The CEPH consortium linkage map of human chromosome 1

doi:10.1016/0888-7543(91)90362-I

Genomics

Volume 9, Issue 4, April 1991, Pages 686-700

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https://doi.org/10.1016/0888-7543(91)90362-I Get rights and content

Abstract

This paper describes the Centre d'Etude du Polymorphisme Humain (CEPH) consortium linkage map of human chromosome 1. The map contains 101 loci defined by genotypes generated from CEPH family DNAs with 146 different contributions from 11 laboratories. A total of 58 loci are uniquely placed on the map with likelihood support of at least 1000:1. The map extends from loci in the terminal bands of both chromosome arms (locus D1Z2 in 1p36.3 and D1S68 in 1q44) and is anchored at the centromere by the D1Z5 α-satellite polymorphism. With the exception of a single locus, the remaining loci are arrayed on the fixed map in short intervals and their possible locations are indicated. Multipoint linkage analyses provided estimates that the male, female, and sex-averaged maps extend for 308, 478, and 390 cM, respectively. The sex-averaged map contains only four intervals > 15 cM, and the mean genetic distance between the 58 uniquely placed loci is 6.7 cM.

References (100)

J.A.L. Armour et al.
Analysis of somatic mutations at human minisatellite loci in tumors and cell lines
Genomics
(1989)
K. Buetow et al.
A detailed multipoint gene map of chromosome 1q
Genomics
(1990)
J. Dausset et al.
Centre d'Etude du Polymorphisme Humain (CEPH): Collaborative genetic mapping of the human genome
Genomics
(1990)
H. Donis-Keller et al.
A genetic linkage map of the human genome
Cell
(1987)
N.C. Dracopoli et al.
Two thyroid hormone regulated genes, the beta subunits of nerve growth factor (NGFB) and thyroid stimulating hormone (TSHB), are located less than 310 kb apart in both human and mouse genomes
Genomics
(1988)
N.C. Dracopoli et al.
Localization of the FGR protooncogene on the genetic linkage map of of human chromosome 1p
Genomics
(1988)
N.C. Dracopoli et al.
Mapping the human amylase gene cluster in the proximal short arm of chromosome 1 using a highly informative (CA)_n repeat
Genomics
(1990)
A. Fujisaku et al.
Genomic organization and polymorphisms of the human C3d/Epstein-Barr virus receptor
J. Biol. Chem
(1989)
M.P. Kamps et al.
A new homeobox gene contributes to the DNA-binding binding domain of the t(1:19) translocation protein in pre-B ALL
Cell
(1990)
J.R. Kidd et al.
The locus for the medium-chain acyl-CoA dehydrogenase gene on chromosome 1 is highly polymorphic
Genomics
(1990)

W.J. Kimberling et al.

Localization of Usher syndrome type II to chromosome 1q

Genomics

(1990)

S.F. Kingsmore et al.

Longrange restriction site mapping of a syntenic segment conserved between human chromosome 1 and mouse chromosome 3

Genomics

(1990)

E.S. Lander et al.

MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations

Genomics

(1987)

R.A. Lewis et al.

Mapping recessive ophthalmic diseases: Linkage of the locus for Usher syndrome type II to a DNA marker on 1q

Genomics

(1990)

D.Y. Nishimura et al.

RFLPs and linkage relationships of the human laminin B2 gene

Genomics

(1988)

J. Nourse et al.

Chromosomal translocation t(1;19) results in synthesis of a homeobox fusion mRNA that codes for a potential chimeric transcription factor

Cell

(1990)

P. O'Connell et al.

Twenty-eight loci form a continuous linkage map of markers for human chromosome 1

Genetics

(1989)

G.A. Rouleau et al.

A genetic map of chromosome 1: Comparison of different data sets and linkage programs

Genomics

(1990)

N.J. Royle et al.

Clustering of hypervariable minisatellites in the proterminal regions of human autosomes

Genomics

(1988)

J. Scott et al.

High density lipoprotein composition is altered by a common DNA polymorphism adjacent to apolipoprotein All gene in man

Lancet

(1985)

M. Smith et al.

Regional assignment of the gene for human liver/bone/kidney alkaline phosphatase to chromosome 1p36.1–p34

Genomics

(1988)

J.S. Waye et al.

