1
|
Feder JN, Gnirke A, Thomas W, Tsuchihashi Z, Ruddy DA, Basava A. The discovery of the new haemochromatosis gene. 1996. J Hepatol 2003; 38:704-9. [PMID: 12763361 DOI: 10.1016/s0168-8278(03)00142-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
2
|
Herbon N, Werner M, Braig C, Gohlke H, Dütsch G, Illig T, Altmüller J, Hampe J, Lantermann A, Schreiber S, Bonifacio E, Ziegler A, Schwab S, Wildenauer D, van den Boom D, Braun A, Knapp M, Reitmeir P, Wjst M. High-resolution SNP scan of chromosome 6p21 in pooled samples from patients with complex diseases. Genomics 2003; 81:510-8. [PMID: 12706109 DOI: 10.1016/s0888-7543(02)00035-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We apply a high-throughput protocol of chip-based mass spectrometry (matrix-assisted laser desorption/ionization time-of-flight; MALDI-TOF) as a method of screening for differences in single-nucleotide polymorphism (SNP) allele frequencies. Using pooled DNA from individuals with asthma, Crohn's disease (CD), schizophrenia, type 1 diabetes (T1D), and controls, we selected 534 SNPs from an initial set of 1435 SNPs spanning a 25-Mb region on chromosome 6p21. The standard deviations of measurements of time of flight at different dots, from different PCRs, and from different pools indicate reliable results on each analysis step. In 90% of the disease-control comparisons we found allelic differences of <10%. Of the T1D samples, which served as a positive control, 10 SNPs with significant differences were observed after taking into account multiple testing. Of these 10 SNPs, 5 are located between DQB1 and DRB1, confirming the known association with the DR3 and DR4 haplotypes whereas two additional SNPs also reproduced known associations of T1D with DOB and LTA. In the CD pool also, two earlier described associations were found with SNPs close to DRB1 and MICA. Additional associations were found in the schizophrenia and asthma pools. They should be confirmed in individual samples or can be used to develop further quality criteria for accepting true differences between pools. The determination of SNP allele frequencies in pooled DNA appears to be of value in assigning further genotyping priorities also in large linkage regions.
Collapse
Affiliation(s)
- Nicole Herbon
- Institut für Epidemiologie, GSF Forschungszentrum für Umwelt und Gesundheit, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
3
|
Lonjou C, Collins A, Ajioka RS, Jorde LB, Kushner JP, Morton NE. Allelic association under map error and recombinational heterogeneity: a tale of two sites. Proc Natl Acad Sci U S A 1998; 95:11366-70. [PMID: 9736742 PMCID: PMC21648 DOI: 10.1073/pnas.95.19.11366] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/1998] [Indexed: 11/18/2022] Open
Abstract
Recombination acts on the genetic map, not on the physical map. On the other hand, the physical map is usually more accurate. Choice of the genetic or physical map for positional cloning by allelic association depends on the goodness of fit of data to each map under an established model. Huntington disease illustrates the usual case in which the greater reliability of physical data outweighs recombinational heterogeneity. Hemochromatosis represents an exceptional case in which unrecognized recombinational heterogeneity retarded positional cloning for a decade. The Malecot model performs well for major genes, but no approach assuming either equilibrium or disequilibrium has been validated for oligogenes contributing to common disease. In this case of greatest interest, the power of allelic association relative to linkage is less clear than for major genes.
