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Perspective

Comparing the human and chimpanzee genomes: Searching for needles in a haystack

Glycobiology Research and Training Center, Departments of Medicine and Cellular & Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA

The chimpanzee genome sequence is a long-awaited milestone, providing opportunities to explore primate evolution and genetic contributions to human physiology and disease. Humans and chimpanzees shared a common ancestor 5-7 million years ago (Mya). The difference between the two genomes is actually not 1%, but 4%—comprising 35 million single nucleotide differences and 90 Mb of insertions and deletions. The challenge is to identify the many evolutionarily, physiologically, and biomedically important differences scattered throughout these genomes while integrating these data with emerging knowledge about the corresponding "phenomes" and the relevant environmental influences. It is logical to tackle the genetic aspects via both genome-wide analyses and candidate gene studies. Genome-wide surveys could eliminate the majority of genomic sequence differences from consideration, while simultaneously identifying potential targets of opportunity. Meanwhile, candidate gene approaches can be based on such genomic surveys, on genes that may contribute to known differences in phenotypes or disease incidence/severity, or on mutations in the human population that impact unique aspects of the human condition. These two approaches will intersect at many levels and should be considered complementary. We also cite some known genetic differences between humans and great apes, realizing that these likely represent only the tip of the iceberg.

Reich, D.E., Lander, E.S., Waterston, R., Pääbo, S., Ruvolo, M., and Varki, A. 2002. Sequencing the chimpanzee genome (white paper submitted to NHGRI, February 2002).

¹ Corresponding author.
E-mail a1varki{at}ucsd.edu; fax (858) 534-5611.

² The term "great apes" is used here in the now colloquial sense, as genomic information no longer supports this species grouping (Goodman 1999). Under the currently more common classification, these species are now grouped together with humans in the family Hominidae.

³ The term "phenome" has been used in multiple publications (e.g., Mahner and Kary 1997; Varki et al. 1998; Paigen and Eppig 2000; Nevo 2001; Walhout et al. 2002; Freimer and Sabatti 2003), but still lacks an accepted definition. Discussions with researchers who have used the term suggest the following definition: "The body of information describing an organism's phenotypes, under the influences of genetic and environmental factors."

⁴ Olson, M.V., Eichler, E.E., Varki, A., Myers, R.M., Erwin, J.M., and McConkey, E.H.A. 2002. White paper advocating complete sequencing of the genome of the common chimpanzee, Pan troglodytes (white paper submitted to NHGRI, February 2002).

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