Deep sequencing undoes gene knot

Researchers are using high-throughput sequencing technology in high-resolution human leukocyte antigen genotyping. In a study, researchers performed ultra-deep amplicon sequencing--using technology from Roche company 454 Life Sciences--of specific HLA class I and II gene loci with the Genome Sequencer FLX System. They successfully assigned allele-level genotypes using software developed by Conexio Genomics.

The effort is expected to aid in human disease treatment and tissue transplantation efforts.

The typing of the HLA genes, which play a role in the adaptive immune response, is complicated by their polymorphic nature. "The challenge is to determine which polymorphic sequences go together on which alleles," says Henry Erlich of Roche Molecular Systems, in an announcement. "We were able to assign allele-level HLA genotypes at eight loci in 48 samples from the data produced in a single Genome Sequencer FLX System run."

He says the long sequencing reads yielded no ambiguity in assigning HLA alleles in a process that is faster and more cost efficient than traditional technologies. "We were also able to detect rare variants, such as the non-transmitted maternal allele in a SCIDS [Severe Combined Immunodeficiency Syndrome] sample, reflecting the presence of maternal cells in the subject's circulation."

- here's the announcement

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