Collapse
Affiliation(s)
- C Lonjou
- Human Genetics, University of Southampton, Princess Anne Hospital, Southampton SO16 54A, United Kingdom
| | | | | | | | | | | |
Collapse
|
4
|
Jouanolle AM, Gandon G, Jézéquel P, Blayau M, Campion ML, Yaouanq J, Mosser J, Fergelot P, Chauvel B, Bouric P, Carn G, Andrieux N, Gicquel I, Le Gall JY, David V. Haemochromatosis and HLA-H. Nat Genet 1996; 14:251-2. [PMID: 8896550 DOI: 10.1038/ng1196-251] [Citation(s) in RCA: 269] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
5
|
Feder JN, Gnirke A, Thomas W, Tsuchihashi Z, Ruddy DA, Basava A, Dormishian F, Domingo R, Ellis MC, Fullan A, Hinton LM, Jones NL, Kimmel BE, Kronmal GS, Lauer P, Lee VK, Loeb DB, Mapa FA, McClelland E, Meyer NC, Mintier GA, Moeller N, Moore T, Morikang E, Prass CE, Quintana L, Starnes SM, Schatzman RC, Brunke KJ, Drayna DT, Risch NJ, Bacon BR, Wolff RK. A novel MHC class I-like gene is mutated in patients with hereditary haemochromatosis. Nat Genet 1996; 13:399-408. [PMID: 8696333 DOI: 10.1038/ng0896-399] [Citation(s) in RCA: 2524] [Impact Index Per Article: 90.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Hereditary haemochromatosis (HH), which affects some 1 in 400 and has an estimated carrier frequency of 1 in 10 individuals of Northern European descent, results in multi-organ dysfunction caused by increased iron deposition, and is treatable if detected early. Using linkage-disequilibrium and full haplotype analysis, we have identified a 250-kilobase region more than 3 megabases telomeric of the major histocompatibility complex (MHC) that is identical-by-descent in 85% of patient chromosomes. Within this region, we have identified a gene related to the MHC class I family, termed HLA-H, containing two missense alterations. One of these is predicted to inactivate this class of proteins and was found homozygous in 83% of 178 patients. A role of this gene in haemochromatosis is supported by the frequency and nature of the major mutation and prior studies implicating MHC class I-like proteins in iron metabolism.
Collapse
Affiliation(s)
- J N Feder
- Mercator Genetics, Inc., Menlo Park, California 94025, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Pichon L, Giffon T, Chauvel B, Carn G, Bouric P, El Kahloun A, Legall JY, David V. Physical map of the HLA-A/HLA-F subregion and identification of two new coding sequences. Immunogenetics 1996; 43:175-81. [PMID: 8575815 DOI: 10.1007/bf00587297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
As part of an effort to characterize the hemochromatosis gene, we selected three non-chimeric yeast artificial chromosomes (YACs) overlapping with the YAC B30 previously described and forming an 800 kilobase contig covering the HLA-A/HLA-F region. The precise physical map of these YACs and of the corresponding genomic region were established. Nine concentrated sites of CpG cutter elements, potentially HTF islands, were mapped. In addition, several probes have been generated as tools for mapping and examining transcripts produced in the region. This allowed for the characterization and localization of two new coding sequences, provisionally named HCG (for hemochromatosis candidate gene) and numbered VIII and IX.
Collapse
MESH Headings
- Blotting, Northern
- Chromosomes, Artificial, Yeast
- Chromosomes, Human, Pair 6
- Cloning, Molecular
- DNA Fingerprinting
- DNA, Complementary/genetics
- Electrophoresis, Gel, Pulsed-Field
- Gene Library
- HLA Antigens/genetics
- HLA-A Antigens/genetics
- Hemochromatosis/genetics
- Histocompatibility Antigens Class I/genetics
- Humans
- Molecular Sequence Data
- Open Reading Frames
- Restriction Mapping
- Sequence Analysis, DNA
- Transcription, Genetic
Collapse
Affiliation(s)
- L Pichon
- Department of Biochemistry and Molecular Biology, UPR 41 CNRS - "Recombinaisons génétiques" Faculté de Médecine, 2 avenue du Professeur Léon Bernard, 35043 Rennes Cedex, France
| | | | | | | | | | | | | | | |
Collapse
|
7
|
Sallie R. Isolation of candidate genes by subtractive and sequential (Boolean) hybridization: an hypothesis. Med Hypotheses 1995; 45:142-6. [PMID: 8531837 DOI: 10.1016/0306-9877(95)90063-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This paper describes a theoretical method of isolating candidate disease-specific genes by polymerase chain reaction (PCR)-based subtractive hybridization and subsequent (Boolean) hybridization of the subtracted library to arrays of chromosome-specific cosmid clones. A specific application of this technique to isolate genes potentially related to Wilson's disease is outlined.
