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

Table 3 HGMD-derived mutations identified as PCMs in the Denisovan genome and/or chimpanzee genome

	Mutation type and basis of disease aetiology
Mutation/ regulatory type	PCM state	DM	DP	FP	DFP	Total
Coding sequence	Ancestral	5/5	24/29	9/9	5/7	43/50
	Derived	4/4	7/7	4/5	4/4	19/20
	Denisovan	0/0	4/6	2/2	0/0	6/8
	Others	0/0	1/1	0/0	0/0	1/1
	Total	9/9	36/43	15/16	9/11	69/79
Regulatory	Ancestral	2	6	9	12	29
	Derived	1	2	1	2	6
	Denisovan	0	1	0	2	3
	Total	3	9	10	16	38

Ancestral: Both the Denisovan nucleotide and the chimpanzee nucleotide were identical to the human DM/disease-associated mutation; Derived: The chimpanzee nucleotide was identical to the human DM/disease-associated mutation, whereas the Denisovan nucleotide was identical to the human wild-type nucleotide; Denisovan: The Denisovan nucleotide was identical to the human DM/disease-associated mutation, whereas the chimpanzee nucleotide was identical to the human wild-type nucleotide. Under coding sequence, 'a/b' means there were a total number of 'b' mutations, of which 'a' were non- synonymous mutations.
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.

ISSN: 1479-7364