and green for his maternal line but whatever colors work is fine with me. Your chromosome mapper is such a great tool, Kitty. Thank you for doing it.. I am one of your Mac testers.. ...
  http://blog.kittycooper.com/2013/07/first-version-of-chromosome-mapping-tool/?replytocom=3854
*  Moving: Necessary PTSD Fallout: I could have lived without it.
I was dealing with sensory overload. The one factor that had changed from the old place to the new was the elimination of a physical location for my PTSD 'Fallout Shelter'. I no longer had a man-cave. I didn't realize how significant the effects of losing it would be until I thought about what I gained from it. Whenever I needed to get away from sensory overload, I went down into the basement and simplified things. I would use gaming as my focal point for cutting out all of the chatter. Now, as much as I love the new place, I don't have that. The place I try to get away from everything is right in the middle of the apartment. It doesn't allow me to get away from anything for even a millisecond. THAT's what was causing all of this stress. Finally recognizing this is a good thing, but now I need to find a way to shut out all of the chatter without having a physical location to do so. I will talk to Dani about this issue and see what we can come up with ...
  http://www.combatveteranswithptsd.org/blog/moving-necessary-ptsd-fallout-i-could-have-lived-without-it
*  Antibody-based Protein Profiling of the Human Chromosome 21
The Human Proteome Project has been proposed to create a knowledge-based resource based on a systematical mapping of all human proteins, chromosome by chromosome, in a gene-centric manner. With this background, we here describe the systematic analysis of chromosome 21 using an antibody-based approach for protein profiling using both confocal microscopy and immunohistochemistry, complemented with transcript profiling using next generation sequencing data. We also describe a new approach for protein isoform analysis using a combination of antibody-based probing and isoelectric focusing. The analysis has identified several genes on chromosome 21 with no previous evidence on the protein level, and the isoform analysis indicates that a large fraction of human proteins have multiple isoforms. A chromosome-wide matrix is presented with status for all chromosome 21 ...
  http://uu.diva-portal.org/smash/record.jsf?pid=diva2:510337
*  Mapping of Metabolic QTL in Congenic and RI Strains
Identification of genes influencing obesity and type 2 diabetes remains a significant challenge. We have used the polygenic obese mouse strain NZO to map genes which regulate various parameters relevant to body weight regulation, eg food intake, physical activity, insulin secretion, fat pad weights, heart size, etc. Congenic mice have been produced to confirm the mapping data and to fine map the QTL loci. A major locus resulting in deficient insulin production was mapped to a 2cM region. We have also examined regulation of insulin production in crosses between the C57BL/6 and DBA/2 strains. Mapping of two loci that affect insulin production was achieved from analysis of backcross mice, and characterization of RIX strains bred from selected BXD RI strains will allow fine mapping of these loci ...
  http://www.complextrait.org/archive/2002/HTML/morahan.html
*  Clues to the Evolution of the Malarial Chromosome
Understanding the recombination patterns across a chromosome determining the positions and frequency of genetic exchanges between homologous chromosomes is crucial for understanding and tracking inheritance of traits. Mapping genes that affect parasites' traits, such as responses to various antimalarial agents, is possible because, during meiosis, homologous chromosomes line up and may exchange segments. Genes or any polymorphic bits of DNA that are close together tend to remain linked during this process, while those far apart tend to become separated. Identifying and following polymorphic markers through multiple generations is a key technique for genetic mapping ...
  http://www.rxpgnews.com/malaria/Clues_to_the_Evolution_of_the_Malarial_Chromosome_2382_printer.shtml
*  Human chromosome 11 DNA sequence and analysis including novel gene identification.
Taylor T.D., Noguchi H., Totoki Y., Toyoda A., Kuroki Y., Dewar K., Lloyd C., Itoh T., Takeda T., Kim D.-W., She X., Barlow K.F., Bloom T., Bruford E., Chang J.L., Cuomo C.A., Eichler E., FitzGerald M.G., Jaffe D.B., LaButti K., Nicol R., Park H.-S., Seaman C., Sougnez C., Yang X., Zimmer A.R., Zody M.C., Birren B.W., Nusbaum C., Fujiyama A., Hattori M., Rogers J., Lander E.S., Sakaki Y.. Chromosome 11, although average in size, is one of the most gene- and disease-rich chromosomes in the human genome. Initial gene annotation indicates an average gene density of 11.6 genes per megabase, including 1,524 protein-coding genes, some of which were identified using novel methods, and 765 pseudogenes. One-quarter of the protein-coding genes shows overlap with other genes. Of the 856 olfactory receptor genes in the human genome, more than 40% are located in 28 single- and multi-gene clusters along this chromosome. Out of the 171 ...
