Human genome needs fixing

Researchers have discovered 2,363 new DNA sequences corresponding to 730 regions on the human genome that were not charted in the reference map produced to date.

"A large portion of those sequences are either missing, fragmented or misaligned when compared to results from next-generation sequencing genome assemblies on the same samples," said Dr Evan Eichler, from the University of Washington (UW) and senior author on the findings published April 19 in the advanced online edition of Nature Methods.

"These findings suggest that new genome assemblies based solely on next-generation sequencing might miss many of these sites."

Dr Jeffrey Kidd, now a postdoctoral fellow at Stanford University, was lead author of the article, which describes the new techniques the research team used to find some of the missing sequences.

"Over the past several years, the extent to which the structure of the genome varies among humans has become clearer. This variation suggested that there must be portions of the human genome where DNA sequences had yet to be discovered, annotated and characterised," he said.

"We hope that these sequences ultimately will be included as part of future releases of the reference human genome sequence."

The reference genome is a yardstick – or standard for comparison – for studies of human genetics.

The human reference genome was first created in 2001 and is updated every couple of years. It's a mosaic of DNA sequences derived from several individuals. About 80 per cent of the reference genome came from eight people. One of them actually accounts for more than 66 percent of the total.

Along with their collaborators at Agilent, the team designed ways to examine these newly identified sequences in a panel of people representing populations from around the world. The researchers found that, in some cases, the number of copies of these sequences varied from person to person.

The fact that a person can have one or more copies, or no copy at all, of a particular DNA sequence may account for why these sequences were missing from the reference genome. The researchers also found that some of these sequences were common or rare in different populations, depending on from which part of the globe their ancestors originated.

"Each segment of the reference genome is from a single person, and reflects the genome of that individual. If the donor sample was missing a sequence that many other people have, that sequence would not be represented in the reference genome," Kidd said.

"That is why some of the positions on the reference genome represent rare structural configurations or entirely omit sequences found in the majority of people."

Kidd said that the study used information from nine individuals, representing various world populations, to search for and fill in some of the missing pieces.

By looking at genomes from seven kinds of animals, the researchers were also able to show that some of the newly identified DNA sequences appear to have been conserved during the evolution of mammals and man. The animals whose genomes were studied were chimpanzee, Bornean orangutan, Rhesus monkey, house mouse, Norway rat, dog and horse.

"Some of the sequences were present in several different species, but were absent from the reference genome," Kidd said.

"Some of the sequences present in several mammals actually correspond to sites of variations in humans – some people have retained a particular sequence, and others have lost it."

The researchers also developed a method to accurately genotype many of the newly found DNA sequences and created a way to look at variations in the number of copies of these sequences, thereby opening up regions of the human genome previously inaccessible to such studies.

"Scientists can now begin trying to understand the functional importance of these sequences and their variations," Kidd said.

The 1,000 Genomes Project and other genome studies are amassing massive amounts of data on DNA sequences that are then mapped to the reference genome, he added. Any study, he continued, that improves the completeness and quality of the reference genome assembly will thereby benefit these projects and lead to a fuller picture of the extent of human genomic variation.

The findings are published as "Characterization of missing human genome sequences and copy-number polymorphic insertions", in Nature Methods (DOI 10.1038/nmeth.1451).