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Mendelian Inheritance in Man
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1997-05-02
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Key to OMIM gene map in file genemap.txt
Each entry is a list of fields, separated by the '|' character. The
fields are, in order :
1 - Numbering system, in the format Chromosome.Map_Entry_Number2 - Month entered3 - Day "4 - Year "5 - Location6 - Gene Symbol(s)7 - Gene Status (see below for codes)8 - Title9 - 10 - MIM Number11 - Method (see below for codes)12 - Comments13 -14 - Disorders15 - Disorders, cont.16 - Disorders, cont17 - Mouse correlate18 - Reference
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Status codes:
The certainty with which assignment of loci to chromosomes or the
linkage between two loci has been established has been graded into
the following classes:
C = confirmed - observed in at least two laboratories or in several
families.
P = provisional - based on evidence from one laboratory or one
family.
I = inconsistent - results of different laboratories disagree.
L = limbo - evidence not as strong as that provisional, but included
for heuristic reasons. (Same as `tentative'.)
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Method codes :
The methods for mapping genes are symbolized as follows:
A = in situ DNA-RNA or DNA-DNA annealing (`hybridization'); e.g.,
ribosomal RNA genes to acrocentric chromosomes; kappa light chain
genes to chromosome 2.
AAS = deductions from the amino acid sequence of proteins; e.g.,
linkage of delta and beta hemoglobin loci from study of hemoglobin
Lepore. (Includes deductions of hybrid protein structure by
monoclonal antibodies; e.g., close linkage of MN and SS from study of
Lepore-like MNSs blood group antigen.) Also includes examples of
hybrid genes as in one form of hypertrophic cardiomyopathy and in
apolipoprotein (Detroit).
C = chromosome mediated gene transfer (CMGT); e.g., cotransfer of
galactokinase and thymidine kinase. (In conjunction with this
approach fluorescence-activated flow sorting can be used for transfer
of specific chromosomes.)
Ch = chromosomal change associated with particular phenotype and not
proved to represent linkage (Fc), deletion (D), or virus effect (V);
e.g., loss of 13q14 band in some cases of retinoblastoma. (`Fragile
sites,' observed in cultured cells with or without folate-deficient
medium or BrdU treatment, fall into this class of method; e.g.,
fragile site at Xq27.3 in one form of X-linked mental retardation.
Fragile sites have been used as markers in family linkage studies;
e.g., FS16q22 and haptoglobin.)
D = deletion or dosage mapping (concurrence of chromosomal deletion
and phenotypic evidence of hemizygosity), trisomy mapping (presence
of three alleles in the case of a highly polymorphic locus), or gene
dosage effects (correlation of trisomic state of part or all of a
chromosome with 50% more gene product). Includes "loss of
heterozygosity" (loss of alleles) in malignancies. Examples:
glutathione reductase to chromosome 8. Includes DNA dosage; e.g.,
fibrinogen loci to 4q2. Dosage mapping also includes coamplification
in tumor cells.
EM = exclusion mapping, i.e., narrowing the possible location of loci
by exclusion of parts of the map by deletion mapping, extended to
include negative lod scores from families with marker chromosomes and
negative lod scores with other assigned loci; e.g., support for
assignment of MNSs to 4q.
F = linkage study in families; e.g., linkage of ABO blood group and
nail-patella syndrome. (When a chromosomal heteromorphism or
rearrangement is one trait, Fc is used; e.g., Duffy blood group locus
on chromosome 1. When 1 or both of the linked loci are identified by
a DNA polymorphism, Fd is used; e.g., Huntington disease on
chromosome 4. F = L in the HGM workshops.)
H = based on presumed homology; e.g., proposed assignment of TF to
3q. Includes Ohno's law of evolutionary conservatism of X chromosome
in mammals. Mainly heuristic or confirmatory.
HS = DNA/cDNA molecular hybridization in solution (`Cot analysis');
e.g., assignment of Hb beta to chromosome 11 in derivative hybrid
cells.
L = lyonization; e.g., OTC to X chromosome. (L = family linkage study
in the HGM workshops.)
LD = linkage disequilibrium; e.g., beta and delta globin genes (HBB,
HBD).
M = Microcell mediated gene transfer (MMGT); e.g., a collagen gene
(COL1A1) to chromosome l7.
OT = ovarian teratoma (centromere mapping); e.g., PGM3 and centromere
of chromosome 6.
Pcm = PCR of microdissected chromosome segments (see REl).
Psh = PCR of somatic cell hybrid DNA.
R = irradiation of cells followed by `rescue' through fusion with
nonirradiated (nonhuman) cells (Goss-Harris method of
radiation-induced gene segregation); e.g., order of genes on Xq.
(Also called cotransference. The complement of cotransference =
recombination.)
RE = Restriction endonuclease techniques; e.g., fine structure map of
the beta-globin cluster (HBBC) on 11p; physical linkage of 3
fibrinogen genes (on 4q) and APOA1 and APOC3 (on 11p).
REa = combined with somatic cell hybridization; e.g., NAG (HBBC) to
11p.
REb = combined with chromosome sorting; e.g., insulin to 11p.
Includes Lebo's adaptation (dual laser chromosome sorting and spot
blot DNA analysis); e.g., MGP to 11q. (For this method, using flow
sorted chromosomes, W is the symbol adopted by the HGM workshops.)
REc = hybridization of cDNA to genomic fragment (by YAC, PFGE,
microdissection, etc.), e.g., A11 on Xq.
REf = isolation of gene from genomic DNA; includes 'exon trapping'
REl = isolation of gene from chromosome-specific genomic library (see
Pcm).
REn = neighbor analysis in restriction fragments, e.g., in PFGE.
S = `segregation' (cosegregation) of human cellular traits and human
chromosomes (or segments of chromosomes) in particular clones from
interspecies somatic cell hybrids; e.g., thymidine kinase to
chromosome 17. When with restriction enzyme, REa; with hybridization
in solution, HS.
T = TACT = telomere-associated chromosome fragmentation; e.g.,
interferon-inducible protein 6-16.
V = induction of microscopically evident chromosomal change by a
virus; e.g., adenovirus 12 changes on chromosomes 1 and 17.
X/A = X-autosome translocation in female with X-linked recessive
disorder; e.g., assignment of Duchenne muscular dystrophy to Xp21.