The DNA sequence and analysis of human chromosome 13

Genomics, 1998

cate that this is a gene-rich region of the human genome. ᭧ 1998 Academic Press Despite the localization of several human diseases to 11q13, the majority of the genes responsible for these disorders have not yet been cloned. Exon amplification and EST mapping were performed using INTRODUCTION clones derived from an Ç1.65-Mb P1 artificial chromosome contig encompassing the region that reportedly Transcription maps facilitate faster positional clonharbors the gene mutated in the dominantly inherited ing of disease genes (Collins, 1995). These maps are eye disorder, Best disease. Fifty-eight exons isolated being constructed either at a relatively low resolution from the region were sequenced, resulting in 41.3% by the systematic mapping of expressed sequence tags showing weak or no similarity to database sequences. (ESTs) in the whole genome or at a higher resolution by Four exons had exact matches with human ESTs and positional cloning projects. While the high-resolution 2 exons were highly similar to mouse ESTs. The seapproaches are costly and laborious, they produce more quence of 1 of these human ESTs was highly similar to detailed maps, providing information on region-specific that of the rat Rabin3 and mouse Pat-12 genes, which gene density and transcript orientation, and at the inpotentially encode Ras-like GTPase binding proteins. dividual gene level they provide information regarding Three exon sequences were similar to those of the inexpression pattern and evolutionary conservation. ner centromere proteins of Gallus gallus and Xenopus Gene identification from large genomic regions can be laevis, which are mitotic phosphoproteins, and 1 exon a rate-limiting step in such positional cloning projects. sequence had similarity to the epidermal growth fac-To overcome this obstacle a number of techniques pretor-like repeat from several proteins. High-resolution sented below are being utilized. mapping of 34 ESTs binned to the 11q12-q13 region by the Human Transcript Mapping Project identified Although direct hybridization to arrayed cDNA li-5 present in the PAC contig, with 1 of these ESTs iden-braries and identification of genomic fragments showtifying a human homologue of the rat synaptotagmin ing cross-species sequence conservation have been used VII gene. Database searches identified two overlapsuccessfully to identify disease genes (Monaco et al., ping cDNA clones representing almost the entire open 1986; Rommens et al., 1989), they have now been superreading frame of this human gene and a sequenced seded by more efficient and less laborious techniques cosmid indicating its partial genomic structure. Fursuch as cDNA selection and exon trapping (Lovett et ther database analyses identified another sequenced al., 1991; Parimoo et al., 1991; Buckler et al., 1991; cosmid from this region that contained both exon-Church et al., 1994). These methodologies have retrap and mapped EST sequences. PowerBLAST and sulted in the accelerated discovery of disease genes GRAIL analysis of this cosmid sequence identified from large genomic regions (Derry et al., 1994; Miki matches with several other ESTs, the previously deet al., 1994; The Huntington's Disease Collaborative scribed FEN1 gene, and a novel evolutionarily con-Research Group, 1993; The Treacher Collins Syndrome served gene. These experiments identify candidate Collaborative Group, 1996). genes for disorders that map to this region and indi-More recently, gene identification has resulted from the need to analyze large-scale genomic sequence and 1 To whom correspondence should be addressed at the Department to predict positions of potential coding regions. Comof Human Genetics, Roswell Park Cancer Institute, Elm & Carlton puter-based gene prediction programs such as Genota

Genomics, 1998

affected families using polymorphic markers (Schuler We have assembled a high-resolution physical map et al., 1996). Useful in this regard are framework maps of human chromosome 13 DNA (Ç114 Mb) from hybridconstructed by sequence-tagged site (STS) content ization, PCR, and FISH mapping data using a specifianalysis of yeast artificial chromosomes (YACs) and cally designed set of computer programs. Although the radiation hybrids and further annotated with addimapping of 13p is limited, 13q (Ç98 Mb) is covered by tional markers, including expressed sequences (Chuan almost continuous contig of 736 YACs aligned to 597 makov et al., 1992; contigs of cosmids. Of a total of 10,789 cosmids initially . Howselected from a chromosome 13-specific cosmid library ever, the resolution of such maps is not always high, (16,896 colonies) using inter-Alu PCR probes from the and they do not provide direct substrates for DNA se-YACs and probes for markers mapped to chromosome quencing (Green et al., 1991; Cox et al., 1994; Kouprina 13, 5111 were assembled in contigs that were estab- lished from cross-hybridization relationships between Bouffard et al., 1997). Finer maps providing sequencethe cosmids. The 13q YAC-cosmid map was annotated ready reagents and also circumventing the potential with 655 sequence tagged sites (STSs) with an average imprecision of STS-based YAC contigs, due to internal spacing of 1 STS per 150 kb. This set of STSs, each deletions, chimerism, and rearrangements of YAC identified by a D number and cytogenetic location, inclones, can be assembled using cosmids, PACs, and cludes database markers (198), expressed sequence BACs (Shizuya et al., 1992; Ioannou et al., 1994). Using tags (93), and STSs generated by sequencing of the this approach, high-resolution (õ100 kb), annotated ends of cosmid inserts (364). Additional annotation has physical maps have been constructed, for example, for been provided by positioning 197 cosmids mapped by chromosomes 16, 19, 21, and 22 and for selected seg-FISH on 13q. The final (comprehensive) map, a list of STS primers, and raw data used in map assembly are ments of chromosome 13 (Doggett et al., 1995; Ashavailable at our Web site (genome1.ccc.columbia.edu/ worth et al., 1995a,b; Kim et al., Çgenome/) and can serve as a resource to facilitate Schutte et al., 1995; Fiaccurate localization of additional markers, provide scher et al., 1996;.

Nature, 2006

Human chromosome 12 contains more than 1,400 coding genes 1 and 487 loci that have been directly implicated in human disease 2 . The q arm of chromosome 12 contains one of the largest blocks of linkage disequilibrium found in the human genome 3 . Here we present the ...