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Study suggests that publicly available genome data may contain small but significant errors

heir results and that of the map derived from the public sequence released in 2002. S. pombe's genome is only about 14 million bases long (almost a thousandth of the human genome), and is widely considered to be a gold-standard in whole-genome assembly.

The authors show that with appropriate experimental conditions, array hybridization data can be used to establish a physical distance between unique arrayed probes--a sequence of DNA which in this case was 70 base pairs long. Each of the 70 base pairs is unique in the target organism's genome and serves as a landmark in that genome. These probes can then be ordered in the correct sequence in which they occur in the target genome in much the same way as a mapmaker can locate landmarks at the correct coordinates by consulting a three-dimensional rendering of a geographical map. The distance between pairs of landmarks can be used to assemble physical maps, as an aid to sequence assembly, or as an independent method for validating sequence assembly and indicating where errors need correction.

Comparing data from their inferred probe maps to the available sequence assembly, the new method provides insights into the difficulties of establishing a canonical and accurate sequence or physical map, and suggests ways that the two types of data can be combined to render increased confidence levels of the assembly.

This physical mapping technology is simple to implement and is relatively inexpensive. It is likely to have significant commercial impact through disease-related genetics studies, such as cancer and autism. In addition, it complements other mapping and sequencing technologies (e.g., Optical Mapping and Sequencing being developed by Mishra) and cancer array CGH studies (e.g., ROMA project of Wigler and a versatile cancer genome analysis project of Mishra).


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Source:New York University


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