Collapse
Affiliation(s)
- R Sallie
- Liver Unit, National Institute for Health, Bethesda, Maryland 20892, USA
| |
Collapse
|
8
|
Raha-Chowdhury R, Bowen DJ, Burnett AK, Worwood M. Allelic associations and homozygosity at loci from HLA-B to D6S299 in genetic haemochromatosis. J Med Genet 1995; 32:446-52. [PMID: 7666396 PMCID: PMC1050484 DOI: 10.1136/jmg.32.6.446] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Haemochromatosis (GH) is an autosomal recessive disorder in which increased iron absorption causes iron overload. The gene (HFE) is closely linked to HLA-A on chromosome 6 (6p21.3) but has not yet been identified. We have examined eight polymorphic loci, HLA-B (most centromeric), I82, D6S265, HLA-A, D6S128, HLA-F, D6S105, and D6S299 (most telomeric) in 37 unrelated patients and 60 control subjects. There are also significant positive associations between GH and alleles at all loci except D6S299. Analysis of 48 GH chromosomes in which haplotypes could be established showed that the most common haplotype was I82-2:D6S265-1:HLA-A3:D6S128-2:HLA-F1:D6S105-8. This was present in 28 of 48 chromosomes. In 14 the haplotype included HLA-B7 but only in seven did this extend beyond the telomere to D6S299-2 (the most common allele on GH chromosomes at this locus). In 36 out of 48 chromosomes the two locus haplotype, F1:D6S105-8 was present. Since haemochromatosis appears to originate from a founder mutation we have examined linkage disequilibrium between these various loci and GH using calculations of pexcess. The maximum value (0.72, 95% CI 0.55-0.85) is given by D6S105-8 but is not significantly different from values for HLA-A3 and HLA-F1 (0.50, 95% CI 0.34-0.61 and 0.49, 0.25-0.66 respectively). However, both HLA-A and D6S105 give a value for pexcess which is significantly higher than that for the most centromeric marker, HLA-B (0.17, 95% CI 0.02-0.30). We have counted the number of patients who are homozygous for the common allele at each locus. At D6S105, 22 patients are homozygous for allele 8, with 18 homozygous for HLA-F1 and 10 homozygous for A3. The pattern of cumulative homozygosity suggests a gene location closer to D6S105 than HLA-A. We have also analysed our data for divergence from the apparent founder haplotype (A3:F1:105-8) and have calculated the theoretical frequencies of crossovers between loci. These data suggest a location telomeric to D6S105. A more precise localisation of the gene may be possible with the identification of new markers around D6S105.
Collapse
Affiliation(s)
- R Raha-Chowdhury
- Department of Haematology, University of Wales College of Medicine, Heath Park, Cardiff, UK
| | | | | | | |
Collapse
|
9
|
Dorak MT, Wilson DW, Galbraith I, Henderson N, Burnett AK, Worwood M. A molecular analysis of the telomeric end of the major histocompatibility complex. DNA typing of HLA-A3 subtypes and -B7. Hum Immunol 1995; 42:1-8. [PMID: 7751155 DOI: 10.1016/0198-8859(94)00054-t] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A molecular investigation of the HLA-A, -B, -C, I82, D6S128, and D6S265 loci was carried out using RFLP and PCR analyses in 331 healthy individuals, 21 HLA-A3B7 homozygous subjects, and 17 HLA homozygous cell lines. New polymorphic RFLP patterns were noted at the HLA-A and -B loci which were useful for distinguishing subtypes of HLA-A3 and -B44. Strictly specific bands were observed for HLA-A3, -A11, -B7, -B57. and -Cw4. Molecular identification of two HLA-A3 subtypes was possible by HLA-A RFLP and D6S265 PCR analyses. The two alleles of the I82 locus were associated with different HLA-A3 subtypes. It was shown that the serologically HLA-A3 homozygous cell line EHM was heterozygous for the two subtypes. The common subtype formed 91% of HLA-A3 antigens. Some serologically HLA-A3 homozygous healthy individuals were heterozygous for the subtypes. Using these new polymorphisms, a thorough molecular analysis of the haplotype HLA-A3B7DR15 at the three regions of the MHC was performed. The results have implications on HLA matching in transplantation, population genetics of the MHC, and disease association studies.
