While germline mutations in the adenomatous polyposis coli (APC) gene cause the hereditary colon cancer syndrome (familial adenomatous polyposis (FAP)), the role of common germline APC variants in sporadic adenomatous polyposis remains unclear. We studied the association of eight APC single nucleotide polymorphisms (SNPs), possibly associated with functional consequences, and previously identified gene–environment (dietary fat intake and hormone replacement therapy (HRT) use) interactions, in relation to advanced colorectal adenoma in 758 cases and 767 sex- and race-matched controls, randomly selected from the screening arm of the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. Cases had at least one verified advanced adenoma of the distal colon; controls, a negative sigmoidoscopy. We did not observe an association between genotypes for any of the eight APC SNPs and advanced distal adenoma risk (Pglobal gene-based = 0.92). Frequencies of identified common haplotypes did not differ between cases and controls (Pglobal haplotype test = 0.97). However, the risk for advanced distal adenoma was threefold higher for one rare haplotype (cases: 2.7%; controls: 1.6%) (odds ratio (OR) = 3.27; 95% confidence interval (CI) = 1.08–9.88). The genetic association between D1822V and advanced distal adenoma was confined to persons consuming a high-fat diet (Pinteraction = 0.03). Similar interactions were not observed with HRT use. In our large, nested case-control study of advanced distal adenoma and clinically verified adenoma-free controls, we observed no association between specific APC SNPs and advanced adenoma. Fat intake modified the APC D1822V-adenoma association, but further studies are warranted.

To test the reliability of linkage-disequilibrium analysis for gene mapping, we compared physical distance and linkage disequilibrium among seven polymorphisms in the adenomatous polyposis coli (APC) region on chromosome 5. Three of them lie within the APC gene, and two lie within the nearby MCC (mutated in colon cancer) gene. One polymorphism lies between the two genes, and one is likely to be 5' of MCC. Five of these polymorphisms are newly reported. All polymorphisms were typed in the CEPH kindreds, yielding 179-205 unrelated two-locus haplotypes. Linkage disequilibrium between each pair of polymorphisms is highly correlated with physical distance in this 550-kb region (correlation coefficient -.80, P < .006). This result is replicated in both the Utah and non-Utah CEPH kindreds. There is a tendency for greater disequilibrium among pairs of polymorphisms located within the same gene than among other pairs of polymorphisms. Trigenic, quadrigenic, three-locus, and four-locus disequilibrium measures were also estimated, but these measures revealed much less disequilibrium than did the two-locus disequilibrium measures. A review of 19 published disequilibrium studies, including this one, shows that linkage disequilibrium nearly always correlates significantly with physical distance in genomic regions > 50-60 kb but that it does not do so in smaller genomic regions. We show that this agrees with theoretical predictions. This finding helps to resolve controversies regarding the use of disequilibrium for inferring gene order. Disequilibrium mapping is unlikely to predict gene order correctly in regions < 50-60 kb in size but can often be applied successfully in regions of 50-500 kb or so in size. It is convenient that this is the range in which other mapping techniques, including chromosome walking and linkage mapping, become difficult.

An attenuated form of familial adenomatous polyposis coli, AAPC, causes relatively few colonic polyps, but still carries a significant risk of colon cancer. The mutant alleles responsible for this attenuated phenotype have been mapped in several families to the adenomatous polyposis coli (APC) locus on human chromosome 5q. Four distinct mutations in the APC gene have now been identified in seven AAPC families. These mutations that predict truncation products, either by single base pair changes or frameshifts, are similar to mutations identified in families with classical APC. However, they differ in that the four mutated sites are located very close to one another and nearer the 5' end of the APC gene than any base substitutions or small deletions yet discovered in patients with classical APC.

Small (100-260 kb), nested deletions were characterized in DNA from two unrelated patients with familial adenomatous polyposis coli (APC). Three candidate genes located within the deleted region were ascertained and a previous candidate gene, MCC, was shown to be located outside the deleted region. One of the new genes contained sequence identical to SRP19, the gene coding for the 19 kd component of the ribosomal signal recognition particle. The second, provisionally designated DP1 (deleted in polyposis 1), was found to be transcribed in the same orientation as MCC. Two other cDNAs, DP2 and DP3, were found to overlap, forming a single gene, DP2.5, that is transcribed in the same orientation as SRP19.

