Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels

Britten, Roy J.

doi:10.1073/pnas.172510699

Cited by 265 publications

(157 citation statements)

References 14 publications

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“…(The latter criterion corresponds to resolvable ambiguities in two-array designs, see §3.3.) We found that 1543 (74%) of the reads were informative, in accordance with the table above given that the divergence between human and chimpanzee genomes is 5% (Britten 2002), and we corrupted the shotgun sequences with an additional 1% error. We further analyzed the matches to see if this ratio of "informative reads" is uniform across clones.…”

Section: Closely Related Speciessupporting

confidence: 82%

Pooled Genomic Indexing (PGI): Analysis and Design of Experiments

Csűrös

Milosavljevic

2004

Journal of Computational Biology

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Pooled Genomic Indexing (PGI) is a novel method for physical mapping of clones onto known sequences. PGI is carried out by pooling arrayed clones, and generating shotgun sequence reads from the pools. The shotgun sequences are compared to a reference sequence. In the simplest case clones are placed on an array and are pooled by rows and columns. If a shotgun sequence from a row pool and another shotgun sequence from a column pool match the reference sequence at a close distance, they are both assigned to the clone at the intersection of the two pools. Accordingly, the clone is mapped onto the region of the reference sequence between the two matches. A probabilistic model for PGI is developed, and several pooling designs are described and analyzed, including transversal designs and designs from linear codes. The probabilistic model and the pooling schemes are validated in simulated experiments where 625 rat BAC clones and 207 mouse BAC clones are mapped onto homologous human sequence.

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Section: Closely Related Speciessupporting

confidence: 82%

Pooled Genomic Indexing (PGI): Analysis and Design of Experiments

Csűrös

Milosavljevic

2004

Journal of Computational Biology

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“…Humans are ∼98.8% similar to chimpanzees at the nucleotide level 20 and are considerably more similar to each other, differing on average at only 1 of every 500-1,000 nucleotides between chromosomes 21,22 . This degree of diversity is less than what typically exists among chimpanzees [23][24][25] .…”

Section: Amounts Of Genetic Variationmentioning

confidence: 96%

Implications of biogeography of human populations for 'race' and medicine

2004

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In this review, we focus on the biogeographical distribution of genetic variation and address whether or not populations cluster according to the popular concept of 'race'. We show that racial classifications are inadequate descriptors of the distribution of genetic variation in our species. Although populations do cluster by broad geographic regions, which generally correspond to socially recognized races, the distribution of genetic variation is quasicontinuous in clinal patterns related to geography. The broad global pattern reflects the accumulation of genetic drift associated with a recent African origin of modern humans, followed by expansion out of Africa and across the rest of the globe. Because disease genes may be geographically restricted due to mutation, genetic drift, migration and natural selection, knowledge of individual ancestry will be important for biomedical studies. Identifiers based on race will often be insufficient.

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“…Estimates of nucleotide substitution rates of aligned sequences range from 1.23% by bacterial artificial chromosome (BAC) end sequencing 3 to about 2% by molecular analysis 1,[6][7][8] , whereas the overall sequence difference was estimated to be approximately 5% by taking regions of insertions or deletions (indels) into account 9 . Chromosomal rearrangements including duplications, translocations and transpositions have also been identified 10,11 .…”

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confidence: 99%

DNA sequence and comparative analysis of chimpanzee chromosome 22

Watanabe

Fujiyama²,

Hattori³

et al. 2004

Nature

207

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Human–chimpanzee comparative genome research is essential for narrowing down genetic changes involved in the acquisition of unique human features, such as highly developed cognitive functions, bipedalism or the use of complex language. Here, we report the high-quality DNA sequence of 33.3 megabases of chimpanzee chromosome 22. By comparing the whole sequence with the human counterpart, chromosome 21, we found that 1.44% of the chromosome consists of single-base substitutions in addition to nearly 68,000 insertions or deletions. These differences are sufficient to generate changes in most of the proteins. Indeed, 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level. Furthermore, we demonstrate different expansion of particular subfamilies of retrotransposons between the lineages, suggesting different impacts of retrotranspositions on human and chimpanzee evolution. The genomic changes after speciation and their biological consequences seem more complex than originally hypothesized

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Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels

Cited by 265 publications

References 14 publications

Pooled Genomic Indexing (PGI): Analysis and Design of Experiments

Pooled Genomic Indexing (PGI): Analysis and Design of Experiments

Implications of biogeography of human populations for 'race' and medicine

DNA sequence and comparative analysis of chimpanzee chromosome 22

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