Construction of an approximately 700-kb transcript map around the familial Mediterranean fever locus on human chromosome 16p13.3.

We used a combination of cDNA selection, exon amplification, and computational prediction from genomic sequence to isolate transcribed sequences from genomic DNA surrounding the familial Mediterranean fever (FMF) locus. Eighty-seven kb of genomic DNA around D16S3370, a marker showing a high degree of linkage disequilibrium with FMF, was sequenced to completion, and the sequence annotated. A transcript map reflecting the minimal number of genes encoded within the approximately 700 kb of genomic DNA surrounding the FMF locus was assembled. This map consists of 27 genes with discreet messages detectable on Northerns, in addition to three olfactory-receptor genes, a cluster of 18 tRNA genes, and two putative transcriptional units that have typical intron-exon splice junctions yet do not detect messages on Northerns. Four of the transcripts are identical to genes described previously, seven have been independently identified by the French FMF Consortium, and the others are novel. Six related zinc-finger genes, a cluster of tRNAs, and three olfactory receptors account for the majority of transcribed sequences isolated from a 315-kb FMF central region (between D16S468/D16S3070 and cosmid 377A12). Interspersed among them are several genes that may be important in inflammation. This transcript map not only has permitted the identification of the FMF gene (MEFV), but also has provided us an opportunity to probe the structural and functional features of this region of chromosome 16.

A transcript map of the newly defined 165 kb Wolf-Hirschhorn syndrome critical region.

Wolf-Hirschhorn syndrome (WHS) is a multiple malformation syndrome characterised by mental and developmental defects resulting from the absence of a segment of one chromosome 4 short arm (4p16.3). Due to the complex and variable expression of this disorder, it is thought that the WHS is a contiguous gene syndrome with an undefined number of genes contributing to the phenotype. In an effort to identify genes that contribute to human development and whose absence results in this syndrome, we have utilised a series of landmark cosmids to characterise a collection of WHS patient derived cell lines. Fluorescence in situ hybridisation with these cosmids was used to refine the WHS critical region (WHSCR) to 260 kb. The genomic sequence of this region is available and analysis of this sequence through BLAST detected several cDNA clones in the dbEST data base. A total of nine independent cDNAs, and their predicted translation products, from this analysis show no significant similarity to members of DNA or protein databases. Furthermore, these genes have been localised within the WHS critical region and reveal an interesting pattern of transcriptional organisation. A previously published report of a patient with proximal 4p- syndrome further refines the WHSCR to 165 kb defined by the loci D4S166 and D4S3327. This work provides the starting point to understand how multiple genes or other mechanisms can contribute to the complex phenotype associated with the Wolf-Hirschhorn syndrome.

Database of mutations in the p53 and APC tumor suppressor genes designed to facilitate molecular epidemiological analyses.

Germline and somatic mutations in the p53 and APC genes contribute to neoplasia. The patterns of these and other acquired mutations in cancers reflect environmental mutagens and endogenous factors that contribute to carcinogenesis. Herein, we describe a database of almost 2,300 mutations in the p53 and APC genes published until September 1, 1993. In addition to cataloging the mutations, multiple fields of information have been added to facilitate future molecular epidemiological analyses of human cancer. The accuracy of the database has been checked by the present authors and, by soliciting feedback from the original corresponding authors. The strengths and limitations of the primary literature are discussed.

Nonrandom patterns of simple and cryptic triplet repeats in coding and noncoding sequences.

Triplet repeats of the sequence purine, purine, and pyrimidine [RRY(i)] are frequent and often polymorphic in humans. Some RRY(i) are composed predominantly of a continuous repeat of one sequence [simple RRY(i)], but the majority are cryptic RRY(i) that are not obvious until the bases are classified into R or Y before the full extent of the repeat becomes apparent. RRY(i) can be divided into 18 classes based on predominant nucleotides. These classes are highly nonrandom in abundance and in location within genes. In humans, simple or cryptic RRY(i), in which AAT or AAC triplets predominate, are preferentially located 3' of Alu repeats. RRY(i) with a predominance of AGC or GGC show a dramatic enrichment in coding sequence, and GGC also shows a dramatic enrichment in 5' untranslated regions of genes. Characterization of RRY(i) present in coding regions identify 10 protein motifs (An, Dn, Hn, Pn, Qn, Tn, GnS0-3Gm, (G/S)n, (S/G/N)n, and (L/P)n). Six of the protein motifs appear predominantly in DNA-binding proteins/transcription factors. Alignment of homologous protein sequences from other mammals reveals that both simple and cryptic RRY(i) are a major source of deletions or insertions in the genes that contain them. Cryptic RRY(i) may be candidates for triplet repeat genetic diseases and, when mutated in somatic cells, may contribute to carcinogenesis.

Deletions with inversions: report of a mutation and review of the literature.

Herein we report a 10.9 kb deletion and a 95 bp inversion in a patient with severe hemophilia B (factor IXHB209). With the addition of factor IXHB209, three of six characterized deletions in the factor IX gene are now known to include inversions. A high frequency of combined deletions and inversions has not previously been described in a human gene.