Chromosome specific α-satellite DNA from human chromosome 1: Hierarchical structure and genomic organization of a polymorphic domain spanning several hundred kilobase pairs of centromeric DNA

Genomics

(1987)

R.L. White et al.

The CEPH consortium primary linkage map of human chromosome 10

Genomics

(1990)

T.L. Yang-Feng et al.

Chromosomal localization of human Na+, K+-ATPase α- and β-subunit genes

Genomics

(1988)

L.A. Anderson et al.

Polymorphisms near 1cen

Cytogenet. Cell Genet

(1989)

S.J. Bale et al.

Mapping the gene for hereditary cutaneous malignant melanoma-dysplastic nevus to chromosome 1p

N. Engl. J. Med

(1989)

T.D. Bird et al.

Evidence for linkage of Charcot-Marie-Tooth neuropathy to the Duffy locus on chromosome 1

Amer. J. Hum. Genet

(1982)

S.C. Bock et al.

Characterization of an unusual DNA length polymorphism 5′ to the human antithrombin III gene

Nucleic Acids Res

(1983)

D. Botstein et al.

Construction of a genetic linkage map in man using restriction fragment length polymorphisms

Amer. J. Hum. Genet

(1980)

X.O. Breakefield et al.

Structural gene for the beta-nerve growth factor not defective in familial dysautonomia

G.A.P. Bruns et al.

Report of the committee on the genetic constitution of chromosome 1

Cytogenet. Cell Genet

(1989)

N. Buroker et al.

A hypervariable repeated sequence on human chromosome 1p36

Hum. Genet

(1987)

M. Carlson et al.

Isolation and mapping of a polymorphism DNA sequence for NRAS pMCR3 on chromosome 1

Nucleic Acids Res

(1987)

J.M. Chirgwin et al.

Human renin gene is on chromosome 1

Somat. Cell Mol. Genet

(1984)

C. Dacou-Voutetakis et al.

Familial hypothyroidism caused by a nonsense mutation in the TSHB gene

Amer. J. Hum. Genet

(1990)

J.K. Darby et al.

PvuII RFLP at the human chromosome 1 alpha-l-fucosidase gene locus (FUCA1)

Nucleic Acids Res

(1986)

N.C. Dracopoli et al.

A genetic linkage map of 27 loci from PND to FY on the short arm of human chromosome 1

Amer. J. Hum. Genet

(1988)

N.C. Dracopoli et al.

Loss of alleles from the distal short arm of chromosome 1 occurs late in melanoma tumor progression

C.-T. Fong et al.

Loss of heterozygosity for the short arm of chromosome 1 in human neuroblastomas: Correlation with N-myc amplification

P.M. Frossard et al.

Human renin (REN) gene locus: BglII, RsaI, and TaqI RFLPs

Nucleic Acids Res

(1986)

E. Fujimoto et al.

Isolation and mapping of a polymorphic DNA sequence (pEFD53.2) on chromosome 1 (D1S73)

Nucleic Acids Res

(1988)

S.J. Goss et al.

Gene transfer by means of cell fusion. II. The mapping of 8 loci on human chromosome 1 by statistical analysis of gene assortment in somatic cell hybrids

J. Cell Sci

(1977)

J. Hall et al.

Polymorphism of HLM2 and linkage relationships on chromosome 1p

Cytogenet. Cell Genet

(1987)

J.L. Hamerton et al.

Report of the Committee on the Genetic Constitution of Chromosome 1. Human Gene Mapping 1 (New Haven Conference 1973) National Foundation

Y. Hayashizaki et al.

Thyroid stimulating hormone (TSH) deficiency caused by a single base substitution in the CAGYC region of the β-subunit

EMBO J

(1989)

M. Hoff et al.

Isolation and mapping of a polymorphic DNA sequence (pHHH119) on chromosome 1 (D1S59)

Nucleic Acids Res

(1988)

N. Hoffman et al.

Three RFLPs are detected by an alpha spectrin genomic clone

Nucleic Acids Res

(1987)

T. Holm et al.

Isolation and mapping of a polymorphic DNA sequence (pTH154) on chromosome 1p (D1S62)

Nucleic Acids Res

(1988)

M.A. Hultén et al.

