Terms from CHLC documents
- Skeletal Maps
- CHLC version 2 integrated skeletal maps are constructed from STRP markers only, using a rigorous algorithm which incorporates diagnostic evaluation of the map during the map-making process.
First, markers are evaluated for heterogeneity among families. Those which display significant heterogeneity are excluded from the skeletal build. A likely pair of starting points are selected, and remaining STRP markers are offered for insertion. With the addition of each marker to the map, a diagnostic which successively drops each locus and attempts to reinsert it in the remaining map at lod 3 criteria is run. Any locus whose addition causes instability as detected by this diagnostic is removed from the map, and placed at the end of the insert list. When a map order has been constructed and no additional markers can be inserted at lod 3, the "lenloc" diagnostic is run to evaluate map expansion caused by each internal locus. If any locus is found to expand the map by more than 2 cM (an exception is the map of chromosome X, which was allowed greater map expansion because only the female map was considered), the build process backtracks to a point just prior to its inclusion and the locus is placed at the end of the insert list. Maps constructed by this algorithm tend to be shorter and sparser than usual, but more reliable.
- Framework Maps
- The skeletal maps are used as a starting order for framework maps. Additional loci from the integrated data set, including rflp's and markers excluded from the skeletal build because of heterogeneity, are presented for insertion according to information content. A standard CRIMAP build is run using lod 3 criteria. The resulting map is evaluated by CRIMAP flips, and if any pair shows a greater likelihood in the reverse order, one of the loci is dropped.
- Recombination Minimization (RECMIN) Maps
- The recombination minimization (recmin) maps are composed of STRP loci. Maps are constructed using a subset of 15 families from the CEPH reference panel. The starting order for markers for each map is the v2.0 CHLC skeletal map. Each of the loci in these maps defines the boundary of a meiotic bin. Additonal loci are assigned to the bins if they can be excluded from all other skeletal map intervals by odds of 1000:1. The order of the loci within one bin is determined by permuting all possible orders within that bin. The order that results in the minimum number of recombination events is selected.
Map distances (female, male and sex-averaged) for the complete set of ordered loci over all bins on each chromosome are calculated using the maximum likelihood method as implemented in the program CRIMAP.
- Scaffold Maps
- Scaffold maps consist of tri-,tetra-, and penta-nucleotide repeat markers which can be ordered uniquely, and which can be taken to constitute a screening set. They were constructed by determining the likely locations of the tri's, tetra's, and penta's against the CHLC skeletal and framework maps. For each chromosome, a subset of tri's, tetra's and penta's with non-overlapping likely-location intervals was selected, and a map was constructed from them. The majority of markers in the scaffold maps are CHLC markers, but these have been supplemented with other markers from our integrated data sets as necessary to achieve the most dense possible map. As a result of the method of construction, two sets of maps are available: one constructed using the CHLC version 1 skeletal maps, and the other using the CHLC version 1 framework maps.
- Integrated Genetic Maps
- Integrated maps consist of skeletal, framework, and recombination minimization maps of the genome, constructed from publically available genotype data from the CEPH reference panel.
- CHLC Genetic Maps
- CHLC Maps are maps generated by extending publically available maps (such as CHLC Integrated maps, Genethon maps and Weber's Screening set maps) with CHLC generated markers. In addition, maps solely consisting of CHLC-generated markers are available (e.g., scaffold maps).
- CHLC Generated Markers
- Within the CHLC project we generate tri-, tetra- and penta-nucleotide repeat markers, UTRs and ESTs. Genotypes are generated for members of the CEPH reference panel. Marker specific information for CHLC markers is accessible via the Marker Search tool.
Information provided by the Marker Search tool can include:
- marker name aliases, including GenBank and GDB accession numbers
- listing of maps in which the marker appears
- marker (genotype) descriptive information
- chromosome assignment
- allele frequencies
- primer information
- template sequence
Other sources of information on CHLC markers include:
- likely locations of CHLC markers with respect to various meiotic maps.
- complete listings of CHLC generated markers.
- genotype files used in our mapping construction process.
- Likely Locations
- Likely locations of all the markers in our Integrated and CHLC datasets are presented in tabular form. Todate we have generated likely locations mainly with respect to CHLC version 2 (v2) skeletal maps. Other reference maps are used (eg. framework map) to determine a marker's genetic location.
For each marker we indicate the full interval over which its placement is within lod 3 of the most likely location. The best location is the interval that has the highest support for marker placement. Multiple reference intervals can have equal support for marker placement. In such cases, the outer boundaries of the combined intervals are listed.
Note: If a marker is haplotyped, only the primary member of the haplotype is listed with a likely location. The calculation is done on the haplotyped locus.
- Interval Distributions of Markers Categorized by Locus Type (markerbycat)
- Interval distribution files for CHLC maps and Integrated maps list the location of each of the markers mapped by CHLC. The intervals are described by a subset of the markers in the version 2 CHLC skeletal markers. Each interval is approximately 10 cM. Each marker was categorized as either a gene, strp or other (incl. RFLPs, VNTRs etc.) and its statiscally best location was determined (refer to likely location tables for more detail) with respect to the version 2 CHLC skeletal map. The tables list all chlc mapped markers in their best location by category. (NOTE: If a marker is haplotyped, only the primary member of the haplotype is listed in the interval distribution table.)
- CGAP-GAI
- CGAP Genetic Annotation Initiative is a research program that focuses on the identification and characterization of genetic variation in genes important in cancer. GAI is part of the Cancer Genome Anatomy Project (CGAP), an interdisciplinary program to establish the information and technological tools needed to decipher the molecular anatomy of the cancer cells.
- CHLC version 2 integrated skeletal maps are constructed from STRP markers only, using a rigorous algorithm which incorporates diagnostic evaluation of the map during the map-making process.
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