Gene Index analysis of the human genome estimates approximately 120,000 genes

Although sequencing of the human genome will soon be completed, gene identification and annotation remains a challenge. Early estimates suggested that there might be 60,000‐100,000 (ref. 1) human genes, but recent analyses of the available data from EST sequencing projects have estimated as few as 45,000 (ref. 2) or as many as 140,000 (ref. 3) distinct genes. The Chromosome 22 Sequencing Consortium estimated a minimum of 45,000 genes based on their annotation of the complete chromosome, although their data suggests there may be additional genes 4 . The nearly 2,000,000 human ESTs in dbEST provide an important resource for gene identification and genome annotation, but these single-pass sequences must be carefully analysed to remove contaminating sequences, including those from genomic DNA, spurious transcription, and vector and bacterial sequences. We have developed a highly refined and rigorously tested protocol for cleaning, clustering and assembling EST sequences to produce high-fidelity consensus sequences for the represented genes (F.L. et al., manuscript submitted) and used this to create the TIGR Gene Indices5─databases of expressed genes for human, mouse, rat and other species (http://www.tigr.org/tdb/tgi.html). Using highly refined and tested algorithms for EST analysis, we have arrived at two independent estimates indicating the human genome contains approximately 120,000 genes. To assemble the Human Gene Index (HGI 5.0), we began with 1,610,947 EST sequences downloaded from the dbEST division of GenBank. These were ‘cleaned’ to remove contaminating sequences (see Methods, http://genetics.nature.com/supplementary_info), which eliminated 82,228 ESTs (5.1%) containing mitochondrial, ribosomal, vector, adaptor and bacterial sequences. We included 54,506 human gene sequences: 47,283 human transcripts (NP sequences) parsed through Entrez from CDS and CDS-join features in GenBank records; and 7,223 curated expressed transcript (ET) sequences from the TIGR expressed gene anatomy database (EGAD; http://www.tigr.org/ tdb/egad/egad.html).