title: Whole-exome sequencing of a rare case of familial childhood acute lymphoblastic leukemia reveals putative predisposing mutations in Fanconi anemia genes.
abstract: BACKGROUND
  Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer. While the multi-step model of pediatric leukemogenesis suggests interplay between constitutional and somatic genomes, the role of inherited genetic variability remains largely undescribed. Nonsyndromic familial ALL, although extremely rare, provides the ideal setting to study inherited contributions to ALL. Toward this goal, we sequenced the exomes of a childhood ALL family consisting of mother, father and two non-twinned siblings diagnosed with concordant pre-B hyperdiploid ALL and previously shown to have inherited a rare form of PRDM9, a histone H3 methyltransferase involved in crossing-over at recombination hotspots and Holliday junctions. We postulated that inheritance of additional rare disadvantaging variants in predisposing cancer genes could affect genomic stability and lead to increased risk of hyperdiploid ALL within this family.
  
  
  METHODS
  Whole exomes were captured using Agilent's SureSelect kit and sequenced on the Life Technologies SOLiD System. We applied a data reduction strategy to identify candidate variants shared by both affected siblings. Under a recessive disease model, we focused on rare non-synonymous or frame-shift variants in leukemia predisposing pathways.
  
  
  RESULTS
  Though the family was nonsyndromic, we identified a combination of rare variants in Fanconi anemia (FA) genes FANCP/SLX4 (compound heterozygote - rs137976282/rs79842542) and FANCA (rs61753269) and a rare homozygous variant in the Holliday junction resolvase GEN1 (rs16981869). These variants, predicted to affect protein function, were previously identified in familial breast cancer cases. Based on our in-house database of 369 childhood ALL exomes, the sibs were the only patients to carry this particularly rare combination and only a single hyperdiploid patient was heterozygote at both FANCP/SLX4 positions, while no FANCA variant allele carriers were identified. FANCA is the most commonly mutated gene in FA and is essential for resolving DNA interstrand cross-links during replication. FANCP/SLX4 and GEN1 are involved in the cleavage of Holliday junctions and their mutated forms, in combination with the rare allele of PRDM9, could alter Holliday junction resolution leading to nondisjunction of chromosomes and segregation defects.
  
  
  CONCLUSIONS
  Taken together, these results suggest that concomitant inheritance of rare variants in FANCA, FANCP/SLX4 and GEN1 on the specific genetic background of this familial case, could lead to increased genomic instability, hematopoietic dysfunction, and higher risk of childhood leukemia.
authors.affiliation: Sainte-Justine UHC Research Center, University of Montreal, Montreal, Qc, Canada. jf.spinella@gmail.com.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Spinella
authors.affiliation: Sainte-Justine UHC Research Center, University of Montreal, Montreal, Qc, Canada. jasmine.healy@umontreal.ca.
authors.forename: Jasmine
authors.initials: J
authors.lastname: Healy
authors.affiliation: Sainte-Justine UHC Research Center, University of Montreal, Montreal, Qc, Canada. vr.saillour@gmail.com.
authors.forename: Virginie
authors.initials: V
authors.lastname: Saillour
authors.affiliation: Sainte-Justine UHC Research Center, University of Montreal, Montreal, Qc, Canada. cricher.hsj@gmail.com.
authors.forename: Chantal
authors.initials: C
authors.lastname: Richer
authors.affiliation: Sainte-Justine UHC Research Center, University of Montreal, Montreal, Qc, Canada. cassart.pauline@gmail.com.
authors.forename: Pauline
authors.initials: P
authors.lastname: Cassart
authors.affiliation: Sainte-Justine UHC Research Center, University of Montreal, Montreal, Qc, Canada. manon.ouimet@recherche-ste-justine.qc.ca.
authors.forename: Manon
authors.initials: M
authors.lastname: Ouimet
authors.affiliation: Sainte-Justine UHC Research Center, University of Montreal, Montreal, Qc, Canada. daniel.sinnett@umontreal.ca.|Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Qc, Canada. daniel.sinnett@umontreal.ca.|Division of Hematology-Oncology, Sainte-Justine UHC Research Center, 3175 Côte Ste-Catherine, Montréal (Québec), H3T 1C5, Canada. daniel.sinnett@umontreal.ca.
authors.forename: Daniel
authors.initials: D
authors.lastname: Sinnett
mesh_terms: D000293:Adolescent; D000483:Alleles; D002675:Child, Preschool; D059472:Exome; D051856:Fanconi Anemia Complementation Group Proteins / Q000235:genetics*; D020022:Genetic Predisposition to Disease; D059014:High-Throughput Nucleotide Sequencing; D011495:Histone-Lysine N-Methyltransferase / Q000235:genetics; D006801:Humans; D008297:Male; D009154:Mutation; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D015452:Precursor B-Cell Lymphoblastic Leukemia-Lymphoma / Q000175:diagnosis / Q000235:genetics; D054198:Precursor Cell Lymphoblastic Leukemia-Lymphoma / Q000175:diagnosis / Q000235:genetics*; D035781:Siblings
chemical_list: D051856:Fanconi Anemia Complementation Group Proteins; D011495:Histone-Lysine N-Methyltransferase; C544431:PRDM9 protein, human