Collapse
Affiliation(s)
- M T Dorak
- Department of Hematology, University of Wales College of Medicine, Cardiff, United Kingdom
| | | | | | | | | | | |
Collapse
|
10
|
Abstract
This review is largely concerned with the frequency of genetic haemochromatosis (GH) and attempts to find the gene responsible. Studies of disease prevalence are reviewed along with the association of GH with other inherited disorders. The high prevalence of the disorder found in a number of surveys of populations of European origin along with the relatively few patients presenting with the clinical features of the advanced disease remains a paradox. The tight linkage between HLA-A and GH has been known since 1975 but it has not been possible to distinguish between a telomeric or centromeric location for the gene (HFE) relative to HLA-A. The recent explosion in detailed knowledge of the genetic map of the region telomeric of HLA-A on chromosome 6p has made it possible to examine new genetic markers. The very strong association between GH and D6S105-8 suggests a gene location telomeric to HLA-A. The lack of a precise location, and uncertainty about either the primary biochemical abnormality or the tissues involved has delayed the identification of the gene but expressed genes in the region around HLA-A are now being isolated and tested.
Collapse
Affiliation(s)
- M Worwood
- University of Wales College of Medicine, Cardiff, UK
| |
Collapse
|
11
|
Dorak MT, Burnett AK, Worwood M. Thymus-leukaemia antigens: the haemochromatosis gene product? Immunol Cell Biol 1994; 72:435-9. [PMID: 7835988 DOI: 10.1038/icb.1994.64] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The gene for hereditary haemochromatosis (HFE) lies telomeric to HLA-A and is believed to be expressed in the intestinal mucosa. Its product has not been characterized, but iron overload and its pathological consequences occur only in homozygotes for this putative gene. The genes encoding the putative human counterparts of the mouse thymus-leukaemia (TL) antigens map to the area where the HFE gene lies. Here, we postulate that a human TL gene may encode a protein acting as or interacting with the transferrin (Tf) receptor in the intestinal mucosa. This hypothesis is based on the following observations: (i) hereditary haemochromatosis (HH) is due to excessive absorption of iron through the intestinal mucosa. HH has a strong association with HLA-A3, but HLA-A3 has no direct role in the pathogenesis and reflects linkage disequilibrium with a telomeric gene. (ii) An HLA-A3 homozygous genotype is associated with the highest relative risks for both early-onset leukaemia and HH. In analogy to the susceptibility locus in mice, this genotype may reflect a TL gene association in leukaemia and raise the possibility of a TL gene involvement in HH. (iii) A TL antigen-like human molecule encoded in the region telomeric to HLA-A, TCA, is expressed in leukaemia and recognized by a Tf receptor-specific monoclonal antibody. The Tf receptor is believed to have a role in the control of intestinal iron absorption. (iv) In mice, particular TL antigens are exclusively expressed in the intestinal mucosa.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- M T Dorak
- Department of Haematology, University of Wales College of Medicine, Heath Park, Cardiff, UK
| | | | | |
Collapse
|
12
|
Worwood M, Raha-Chowdhury R, Dorak MT, Darke C, Bowen DJ, Burnett AK. Alleles at D6S265 and D6S105 define a haemochromatosis-specific genotype. Br J Haematol 1994; 86:863-6. [PMID: 7918084 DOI: 10.1111/j.1365-2141.1994.tb04843.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Hereditary haemochromatosis is an HLA-linked, recessive disorder with HLA-A3 a strong marker for the gene. We have identified molecular markers for two serologically indistinguishable subtypes of HLA-A3 and examined these in 42 patients with haemochromatosis. The common HLA-A3 subtype HLA-A*0301 (highly correlated with allele 1 of D6S265) was a slightly better marker for haemochromatosis (RR = 10.1, Chi2 = 30) than the serologically recognized A3 antigen (RR = 9.1; Chi2 = 27.3). Allele 8 of the more telomeric locus D6S105 was also strongly associated with haemochromatosis (RR = 13.0; Chi2 = 21.1) but alleles at this locus were not in strong linkage disequilibrium with HLA-A alleles in the control subjects. The co-occurrence of D6S265-1 and D6S105-8 alleles yielded a higher risk (RR = 16.9; Chi2 = 44). Homozygosity for the haplotype including these markers was specific for haemochromatosis, i.e. did not occur in 376 healthy subjects but was observed in 21.4% of patients. These results refine the HLA-A3 association with haemochromatosis, suggest that the haemochromatosis gene is located on the telomeric side of HLA-A and define a possible haplotype in which the first mutation may have occurred.