Chiasma derived genetic maps and recombination fractions: Chromosome 1

Ann. Hum. Genet

(1982)

A.J. Jeffreys et al.

Spontaneous mutation rates to new length alleles at tandem-repetitive hypervariable loci in human DNA

Nature (London)

(1988)

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^☆: Centre d'Etude du Polymorphisme Humain (CEPH), 27, rue Juliette Dodu, 75010 Paris, France.

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The CEPH consortium linkage map of human chromosome 1☆

Abstract

Genomics

Genomics

Genomics

Cell

Genomics

Genomics

Genomics

J. Biol. Chem

Cell

Genomics

Genomics

Genomics

Genomics

Genomics

Genomics

Cell

Genetics

Genomics

Genomics

Lancet

Genomics

Genomics

Genomics

Genomics

Polymorphisms near 1cen

Cytogenet. Cell Genet

Mapping the gene for hereditary cutaneous malignant melanoma-dysplastic nevus to chromosome 1p

N. Engl. J. Med

Evidence for linkage of Charcot-Marie-Tooth neuropathy to the Duffy locus on chromosome 1

Amer. J. Hum. Genet

Characterization of an unusual DNA length polymorphism 5′ to the human antithrombin III gene

Nucleic Acids Res

Construction of a genetic linkage map in man using restriction fragment length polymorphisms

Amer. J. Hum. Genet

Structural gene for the beta-nerve growth factor not defective in familial dysautonomia

Report of the committee on the genetic constitution of chromosome 1

Cytogenet. Cell Genet

A hypervariable repeated sequence on human chromosome 1p36

Hum. Genet

Isolation and mapping of a polymorphism DNA sequence for NRAS pMCR3 on chromosome 1

Nucleic Acids Res

Human renin gene is on chromosome 1

Somat. Cell Mol. Genet

Familial hypothyroidism caused by a nonsense mutation in the TSHB gene

Amer. J. Hum. Genet

PvuII RFLP at the human chromosome 1 alpha-l-fucosidase gene locus (FUCA1)

Nucleic Acids Res

A genetic linkage map of 27 loci from PND to FY on the short arm of human chromosome 1

Amer. J. Hum. Genet

Loss of alleles from the distal short arm of chromosome 1 occurs late in melanoma tumor progression

Loss of heterozygosity for the short arm of chromosome 1 in human neuroblastomas: Correlation with N-myc amplification

Human renin (REN) gene locus: BglII, RsaI, and TaqI RFLPs

Nucleic Acids Res

Isolation and mapping of a polymorphic DNA sequence (pEFD53.2) on chromosome 1 (D1S73)

Nucleic Acids Res

Gene transfer by means of cell fusion. II. The mapping of 8 loci on human chromosome 1 by statistical analysis of gene assortment in somatic cell hybrids

J. Cell Sci

Polymorphism of HLM2 and linkage relationships on chromosome 1p

Cytogenet. Cell Genet

Report of the Committee on the Genetic Constitution of Chromosome 1. Human Gene Mapping 1 (New Haven Conference 1973) National Foundation

Thyroid stimulating hormone (TSH) deficiency caused by a single base substitution in the CAGYC region of the β-subunit

EMBO J

Isolation and mapping of a polymorphic DNA sequence (pHHH119) on chromosome 1 (D1S59)

Nucleic Acids Res

Three RFLPs are detected by an alpha spectrin genomic clone

Nucleic Acids Res

Isolation and mapping of a polymorphic DNA sequence (pTH154) on chromosome 1p (D1S62)

Nucleic Acids Res

Chiasma derived genetic maps and recombination fractions: Chromosome 1

Ann. Hum. Genet

Spontaneous mutation rates to new length alleles at tandem-repetitive hypervariable loci in human DNA

Nature (London)