Cross-comparison of the genome sequences from human, chimpanzee, Neanderthal and a Denisovan hominin identifies novel potentially compensated mutations

Zhang, Guojie; Pei, Zhang; Ball, Edward V; Mort, Matthew; Kehrer-Sawatzki, Hildegard; Cooper, David N

doi:10.1186/1479-7364-5-5-453

Human Genomics

Table 2 HGMD-derived mutations identified as PCMs in the Denisovan, Neanderthal and/or chimpanzee genomes

From: Cross-comparison of the genome sequences from human, chimpanzee, Neanderthal and a Denisovan hominin identifies novel potentially compensated mutations

	Mutation type and basis of disease aetiology
Mutation/ regulatory type	PCM state	DM	DP	FP	DFP	Total
Coding sequence	Human	5/5	38/43	11/11	17/18	71/77
	Neanderthal	0/0	1/1	0/0	0/0	1/1
	Denisovan	1/1	0/0	0/0	0/0	1/1
	Ancient	0/0	1/1	2/4	0/0	3/5
	Chimpanzee	4/4	7/8	2/4	0/0	13/16
	Denisovan and chimpanzee	3/3	4/5	0/0	0/0	7/8
	Neanderthal and chimpanzee	2/2	4/6	1/1	1/1	8/10
	Others	1/1	0/1	0/0	0/0	1/2
	Total	16/16	55/65	16/20	18/19	105/120
Regulatory	Human	0	23	10	13	46
	Neanderthal	0	0	2	1	3
	Denisovan	0	0	0	3	3
	Ancient	0	2	0	1	3
	Chimpanzee	0	5	5	4	14
	Denisovan and chimpanzee	0	4	1	1	6
	Neanderthal and chimpanzee	0	1	1	0	2
	Others	0	0	0	1	1
	Total	0	35	19	24	78

'Human': The Denisovan nucleotide, Neanderthal nucleotide and chimpanzee nucleotide were identical to a human DM/disease-associated mutation; 'Neanderthal': The Neanderthal nucleotide was identical to the human DM/disease-associated mutation, whereas both the chimpanzee nucleotide and the Denisovan nucleotide were identical to the human wild-type nucleotide; 'Denisovan': The Denisovan nucleotide was identical to the human DM/disease-associated mutation, whereas both the chimpanzee nucleotide and the Neanderthal nucleotide were identical to the human wild-type nucleotide; 'Ancient': Both the Denisovan nucleotide and the Neanderthal nucleotide were identical to the human DM/disease-associated P mutation, whereas the chimpanzee nucleotide was identical to the human wild-type nucleotide. 'Chimpanzee': The chimpanzee nucleotide was identical to the human DM/disease-associated mutation, whereas both the Neanderthal nucleotide and the Denisovan nucleotide were identical to the modern human wild-type nucleotide. 'Denisovan and chimpanzee': Both the Denisovan nucleotide and the chimpanzee nucleotide were identical to the human DM/disease-associated mutation, whereas the Neanderthal nucleotide was identical to the human wild-type nucleotide; 'Neanderthal and chimpanzee': Both the Neanderthal nucleotide and the chimpanzee nucleotide were identical to the human DM/disease-associated mutation, whereas the Denisovan nucleotide was identical to the human wild-type nucleotide. Under coding sequence, 'a/b' means that there were a total number of 'b' mutations, of which 'a' were non-synonymous mutations (there were some synonymous mutations within the coding sequence; eg CM068190, CM077900).
PCM, potentially compensated mutations; DM, disease-causing mutation; DP, disease-associated polymorphism with functional evidence; FP, polymorphism with functional evidence but lacking a reported disease association as yet; DFP, disease-associated polymorphism with functional evidence.

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ISSN: 1479-7364

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