Ancient human genome sequence of an extinct Palaeo-Eskimo

Abstract

We report here the genome sequence of an ancient human. Obtained from ∼4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20×, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing

“…Deamination-based damage, as the most common modification in ancient DNA 5,6 , potentially complicates correct identification of base substitutions that result from evolutionary processes. The sequencing of a 4,000-year-old palaeo-eskimo's DNA sequence demonstrated that exclusion of postmortem, damage-based changes had little impact on the high-throughput sequencing result 5 .…”

“…The sequencing of a 4,000-year-old palaeo-eskimo's DNA sequence demonstrated that exclusion of postmortem, damage-based changes had little impact on the high-throughput sequencing result 5 . However, to estimate the extent of miscoding lesions (that is, postmortem changes in DNA), we determined the transition and transversion ratios (Supplementary Table S2 and Supplementary Table S3) and found them to be largely consistent with ratios observed for other genomes recently analysed by high-throughput sequencing.…”

Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing

“…Another commonly used approach is to apply quality filters that are aimed at selectively removing errors. Every whole-genome sequence reported so far has used filtering to some extent: the most commonly used filters being those that remove sequences with a too-low coverage depth, discard variants with a low-confidence score or eliminate variants located within a cluster of variants 3,7,[10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25] . Surprisingly, there is little consensus with respect to which filters should be used and at which threshold they should be applied.…”

Human genome at ten: The sequence explosion

“…G r e e n p l a n t s Metagenomes (multiple species) P r o t o z o a N o n -h u m a n v e r t e b r a t e s H u m a n s I n v e r t e b r a t e s First drafts of two composite haploid human genomes 1,2 Human Genome Project completed 3 Two Korean males including Seong-Jin Kim 9,10 , Stephen Quake 11 , another cancer genome 12 , George Church, a Yoruban female, another male 13 , and four others [14][15][16] A glioma cell line 17 , Inuk 18 , !Gubi and Archbishop Desmond Tutu 19 , James Lupski 20 , and a family of four 21 James Watson 5 , a woman with acute myeloid leukemia 6 , a Yoruba male from Nigeria 7 and the first Asian genome 8…”