OMIM Gene Map Methods

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.