Methods for finding genes. A major rate-limiting step in positional cloning

Novel expressed sequences obtained by means of a suppression subtractive hybridisation analysis from the 6q21 region that is frequently deleted in gastric cancer

In our search for genomic regions that are involved in the development of gastric cancer, we recently identified a 2-cM minimal region of overlapping heterozygous deletions in 6q16.3-q23.1. Here, we describe an application of the suppression subtraction method (SSH) to search for genes in this small region of the genome, taking advantage of the fact that many human genes present on yeast artificial chromosomes (YACs) are expressed in yeast. Subtraction was performed with two virtually contiguous YACs that cover a region of approximately 2.5 Mb. Combined forward and reversed subtractions resulted in the identification of 12 clones of human origin, all of which could be confirmed by sequence analysis as originating from the 6q21 region. Expression in human tissues could be confirmed by Northern analysis for two of the clones, one of them showing a high level of expression in stomach tissue.

Combinatorial approaches to gene recognition

Recognition of genes via exon assembly approaches leads naturally to the use of dynamic programming. We consider the general graph-theoretical formulation of the exon assembly problem and analyze in detail some specific variants: multicriterial optimization in the case of non-linear gene-scoring functions; context-dependent schemes for scoring exons and related procedures for exon filtering; and highly specific recognition of arbitrary gene segments, oligonucleotide probes and polymerase chain reaction (PCR) primers.

Positional cloning reaches maturity

The identification of genes involved in human genetic disease is no longer the province of those who would make a career of 'not finding' a gene. Developments from the human genome initiative have vastly facilitated the process of localizing genetic intervals segregating mutations, as well as that of obtaining the physical regents necessary for characterizing the region. In a few years' time, efforts aimed at the assignment of genes to the physical map, coupled with increasing quantities of sequence data from both cDNA and genomic sources, will provide numerous candidate genes for analysis, with consequences for the approaches used to define the gene and mutations(s) involved in the disease of interest.

Identifying genes within microdissected genomic DNA: isolation of brain expressed genes from a translocation region associated with inherited mental illness

An improved protocol has been developed for physical enrichment of cDNA sequences by hybridization to genomic DNA. When applied to microdissection recombinants derived from a translocation breakpoint region associated with inherited mental illness, a single cycle of the procedure permitted enriched cDNAs to be visualized directly by agarose gel electrophoresis. Hybridization screening of a library of clones derived from the enriched cDNAs, employing the genomic resource as a probe, led to the identification of six novel gene fragments. This general approach to the isolation of regionally encoded genes could be applied to any subchromosomal interval as a first step towards global transcription map construction.

Cloning mammary cell cDNAs from 17q12-q23 using interspecific somatic cell hybrids and subtractive hybridization

We have cloned human genes that are encoded in the region 17q12-q23 and expressed in breast tissue using interspecific somatic cell hybrids and subtractive hybridization. Two mouse microcell hybrids containing fragments of human chromosome 17 with a nonoverlap region at 17q12-q23 were generated by microcell transfer. Radiolabeled cDNA was synthesized from the hybrid cell containing the 17q12-q23 interval and was subtracted with an excess of RNA from the hybrid cell lacking the interval. Resulting cDNA probes enriched for sequences from 17q12-q23 were used to screen a human premenopausal breast cDNA library, and 60 cDNAs were identified. Three of these cDNAs mapped to the hybrid cell nonoverlap region. These cDNAs were expressed in mammary epithelial cell hybrids, although none appeared to be breast-specific. Sequence analysis of the cDNAs revealed that clone 93A represents a previously unidentified gene, clone 98C has homology to an expressed sequence tag from goat mammary tissue, and clone 200A is identical to the human homologue of the Drosophila melanogaster flightless-I gene. These genes map outside a 1-cM region linked to early onset familial breast cancer but may be useful genetic markers in the 17q12-q23 region.

Towards cloning the familial breast-ovarian cancer gene on chromosome 17

The past year has seen a great deal of excitement in the field of breast cancer genetics. Since linkage of the familial breast-ovarian cancer gene (BRCA1) to chromosome 17, the critical region has been narrowed to 1.0-1.5 Mb by recombination studies, a detailed physical map has been constructed and much of the region has been cloned in yeast artificial chromosome, bacteriophage P1 and cosmid vectors. The focus now lies on identifying the genes housed within the BRCA1 region and scanning them for oncogenic mutations.

Screening cosmid libraries with oligonucleotides corresponding to splice-site consensus sequences

To facilitate the identification of genes within genomic DNA, we have developed a method based on the use of short oligonucleotides designed from the consensus sequences of splice sites. We describe here the hybridization and washing conditions under which such oligonucleotides can be used to screen cosmid libraries. We confirm the presence of genes within cosmids identified by screening with one oligonucleotide by showing that DNA isolated from such cosmids will hybridize to another splice-site oligonucleotide.