Human Genome Quality Assessment

The goal of the Human Genome Project (HGP) was to produce a sequence of human DNA that was of sufficiently high accuracy and long-range contiguity to allow a full interpretation of all the information encoded in the human genome, and that will stand the test of time. The HGP sequencing effort had also adopted an intermediate product for human genomic sequence termed "working draft" sequence because, although it cannot be used for all conceivable methods of DNA analysis, draft quality sequence can be very useful in identifying a number of features in DNA, e.g. coding sequences and repeats.

In establishing different sequence "products," it was also important to develop quality standards appropriate to each. In addition, some of the quality standards that had been developed were specific for the particular strategy employed in generating the sequence data. As different strategies were implemented to improve large-scale DNA sequencing (for example, for future target genomes), it was likely that additional or different quality standards would need to be developed.

The first quality assessment of human working draft sequence was conducted in November of 1999. The finished sequence produced by the three largest NHGRI-funded sequencing centres was evaluated. Trace files were transferred from their 10 most recent projects to Dr. Richard Myers and Jeremy Schmutz at the SHGC for re-assembly and assessment against the coverage standard established for human working draft sequence. Read data quality and assembly was also assessed (even though no standards for these had been established). In all cases, the submitted data met or exceeded standards. 

The HGP regularly revisits quality standards to ensure that they remain relevant to the overall sequencing program.

For more information on Human Genome Quality Assessment, you can download the following journal publications:

• Schmutz J, Wheeler J, Grimwood J, Dickson M, Myers RM. "Assessing the Quality of Finished Genomic Sequence." Cold Spring Harbor Symposia on Quantative Biology.  Vol. 68: Cold Spring Harbor Laboratory Press, 2003. 31-7.(PDF)
• Schmutz J, Wheeler J, Grimwood J, Dickson M, Yang J, Caoile C, Bajorek E, Black S, Chan YM, Denys M, Escobar J, Flowers D, Fotopulos D, Garcia C, Gomez M, Gonzales E, Haydu L, Lopez F, Ramirez L, Retterer J, Rodriguez A, Rogers S, Salazar A, Tsai M, Myers RM. (2004). Quality assessment of the human genome sequence. Nature. 429(6990):365-8. (PDF)