Hypodiploid ALL (St. Jude, Nature Genetics 2013)

Overview

A St. Jude Children’s Research Hospital cohort of 124 pediatric hypodiploid acute lymphoblastic leukemia (ALL) cases profiled by whole-genome sequencing, whole-exome sequencing, SNP microarray copy number profiling, and gene expression arrays. The study defined two genetically and clinically distinct subtypes: near haploid ALL (24–31 chromosomes) and low hypodiploid ALL (32–39 chromosomes). dbGaP accession: phs000341.v1.p1.

Composition

• 124 pediatric hypodiploid ALL cases: 50 near haploid, 26 low hypodiploid, 18 masked hypodiploid, 22 near diploid, plus 8 masked low hypodiploid.
• Additional adult ALL cohort of 117 cases including 11 low hypodiploid cases.
• Matched remission DNA available for 89 cases.
• Cancer type: BLL.

Assays / panels (linked)

• Whole-genome sequencing — 20 cases (11 near haploid, 9 low hypodiploid).
• Whole-exome sequencing — 20 cases (14 near haploid, 6 low hypodiploid).
• Affymetrix SNP 6.0 — genome-wide copy number profiling.
• Sanger sequencing — validation in 8 genes (all coding exons in 11 genes) across the full cohort.

Papers using this cohort

• PMID:23334668 — Genomic characterization of pediatric hypodiploid ALL (St. Jude, Nature Genetics 2013).

Notable findings derived from this cohort

• Near haploid ALL harbors RTK/Ras signaling alterations in 70.6% of cases, including NF1 (44.1%), NRAS, KRAS, FLT3, PTPN11, and MAPK1 PMID:23334668.
• Low hypodiploid ALL has TP53 alterations in 91.2% of pediatric cases; 43.3% of TP53 mutations were inherited, linking this subtype to Li-Fraumeni syndrome PMID:23334668.
• IKZF2 deletions in 52.9% of low hypodiploid ALL; IKZF3 alterations in 13.2% of near haploid ALL PMID:23334668.
• Both subtypes show PI3K pathway dependence and ex vivo sensitivity to GDC-0941 and BEZ235 PMID:23334668.

Sources

• PMID:23334668

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