Haplotype Counting for Sensitive Chimerism Testing: Potential for Early Leukemia Relapse Detection

Marija Debeljak, Evelina Mocci, Max C. Morrison, Aparna Pallavajjalla, Katie Beierl, Marie Amiel, Michaël Noë, Laura D. Wood, Ming Tseh Lin, Christopher D. Gocke, Alison P. Klein, Ephraim J. Fuchs, Richard J. Jones, James R. Eshleman

Research output: Research - peer-reviewArticle

Abstract

Fields of forensics, transplantation, and paternity rely on human identity testing. Currently, this is accomplished through amplification of microsatellites followed by capillary electrophoresis. An alternative and theoretically better approach uses multiple single-nucleotide polymorphisms located within a small region of DNA, a method we initially developed using HLA-A and called haplotype counting. Herein, we validated seven additional polymorphic loci, sequenced a total of 45 individuals from three of the 1000 Genomes populations (15 from each), and determined the number of haplotypes, heterozygosity, and polymorphic information content for each locus. In addition, we developed a multiplex PCR that amplifies five of these loci simultaneously. Using this strategy with a small cohort of leukemic patients who underwent allogeneic bone marrow transplantation, we first attempted to define a threshold (0.26% recipient) by examining seven patients who tested all donor and did not relapse. Although this initial threshold will need to be confirmed in a larger cohort, we detected increased recipient DNA above this threshold 90 to 145 days earlier than microsatellite positivity, and 127 to 142 days before clinical relapse in four of eight patients (50%). Haplotype counting using these novel loci may be useful for ultrasensitive detection in fields such as bone marrow transplantation, solid organ transplant rejection, patient identification, and forensics.

LanguageEnglish (US)
Pages427-436
Number of pages10
JournalJournal of Molecular Diagnostics
Volume19
Issue number3
DOIs
StatePublished - May 1 2017

Fingerprint

Chimerism
Haplotypes
Leukemia
Recurrence
Bone Marrow Transplantation
Microsatellite Repeats
DNA
Paternity
HLA-A Antigens
Multiplex Polymerase Chain Reaction
Homologous Transplantation
Capillary Electrophoresis
Graft Rejection
Single Nucleotide Polymorphism
Transplantation
Tissue Donors
Genome
Transplants
Population

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Molecular Medicine

Cite this

Haplotype Counting for Sensitive Chimerism Testing : Potential for Early Leukemia Relapse Detection. / Debeljak, Marija; Mocci, Evelina; Morrison, Max C.; Pallavajjalla, Aparna; Beierl, Katie; Amiel, Marie; Noë, Michaël; Wood, Laura D.; Lin, Ming Tseh; Gocke, Christopher D.; Klein, Alison P.; Fuchs, Ephraim J.; Jones, Richard J.; Eshleman, James R.

In: Journal of Molecular Diagnostics, Vol. 19, No. 3, 01.05.2017, p. 427-436.

Research output: Research - peer-reviewArticle

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