Development and Role of the Human Reference Sequence in Personal Genomics

A few weeks back, we published a review about the development and role of the human reference genome. A key point of the reference genome is that it is not a single sequence. Instead it is an assembly of consensus sequences that are designed to deal with variation in the human population and uncertainty in the data. The reference is a map and like a geographical maps evolves though increased understanding over time.

From the Wiley On Line site:


Genome maps, like geographical maps, need to be interpreted carefully. Although maps are essential to exploration and navigation they cannot be completely accurate. Humans have been mapping the world for several millennia, but genomes have been mapped and explored for just a single century with the greatest advancements in making a sequence reference map of the human genome possible in the past 30 years. After the deoxyribonucleic acid (DNA) sequence of the human genome was completed in 2003, the reference sequence underwent several improvements and today provides the underlying comparative resource for a multitude genetic assays and biochemical measurements. However, the ability to simplify genetic analysis through a single comprehensive map remains an elusive goal.

Key Concepts:

  • Maps are incomplete and contain errors.

  • DNA sequence data are interpreted through biochemical experiments or comparisons to other DNA sequences.

  • A reference genome sequence is a map that provides the essential coordinate system for annotating the functional regions of the genome and comparing differences between individuals' genomes.

  • The reference genome sequence is always product of understanding at a set point in time and continues to evolve.

  • DNA sequences evolve through duplication and mutation and, as a result, contain many repeated sequences of different sizes, which complicates data analysis.

  • DNA sequence variation happens on large and small scales with respect to the lengths of the DNA differences to include single base changes, insertions, deletions, duplications and rearrangements.

  • DNA sequences within the human population undergo continual change and vary highly between individuals.

  • The current reference genome sequence is a collection of sequences, an assembly, that include sequences assembled into chromosomes, sequences that are part of structurally complex regions that cannot be assembled, patches (fixes) that cannot be included in the primary sequence, and high variability sequences that are organised into alternate loci.

  • Genetic analysis is error prone and the data require validation because the methods for collecting DNA sequences create artifacts and the reference sequence used for comparative analyses is incomplete.

More like this

"Come quickly, Watson," said Sherlock Holmes, "I've been asked to review a mysterious sequence, whose importance I'm only now beginning to comprehend." The unidentified stranger handed Holmes a piece of paper inscribed with symbols and said it was a map of unparalleled value. Holmes gazed…
Nature Genetics is asking: What would you do if it became possible to sequence the equivalent of a full human genome for only $1,000? George Church would repeat the Applera dataset for everyone on earth, sequencing every exon from every human being. Francis Collins would sequence people with…
In which I present a quick guide for the omically challenged and a defense of 'arth and "ome." Other SciBloggers have shared their thoughts on the use of ome here and here. Sometimes I get frustrated too, with the way language is abused and tweaked by those around me. So many word pairs that once…
In our series on why $1000 genomes cost $2000, I raised the issue that the $1000 genome is a value based on simplistic calculations that do not account for the costs of confirming the results. Next, I discussed how errors are a natural occurrence of the many processing steps required to sequence…