Recent studies have suggested the existence of a tumor suppressor gene located at chromosome region 5q21. DNA probes from this region were used to study a panel of sporadic colorectal carcinomas. One of these probes, cosmid 5.71, detected a somatically rearranged restriction fragment in the DNA from a single tumor. Further analysis of the 5.71 cosmid revealed two regions that were highly conserved in rodent DNA. These sequences were used to identify a gene, MCC (mutated in colorectal cancer), which encodes an 829-amino acid protein with a short region of similarity to the G protein-coupled m3 muscarinic acetylcholine receptor. The rearrangement in the tumor disrupted the coding region of the MCC gene. Moreover, two colorectal tumors were found with somatically acquired point mutations in MCC that resulted in amino acid substitutions. MCC is thus a candidate for the putative colorectal tumor suppressor gene located at 5q21. Further studies will be required to determine whether the gene is mutated in other sporadic tumors or in the germ line of patients with an inherited predisposition to colonic tumorigenesis.

DNA from 61 unrelated patients with adenomatous polyposis coli (APC) was examined for mutations in three genes (DP1, SRP19, and DP2.5) located within a 100 kb region deleted in two of the patients. The intron-exon boundary sequences were defined for each of these genes, and single-strand conformation polymorphism analysis of exons from DP2.5 identified four mutations specific to APC patients. Each of two aberrant alleles contained a base substitution changing an amino acid to a stop codon in the predicted peptide; the other mutations were small deletions leading to frameshifts. Analysis of DNA from parents of one of these patients showed that his 2 bp deletion is a new mutation; furthermore, the mutation was transmitted to two of his children. These data have established that DP2.5 is the APC gene.

Multiple endocrine neoplasia type I (MEN-1), a Mendelian disorder with an autosomal dominant mode of inheritance, causes hyperplasia in the parathyroid glands and hyperplasia or neoplasm in the anterior pituitary gland and/or the pancreatic islets. The genetic defect responsible for MEN-1 in three families was recently mapped to the long arm of chromosome II by linkage between the MEN-1 locus and the gene for skeletal muscle glycogen phosphorylase (PYGM) at 11q13. We have constructed a genetic linkage map of seven markers in the vicinity of the MEN-1 locus that has allowed us to map more precisely the gene associated with MEN-1; the target region has been narrowed to about 12 cM. The closely linked markers will be useful also for identification of likely carriers in families in which an allele responsible for MEN-1 segregates.

Journal Article Isolation and mapping of a polymorphic DNA sequence (pMCA1-1) on chromosome 15 [D15S33] Get access M. Carlson, M. Carlson The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Y. Nakamura, Y. Nakamura The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar L. Sargeant, L. Sargeant The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar P. O'Connell, P. O'Connell The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar M. Leppert, M. Leppert The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar G.M. Lathrop, G.M. Lathrop The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar J.-M. Lalouel, J.-M. Lalouel The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar R. White R. White The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 3, 11 February 1988, Page 1225, https://doi.org/10.1093/nar/16.3.1225 Published: 11 February 1988

SOURCE/DESCRIPTION; A 4.5 kb (pMCT96.1) or a 3.7 kb (pMCT96.2) of Mspl fragment from cosmid MCT96 isolated by an oligonucleotide (GTGTGTGTGTGTGTGTGTGT) (1) was subcloned into the Accl site of pUC18. POLYMORPHISM: pMCT96.1 : Rsal identifies 3 systems of site polymorphisms; system 1: 4.7 kb (Rl) or 3.7 kb (R2); system 2: 3.0 (R3) kb or 2.8 kb (R4); system 3: 1.0 kb (R5) or 0.9 kb (R6) pMCT96.2 : Hinfl resolves a 4 allele VNTR polymorphism with bands between 1.5 kb and 3.0 kb. Mspl, TaqI, Rsal, PvuII and PstI also detect this polymorphism. HOT POLYMORPHIC FOR: none known CHROMOSOMAL LOCALIZATION: pMCT96.1 and pMCT96.2 have been assigned to chromosome 9q by multipoint linkage analysis(2) with loci (ABO, ABL, AK1, ORM) known to span this region(3). MENDELIAN INHERITANCE: Co-dominant segregation of the polymorphism was observed in 43 three generation families. PROBE AVAILABILITY: Freely available (contact Y.N.) or will be available from ATCC. OTHER COMMENTS: RFLPs were observed after competitive hybridization with total human DNA for pMCT96.2. For pMCT96.1, RFLPs were observed under normal hybridization and washing condition.

