title: Quantitative shearing linear amplification polymerase chain reaction: an improved method for quantifying lentiviral vector insertion sites in transplanted hematopoietic cell systems.
abstract: In gene therapy trials targeting blood disorders, it is important to detect dominance of transduced hematopoietic stem cell (HSC) clones arising from vector insertion site (VIS) effects. Current methods for VIS analysis often do not have defined levels of quantitative accuracy and therefore can fail to detect early clonal dominance. We have developed a rapid and inexpensive method for measuring clone size based on random shearing of genomic DNA, minimal exponential PCR amplification, and shear site counts as a quantitative endpoint. This quantitative shearing linear amplification PCR (qsLAM PCR) assay utilizes an internal control sample containing 19 lentiviral insertion sites per cell that is mixed with polyclonal samples derived from transduced human CD34+ cells. Samples were analyzed from transplanted pigtail macaques and from a participant in our X-linked severe combined immunodeficiency (XSCID) lentiviral vector trial and yielded controlled and quantitative results in all cases. One case of early clonal dominance was detected in a monkey transplanted with limiting numbers of transduced HSCs, while the clinical samples from the XSCID trial participant showed highly diverse clonal representation. These studies demonstrate that qsLAM PCR is a facile and quantitative assay for measuring clonal repertoires in subjects enrolled in human gene therapy trials using lentiviral-transduced HSCs.
authors.affiliation: 1 Division of Experimental Hematology, Department of Hematology, St. Jude Children's Research Hospital , Memphis, TN 38120.
authors.forename: Sheng
authors.initials: S
authors.lastname: Zhou
authors.forename: Melissa A
authors.initials: MA
authors.lastname: Bonner
authors.forename: Yong-Dong
authors.initials: YD
authors.lastname: Wang
authors.forename: Samuel
authors.initials: S
authors.lastname: Rapp
authors.forename: Suk See
authors.initials: SS
authors.lastname: De Ravin
authors.forename: Harry L
authors.initials: HL
authors.lastname: Malech
authors.forename: Brian P
authors.initials: BP
authors.lastname: Sorrentino
mesh_terms: D000818:Animals; D018390:Gene Targeting / Q000379:methods*; D015316:Genetic Therapy / Q000379:methods*; D005822:Genetic Vectors / Q000235:genetics; D057809:HEK293 Cells; D018380:Hematopoietic Stem Cell Transplantation / Q000379:methods*; D006801:Humans; D019169:Jurkat Cells; D016086:Lentivirus / Q000235:genetics*; D008254:Macaca nemestrina; D016133:Polymerase Chain Reaction / Q000379:methods*; D053632:X-Linked Combined Immunodeficiency Diseases / Q000628:therapy*; D055815:Young Adult