Leland Stanford Junior University

Sujatha Krishnakumar

Ronald W Davis

Michael Nicholas Mindrinos

Mark M Davis

Chunlin Wang

Peidong Shen

Curt Scharfe

Methods are provided to determine the entire genomic region of a particular HLA locus including both intron and exons. The resultant consensus sequences provides linkage information between different exons, and produces the unique sequence from each of the two genes from the individual sample being typed. The sequence information in intron regions along with the exon sequences provides an accurate HLA haplotype.

Haplotying of HLA loci with ultra-deep shotgun sequencing

A method for producing a single stranded DNA (ssDNA) molecule of a defined length and sequence is disclosed. This method enables the preparation of, inter alia, probes of greater length than can be chemically synthesized. The method starts with a double stranded molecule, such as genomic, double stranded DNA (dsDNA) from any organism. A fragment of the starting molecule (dsDNA) is amplified by specific primers engineered to introduce cleavage sites on either side of the desired sequence. Cleavage steps on the amplified, engineered fragment are combined with a phosphate removal step, thereby creating a construct that can be digested with an exonuclease without damage to the desired ssDNA. Probes, which hybridize with large gaps between the ends of the probes, are also disclosed.

Method to produce DNA of defined length and sequence and DNA probes produced thereby

Method to produce single stranded DNA of defined length and sequence and DNA probes produced thereby

Growing community of inventors

Palo Alto, CA, United States of America

Sujatha Krishnakumar