Seven-array set enables rapid resequencing of the entire smallpox genome and can be used to quickly identify a new smallpox strain as well as determine if it has been genetically engineered
Affymetrix has announced the completion of the GeneChip brand smallpox resequencing array set, seven smallpox arrays that will enable rapid resequencing of the entire smallpox genome.
These arrays, developed in collaboration with the Centers for Disease Control and Prevention (CDC), contain genomic sequence common to all strains of smallpox, as well as variant DNA from different smallpox isolates.
The Affymetrix smallpox resequencing array set will be used to identify and catalogue hundreds of different smallpox strains within the World Health Organisation collection maintained at the CDC and will also help researchers differentiate smallpox from other orthopox viruses like monkeypox or cowpox.
The smallpox array set can potentially be used to quickly identify a new smallpox strain as well as determine if a particular strain has been genetically engineered.
The array set may also have clinical applications, such as epidemiological studies and vaccine research.
"This array set joins a growing list of pathogen arrays developed using the CustomSeq array programme, including a Sars virus array and numerous other custom arrays," said Greg Yap, senior marketing director, DNA Analysis.
"Through this programme, researchers can design custom arrays to completely resequence an entire viral organism, such as Sars or smallpox, or design a single array to interrogate unique sequences from multiple pathogens". Pathogen arrays can be used to identify and catalogue outbreaks, as well as to compare patient outcome among different pathogen subtypes.
Such arrays allow scientists to better understand which strains are most dangerous and to discover key factors in developing therapies.
In addition, epidemiologists can use the arrays to study how viruses are evolving over time, during their spread into different geographies and populations.
One CustomSeq array can sequence about 30,000 bases of unique sequence quickly and with a high degree of accuracy.
Compared to capillary methods, CustomSeq arrays make sequencing faster and more effective by delivering completed sequence with minimal assembly and alignment.
Understanding pathogens is one of many CustomSeq array applications.
Other uses of CustomSeq arrays include SNP discovery, comparative sequencing of drug targets and investigation of candidate gene regions.