  http://www.uniprot.org/citations/16554811
*  New Mapping Project Splits the Community | Science
A new type of genomic map, known as the haplotype map, promises to speed the search for elusive genes involved in complex diseases. But to many biologists, it's an untested concept hardly worthy of the $110 million it will consume. Welcome to the haplotype map, a new type of genome map that, depending on where you look, is eliciting exuberance or exasperation. ...
  http://science.sciencemag.org/content/296/5572/1391
*  Refined mapping finds over 200 Crohn's Disease genes
Researchers have used a genetic mapping technique to identify more than 200 genes associated with Crohn's Disease, making it the most well-characterized disorder to date.
  https://www.news-medical.net/news/20121231/Refined-mapping-finds-over-200-Crohne28099s-Disease-genes.aspx
*  DBA/2J Haplotype on Distal Chromosome 2 Reduces Mertk Expression, Restricts Efferocytosis, and Increases Susceptibility to...
Each QTL identified in the crosses of inbred mice generally spans a large genomic distance, sometimes almost an entire chromosome. In complex phenotypes such as atherosclerosis, where a large number of genes are involved, transferring a target region onto an inbred background and creating congenic line is a powerful step toward identifying causative genes. Here we have analyzed the effect of the atherosclerosis QTL Aath4 by establishing a congenic line (Aath4aDBA/DBA), where the 5′ region of DBA Aath4 was backcrossed onto a 129S6-Apoe−/− background. As expected, the resulting Aath4aDBA/DBA males had significantly larger plaques, and macrophages isolated from these mice exhibited reduced efferocytosis as a consequence of allele-specific decrease in MERTK expression. Together, our results provide strong evidence that the increased susceptibility to atherosclerosis determined by the DBA allele of Aath4 is, at least in part, due to decreased MERTK expression.. MERTK is known to play a ...
  http://atvb.ahajournals.org/content/37/7/e82
*  Plus it
Genetics. Four synaptotagmin mutant lines were used for analysis. syt AD4is a null mutation with a stop codon at amino acid 32. This mutant will be referred to as syt null.syt AD3 is a hypomorph with a Y to N mutation at amino acid 364 (DiAntonio and Schwarz, 1994).*,syt AD3 and*,syt null are chromosomes on which the syt alleles were placed in a different genetic background. These chromosomes were generated by homologous recombination between a second chromosome bearing one of thesyt mutations (syt null orsyt AD3 chromosomes) and one bearing a P-element (P[HsGal4]). When the P-element containing portion of these recombined chromosomes is made homozygous, the increase in spontaneous transmitter release normally seen insyt mutants is suppressed (see Results). It is possible that the change in spontaneous release frequency is attributable to a novel mutation caused by the insertion of this P-element. Indeed, when the P-element ...
  http://www.jneurosci.org/content/18/19/7662
*  Glossary | CaBRI
Also known as a genetic marker, a segment of DNA with an identifiable physical location on a chromosome whose inheritance can be followed. A marker can be a gene, or it can be some section of DNA with no known function. Because DNA segments that lie near each other on a chromosome tend to be inherited together, markers are often used as indirect ways of tracking the inheritance pattern of genes that have not yet been identified, but whose approximate locations are known ...
  http://cabrimed.org/glossary.jsp
*  Glossary | CaBRI
Also known as a genetic marker, a segment of DNA with an identifiable physical location on a chromosome whose inheritance can be followed. A marker can be a gene, or it can be some section of DNA with no known function. Because DNA segments that lie near each other on a chromosome tend to be inherited together, markers are often used as indirect ways of tracking the inheritance pattern of genes that have not yet been identified, but whose approximate locations are known ...
  http://www.cabrimed.org/glossary.jsp
*  SyMAP Tour
The Chromosome Explorer allows you to select multiple chromosomes from different species and view their alignment using several views: 3D (shown here); dot-plot; circular; and side-by-side. Chromosomes, and a reference chromosome, are selected through the lefthand panel, and the desired alignment view is shown to the right. Below is an example showing three chromosomes from Maize, Rice, and Sorghum against Maize chromosome 9. The 3D view, shown here, is available in the standalone Java application (not over the web). It shows a three-dimensional display of the syntenic regions ("synteny blocks") for selected chromosomes against the reference chromosome. Inverted blocks are shown in green. ...
  http://www.agcol.arizona.edu/software/symap/v4.2/Tour.html
*  Gene mapping project offers new clues about humans | Health24
Early data from the 1,000 Genomes Project is already offering new clues about human disease, including why some people are more severely affected by disease than others.
  http://www.health24.com/Medical/Genetics/News/Gene-mapping-project-offers-new-clues-about-humans-20120721
*  The expression ratios of 5p arm miRNA to 3p arm miRNA. | Open-i
The expression ratios of 5p arm miRNA to 3p arm miRNA. Several pre-miRNAs have significantly different ratios, demonstrating the arm selection preferences withi
  https://openi.nlm.nih.gov/detailedresult.php?img=PMC3303722_1471-2164-13-S1-S13-3&req=4