Collapse
Affiliation(s)
- M Worwood
- Department of Haematology, University of Wales College of Medicine
| | | | | | | | | | | |
Collapse
|
13
|
Bhavsar D, Chen Y, Zheng HD, Drysdale J. Searching for the hemochromatosis grail. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1994; 356:331-42. [PMID: 7887239 DOI: 10.1007/978-1-4615-2554-7_35] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- D Bhavsar
- Department of Biochemistry, Tufts Medical School, Boston, MA 02025
| | | | | | | |
Collapse
|
14
|
Worwood M, Dorak MT, Raha-Chowdhury R, Darke C. Genetics of haemochromatosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1994; 356:309-18. [PMID: 7887236 DOI: 10.1007/978-1-4615-2554-7_33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- M Worwood
- Department of Haematology, University of Wales College of Medicine, Cardiff
| | | | | | | |
Collapse
|
15
|
el Kahloun A, Chauvel B, Mauvieux V, Dorval I, Jouanolle AM, Gicquel I, le Gall JY, David V. Localization of seven new genes around the HLA-A locus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1994; 356:319-30. [PMID: 7887238 DOI: 10.1007/978-1-4615-2554-7_34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- A el Kahloun
- Laboratoire de Biochimie Médicale B, Faculté de Médecine- 2, Rennes, France
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Crouau-Roy B, Bouissou C, Sommer E, Pontarotti P, Thomsen M. Analysis of HLA-A/B recombinant families with new polymorphic markers. Hum Immunol 1993; 38:132-6. [PMID: 7906260 DOI: 10.1016/0198-8859(93)90530-e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The MHC in humans is a much studied region of the genome, the genes of which display a high rate of polymorphism and a high rate of linkage disequilibrium. Four families in which intra-class-I recombination has occurred have been analyzed with six polymorphic markers between HLA-A and -B in order to determine the full haplotypes of the whole families and to localize the points of crossover. The previously proposed order of the markers was confirmed by recombination mapping. In one family, the crossover was shown to have occurred in the 20-kb stretch of DNA bounded by the two markers (P3B and P5) between which no evidence of linkage disequilibrium was found, a region which constitutes of only about 1% of the distance between HLA-A and HLA-B. Although supportive of the suggestion of a hot spot of recombination in this region, based on the apparent lack of linkage disequilibrium between the markers P3B and P5, more such families need to be tested in order to confirm or refute this hypothesis.
Collapse
Affiliation(s)
- B Crouau-Roy
- Center for Research into Genetic Polymorphisms of the Human Population, CNRS, CHU Purpan, Toulouse, France
| | | | | | | | | |
Collapse
|
17
|
Affiliation(s)
- C Q Edwards
- Department of Medicine, University of Utah College of Medicine, Salt Lake City 84132
| | | |
Collapse
|