title: A Quantitative Analysis of Subclonal and Clonal Gene Mutations before and after Therapy in Chronic Lymphocytic Leukemia.
abstract: OBJECTIVE
  Chronic lymphocytic leukemia (CLL)-associated gene mutations that influence CLL cell fitness and chemotherapy resistance should increase in clonal representation when measured before therapy and at relapse.
  
  
  METHODS
  To uncover mutations associated with CLL relapse, we have performed whole-exome sequencing in a discovery cohort of 61 relapsed CLL patients identifying 86 recurrently mutated genes. The variant allele fractions (VAF) of 19 genes with mutations in ≥3 of 61 cases were measured in 53 paired pre- and posttreatment CLL samples sorted to purity using panel-based deep resequencing or by droplet digital PCR.
  
  
  RESULTS
  We identify mutations in TP53 as the dominant subclonal gene driver of relapsed CLL often demonstrating substantial increases in VAFs. Subclonal mutations in SAMHD1 also recurrently demonstrated increased VAFs at relapse. Mutations in ATP10A, FAT3, FAM50A, and MGA, although infrequent, demonstrated enrichment in ≥2 cases each. In contrast, mutations in NOTCH1, SF3B1, POT1, FBXW7, MYD88, NXF1, XPO1, ZMYM3, or CHD2 were predominantly already clonal prior to therapy indicative of a pretreatment pathogenetic driver role in CLL. Quantitative analyses of clonal dynamics uncover rising, stable, and falling clones and subclones without clear evidence that gene mutations other than in TP53 and possibly SAMHD1 are frequently selected for at CLL relapse.
  
  
  CONCLUSIONS
  Data in aggregate support a provisional categorization of CLL-associated recurrently mutated genes into three classes (i) often subclonal before therapy and strongly enriched after therapy, or, (ii) mostly clonal before therapy or without further enrichments at relapse, or, (iii) subclonal before and after therapy and enriching only in sporadic cases. Clin Cancer Res; 22(17); 4525-35. ©2016 AACR.
authors.affiliation: Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.
authors.forename: Nisar A
authors.initials: NA
authors.lastname: Amin
authors.affiliation: Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.
authors.forename: Erlene
authors.initials: E
authors.lastname: Seymour
authors.affiliation: Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.
authors.forename: Kamlai
authors.initials: K
authors.lastname: Saiya-Cork
authors.affiliation: Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.
authors.forename: Brian
authors.initials: B
authors.lastname: Parkin
authors.affiliation: Division of Statistics, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.
authors.forename: Kerby
authors.initials: K
authors.lastname: Shedden
authors.affiliation: Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan. smalek@med.umich.edu.
authors.forename: Sami N
authors.initials: SN
authors.lastname: Malek
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000483:Alleles; D014408:Biomarkers, Tumor; D060965:Clonal Evolution / Q000235:genetics*; D018450:Disease Progression; D005260:Female; D006801:Humans; D015451:Leukemia, Lymphocytic, Chronic, B-Cell / Q000188:drug therapy / Q000235:genetics* / Q000473:pathology; D008297:Male; D008875:Middle Aged; D009154:Mutation; D009367:Neoplasm Staging; D011379:Prognosis; D000073359:Exome Sequencing
chemical_list: D014408:Biomarkers, Tumor