_UCDE/IPTO: A 5.3 kb BamHI fragment from cosmid MCT46 was subcloned into the BauHI site of pUC18.POLYMORPRIIS: PvuII identifies a two allele polymorphism (P1 5.9 kb, P2 : 5.3 kb).FREOUENCY: Estimated from

POLYMORPHISM: PvuII identifies >10 allelic VNTR polymorphisms with bands between 4.0 and 10.0 kb. TaqI, Rsal Mspl and Pstl identify the same VNTR polymorphism. FREQUENCY; With PvuII, 85 % heterozygosity was observed in 97 unrelated Caucasians. NOT POLYMORPHIC FOR; Bglll CHROMOSOMAL LOCALIZATION: MCOD13 has been assigned to chromosome 3 by linkage analysis (2) with loci (APOD) known to span this chromosome(3). MENDELIAN INHERITANCE: Co-dominant segregation of the Hinfl RFLP was observed in 49 three generation families. PROBE AVAILABILITY: Freely available (contact Y.N.) or will be available from ATCC. OTHER COMMENTS: RFLPs were observed after competitive hybridization with total human DNA. REFERENCES: 1. Y. Nakamura et al., submitted 2. G.M. Lathrop et al., Am. J. Hum. Genet. 12:482-498 (1985) 3. D. Drayna et al., DNA, £:194-204 (1987)

Elsewhere we have reported an efficient method for isolating VNTR (Variable Number of Tandem Repeats) markers. Several of the VNTR markers isolated in those experiments were sequenced, and a DNA sequence of 9 bp (GNNGTGGG) emerged as an apparent consensus sequence for VNTR markers. To confirm this result and to develop more VNTR markers, we synthesized nine different 18-base-long oligonucleotides whose sequences each included GNNGTGGG. When 102 cosmid clones selected by these oligonucleotides were tested for polymorphism, 34 (33%) of them showed multiallelic VNTR polymorphisms (average heterozygosity 68%). This procedure represents a new and efficient approach for isolating additional VNTR markers and supports the idea that the GNNGTGGG sequence may play an important role in the generation of the multiallelic systems within the human genome.

Journal Article Isolation and mapping of a polymorphic DNA sequence (pMCT149.2) on chromosome 15 [D15S34] Get access M. Carlson, M. Carlson The Howard Hughes Medical institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Y. Nakamura, Y. Nakamura The Howard Hughes Medical institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar K. Krapcho, K. Krapcho The Howard Hughes Medical institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar R. Payson, R. Payson The Howard Hughes Medical institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar P. O'Connell, P. O'Connell The Howard Hughes Medical institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar M. Leppert, M. Leppert The Howard Hughes Medical institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar J.-M. Lalouel, J.-M. Lalouel The Howard Hughes Medical institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar R. White R. White The Howard Hughes Medical institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 22, 25 November 1988, Page 10941, https://doi.org/10.1093/nar/16.22.10941 Published: 25 November 1988

Familial adenomatous polyposis (FAP), a Mendelian disorder that includes familial polyposis coli (FPC) and Gardner syndrome (GS), has an autosomal dominant mode of inheritance. It is characterized by hundreds to thousands of adenomatous polyps that can progress to carcinoma of the colon, suggesting that the gene that harbors the FAP germ-line mutation may play an important role in the somatic genetic pathway to colon cancer. The defect responsible for FAP was recently mapped to the long arm of chromosome 5 by linkage between the FPC phenotype and a locus defined by DNA probe pC11p11 (D5S71), located at 5q21-22. Because an important next step in the paradigm for identification of a disease gene is to obtain a more precise localization, we isolated and mapped by linkage six additional polymorphic DNA markers in the FAP region. Subsequent linkage analysis in six pedigrees, three having the FPC phenotype and three segregating GS, placed the FAP locus very close to a new marker, YN5.48 (D5S81), that is approximately 17 centimorgans distal to C11p11 on the genetic map. The analysis revealed no evidence of genetic heterogeneity between the two phenotypes, a question that had not been clearly resolved by the earlier studies. The new set of markers in the near vicinity of the FAP locus represents a further step toward isolation of the genetic defect and provides the opportunity for preclinical diagnosis of risk status for colon cancer among individuals in families that are segregating adenomatous polyposis.

Journal Article Isolation and mapping of a polymorphic DNA sequence (pMCT128.2) on chromosome 8 [D8S39] Get access Y. Nakamura, Y. Nakamura The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar M. Carlson, M. Carlson The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar K. Karpcho, K. Karpcho The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar L. Ballard, L. Ballard The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar M. Leppert, M. Leppert The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar P. O'Connell, P. O'Connell The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar G.M. Lathrop, G.M. Lathrop The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar J.-M. Lalouel, J.-M. Lalouel The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar R. White R. White The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 8, 25 April 1988, Page 3590, https://doi.org/10.1093/nar/16.8.3590 Published: 25 April 1988

CHROMOSOMAL LOCALIZATION: This probe has been assigned to chromosome 21 by linkage analysis (2) with the loci known to span this chromosome (3). MENDELIAN INHERITANCE: Co-dominant segregation has been + observed in 40 three generation families.